ORCID Profile
0000-0001-5157-7422
Current Organisations
University of Technology Sydney
,
Shanghai University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Organic Chemical Synthesis | Organic Chemistry | Theoretical and Computational Chemistry | Quantum Chemistry | Nanotechnology | Quantum Chemistry | Condensed Matter Physics—Structural Properties | Condensed Matter Physics—Electronic And Magnetic Properties; | Chemical Spectroscopy | Colloid And Surface Chemistry | Mathematical Physics | Nanophotonics | Theoretical And Computational Chemistry Not Elsewhere Classified | Molecular and Organic Electronics | Biological And Medical Chemistry | Condensed Matter Physics | Organic Chemical Synthesis | Photodetectors, Optical Sensors and Solar Cells | Structural Biology (incl. Macromolecular Modelling) | Functional Materials | Other Electronic Engineering | Nanotechnology | Petroleum and Reservoir Engineering | Interdisciplinary Engineering | Composite and Hybrid Materials | Medical Biotechnology Diagnostics (incl. Biosensors) | Structural Engineering | Physical Chemistry (Incl. Structural) | Theory Of Materials | Structural Chemistry and Spectroscopy | Nanomanufacturing | Turbulent Flows | Carbon Sequestration Science | Industrial Biotechnology Diagnostics (incl. Biosensors) | Nanofabrication, Growth and Self Assembly
ANZSRC Socio-Economic Objective (SEO)
Integrated circuits and devices | Chemical sciences | Solar-photoelectric | Expanding Knowledge in the Chemical Sciences | Physical sciences | Polymeric materials (e.g. paints) | Oil and gas | Biological sciences | Education and Training not elsewhere classified | Information and Communication Services not elsewhere classified | Renewable energy not elsewhere classified (e.g. geothermal) | Structural glass and glass products | Diagnostic methods | Solar-Photovoltaic Energy | Cement and concrete materials | Expanding Knowledge in the Information and Computing Sciences | Public health not elsewhere classified |
Related Links
Publications
N-Silylamine Junctions for Molecular Wires to Gold: The Effect of Binding Atom Hybridization on the Electronic Transmission
Publisher: American Chemical Society (ACS)
Date: 03-11-2009
DOI: 10.1021/JP9054457
Polymeric di- and discrete trinuclear silver(I) assemblies incorporating γ-carbon bonded, neutral acetylacetone-imine motifs assembled from racemic and diastereopure N,N′-bis(acetylacetone)cyclohexane
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B903467F
Abstract: Diastereopure (1R,2R)-N,N'-bis(acetylacetone)cyclohexanedi-imine L(1) and its corresponding (1R,2R)L(1)/(1S,2S)L(2) enantiomeric mixture react with AgNO(3) to yield the unusual coordination polymer [Ag(2)(L(1))(L(2))(NO(3))(2)](n) (1) and the unique trimetallic discrete species {[Ag(3)(L(1))(3)(micro(3)-O,O,O-NO(3))(H(2)O)(3)](2)(NO(3))}(NO(3))(3) x 8.5H(2)O (2) which incorporates a symmetrical micro(3)-bridging nitrato group that gives rise to a C(3)-symmetric triskelion motif both species also feature gamma-carbon eta(1) aryl-like coordination of neutral bridging acetylacetone-imine units to the respective Ag(I) centres.
The structure and vibrational spectra of small clusters of water molecules
Publisher: Elsevier BV
Date: 03-1984
First Singlet (n,π*) Excited State of Hydrogen-Bonded Complexes between Water and Pyrimidine
Publisher: American Chemical Society (ACS)
Date: 05-02-2005
DOI: 10.1021/JP048309I
Abstract: Hydrogen bonds from water to excited-state formaldehyde and from water to excited-state pyridine have been shown to display novel motifs to traditional hydrogen bonds involving ground states, with, in particular for H2O:pyridine, strong interactions involving the electron-rich pi cloud dominating the (n,pi) excited state. We investigate H2O:pyrimidine and various dihydrated species and reveal another motif, one in which the hydrogen bonding can dramatically alter the electronic structure of the excited state. Such effects are rare for ground-state interactions for which hydrogen bonding usually acts to merely perturb the electronic structure of the participating molecules. It arises as the (n,pi*) excitation of isolated pyrimidine is delocalized over both nitrogens but asymmetric hydrogen bonding causes it to localize on just the noninteracting atom. As a result, the excited-state hydrogen bond in H2O:pyrimidine is suprisingly very similar to the ground-state structure. These results lead to an improved understanding of the spectroscopy of pyrimidine in liquid water, and to the prediction that stable excited-state hydrogen bonds in H2O:pyrimidine should be observable, despite failure of experiments to actually do so. They also provide a simple model for the intricate control over primary charge separation in photosynthesis exerted by hydrogen bonding, and for solvent-induced electron localization in symmetric mixed-valence complexes. All conclusions are based on strong parallels found between the results of calculations performed using density-functional theory (DFT) and time-dependent DFT (TDDFT), complete-active-space self-consistent-field (CASSCF) with second-order perturbation-theory correction (CASPT2) theory, and equation-of-motion coupled cluster (EOM-CCSD) theory, calculations that are verified through detailed comparison of computed properties with experimental data for both the isolated molecules and the ground-state hydrogen bond.
Density functionals with asymptotic-potential corrections are required for the simulation of spectroscopic properties of materials
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D1SC03738B
Abstract: Spectroscopic transitions in materials that involve charge transfer require asymptotically corrected density functionals. As most transitions do have some charge transfer character, use of such methods are generally warranted.
The conduction properties of α,ω-diaminoalkanes and hydrazine bridging gold electrodes
Publisher: Elsevier BV
Date: 03-2008
Adsorption of pyridine on the gold(111) surface: Implications for alligator clips for molecular wires
Publisher: American Chemical Society (ACS)
Date: 12-06-2002
DOI: 10.1021/JP020590I
Reply to Comment on “Solvent Effects on the Electronic Spectrum of C60”
Publisher: American Chemical Society (ACS)
Date: 1996
DOI: 10.1021/JP953435V
Computational Methods for Large Systems
Publisher: Wiley
Date: 05-07-2011
Quantum entanglement between electronic and vibrational degrees of freedom in molecules
Publisher: AIP Publishing
Date: 28-12-2011
DOI: 10.1063/1.3671386
Abstract: We consider the quantum entanglement of the electronic and vibrational degrees of freedom in molecules with tendencies towards double welled potentials. In these bipartite systems, the von Neumann entropy of the reduced density matrix is used to quantify the electron-vibration entanglement for the lowest two vibronic wavefunctions obtained from a model Hamiltonian based on coupled harmonic diabatic potential-energy surfaces. Significant entanglement is found only in the region in which the ground vibronic state contains a density profile that is bimodal (i.e., contains two separate local maxima). However, in this region two distinct types of density and entanglement profiles are found: one type arises purely from the degeneracy of energy levels in the two potential wells and is destroyed by slight asymmetry, while the other arises through strong interactions between the diabatic levels of each well and is relatively insensitive to asymmetry. These two distinct types are termed fragile degeneracy-induced entanglement and persistent entanglement, respectively. Six classic molecular systems describable by two diabatic states are considered: ammonia, benzene, BNB, pyridine excited triplet states, the Creutz-Taube ion, and the radical cation of the “special pair” of chlorophylls involved in photosynthesis. These chemically erse systems are all treated using the same general formalism and the nature of the entanglement that they embody is elucidated.
Two-photon fluorescence excitation spectrum of a naphthalene norbornylog: Implications for electron transfer
Publisher: Elsevier BV
Date: 06-1990
Gold mining by alkanethiol radicals: Vacancies and pits in the self-assembled monolayers of 1-propanethiol and 1-butanethiol on Au(111)
Publisher: American Chemical Society (ACS)
Date: 06-05-2011
DOI: 10.1021/JP111811G
Molecular Design Principles for Linearly Scalable, Frequency-Based, Universal Quantum Computers
Publisher: OSA
Date: 2011
Decomposition of Ferrocene on Pt(111) and Its Effect on Molecular Electronic Junctions
Publisher: American Chemical Society (ACS)
Date: 18-11-190728635
Chemical Analysis Of The Superatom Model For Sulfur-Stabilized Gold Nanoparticles
Publisher: American Chemical Society (ACS)
Date: 02-06-2010
DOI: 10.1021/JA101083V
Abstract: The superatom model for nanoparticle structure is shown to be inadequate for the prediction of the thermodynamic stability of gold nanoparticles. The observed large HOMO-LUMO gaps for stable nanoparticles predicted by this model are, for sulfur-stabilized gold nanoparticles, attributed to covalent interactions of the metal with thiyl adsorbate radicals rather than ionic interactions with thiolate adsorbate ions, as is commonly presumed. In particular, gold adatoms in the stabilizing layer are shown to be of Au(0) nature, subtle but significantly different from the atoms of the gold core owing to the variations in the proportion of gold-gold and gold-sulfur links that form. These interactions explain the success of the superatom model in describing the electronic structure of both known and informatory nanoparticle compositions. Nanoparticle reaction energies are, however, found not to correlate with the completion of superatom shells. Instead, local structural effects are found to dominate the chemistry and in particular the significantly different chemical properties of gold nanoparticle and bulk surfaces. These conclusions are drawn from density-functional-theory calculations for the Au(102)(p-mercaptobenzoic acid)(44) nanoparticle based on the X-ray structure (Jadzinsky, P. D. et al. Science 2007, 318, 430), as well calculations for the related Au(102)(S(*)-CH(3))(44) nanoparticle, for the inner gold-cluster cores, for partially and overly reacted cores, and for Au(111) surface adsorbates.
Incoherent tunneling and heat dissipation in molecular bridges
Publisher: IOP Publishing
Date: 04-2006
Mixed Valency Systems: Applications in Chemistry, Physics and Biology
Publisher: Springer Netherlands
Date: 1991
Convergence of Defect Energetics Calculations
Publisher: American Chemical Society (ACS)
Date: 18-08-2020
The Manganite-Water Interface
Publisher: American Chemical Society (ACS)
Date: 26-06-2007
DOI: 10.1021/JP068842T
Inter-porphyrin coupling: How strong should it be for molecular electronics applications?
Publisher: World Scientific Pub Co Pte Ltd
Date: 12-2002
DOI: 10.1142/S1088424602000919
Abstract: Porphyrins and phthalocyanines have now been assembled in a multitude of different architectures, each of which may be identified with a different scenario of the coupling acting between the porphyrins. The synthetic flexibility of these compounds makes possible the design of particular molecules for specific applications in molecular electronics, both in naturally occurring and synthetic devices. Here, we form an overview of these features and focus on the coupling strength, considering what values are appropriate for different molecular electronics applications. In particular, we focus on model compounds that have been prepared as mimics of naturally occurring photosynthetic functional units, oligoporphyrins molecular wires, and stacked systems in which small changes in geometry can affect significant changes in the inter-porphyrin coupling and hence produce dramatic changes in device properties.
Diabatic models with transferrable parameters for generalized chemical reactions
Publisher: IOP Publishing
Date: 04-2017
DOI: 10.1088/1742-6596/833/1/012014
Abstract: Diabatic models applied to adiabatic electron-transfer theory yield many equations involving just a few parameters that connect ground-state geometries and vibration frequencies to excited-state transition energies and vibration frequencies to the rate constants for electron-transfer reactions, utilizing properties of the conical-intersection seam linking the ground and excited states through the Pseudo Jahn-Teller effect. We review how such simplicity in basic understanding can also be obtained for general chemical reactions. The key feature that must be recognized is that electron-transfer (or hole transfer) processes typically involve one electron (hole) moving between two orbitals, whereas general reactions typically involve two electrons or even four electrons for processes in aromatic molecules. Each additional moving electron leads to new high-energy but interrelated conical-intersection seams that distort the shape of the critical lowest-energy seam. Recognizing this feature shows how conical-intersection descriptors can be transferred between systems, and how general chemical reactions can be compared using the same set of simple parameters. Mathematical relationships are presented depicting how different conical-intersection seams relate to each other, showing that complex problems can be reduced into an effective interaction between the ground-state and a critical excited state to provide the first semi-quantitative implementation of Shaik’s “twin state” concept. Applications are made (i) demonstrating why the chemistry of the first-row elements is qualitatively so different to that of the second and later rows, (ii) deducing the bond-length alternation in hypothetical cyclohexatriene from the observed UV spectroscopy of benzene, (iii) demonstrating that commonly used procedures for modelling surface hopping based on inclusion of only the first-derivative correction to the Born-Oppenheimer approximation are valid in no region of the chemical parameter space, and (iv), demonstrating the types of chemical reactions that may be suitable for exploitation as a chemical qubit in some quantum information processor.
Solvent effects on molecular spectra. I. Normal pressure and temperature Monte Carlo simulations of the structure of dilute pyrimidine in water
Publisher: AIP Publishing
Date: 08-1993
DOI: 10.1063/1.465317
Abstract: In this series, our aim is to develop a new scheme based upon a perturbation expansion of the weak intermolecular interactions for the solvent (solvatochromatic) shift of the center of an electronic absorption band in a condensed phase. It is tested by calculation of the shift of the 1(n,π*) absorption and fluorescence spectra of pyrimidine in water. Herein, NPT-ensemble Monte Carlo simulations are performed to determine the structure of dilute pyrimidine in water at 25 °C and 1 atm. pressure. Six different intermolecular effective pair potentials are used to produce a wide range of hydrogen-bond structures ranging from 0 to 2 hydrogen bonds per pyrimidine molecule, suitable for subsequent investigations into the correlation of spectral shift with solvent structure. One potential obtained using Kollman’s Lennard-Jones parameters combined with ab initio electrostatic-potential charges produces the most accurate potential function this correctly reproduces the observed enthalpy of hydration and partial specific volume of pyrimidine, and produces a chemically reasonable description of the hydrogen-bond structure.
Medium effects on molecular and ionic electronic spectra. Application to the lowest 1(n, π*) state of dilute pyridine in water
Publisher: Elsevier BV
Date: 04-1993
A practical method for the use of curvilinear coordinates in calculations of normal-mode-projected displacements and Duschinsky rotation matrices for large molecules
Publisher: AIP Publishing
Date: 22-11-2001
DOI: 10.1063/1.1412875
Abstract: While use of curvilinear coordinates such as bond lengths and bond angles is common in accurate spectroscopic and/or scattering calculations for triatomic and other small molecules, their use for large molecules is uncommon and restricted. For large molecules, normal-mode analysis is feasible but gives sensible results only if the dynamical or spectroscopic process being considered involves changes in angular coordinates, including ring deformations, which are so small that the motion can be approximated by its tangential component. We describe an approximate method by which curvilinear normal-mode-projected displacements and hence Franck–Condon factors, reorganization energies, and vibronic coupling constants, as well as Duschinsky (Dushinsky, Duschinskii) rotation matrices, can be evaluated for large systems. Three illustrative ex les are provided: (i) to understand the nature of the first excited state of water, illustrating properties of large- litude bending motions (ii) to understand the nature of the “boat” relaxation of the first excited state of pyridine, illustrating properties of large- litude torsional motions and (iii) to understand the coupling of vibrational modes to the oxidation of bacteriochlorophyll-a, a paradigm with many applications to both chemical and biological electron transfer, illustrating properties of macrocyclic deformations. The method is interfaced to a wide variety of computational chemistry computer programs.
Solvent effects on molecular spectra. II. Simulations of hydrated clusters and dilute solutions of pyrimidine in its lowest (n,π*) singlet excited state
Publisher: AIP Publishing
Date: 08-1993
DOI: 10.1063/1.465318
Abstract: Hydrogen bonding between pyrimidine in its lowest (n,π*) singlet excited state and water in dilute solution is investigated using NPT-ensemble Monte Carlo simulations, and the properties of the pyrimidine–water complex are examined using molecular dynamics. The 1(n,π*) excitation, known experimentally to be delocalized in the gas phase, is shown to remain delocalized when pyrimidine undergoes hydrogen bonding. Assuming that the intermolecular interactions are electronic state independent, Kollman’s Lennard-Jones interactions are combined with molecular charges obtained in four different ways, generating a variety of intermolecular pair potentials. It is found that, in solution, both pyrimidine–water–hydrogen bonds are considerably weakened in the excited state however, on average, one hydrogen bond per pyrimidine remains. The excited state hydrogen bonding gives rise to structures in the liquid more like those found in van der Waals bonded systems than in strongly hydrogen-bonded systems such as ground-state pyrimidine in water. A blue shift of the absorption band origin is correctly predicted and its magnitude and Franck–Condon contribution are in reasonable agreement with experiment. For pyrimidine–water clusters, minor changes in the intermolecular potential surfaces are shown to cause major qualitative differences in the excited state cluster dynamics, mimicking the observed spectral properties of several different hydrogen-bonded pyrimidine clusters.
Synthetically tuneable biomimetic artificial photosynthetic reaction centres that closely resemble the natural system in purple bacteria
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6SC01076H
Abstract: Synthetically flexible, rigid, tetrad molecules are shown to closely mimic structural and photochemical properties of the bacterial photosynthetic reaction centre.
Solvent Effects On Molecular-Spectra .3. Absorption To And Emission From The Lowest Singlet (N,Pi-Asterisk) State Of Dilute Pyrimidine In Water
Publisher: AIP Publishing
Date: 08-1993
DOI: 10.1063/1.465319
Abstract: A model is developed for the solvent shift of the center of an electronic absorption or emission band and is applied to the interpretation of the spectra of dilute pyrimidine in water. It is based on the use of standard simulation techniques such as molecular dynamics and Monte Carlo to calculate the liquid structure around the chromophore in its initial electronic state the solvent shift is then deduced by considering the changes in the electrostatic distribution of the chromophore on vertical Franck–Condon excitation. During the solvent-shift evaluation only, spherical boundary conditions are used and the s le, containing both the solute and a large number of explicitly polarizable solvent molecules, is placed inside a dielectric continuum. The results show that the solvent shifts of both the absorption and fluorescence spectra of pyrimidine in water are comprised of approximately equal contributions from specific hydrogen-bonding interactions and long-range–plus–nonspecific dipole solvation effects. The solvent shift is shown to be very sensitive to the structure of the liquid. A specific aim of our approach is to develop a method applicable to molecular electronic devices, and to inorganic complexes.
Spontaneous S-Si bonding of alkanethiols to Si(111)-H: towards Si-molecule-Si circuits.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0SC01073A
Abstract: Spontaneously formed Si–S bonds enable monolayer and single-molecule Si–molecule–Si circuits.
The revised Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not scientifically justified Comment on Consciousness in the universe: A review of the 'Orch OR' theory by Hameroff and Penrose
Publisher: Elsevier BV
Date: 03-2014
van der Waals forces control ferroelectric–antiferroelectric ordering in CuInP2S6 and CuBiP2Se6 laminar materials
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8SC01274A
Abstract: We show how van der Waals (vdW) forces outcompete covalent and ionic forces to control ferroelectric ordering in CuInP 2 S 6 nanoflakes as well as in CuInP 2 S 6 and CuBiP 2 Se 6 crystals.
How Equilibrium Gets Mimicked during Kinetic and Thermodynamic Control in Porphyrin and Phthalocyanine Self-Assembled Monolayers
Publisher: American Chemical Society (ACS)
Date: 20-11-2018
DOI: 10.1021/ACS.LANGMUIR.7B03320
Abstract: The recent review of Hipps and Mazur is extended to consider the origins and significance of their conclusion that "surface structures vary with relative component concentration in a way that may mimic equilibria but is not". How this situation can arise during self-assembly is discussed, as well as a range of qualitative and quantitative observations and high-level free-energy calculations that document the effect for meso-tetraalkylporphyrins self-assembled monolayer (SAM) polymorphs. This leads to a discussion of modern challenges facing quantification of the effects caused by kinetic control, as well as to the usefulness of equilibrium mimicking in the design and synthesis of SAMs.
Nature of Nonbonding Molecular Orbitals: Application to Two Symmetric Tetraazanaphthalenes
Publisher: American Chemical Society (ACS)
Date: 04-1999
DOI: 10.1021/JP984565H
Wavepacket propagation using time-sliced semiclassical initial value methods
Publisher: AIP Publishing
Date: 13-12-2004
DOI: 10.1063/1.1825999
Abstract: A new semiclassical initial value representation (SC-IVR) propagator and a SC-IVR propagator originally introduced by Kay [J. Chem. Phys. 100, 4432 (1994)], are investigated for use in the split-operator method for solving the time-dependent Schrödinger equation. It is shown that the SC-IVR propagators can be derived from a procedure involving modified Filinov filtering of the Van Vleck expression for the semiclassical propagator. The two SC-IVR propagators have been selected for investigation because they avoid the need to perform a coherent state basis set expansion that is necessary in other time-slicing propagation schemes. An efficient scheme for solving the propagators is introduced and can be considered to be a semiclassical form of the effective propagators of Makri [Chem. Phys. Lett. 159, 489 (1989)]. Results from applications to a one-dimensional, two-dimensional, and three-dimensional Hamiltonian for a double-well potential are presented.
Analysis of the OH bend and stretch region in the vibrational spectrum of water
Publisher: Elsevier BV
Date: 1983
Comparison of Soliton Geometry and Charge-Density Wave Structure, and Band Gaps, Between Odd Polyene and Symmetrical Polymethine Cyanine (Brooker) Ions and T - Polyacetylene : Scf and Model Hamiltonia
Publisher: Informa UK Limited
Date: 10-1993
Successful a priori modeling of CO adsorption on Pt(111) using periodic hybrid density functional theory
Publisher: American Chemical Society (ACS)
Date: 08-2007
DOI: 10.1021/JA0712367
Abstract: The adsorption of CO on the surface of metals such as Pt(111) is of great interest owing to the industrial importance of the catalytic oxidation of pollutant CO. To date, reliable high-level calculations of this process have not been possible, a situation often referred to as the "CO/Pt(111) puzzle". Standard generalized-gradient-approximation density functional theory approaches fail to capture key details of the binding, such as the location of the adsorption site, while cluster approaches using alternative methods show some but insufficient improvement. Using a new computational methodology combining hybrid density functionals containing non-local Hartree-Fock exchange with periodic imaging plane-wave-based techniques, we demonstrate that key aspects of the adsorption of CO on Pt(111), including the identification of the absorption site and CO frequency change, can now be adequately modeled. The binding is dominated by both CO dative covalent bonding and metal-to-molecule pi back-bonding, effects requiring realistic alignment of both the molecular HOMO and LUMO orbitals with respect to the metal Fermi energy.
Molecular Electronics: From Basic Chemical Principles To Photosynthesis To Steady-State Through-Molecule Conductivity To Computer Architectures
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/CH04132
Abstract: Molecular electronics offers many possibilities for the development of electronic devices beyond the limit of silicon technology. Its basic ideas and history are reviewed, and a central aspect of the delocalization of electrons across molecules and junctions is examined. Analogies between key processes affecting steady-state through-molecule conduction and equilibrium geometric and spectroscopic properties of paradigm molecules, such as hydrogen, ammonia, benzene, and the Creutz–Taube ion are drawn, and the mechanisms by which control can be exerted over molecular-electronic processes during biological photosynthesis are examined. Ab initio molecular dynamics and simulations of conductivity are then presented for carbon nanotube flanged to gold(111), and device characteristics are calculated for a molecular shift register clocked by two gold electrodes.
Photoluminescence and photochemistry of the $V_B^-$ defect in hexagonal boron nitride
Publisher: arXiv
Date: 2020
Singlet and Triplet Valence Excited States of Pyrimidine
Publisher: American Chemical Society (ACS)
Date: 05-04-2003
DOI: 10.1021/JP0221385
Competition of van der Waals and chemical forces on gold–sulfur surfaces and nanoparticles
Publisher: Springer Science and Business Media LLC
Date: 08-02-2017
The exact eigenfunctions and eigenvalues of a particle in a box obtained using Gaussian wavepacket dynamics
Publisher: IOP Publishing
Date: 11-09-1986
A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers
Publisher: Proceedings of the National Academy of Sciences
Date: 28-10-2015
Abstract: First-principles free energy calculations, characterizing polymorphism of self-assembled monolayers (SAMs) of porphyrin molecules formed from solution onto graphite, are performed using efficient methods previously applied only to small-molecule reactivity. SAM structures are typically optimized in the absence of solvent using density functional theory embodying explicit dispersion corrections. Added then are dispersion-dominated implicit solvation energies and SAM formation entropies derived from both molecular and phonon vibration frequencies. Scanning tunneling microscopy (STM) images are measured, and polymorph formation free energies are approximated. Close parallels between experiment and theory support the hypothesis that the first seconds of SAM formation are under thermodynamic control, despite formed SAMs being kinetically trapped. Polymorphism is associated with large opposing changes to entropy and substrate−molecule and solvent−molecule interaction energies.
Photoinduced electron transfer in a β,β′-pyrrolic fused ferrocene-(zinc porphyrin)-fullerene
Publisher: Royal Society of Chemistry (RSC)
Date: 2007
DOI: 10.1039/B704136E
Abstract: A donor-acceptor linked triad with a short spacer (Fc-ZnP-C60) 1 was designed and synthesised to attain the longest charge-separation lifetime, 630 micros, ever reported for triads at room temperature. The ferrocene electron donor and fullerene electron acceptor of triad 1 are attached to imidazole rings fused to opposite beta,beta'-pyrrolic positions of the zinc porphyrin. After excitation of the porphyrin, electron transfer to C60 occurs within 230 ps, followed by hole transfer to ferrocene after 500 ps to produce the long-lived charge-separated state.
CASSCF-wave packet a b i n i t i o p
Publisher: AIP Publishing
Date: 06-1985
DOI: 10.1063/1.448628
Abstract: The combination of ab initio calculation of electronic wave functions with a wave packet calculation of the nuclear motion is used, within the Born–Oppenheimer approximation to compute the vibrational and electronic absorption of a polyatomic molecule. A particular virtue of this approach is that high as well as low temperature spectra are both calculable. This method is applied to C2H, for which the complete active space self-consistent field (CASSCF) method is used to determine full Born–Oppenheimer potential surfaces. Using the assumption that the A(2Π) ← X(2Σ+) absorption can be written as the sum of the A(2A′) ← X and A(2A″) ← X absorptions, the spectra are determined to 60 cm−1 resolution at a temperature of 3000 K. As a result of the large thermal bending litude at 3000 K, the calculated spectra are broad and have little resolved structure. Two bands are resolvable, one is due to the A(2A″) ← X absorption and is centered at 5500 cm−1, while the other is due to A(2A′) ← X absorption and is centered at 9500 cm−1. The dramatic blue shift of the A(2A′) ← X band results from the combination of the large X state thermal bending litude and high bending frequency of the A(2A′) state. We also determine the X state pure vibrational absorption spectrum and show it to be of much lower intensity than the pure electronic spectrum.
Norbornadiene-Based Molecules For Functionalizing The Si(001) Surface
Publisher: American Chemical Society (ACS)
Date: 17-08-2009
DOI: 10.1021/JP903481W
Explanation Of The Anomalous Complexation Of Silver(I) With Ammonia In Terms Of The Poor Affinity Of The Ion For Water
Publisher: American Chemical Society (ACS)
Date: 03-09-2004
DOI: 10.1021/JP0495545
Publisher Correction: A new fundamental type of conformational isomerism.
Publisher: Springer Science and Business Media LLC
Date: 27-07-2018
DOI: 10.1038/S41557-018-0117-5
Abstract: In the version of this Article originally published, the word 'stereoisomerism' was erroneously included in the label of the upper-right box of Fig. 1. The label within the box has been corrected and it now reads: "Constitutional isomerism (same formula, different connectivity)". This has been corrected in the online version of the Article.
The development and validation of a single SNaPshot multiplex for tiger species and subspecies identification - Implications for forensic purposes
Publisher: Elsevier BV
Date: 03-2012
BIOPHYSCHEM2011: A joint meeting of the Australian society for biophysics and the RACI physical chemistry division
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/CH12213
Source code, input data, and sample output concerning the application of multistate density functional theory to the singdoublet and tripdoublet states of the ethylene cation
Publisher: Elsevier BV
Date: 02-2020
Interference-Induced Electron- And Hole-Conduction Asymmetry
Publisher: Springer Science and Business Media LLC
Date: 05-10-2011
Solvent Effects on Molecular and Ionic Spectra IX: The Change in Dipole Moment Accompanying Metal to Ligand Charge Transfer Absorption in Pentaaminopyridylruthenium(II)
Publisher: American Chemical Society (ACS)
Date: 1996
DOI: 10.1021/JP961860Y
Surface Adsorption
Publisher: Elsevier
Date: 2017
Assignment Of The Q(Y) Absorption Spectrum Of Photosystem-I From Thermosynechococcus Elongatus Based On Cam-B3Lyp Calculations At The Pw91-Optimized Protein Structure
Publisher: American Chemical Society (ACS)
Date: 08-2007
DOI: 10.1021/JP070030P
Abstract: The Qy absorption spectrum of Photosystem-I from Thermosynecochoccus elongatus (formerly Synecochoccus elongatus) is calculated using the CAM-B3LYP density functional and INDO schemes based on a quantum-mechanically refined structure for the entire photosystem obtained using the PW91 density functional. These methods present a priori predictions of the absorption and linear dichroism spectra and include protein electrostatic effects, short range inductive effects, long-range and short-range exciton couplings, and superexchange effects involving aromatic residues and carotenes. CAM-B3LYP is used as it is the only known density functional that correctly describes the Q bands of chlorophylls, all other methods contaminating them with erroneous charge-transfer excitations. A critical feature is found to be the use of fully optimized heavy-atom coordinates, with those obtained from just X-ray crystallography providing a poor description of the electronic properties of the chromophores. The result is a realistic first-principles prediction of the observed absorption band that identifies the nature of the red-shifted chlorophylls as well as the energies of the reaction-center chlorophylls and the exciton couplings acting between them. The "special pair" appears more like a dimer of dimers than a self-contained functional unit, with the exciton couplings between its members and the accessory chlorophylls exceeding the internal coupling.
Evanescent-Field Spectroscopy Using Structured Optical Fibers: Detection Of Charge-Transfer At The Porphyrin-Silica Interface
Publisher: American Chemical Society (ACS)
Date: 09-02-2009
DOI: 10.1021/JA8081473
Abstract: The fabrication of porphyrin thin films derived from dichloro[5,10,15,20-tetra(heptyl)porphyrinato]tin(IV) [Cl-Sn(THP)-Cl] in the holes of photonic crystal fibers over 90 cm in length is described. Evanescent field spectroscopy (EFS) is used to investigate the interfacial properties of the films, with the high surface optical intensity and the long path length combining to produce significant absorption. By comparison with results obtained for similar films formed from Cl-Sn(THP)-Cl inside fused-silica cuvettes and on glass slides, the film is shown to be chemisorbed as a surface Si-O-Sn(THP)-X (X = Cl or OH) species. In addition to the usual porphyrin Q and Soret bands, new absorptions in the in-fiber films are observed by EFS at 445 nm and between 660-930 nm. The 660-930 nm band is interpreted as a porphyrin to silicon charge-transfer transition and postulated to arise following chemisorption at mechanical-strain induced defect sites on the silica surface. Such defect sites are caused by the optical fiber production process and are less prevalent on other glass surfaces. EFS within optical fibers therefore offers new ways for understanding interface phenomena such as surface adsorbates on glass. Such understanding will benefit all devices that exploit interface phenomena, both in optical fibers and other integrated waveguide forms. They may be directly exploited to create ultrasensitive molecular detectors and could yield novel photonic devices.
Recent Advances in Stereochemistry Reveal Classification Shortcomings
Publisher: American Chemical Society (ACS)
Date: 18-06-2020
DOI: 10.26434/CHEMRXIV.12488525.V1
Abstract: We contend that the Polytope model utilized by IUPAC to specify stereoisomerism for species ML n with n 3 should be universally applied. Such application recently led to the synthesis of isolable compounds displaying a new fundamental form of isomerism, ak tisomerism, pertinent to ML 2 stereocenters. We review 443807 molecules that could be classified as ak tisomers. Some ak tisomers are described as being “wrong” by existing IUPAC rules, hindering molecular conception. For many classes of medicinal and technology-related molecules, software packages like ChemDraw mostly do not handle ak tisomers correctly, databases such as CAS provide 2D representations inconsistent with those presented in the original publications, and often the ak tisomeric identity of compounds remains unknown. These features hinder both human and machine-learning approaches to chemical design. Further, the existence of previously unrecognized isomeric forms has broad implications for patents and pharmaceutical-registration requirements. Hence, the immediate re-examination of stereochemistry is demanded.
Switchable Electronic Coupling In Model Oligoporphyrin Molecular Wires Examined Through The Measurement And Assignment Of Electronic Absorption Spectra
Publisher: American Chemical Society (ACS)
Date: 16-07-2002
DOI: 10.1021/JA020081U
Abstract: The use of a quinone functionality in the linkage unit of laterally bridged oligoporphyrins as a switch for controlling electronic coupling between the termini is examined. The quinone-bridged bisporphyrin P(2)TA-O(2) was synthesized by condensation of 2 equiv of the dione 2,3-dioxo-5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)chlorin with 2,3,5,6-tetraamino-1,4-benzoquinone. The electronic absorption spectra of P(2)TA-O(2) and its conjugated benzenoid analogue P(2)TA are measured and assigned, in conjunction with the spectra of the fragment monomers and porphyrin-bridge compounds. Band homologies and CASPT2 calculations are used to make the assignments. Chemically, the dimer in one case is bridged by a through-conjugated, pi-delocalized 1,4,5,8-tetraazaanthracene molecule. This is shown to display significant inter-porphyrin coupling, with an observed difference in the exciton couplings of the B(x) and B(y) bands being ca. 0.18 eV. However, the other dimer is bridged using a derivative in which the central ring is converted to a cross-conjugated, pi-localized quinonoid form this molecule displays no observable inter-porphyrin coupling. This scenario provides a paradigm for the use of molecular electronic devices in sensing, control, and high-capacity relatively low-speed data storage applications.
Solvent Effects on Molecular and Ionic Spectra. 7. Modeling the Absorption and Electroabsorption Spectra of Pentaammine- ruthenium(II) Pyrazine and Its Conjugate Acid in Water
Publisher: American Chemical Society (ACS)
Date: 1996
DOI: 10.1021/JA952993K
Dynamics of Wave Packets in Molecular and Nuclear Physics
Publisher: Springer Berlin Heidelberg
Date: 1986
Polymorphism In Porphyrin Monolayers: The Relation Between Adsorption Configuration And Molecular Conformation
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3CP50829C
Abstract: Self-assembled monolayers of meso-5,10,15,20-tetrakis(undecyl)porphyrin copper(II) on a graphite/1-octanoic acid interface have been studied by Scanning Tunnelling Microscopy. Four distinct polymorphs were observed, varying in their unit cell size. Arrays of unit cells of the various polymorphs seamlessly connect to each other via shared unit cell vectors. The monolayers are not commensurate, but coincident with the underlying graphite substrate. The seamless transition between the polymorphs is proposed to be the result of an adaptation of the molecular conformations in the polymorphs and at the boundaries, which is enabled by the conformational freedom of the alkyl tails of these molecules.
Accurate and computationally efficient third-nearest-neighbor tight-binding model for large graphene fragments
Publisher: American Physical Society (APS)
Date: 26-05-2010
ELECTRON AND ION TRANSFER IN CONDENSED MEDIA
Publisher: WORLD SCIENTIFIC
Date: 09-1997
Putting David Craig’s Legacy to Work in Nanotechnology and Biotechnology
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/CH16489
Abstract: David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes inelastic electron-tunnelling spectroscopy (IETS) chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness synthetic design strategies for NMR quantum computing Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.
Inter-porphyrin coupling: rotation-modulation of inter-ring coupling in a μ-oxo-silicon phthalocyanine dimer
Publisher: Elsevier BV
Date: 09-2003
Erratum: Competition of van der Waals and chemical forces on gold–sulfur surfaces and nanoparticles
Publisher: Springer Science and Business Media LLC
Date: 22-03-2017
A multiscale simulation technique for molecular electronics: Design of a directed self-assembled molecular n-bit shift register memory device
Publisher: IOP Publishing
Date: 22-11-2013
DOI: 10.1088/0957-4484/24/50/505202
Abstract: A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.
Modeling the Bacterial Photosynthetic Reaction Center. 4. The Structural, Electrochemical, and Hydrogen-Bonding Properties of 22 Mutants ofRhodobacter sphaeroides
Publisher: American Chemical Society (ACS)
Date: 09-08-2001
DOI: 10.1021/JA0035710
Abstract: Site-directed mutagenesis has been employed by a number of groups to produce mutants of bacterial photosynthetic reaction centers, with the aim of tuning their operation by modifying hydrogen-bond patterns in the close vicinity of the "special pair" of bacteriochlorophylls P identical with P(L)P(M). Direct X-ray structural measurements of the consequences of mutation are rare. Attention has mostly focused on effects on properties such as carbonyl stretching frequencies and midpoint potentials to infer indirectly the induced structural modifications. In this work, the structures of 22 mutants of Rhodobacter sphaeroides have been calculated using a mixed quantum-mechanical molecular-mechanical method by modifying the known structure of the wild type. We determine (i) the orientation of the 2a-acetyl groups in the wild type, FY(M197), and FH(M197) series mutants of the neutral and oxidized reaction center, (ii) the structure of the FY(M197) mutant and possible water penetration near the special pair, (iii) that significant protein chain distortions are required to assemble some M160 series mutants (LS(M160), LN(M160), LQ(M160), and LH(M160) are considered), (iv) that there is competition for hydrogen-bonding between the 9-keto and 10a-ester groups for the introduced histidine in LH(L131) mutants, (v) that the observed midpoint potential of P for HL(M202) heterodimer mutants, including one involving also LH(M160), can be correlated with the change of electrostatic potential experienced at P(L), (vi) that hydrogen-bond cleavage may sometimes be induced by oxidation of the special pair, (vii) that the OH group of tyrosine M210 points away from P(M), and (viii) that competitive hydrogen-bonding effects determine the change in properties of NL(L166) and NH(L166) mutants. A new technique is introduced for the determination of ionization energies at the Koopmans level from QM/MM calculations, and protein-induced Stark effects on vibrational frequencies are considered.
Modelling The Bacterial Photosynthetic Reaction Center. Vi. Use Of Density-Functional Theory To Determine The Nature Of The Vibronic Coupling Between The Four Lowest-Energy Electronic States Of The Special-Pair Radical Cation
Publisher: AIP Publishing
Date: 24-07-2003
DOI: 10.1063/1.1569910
Abstract: It is now over ten years since the first FTIR spectra were recorded of the radical cation of the special-pair, a dimer of bacteriochlorophyll molecules that forms the primary electron donor responsible for primary charge separation in bacterial photosynthesis. While spectra of this type promise to reveal much concerning the role of the special pair electron donor in photosynthesis, attempts to model and interpret them have been limited by poor knowledge of the vibrationally specific aspects of the electron–phonon coupling and have thus been restricted to crude model calculations only. We develop techniques through which density-functional theory can be employed to evaluate most of the unknown properties. This includes symmetric-mode displacements, antisymmetric-mode vibronic coupling constants, and interstate electronic couplings evaluated for interactions between the four lowest-energy states of the special-pair cation radical: the ground state, the primary hole-transfer state, and states involving these two combined with SHOMO to HOMO transitions. Geometry optimizations are performed for all four states of the dimer while vibrational analyses are obtained for the first two vibronic coupling constants are extracted from analysis of stolen infrared transition moments using Herzberg–Teller theory. Quantitatively, these results are employed in the subsequent paper in this series to simulate the observed spectra. Qualitatively, these results indicate that: (1) vibronic coupling occurs through a large number of antisymmetric modes of the dimer rather than through a small number of strongly active modes, (2) the role of symmetric vibrational motions of the dimer is only minor, (3) that the active symmetric modes are significant in number and low in frequency, (4) that vibronic coupling between the hole-transfer state and the SHOMO to HOMO state is relatively weak and influences spectra only near resonance, and (5) that the calculated electronic couplings are qualitatively realistic and may provide an explanation for the much weaker coupling observed in chlorophyll-containing reaction centers.
Failure of density-functional theory and time-dependent density-functional theory for large extended π systems
Publisher: AIP Publishing
Date: 04-09-2002
DOI: 10.1063/1.1501131
Abstract: Density-functional theory (DFT) is widely used for studying large systems such as metals, semiconductors, and large molecules, with time-dependent density-functional theory becoming a very powerful tool for investigating molecular excited states. As part of a systematic study of both the intrinsic weaknesses of DFT and the weaknesses of present implementations, we consider its application to the one and two-dimensional conjugated π systems: polyacetylene fragments and oligoporphyrins, respectively. Very poor results are obtained for the calculated spectra, and polyacetylene is predicted by all functionals considered, including gradient-corrected functionals, to have a triplet ground state. The cause of this is linked to known problems of existing density functionals concerning nonlocality and asymptotic behavior which result in the highest-occupied molecular-orbital being too high in energy so that semiconductors and low-band-gap insulators are predicted to have metal-like properties. The failure of modern density functionals to predict qualitatively realistic molecular hyperpolarizabilities for extended systems is closely related.
Molecular electronics?science and technology
Publisher: Wiley
Date: 1989
Electronic properties of transition-metal complexes determined from electroabsorption (Stark) spectroscopy. 2. Mononuclear complexes of ruthenium(II)
Publisher: American Chemical Society (ACS)
Date: 11-1991
DOI: 10.1021/J100177A032
Ultraviolet photodissociation action spectroscopy of the N-pyridinium cation.
Publisher: AIP Publishing
Date: 05-01-2015
DOI: 10.1063/1.4904267
Abstract: The S1←S0 electronic transition of the N-pyridinium ion (C5H5NH+) is investigated using ultraviolet photodissociation (PD) spectroscopy of the bare ion and also the N2-tagged complex. Gas-phase N-pyridinium ions photodissociate by the loss of molecular hydrogen (H2) in the photon energy range 37 000–45 000 cm−1 with structurally diagnostic ion-molecule reactions identifying the 2-pyridinylium ion as the exclusive co-product. The photodissociation action spectra reveal vibronic details that, with the aid of electronic structure calculations, support the proposal that dissociation occurs through an intramolecular rearrangement on the ground electronic state following internal conversion. Quantum chemical calculations are used to analyze the measured spectra. Most of the vibronic features are attributed to progressions of totally symmetric ring deformation modes and out-of-plane modes active in the isomerization of the planar excited state towards the non-planar excited state global minimum.
Electron and energy transfer through bridged systems. 6. Molecular switches: the critical field in electric field activated bistable molecules
Publisher: American Chemical Society (ACS)
Date: 05-1990
DOI: 10.1021/JA00167A014
Molecular electronics inside optical fibres
Publisher: IEEE
Date: 07-2008
Tautomerization of Nucleobase Model Compounds: The 4-Pyridinol and 4(1H)-Pyridinone Monomers and Their Dimers
Publisher: American Chemical Society (ACS)
Date: 27-04-2000
DOI: 10.1021/JP9939827
Enthalpy of hydration and partial molar specific volume as criteria for evaluation of intermolecular potentials. NPT-ensemble Monte Carlo calculations for dilute neon in water
Publisher: Elsevier BV
Date: 04-1993
Successes and failures of time-dependent density functional theory for the low-lying excited states of chlorophylls
Publisher: Informa UK Limited
Date: 20-03-2005
Unified Understanding of Structure, Reactivity and Spectroscopy Within General Valence Bond Scenarios, Obtained by Transferring Techniques Developed Within Electron-Transfer Theory
Publisher: Elsevier
Date: 2024
Nature of the special-pair radical cation in bacterial photosynthesis
Publisher: Wiley
Date: 2000
Molecular quantum cellular automata cell design trade-offs: latching vs. power dissipation
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8CP02886A
Abstract: A new way of using molecules to enact switches in quantum cellular automata (QCA) is proposed, utilizing monostable molecules that neither provide latching nor consume power properties are compared to those for conventional bistable switches that both latch and consume power.
Modelling the bacterial photosynthetic reaction center. V. Assignment of the electronic transition observed at 2200 cm−1 in the special-pair radical-cation as a second-highest occupied molecular orbit
Publisher: AIP Publishing
Date: 24-07-2003
DOI: 10.1063/1.1569909
Abstract: Primary charge separation in photoexcited photosynthetic reaction centers produces the radical cation P+ of a bacteriochlorophyll dimer known as the special-pair P. P+ has an intense electronic transition in the vicinity of 1800–5000 cm−1 which is usually assigned to the interchromophore hole-transfer excitation of the dimer radical cation in principle, this spectrum can give much insight into key steps of the solar-to-electrical energy-conversion process. The extent to which this transition is localized on one-half of the dimer or delocalized over both is of utmost importance an authoritative deduction of this quantity from purely spectroscopic arguments requires the detailed assignment of the observed high to medium resolution spectra. For reaction centers containing bacteriochlorophylls a or b, a shoulder is observed at 2200 cm−1 on the low-energy side of the main hole-transfer absorption band, a band whose maximum is near 2700 cm−1. Before quantitative analysis of the hole-transfer absorption in these well-studied systems can be attempted, the nature of the processes leading to this shoulder must be determined. We interpret it as arising from an intrachromophore SHOMO to HOMO transition whose intensity arises wholly through vibronic coupling with the hole-transfer band. A range of ab initio and density-functional calculations are performed to estimate the energy of this transition both for monomeric cations and for P+ of Blastochloris viridis, Rhodobacter sphaeroides, Chlorobium limicola, Chlorobium tepidum, Chlamydomonas reinhardtii, Synochocystis S.6803, spinach photosystems I and II, Heliobacillus mobilis, and finally Heliobacterium modesticaldum, with the results found to qualitatively describe the available experimental data. Subsequent papers in this series provide quantitative analyses of the vibronic coupling and complete spectral simulations based on the model developed herein.
FUNCTIONALIZATION OF SEMICONDUCTOR SURFACES BY ORGANIC LAYERS: CONCERTED CYCLOADDITION VERSUS STEPWISE FREE-RADICAL REACTION MECHANISMS
Publisher: PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO.
Date: 05-2006
A priori evaluation of the solvent contribution to the reorganization energy accompanying intramolecular electron transfer: Predicting the nature of the Creutz–Taube ion
Publisher: Elsevier BV
Date: 12-2005
A Unified Description of the Electrochemical, Charge Distribution, and Spectroscopic Properties of the Special-Pair Radical Cation in Bacterial Photosynthesis
Publisher: American Chemical Society (ACS)
Date: 13-03-2004
DOI: 10.1021/JA036883M
Abstract: We apply our four-state 70-vibration vibronic-coupling model for the properties of the photosynthetic special-pair radical cation to: (1) interpret the observed correlations between the midpoint potential and the distribution of spin density between the two bacteriochlorophylls for 30 mutants of Rhodobacter sphaeroides, (2) interpret the observed average intervalence hole-transfer absorption energies as a function of spin density for six mutants, and (3) simulate the recently obtained intervalence electroabsorption Stark spectrum of the wild-type reaction center. While three new parameters describing the location of the sites of mutation with respect to the special pair are required to describe the midpoint-potential data, a priori predictions are made for the transition energies and the Stark spectrum. In general, excellent predictions are made of the observed quantities, with deviations being typically of the order of twice the experimental uncertainties. A unified description of many chemical and spectroscopic properties of the bacterial reaction center is thus provided. Central to the analysis is the assumption that the perturbations made to the reaction center, either via mutations of protein residues or by application of an external electric field, act only to independently modify the oxidation potentials of the two halves of the special pair and hence the redox asymmetry E0. While this appears to be a good approximation, clear evidence is presented that effects of mutation can be more extensive than what is allowed for. A thorough set of analytical equations describing the observed properties is obtained using the Born-Oppenheimer adiabatic approximation. These equations are generally appropriate for intervalence charge-transfer problems and include, for the first time, full treatment of both symmetric and antisymmetric vibrational motions. The limits of validity of the adiabatic approach to the full nonadiabatic problem are obtained.
The Nature of the Near-Infrared Electronic Absorption at 1250 nm in the Spectra of the Radical Cations of the Special Pairs in the Photosynthetic Reaction Centers of Rhodobacter sphaeroides and Rhodop
Publisher: American Chemical Society (ACS)
Date: 02-1995
DOI: 10.1021/JA00109A013
Synthesis And Physical Properties Of Biquinoxalinyl Bridged Bis-Porphyrins: Models For Aspects Of Photosynthetic Reaction Centres
Publisher: Royal Society of Chemistry (RSC)
Date: 2003
DOI: 10.1039/B304161A
Abstract: The synthesis of biquinoxalinyl-bridged bis-porphyrin 4 and metallated derivatives 5-11 was achieved in high yields. UV-visible spectroscopy and electrochemical experiments indicated weak orbital coupling of the two quinoxalinyl units but minimal orbital coupling between the two porphyrins. The weak electronic communication is attributed to non-planarity, on average, of the molecule because of rotation about the inter-quinoxalinyl connection. This, combined with poor coupling across the fused junctions between the porphyrin and quinoxalinyl units, results in minimal inter-porphyrin communication. As a result, the biquinoxalinyl linkage is appropriate for inclusion in more elaborate synthetic compounds, such as the tris-porphyrin 1, that are designed to model the charge-separation apparatus of Photosynthetic Reaction Centres.
Modeling the Bacterial Photosynthetic Reaction Center 3: Interpretation of Effects of Site-Directed Mutagenesis on the Special-Pair Midpoint Potential
Publisher: American Chemical Society (ACS)
Date: 12-2000
DOI: 10.1021/BI001341S
Abstract: Interpretation of changes in midpoint potential of the "special pair" in bacterial photosynthetic reaction centers caused by site-directed mutagenesis is discussed in terms of a simple tight-binding model which relates them to concomitant variations in spin distribution between the two bacteriochlorophyll molecules of the special pair. Our analysis improves on previous similar ones by Allen and co-workers [Artz, K., Williams, J. C., Allen, J. P., Lendzian, F., Rautter, J., and Lubitz, W. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 13582 Ivancich, A., Artz, K., Williams, J. C., Allen, J. P., and Mattioli, T. A. (1998) Biochemistry 37, 11812] in that it is both more complete, including electron-phonon coupling, and more accurate. It is applied to analyze data for a series of M160 mutants of Rhodobacter sphaeroides, yielding a value of 0.18+/-0.03 eV for the electronic coupling energy between the highest occupied levels of the two bacteriochlorophylls in the wild-type and a value of the energy offset E(o) between the highest occupied molecular orbitals of the L and M bacteriochlorophylls of 0.14+/-0.03 eV. For a mutant in which the electron hole in the special pair cation is located entirely on the reactive (L) side, a potential of 641+/-30 mV with respect to the normal hydrogen electrode is predicted. This agrees well with the average value ca. 650 mV observed for the heterodimer mutant HL(M202) in which the bacteriochlorophyll on the unreactive M side has been replaced by a bacteriopheophytin, causing extensive charge localization. However, the deduced coupling is found to be very sensitive to small changes in the assumptions used in the model, and various important chemical effects remain to be included.
Long-Lived Long-Distance Photochemically Induced Spin-Polarized Charge Separation In Beta,Beta '-Pyrrolic Fused Ferrocene-Porphyrin-Fullerene Systems
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C1SC00614B
Flanged nanotube–electrode junctions
Publisher: IOP Publishing
Date: 17-07-2004
Pressure-Induced Spectral Changes For The Special-Pair Radical Cation Of The Bacterial Photosynthetic Reaction Center
Publisher: AIP Publishing
Date: 06-06-2007
DOI: 10.1063/1.2739513
Abstract: The effect of pressure up to 6kbars on the near to mid infrared absorption spectrum (7500–14300cm−1 or 1333–700nm) of the oxidized reaction center of Rhodobacter sphaeroides is measured and interpreted using density-functional B3LYP, INDO, and PM5 calculations. Two weak electronic transition origins at ∼8010 and ∼10210cm−1 are unambiguously identified. The first transition is assigned to a Qy tripdoublet band that involves, in the localized description of the excitation, a triplet absorption on one of the bacteriochlorophyll molecules (PM) in the reaction center’s special pair intensified by the presence of a radical cation on the other (PL). While most chlorophyll transition energies decrease significantly with increasing pressure, the tripdoublet band is found to be almost pressure insensitive. This difference is attributed to the additional increase in the tripdoublet-band energy accompanying compression of the π-stacked special pair. The second band could either be the anticipated second Qy tripdoublet state, a Qx tripdoublet state, or a state involving excitation from a low-lying doubly occupied orbital to the half-occupied cationic orbital. A variety of absorption bands that are also resolved in the 8300–9600cm−1 region are assigned as vibrational structure associated with the first tripdoublet absorption. These sidebands are composites that are shown by the calculations to comprise many unresolved in idual modes while the calculated pressure sensitivity of each in idual mode is small, the calculated pressure dependence of the combined sideband structure is qualitatively similar to the observed pressure dependence, preventing the positive identification of possible additional electronic transitions in this spectral region.
Classical and semiclassical approximations for incoherent neutron scattering
Publisher: American Physical Society (APS)
Date: 09-1987
Reconstructing mammalian phylogenies: a detailed comparison of the cytochrome B and cytochrome oxidase subunit I mitochondrial genes.
Publisher: Public Library of Science (PLoS)
Date: 30-11-2010
Molecular dynamics of the A+BC reaction in rare gas solution
Publisher: AIP Publishing
Date: 15-11-1986
DOI: 10.1063/1.451576
Abstract: Molecular dynamics are computed for model atom transfers A+BC→AB+C in rare gas solvents at liquid densities. We find that the reaction dynamics can be understood in terms of a simple picture which consists of three stages: (1) activation of reactants, (2) barrier crossing, and (3) deactivation of products. The effects seen in stages (1) and (3) can be largely interpreted in terms of existing models of energy and phase decay in solution, while the effects seen in stage (2) can be largely interpreted in terms of gas phase A+BC barrier crossing dynamics. We find that transition state theory is in perfect agreement with the simulations for the 20 and 10 kcal/mol barrier reactions and is a very good description for a 5 kcal/mol reaction barrier. At low barrier curvature, dynamical effects due to the solvent are shown to induce some recrossings of the transition state barrier, thus causing rate constants calculated by simple transition state theory to be slightly too high. The Grote–Hynes modification of transition state theory, which considers the effect of the time dependent friction of the solvent on the dynamics at the transition state, predicts corrections to the rate constants in good agreement with the results from the simulations.
A new fundamental type of conformational isomerism.
Publisher: Springer Science and Business Media LLC
Date: 21-05-2018
DOI: 10.1038/S41557-018-0043-6
Abstract: Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol
Density-functional geometry optimization of the 150 000-atom photosystem-I trimer
Publisher: AIP Publishing
Date: 09-01-2006
DOI: 10.1063/1.2148956
Abstract: We present a linear-scaling method based on the use of density-functional theory (DFT) for the system-wide optimization of x-ray structural coordinates and apply it to optimize the 150 000 atoms of the photosystem-I (PS-I) trimer. The method is based on repetitive applications of a multilevel ONIOM procedure using the PW91∕6-31G(d) DFT calculations for the high level and PM3 for the lower level this method treats all atoms in the structure equivalently, a structure in which the majority of the atoms can be considered as part of some internal “active site.” To obtain a realistic single structure, some changes to the original protein model were necessary but these are kept to a minimum in order that the optimized structure most closely resembles the original x-ray one. Optimization has profound effects on the perceived electronic properties of the cofactors, with, e.g., optimization lowering the internal energy of the chlorophylls by on average 53kcalmol−1 and eliminates the enormous 115kcalmol−1 energy spread depicted by the original x-ray heavy-atom coordinates. A highly precise structure for PS-I results that is suitable for analysis of device function. Significant qualitative features of the structure are also improved such as correction of an error in the stereochemistry of one of the chlorophylls in the “special pair” of the reaction center, as well as the replacement of a water molecule with a metal cation in a critical region on the C3 axis. The method also reveals other unusual features of the structure, leading both to suggestions concerning device functionality and possible mutations between gene sequencing and x-ray structure determination. The optimization scheme is thus shown to augment the molecular modeling schemes that are currently used to add medium-resolution structural information to the raw scattering data in order to obtain atomically resolved structures. System-wide optimization is now a feasible process and its use within protein x-ray data refinement should be considered.
Adsorption Sites Of Maleic Anhydride On Si(100) Revisited: Inter- Versus Intra-Row Attachment
Publisher: Elsevier BV
Date: 02-2004
Molecular electronics: an Australian perspective
Publisher: CSIRO Publishing
Date: 12-07-2023
DOI: 10.1071/CH23008
Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism
Publisher: Informa UK Limited
Date: 11-11-2016
Controlling the Stereochemistry and Regularity of Butanethiol Self-Assembled Monolayers on Au(111)
Publisher: American Chemical Society (ACS)
Date: 02-12-2014
DOI: 10.1021/JA508100C
Abstract: The rich stereochemistry of the self-assembled monolayers (SAMs) of four butanethiols on Au(111) is described, the SAMs containing up to 12 in idual C, S, or Au chiral centers per surface unit cell. This is facilitated by synthesis of enantiomerically pure 2-butanethiol (the smallest unsubstituted chiral alkanethiol), followed by in situ scanning tunneling microscopy (STM) imaging combined with density functional theory molecular dynamics STM image simulations. Even though butanethiol SAMs manifest strong headgroup interactions, steric interactions are shown to dominate SAM structure and chirality. Indeed, steric interactions are shown to dictate the nature of the headgroup itself, whether it takes on the adatom-bound motif RS(•)Au(0)S(•)R or involves direct binding of RS(•) to face-centered-cubic or hexagonal-close-packed sites. Binding as RS(•) produces large, organizationally chiral domains even when R is achiral, while adatom binding leads to rectangular plane groups that suppress long-range expression of chirality. Binding as RS(•) also inhibits the pitting intrinsically associated with adatom binding, desirably producing more regularly structured SAMs.
Formation of gold-methanethiyl self-assembled monolayers.
Publisher: American Chemical Society (ACS)
Date: 08-11-2007
DOI: 10.1021/JA0743442
Abstract: The energetics of formation of thiyl-gold self-assembled monolayers is investigated using density-functional theory simulations. It is found that the chemisorption of dimethyl disulfide on the reconstructed Au(111) (22 x radical3) surface is most favored at the fcc reconstruction stripe, with initial physisorption leading to disulfide dissociation, adatom/vacancy-pair formation, and then, at a coverage of 7.8% sulfur atoms per gold atom, surface reconstruction lifting. At higher coverages, monolayer formation proceeds similarly on the unreconstructed surface, leading to surface pitting. Formation of the analogous adatom/vacancy-pair bound dissociated adsorbate complex on exposure of the clean unreconstructed surface to methanethiol is shown to be endothermic, however.
Where does this tiger come from?-A robust molecular technique for simultaneous identification of endangered species and subspecies
Publisher: Elsevier BV
Date: 12-2011
An Atomistic Approach to Conduction Between Nanoelectrodes Through a Single Molecule
Publisher: Wiley
Date: 04-2002
DOI: 10.1111/J.1749-6632.2002.TB03027.X
Abstract: Capacitance and other properties of nanoelectrodes, finite-size metal clusters envisaged for use in complex molecular-electronic devices, are discussed. The applicability of classical electrostatics (Coulomb's and Gauss' law, Poisson's equation, etc.) to atomistic systems is investigated and the self-energy necessary to store a finite charge on an atom is found to be of central importance. In particular, the neglect of electron exchange is found to introduce severe limitations, with quantum calculations predicting fundamentally different electronic structures. Also, the well-known poor representation of the atomic self-energy inherent to modern DFT is discussed, along with its implications for molecular electronics calculations. An INDO/S method is introduced with new parameters for gold. This is the simplest approximate computational scheme that correctly includes quantum electrostatic, resonance, and spin effects, and is capable of describing arbitrary excited electronic states. Encouraging results are obtained for some trial problems. In particular, voltage differential between the electrodes in electrode-molecule-electrode conduction is obtained, not through an a priori prescription but rather by moving whole electrons between the electrodes and analyzing the response. The voltage drops across the molecule-electrode junctions and the central molecular region are then deduced. This alternative to the current Landauer-based 1-particle transmission equations for electrode-molecule-electrode conduction is discussed in terms of the use of the electronic states of the system. It provides a proper description not only of conduction via electrode-to-molecule charge or hole transfer but also of conduction via simultaneous charge and hole transfer via low-lying excited molecular electronic states, including the ability to account for electroluminescence and other chemical effects. In addition, various aspects of our research on the quantitative prediction of the I(V) curves for electrode-molecule-electrode conduction are reviewed, including demonstration of the equivalence of the formalisms generated by the Datta and the Mujica-Ratner groups, and the development of analytically solvable paradigms, including the conduction through a linear-chain Hückel wire.
Ab Initio and Density-Functional Calculations of the Vibrational Structure of the Singlet and Triplet Excited States of Pyrazine
Publisher: American Chemical Society (ACS)
Date: 12-11-1999
DOI: 10.1021/JP991404K
The Mechanism Of Inner-Hydrogen Migration In Free-Base Porphyrin - Ab-Initio Mp2 Calculations
Publisher: American Chemical Society (ACS)
Date: 03-1995
DOI: 10.1021/JA00115A018
Edge effects on optically detected magnetic resonance of vacancy defects in hexagonal boron nitride
Publisher: Springer Science and Business Media LLC
Date: 31-08-2012
DOI: 10.1038/S42005-020-00416-Z
Abstract: The chemical and structural nature of defects responsible for quantum emission in hexagonal boron nitride (h-BN) remain unknown. Optically detected magnetic resonance (ODMR) measured from these defects was reported in two recent papers. In one case, the ODMR was tentatively attributed to the negatively charged boron vacancy, $$V_{\\mathrm{B}}^ -$$ V B − . Here we show how the key optical and magnetic properties vary with location within the bulk and along edges of h-BN sheets for this and the negatively charged nitrogen vacancy, $$V_{\\mathrm{N}}^ -$$ V N − . Sign changes of the axial zero-field interaction parameter D are predicted, as well interchange of singlet and triplet ground states. Based on the latest experimental information, we assign the observed ODMR signal to bulk $$V_{\\mathrm{B}}^ -$$ V B − . The other observed ODMR has some features reminiscent of our calculations for $$V_{\\mathrm{N}}^ -$$ V N − edge defects.
Chemical Control of Tautomerization‐Based Molecular Electronic and Color Switches
Publisher: Wiley
Date: 06-1998
Dipole Order in Halide Perovskites: Polarization and Rashba Band Splittings
Publisher: American Chemical Society (ACS)
Date: 06-07-0095
Chlorophyll spectroscopy: conceptual basis, modern high-resolution approaches, and current challenges
Publisher: Estonian Academy Publishers
Date: 2022
The Nature of the Special‐pair Radical Cation Produced by Primary Charge Separation During Photosynthesis
Publisher: Wiley
Date: 05-08-2005
Demonstration and interpretation of significant asymmetry in the low-resolution and high-resolution Q y fluorescence and absorption spectra of bacteriochlorophyll a<
Publisher: AIP Publishing
Date: 11-01-2011
DOI: 10.1063/1.3518685
Abstract: Low- and high-resolution absorption and fluorescence emission Qy spectra of bacteriochlorophyll a (BChl a) were recorded, along with homogeneous band line shapes, revealing significant asymmetry between the absorption and emission profiles that are interpreted using a priori spectral calculations. The spectra were recorded in a range of organic solvents facilitating both penta- and hexa-coordination of Mg at ambient and cryogenic temperatures. Detailed vibrational structure in the ground electronic state, virtually independent of Mg coordination, was revealed at 4.5 K by a hole-burning fluorescence line-narrowing technique, complementing the high-resolution spectrum of the excited state measured previously by hole burning to provide the first complete description of the Qy absorption and fluorescence spectra of BChl a. Spectral asymmetry persists from 4.5 to 298 K. Time-dependent density-functional theory calculations of the gas-phase absorption and emission spectra obtained using the CAM-B3LYP density functional, curvilinear coordinates, and stretch-bend-torsion scaling factors fitted to data for free-base porphyrin quantitatively predict the observed frequencies of the most-significant vibrational modes as well as the observed absorption/emission asymmetry. Most other semi-empirical, density-functional, and ab initio computational methods severely overestimate the electron-vibrational coupling and its asymmetry. It is shown that the asymmetry arises primarily through Duschinsky rotation.
Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events
Publisher: Cold Spring Harbor Laboratory
Date: 04-01-2018
DOI: 10.1101/241448
Abstract: The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that recent uplift of previously submerged portions of land on Sulawesi promoted ersification, and that much of the its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesi’s three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that recent emergence of land on Sulawesi (~1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicates that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
Modeling the Bacterial Photosynthetic Reaction Center. 2. A Combined Quantum Mechanical/Molecular Mechanical Study of the Structure of the Cofactors in the Reaction Centers of Purple Bacteria
Publisher: American Chemical Society (ACS)
Date: 25-05-1999
DOI: 10.1021/JP9833808
Simulation Of The Au(111)-(22 X Root 3) Surface Reconstruction
Publisher: American Physical Society (APS)
Date: 27-06-2007
Ab Initio and Density Functional Calculations of the Energies of the Singlet and Triplet Valence Excited States of Pyrazine
Publisher: American Chemical Society (ACS)
Date: 03-11-1999
DOI: 10.1021/JP991403S
Challenges for the Accurate Simulation of Anisotropic Charge Mobilities through Organic Molecular Crystals: The β Phase of mer-Tris(8-hydroxyquinolinato)aluminum(III) (Alq3) Crystal
Publisher: American Chemical Society (ACS)
Date: 03-07-2012
DOI: 10.1021/JP303724R
Silicon - single molecule - silicon circuits.
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1SC04943G
Abstract: Single-molecule circuits using silicon contacts are robust, conductive, controllable, and highly reproducible in blinking experiments, with enhanced conductance in break-junctions owing to residual dangling bonds.
Molecular Origins of Conduction Channels Observed in Shot-Noise Measurements
Publisher: American Chemical Society (ACS)
Date: 27-09-2006
DOI: 10.1021/NL0614516
Abstract: Measurements of shot noise from single molecules have indicated the presence of various conduction channels. We present three descriptions of these channels in molecular terms showing that the number of conduction channels is limited by bottlenecks in the molecule and that the channels can be linked to transmission through different junction states. We introduce molecular-conductance orbitals, which allow the transmission to be separated into contributions from in idual orbitals and contributions from interference between pairs of orbitals.
Solvent Effects on Molecular and Ionic Spectra. 4. Photochemistry of Fe2+(H2O)6 in Water Revisited: Possible Mechanisms for the Primary Absorption Process Leading to Electron Ejection
Publisher: American Chemical Society (ACS)
Date: 10-1994
DOI: 10.1021/J100094A015
Single-photon emitters in hexagonal boron nitride: a review of progress
Publisher: IOP Publishing
Date: 17-03-2020
Abstract: This report summarizes progress made in understanding properties such as zero-phonon-line energies, emission and absorption polarizations, electron-phonon couplings, strain tuning and hyperfine coupling of single photon emitters in hexagonal boron nitride. The primary aims of this research are to discover the chemical nature of the emitting centres and to facilitate deployment in device applications. Critical analyses of the experimental literature and data interpretation, as well as theoretical approaches used to predict properties, are made. In particular, computational and theoretical limitations and challenges are discussed, with a range of suggestions made to overcome these limitations, striving to achieve realistic predictions concerning the nature of emitting centers. A symbiotic relationship is required in which calculations focus on properties that can easily be measured, whilst experiments deliver results in a form facilitating mass-produced calculations.
Unit cells for the simulation of hexagonal ice
Publisher: AIP Publishing
Date: 22-01-1997
DOI: 10.1063/1.473300
Abstract: A number of periodic lattices have historically been used to represent ice-1h in computer simulations. These vary in size, shape, and method of generation, and while they have served their intended purposes, their properties have rarely been documented in detail and their intercompatibility is unknown. We develop a method for generating sets of internally consistent lattices and apply it to determine eight unit cells containing from 96 to 768 water molecules in both near-cubic and slab arrangements. It can easily be applied to generate additional (larger) cells or representations of specific crystal faces. Each unit cell in this set has zero net dipole moment and minimal net quadrupole moment and is optimized using four different criteria to measure the randomness of the hydrogen bonding if required, these criteria can easily be modified to suit the intended application and alternate sets thus generated. We find that Cota and Hoover’s much used constraint for selecting unit cells with zero dipole moment is too restrictive, not permitting a fully random hydrogen-bonding network also, unit-cell generation methods based on potential-energy minimization are found to prefer unrepresentative, highly ordered structures.
Identifying Carbon as the Source of Visible Single Photon Emission from Hexagonal Boron Nitride
Publisher: arXiv
Date: 2020
van der Waals Forces Control the Internal Chemical Structure of Monolayers within the Lamellar Materials CuInP2S6 and CuBiP2Se6
Publisher: American Chemical Society (ACS)
Date: 05-09-2018
Formation of water-chlorophyll clusters in dilute samples of chlorophyll-a in ether at low temperature
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3CP53729C
Abstract: Simultaneously measured absorption (ABS) and magnetic circular dichroism (MCD) spectra of the Q-bands of chlorophyll-a (Chl-a) in ether over 150-186 K reveal that the species that forms at low temperature is a chlorophyll hydrate rather than a diether complex. We have recently proposed a new assignment paradigm for the spectra of chlorophillides which, for the first time, quantitatively accounts for a wide range of observed data. Observations performed at low temperature in ether have historically been very important for the interpretation of the spectra of Chl-a. While our assignment for this system initially anticipated only small spectral changes as the temperature is lowered, significant changes are known to occur. Extensive CAM-B3LYP time-dependent density-functional theory (TD-DFT) calculations verify that the observed spectra of the hydrated species conforms to expectations based on our new assignment, as well as supporting the feasibility of the proposed hydration reactions.
The Infrared Absorption Spectrum of Water
Publisher: CSIRO Publishing
Date: 1982
DOI: 10.1071/PH820623
Abstract: A combination of quantum calculations and Monte Carlo methods is used to predict the infrared absorption spectrum of the water monomer, water dimer and the pure liquid. Full quantum calculations using internal coordinates are used to fit three Morse oscillators to the fundamental and overtone vibrations of the water monomer. This intramolecular potential is then combined with an accurate intermolecular surface to calculate the dimer spectrum from a normal mode analysis and from classical trajectory studies. The liquid state spectrum is obtained using a Monte Carlo simulation program together with a sequence of normal mode analyses of representative molecular configurations. Results are in good agreement with available experimental data suggesting that the potential energy surfaces used are reasonably accurate.
Control Of The Orbital Delocalization And Implications For Molecular Rectification In The Radical Anions Of Porphyrins With Coplanar 90 Degrees And 180 Degrees Beta,Beta '-Fused Extensions
Publisher: American Chemical Society (ACS)
Date: 2008
DOI: 10.1021/JP076406G
Abstract: Through-porphyrin electronic communication is investigated using "linear-type" and "corner-type" bis(quinoxalino)porphyrins in free-base form and their ZnII, CuII, NiII, and PdII derivatives. These compounds are porphyrins with quinoxalines fused on opposite or adjacent beta,beta'-pyrrolic positions they were synthesized from 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)-porphyrin-2,3,12,13- and -2,3,7,8-tetraone, respectively, by reaction with 1,2-phenylenediamine. The degree of electron spin delocalization into the fused rings in the pi-radical anions of the free-base and metal(II) bisquinoxalinoporphyrins was elucidated by electrochemistry, UV-vis absorption, and electron spin resonance (ESR) spectra of the singly reduced species and density functional theory calculations. Hyperfine splitting patterns in the ESR spectra of the pi-radical anions show that symmetric molecules have delocalized electron spin, indicating that significant inter-quinoxaline interactions are mediated through the central porphyrin unit, these interactions being sufficient to guarantee through-molecule conduction. However, when molecular symmetry is broken by tautomeric exchange of the inner nitrogen hydrogens in the free-base porphyrin with a corner-type quinoxaline substitution pattern, the pi-radical anion becomes confined so that one quinoxaline group is omitted from spin delocalization. This indicates the appearance of a unidirectional barrier to through-molecule conduction, suggesting a new motif for chemically controlled rectification.
Cyanine platelet single crystals: growth, crystal structure and optical spectra
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8CP06034G
Abstract: Micro transmittance spectroscopy of ultrathin crystalline organic salt semiconductors reveals strong low-energy and weak high-energy bands polarized along the crystallographic b - and c -axis. While the excitonic coupling pattern explains the occurrence of polarized bands, the observed intensities are opposite of expectations based on chromophore alignment within the crystal.
The Low-Lying Excited States of Pyridine
Publisher: American Chemical Society (ACS)
Date: 18-08-2000
DOI: 10.1021/JP000962S
Energy flow in the Photosystem I supercomplex: Comparison of approximative theories with DM-HEOM
Publisher: Elsevier BV
Date: 11-2018
The influence of spin-forbidden monomer excitations on spin-allowed electron transfer and electron-localized states of mixed-valence and single-valence dimeric systems
Publisher: Elsevier BV
Date: 11-1994
Time-dependent density-functional determination of arbitrary singlet and triplet excited-state potential energy surfaces: Application to the water molecule
Publisher: AIP Publishing
Date: 11-2000
DOI: 10.1063/1.1312826
Abstract: Over the past few years a large number of density-functional schemes have been developed for molecular excited states, many of which have been shown to produce poor results for water. We apply the time-dependent density-functional method using hybrid and asymptotically corrected functionals to evaluate the vertical excitation energies, C2v-relaxation energies and vibration frequencies, and dissociation pathways for up to eight singlet and six triplet excited states of water. The results are compared to experimental data as well as ab initio calculated data obtained using direct and equations-of-motion coupled-cluster techniques, as well as multireference configuration-interaction techniques. For most properties, the asymptotically corrected density-functional method produces results of comparable quality to those produced by the ab initio methods. However, the time-dependent methods produce very poor results for systems involving molecular dissociation. In fact, only the multireference approaches produce good descriptions of molecular dissociation, but in the regions of the (C2v) minima of the potential energy surfaces single-reference techniques are found to be both more accurate and much more robust.
Electron transfer and energy transfer through bridged systems III. Tight-binding linkages with zero or non-zero asymptotic band gap
Publisher: Elsevier BV
Date: 08-1994
Understanding non-linear effects from Hill-type dynamics with application to decoding of p53 signaling
Publisher: Springer Science and Business Media LLC
Date: 02-2018
DOI: 10.1038/S41598-018-20466-2
Abstract: Analytical equations are derived depicting four possible scenarios resulting from pulsed signaling of a system subject to Hill-type dynamics. Pulsed Hill-type dynamics involves the binding of multiple signal molecules to a receptor and occurs e.g., when transcription factor p53 orchestrates cancer prevention, during calcium signaling, and during circadian rhythms. The scenarios involve: (i) enhancement of high-affinity binders compared to low-affinity ones, (ii) slowing reactions involving high-affinity binders, (iii) transfer of the clocking of low-affinity binders from the signal molecule to the products, and (iv) a unique clocking process that produces incremental increases in the activity of high-affinity binders with each signal pulse. In principle, these mostly non-linear effects could control cellular outcomes. An applications to p53 signaling is developed, with binding to most gene promoters identified as category (iii) responses. However, currently unexplained enhancement of high-affinity promoters such as CDKN1a (p21) by pulsed signaling could be an ex le of (i). In general, provision for all possible scenarios is required in the design of mathematical models incorporating pulsed Hill-type signaling as some aspect.
Solving the scalability issue in quantum-based refinement: Q|R#1.
Publisher: International Union of Crystallography (IUCr)
Date: 30-11-2017
DOI: 10.1107/S2059798317016746
Abstract: Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately as n m , where n is the number of atoms and m (≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package called Q | R , this issue is referred to as Q|R#1. A ide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1. Firstly, the atomic model of a crystal structure is analyzed to detect noncovalent interactions between residues, and the results of the analysis are represented as an interaction graph. Secondly, a graph-clustering algorithm is used to partition the interaction graph into a set of clusters in such a way as to minimize disruption to the noncovalent interaction network. Thirdly, the environment surrounding each in idual cluster is analyzed and any residue that is interacting with a particular cluster is assigned to the buffer region of that particular cluster. A fragment is defined as a cluster plus its buffer region. The gradients for all atoms from each of the fragments are computed, and only the gradients from each cluster are combined to create the total gradients. A quantum-based refinement is carried out using the total gradients as chemical restraints. In order to validate this interaction graph-based fragmentation approach in Q | R , the entire atomic model of an amyloid cross-β spine crystal structure (PDB entry 2oNA) was refined.
Intermolecular potential functions and the properties of water
Publisher: Elsevier BV
Date: 1982
Towards a comprehensive model for the electronic and vibrational structure of the Creutz–Taube ion
Publisher: The Royal Society
Date: 07-09-2007
Abstract: Since the synthesis of the Creutz–Taube ion, the nature of its charge localization has been of immense scientific interest, this molecule providing a model system for the understanding of the operation of biological photosynthetic and electron-transfer processes. However, recent work has shown that its nature remains an open question. Many systems of this type, including photosynthetic reaction centres, are of current research interest, and thereby the Creutz–Taube ion provides an important chemical paradigm: the key point of interest is the details of how such molecules behave. We lay the groundwork for the construction of a comprehensive model for its chemical and spectroscopic properties. Advances are described in some of the required areas including: simulation of electronic absorption spectra quantitative depiction of the large interaction of the ion's electronic description with solvent motions and the physics of Ru–NH 3 spectator-mode vibrations. We show that details of the solvent electron–phonon coupling are critical in the interpretation of the spectator-mode vibrations, as these strongly mix with solvent motions when 0.75 J / λ . In this regime, a double-well potential exists which does not support localized zero-point vibration, and many observed properties of the Creutz–Taube ion are shown to be consistent with the hypothesis that the ion has this character.
Scanning Tunneling Microscopic Observation Of Adatom-Mediated Motifs On Gold-Thiol Self-Assembled Monolayers At High Coverage
Publisher: American Chemical Society (ACS)
Date: 17-08-0012
DOI: 10.1021/JP906216K
Establishing a Core Outcome Set for Autosomal Dominant Polycystic Kidney Disease: Report of the Standardized Outcomes in Nephrology-Polycystic Kidney Disease (SONG-PKD) Consensus Workshop.
Publisher: Elsevier BV
Date: 02-2020
Understanding and Calibrating Density-Functional-Theory Calculations Describing the Energy and Spectroscopy of Defect Sites in Hexagonal Boron Nitride.
Publisher: American Chemical Society (ACS)
Date: 07-02-2018
Abstract: Defect states in 2-D materials present many possible uses but both experimental and computational characterization of their spectroscopic properties is difficult. We provide and compare results from 13 DFT and ab initio computational methods for up to 25 excited states of a paradigm system, the V
Assessing the detectability of antioxidants in two-dimensional high-performance liquid chromatography.
Publisher: Wiley
Date: 17-04-2015
Abstract: This paper explores the analytical figures of merit of two-dimensional high-performance liquid chromatography for the separation of antioxidant standards. The cumulative two-dimensional high-performance liquid chromatography peak area was calculated for 11 antioxidants by two different methods--the areas reported by the control software and by fitting the data with a Gaussian model these methods were evaluated for precision and sensitivity. Both methods demonstrated excellent precision in regards to retention time in the second dimension (%RSD below 1.16%) and cumulative second dimension peak area (%RSD below 3.73% from the instrument software and 5.87% for the Gaussian method). Combining areas reported by the high-performance liquid chromatographic control software displayed superior limits of detection, in the order of 1 × 10(-6) M, almost an order of magnitude lower than the Gaussian method for some analytes. The introduction of the countergradient eliminated the strong solvent mismatch between dimensions, leading to a much improved peak shape and better detection limits for quantification.
“The molecules and methods of chemical, biochemical, and nanoscale electron transfer”
Publisher: Elsevier BV
Date: 07-2006
Physically based molecular device model in a transient circuit simulator
Publisher: Elsevier BV
Date: 07-2006
“The molecules and methods of chemical, biochemical, and nanoscale electron transfer”
Publisher: Elsevier BV
Date: 05-2006
Penrose-Hameroff Orchestrated Objective-Reduction Proposal For Human Consciousness Is Not Biologically Feasible
Publisher: American Physical Society (APS)
Date: 13-08-2009
The critical role of the transition-state cusp diameter in understanding adiabatic and non-adiabatic electron transfer
Publisher: Pleiades Publishing Ltd
Date: 09-2017
Construction Of Building Blocks For Extended Porphyrin Arrays By Nitration Of Porphyrin-2,3-Diones And Quinoxalino[2,3-B]Porphyrins
Publisher: Royal Society of Chemistry (RSC)
Date: 2008
DOI: 10.1039/B712643C
Faraday cage screening reveals intrinsic aspects of the van der Waals attraction.
Publisher: Proceedings of the National Academy of Sciences
Date: 16-10-2018
Abstract: How the van der Waals dispersion interaction relates to chemical electron-correlation effects presents a critical challenge to density functional theory development. Here, recently observed screening of the dispersion force between two insulating objects caused by the insertion of an intermediary graphene layer is explained in terms of Dobson’s general description of dispersion. This then provides a much-needed handle concerning how density functional approaches relate such long-range dispersion interactions to the subtleties of covalent bonding. Screening at intermediate distances appears to change the London expression from r −6 to r −7 , an effect that becomes antiscreening (dispersion enhancement) at distances shorter than van der Waals contact. This provides basic insight into modern revelations that dispersion forces can outcompete covalent forces to control chemical structure.
Electron transfer and energy transfer through bridged systems. 5. Intermetallic coupling and electronic spectra of the bis(pentaammineruthenium) complexes of .alpha.,.omega.-dipyridyl trans-polyenes i
Publisher: American Chemical Society (ACS)
Date: 10-1990
DOI: 10.1021/IC00347A035
Cytochrome b or cytochrome c oxidase subunit I for mammalian species identification-An answer to the debate
Publisher: Elsevier BV
Date: 12-2009
An analytical data inversion method for magnetic circular dichroism spectra dominated by the “B-term”
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3CP53730G
Abstract: A simple procedure is developed enabling the analytical inversion of an (unpolarized) absorption spectrum combined with a Magnetic Circular Dichroism (MCD) spectrum to resolve two overlapping bands of orthogonal polarization. This method is appropriate when (i) the overlapping transitions are well isolated from other bands, and (ii) when their electronic spacing is large enough so that the "A-term" and "C-term" contributions to the MCD spectrum can be ignored and hence only the "B-term" contribution need be considered. We apply this procedure to assign the Q-band system of chlorophylls, though similar challenges also commonly arise throughout both conventional and X-ray MCD (XMCD) spectroscopy. Analytical data inversion has not previously been possible as the inversion process is two-fold underdetermined. We show that the assumptions of isolated spectra and "B-term" dominance yields one generally valid constraint, leaving only one quantity unspecified by the experimental data. For some systems, an approximation leading to equal but opposite sign B-term magnitudes of the two components may be reasonable, but for chlorophyllides we find this constraint to be inappropriate. Instead, we constrain a bounded variable controlling the relative absorption strengths. Derived spectral bandshapes of the in idual components are shown to be insensitive to its particular value, allowing weak spectral components of one polarization overlapped by intense components of the other to be immediately exposed. This is demonstrated for the chlorophylls, molecules for which the failure to detect such weak features historically led to incorrect proposals for the Q-band assignments.
Covalent Linkages of Molecules and Proteins to Si-H Surfaces Formed by Disulfide Reduction.
Publisher: American Chemical Society (ACS)
Date: 03-12-2020
Predicting layered itinerant magnetic Fe3SiSe2 with spontaneous valley polarization
Publisher: AIP Publishing
Date: 26-05-2023
DOI: 10.1063/5.0125336
Abstract: Density functional theory calculations are performed to systematically investigate the electronic and magnetic properties of few-layer and bulk Fe3SiSe2 (FSS). We predict that the bulk FSS has a metallic ground state and a layered structure displaying intralayer ferromagnetic ordering and interlayer antiferromagnetic ordering. The itinerant magnetism in the FSS was determined by the Stoner criterion. Predictions of the absence of unstable phonon modes and a moderate cleavage energy of only 28.3 meV/Å2 suggest the possibility of stabilizing FSS in a monolayer form. The calculated spin–orbit coupling facilitates not only a large magnetocrystalline anisotropy energy, around 500 μeV/Fe, but also spontaneous valley polarization in odd-numbered layer systems. These systems have net magnetic moments as the magnetic moments of AFM-ordered layers are not fully compensated in the odd-numbered layer case and are predicted to show 2D metallic behaviors. The magnitude of the valley polarization in odd-numbered layered systems decreases from 18 meV with layer number but is absent in even-layered structures, thus showing an odd–even oscillation effect. Experimental realization of this bidimensional metallic magnet is, therefore, expected to widen the arena of two-dimensional materials that show exotic phenomena.
Vibrational Stark Spectroscopy. 2. Application to the CN Stretch in HCN and Acetonitrile
Publisher: American Chemical Society (ACS)
Date: 1996
DOI: 10.1021/JP9523985
Multistate density functional theory applied with 3 unpaired electrons in 3 orbitals: The singdoublet and tripdoublet states of the ethylene cation
Publisher: Elsevier BV
Date: 12-2019
Rigid Fused Oligoporphyrins As Potential Versatile Molecular Wires. 2. B3Lyp And Scf Calculated Geometric And Electronic Properties Of 98 Oligoporphyrin And Related Molecules
Publisher: American Chemical Society (ACS)
Date: 18-05-1999
DOI: 10.1021/JP982650J
Macrocyclic Ligand Design. X-Ray, Dft And Solution Studies Of The Effect Of N-Methylation And N-Benzylation Of 1,4,10,13-Tetraoxa-7,16-Diazacyclooctadecane On Its Affinity For Selected Transition And Post-Transition Metal Ions
Publisher: Royal Society of Chemistry (RSC)
Date: 2001
DOI: 10.1039/B008789K
A priori method for propensity rules for inelastic electron tunneling spectroscopy of single-molecule conduction
Publisher: American Physical Society (APS)
Date: 25-05-2007
Models for the Structure and Electronic Transmission of Carbon Nanotubes Covalently Linked by a Molecular Bridge via Amide Couplings
Publisher: American Chemical Society (ACS)
Date: 10-02-2007
DOI: 10.1021/JP0659958
Single molecule conductivity: The role of junction-orbital degeneracy in the artificially high currents predicted by ab initio approaches
Publisher: AIP Publishing
Date: 10-2004
DOI: 10.1063/1.1791011
Abstract: A priori evaluations, using Hartree–Fock self-consistent-field (SCF) theory or density-functional theory (DFT), of the current passing between two electrodes through a single bridging molecule result in predicted conductivities that may be up to one to two orders of magnitude larger than observed ones. We demonstrate that this is, in part, often due to the improper application of the computational methods. Conductivity is shown to arise from tunneling between junction states of the electrodes through the molecule these states are inherently either quasi two-fold or four-fold degenerate and always comprise the (highest occupied molecular orbital) HOMO band at the Fermi energy of the system. Frequently, in previous cluster based molecular conduction calculations, closed-shell SCF or Kohn–Sham DFT methods have been applied to systems that we demonstrate to be intrinsically open shell in nature. Such calculations are shown to induce artificial HOMO-LUMO (LUMO—lowest unoccupied molecular orbital) band splittings that Landauer-based formalisms for steady-state conduction interpret as arising from extremely rapid through-molecule tunneling at the Fermi energy, hence, overestimating the low-voltage conductivity. It is demonstrated that these shortcomings can be eliminated, dramatically reducing calculated current magnitudes, through the alternate use of electronic-structure calculations based on the spin-restricted open-shell formalism and related multiconfigurational SCF of DFT approaches. Further, we demonstrate that most anomalies arising in DFT implementations arise through the use of hybrid density functionals such as B3LYP. While the enhanced band-gap properties of these functionals have made them the defacto standard in molecular conductivity calculations, we demonstrate that it also makes them particularly susceptible to open-shell anomalies.
Back matter
Publisher: Royal Society of Chemistry (RSC)
Date: 2008
DOI: 10.1039/B820726G
Dissociated Water On Si(100): Relation Between Stm Topograph And Actual Geometry
Publisher: World Scientific Pub Co Pte Lt
Date: 04-2004
DOI: 10.1142/S0218625X04006049
Abstract: We have modeled the dissociative chemisorption of water on the Si (100)-(2×1) surface using a generalized gradient approximation of density functional theory and a periodic slab model of the surface. For the energetically favorable structures, scanning tunneling microscope topographs of the filled states are simulated. These exhibit distinctively dark characteristics where water "islands" are formed, in agreement with experimental findings. In addition, they indicate that the hydrogen-atom and hydroxyl-radical adducts display somewhat different contrasts. Furthermore, in the case of a partial saturation of a Si dimer a prominent brightness is predicted for the unsaturated Si atoms if their dimer-forming counterparts are saturated by hydroxyl species, while in the case of hydrogen saturation the contrast is rather dim.
Complexation, computational, magnetic, and structural studies of the maillard reaction product isomaltol including investigation of an uncommon π interaction with copper(II)
Publisher: American Chemical Society (ACS)
Date: 26-01-2011
DOI: 10.1021/IC102117D
Abstract: The metal complexation properties of the naturally occurring Maillard reaction product isomaltol HL(2) are investigated by measurement of its stability constants with copper(II), zinc(II), and iron(III) using potentiometric pH titrations in water, by structural and magnetic characterization of its crystalline complex, [Cu(L(2))(2)]·8H(2)O, and by density functional theory calculations. Strong complexation is observed to form the bis(isomaltolato)copper(II) complex incorporating copper in a typical (pseudo-)square-planar geometry. In the solid state, extensive intra- and intermolecular hydrogen bonding involving all three oxygen functions per ligand assembles the complexes into ribbons that interact to form two-dimensional arrays further hydrogen bonds and π interactions between the furan moiety of the anionic ligands and adjacent copper(II) centers connect the complexes in the third dimension, leading to a compact polymeric three-dimensional (3D) arrangement. The latter interactions involving copper(II), which represent an underappreciated aspect of copper(II) chemistry, are compared to similar interactions present in other copper(II) 3D structures showing interactions with benzene molecules the results indicate that dispersion forces dominate in the π system to chelated copper(II) ion interactions.
Understanding And Improving Solid-State Polymer/C-60-Fullerene Bulk-Heterojunction Solar Cells Using Ternary Porphyrin Blends
Publisher: American Chemical Society (ACS)
Date: 10-2007
DOI: 10.1021/JP0748664
An assessment of the genetic diversity of the founders of the European captive population of Asian lion (Panthera leo leo), using microsatellite markers and studbook analysis
Publisher: Springer Science and Business Media LLC
Date: 2018
Optimization And Chemical Control Of Porphyrin-Based Molecular Wires And Switches
Publisher: Wiley
Date: 06-1998
Rigid Fused Oligoporphyrins As Potential Versatile Molecular Wires .1. Geometry And Connectivity Of 1,4,5,8-Tetraazaanthracene-Bridged Systems
Publisher: American Chemical Society (ACS)
Date: 11-1994
DOI: 10.1021/J100097A013
Assigning confidence to sequence comparisons for species identification: A detailed comparison of the cytochrome b and cytochrome oxidase subunit I mitochondrial genes
Publisher: Elsevier BV
Date: 12-2011
Application of time-dependent density-functional theory to the Σu−3 first excited state of H2
Publisher: AIP Publishing
Date: 08-01-2000
DOI: 10.1063/1.480544
Abstract: Recently, time-dependent density-functional (TDDFT) methods have been developed for determining the energies of molecular excited states. This, along with the somewhat similar equations-of-motion coupled-cluster (EOM-CCSD) methods, offer advantages of speed, reliability, and often accuracy over alternate complete-active-space self-consistent-field (CASSCF) based approaches, with the disadvantages associated with being essentially “single-reference” calculations. We compare results obtained using both approaches for the Σg+1 (ground) and Σu−3 (first excited) states of the simplest molecule, H2. For the excited state of this two-electron system, EOM-CCSD is equivalent to full configuration interaction, while results obtained using TDDFT are good at short bond lengths but become quite poor as the bond is stretched from its equilibrium length. The poor TDDFT result is attributed to the fact that the spin-restricted Kohn–Sham (RKS) method used to generate the ground-state density is not size consistent. We suggest that TDDFT calculations based on spin-unrestricted Kohn–Sham (UKS) calculations should provide better descriptions of molecular excited states than do current RKS-based methods, spin-contamination effects notwithstanding.
Charge Delocalization in the Special-Pair Radical Cation of Mutant Reaction Centers of Rhodobacter sphaeroides from Stark Spectra and Nonadiabatic Spectral Simulations
Publisher: American Chemical Society (ACS)
Date: 30-08-2006
DOI: 10.1021/JP0623894
Abstract: Stark and absorption spectra for the hole-transfer band of the bacteriochlorophyll special pair in the wild-type and L131LH, M160LH, and L131LH/M160LH mutants of the bacterial reaction center of Rhodobacter sphaeroides are presented, along with extensive analyses based on nonadiabatic spectral simulations. Dramatic changes in the Stark spectra are induced by the mutations, changes that are readily interpreted in terms of the redox-energy asymmetry and degree of charge localization in the special-pair radical cation. The effect of mutagenesis on key properties such as the electronic coupling within the special pair and the reorganization energy associated with intervalence hole transfer are determined for the first time. Results for the L131LH and M160LH/L131LH mutants indicate that these species can be considered as influencing the special pair primarily through modulation of the redox asymmetry, as is usually conceptualized, but M160LH is shown to develop a wide range of effects that can be interpreted in terms of significant mutation-induced structural changes in and around the special pair. The nonadiabatic spectra simulations are performed using both a simple two-state 1-mode and an extensive four-state 70-mode model, which includes the descriptions of additional electronic states and explicitly treats the major vibrational modes involved. Excellent agreement between the two simulation approaches is obtained. The simple model is shown to reproduce key features of the Stark effect of the main intervalence transition, while the extensive model quantitatively reproduces most features of the observed spectra for both the electronic and the phase-phonon regions, thus giving a more comprehensive description of the effect of the mutations on the properties of the special-pair radical cation. These results for a series of closely related mixed-valence complexes show that the Stark spectra provide a sensitive indicator for the properties of the mixed-valence complexes and should serve as an instructive ex le on the application of nonadiabatic simulations to the study of mixed-valence complexes in general as well as other chemical systems akin to the photosynthetic special pair.
An azanorbornadiene anchor for molecular-level construction on silicon(100)
Publisher: IOP Publishing
Date: 22-12-2004
The Need for Quantum-Mechanical Treatment of Capacitance and Related Properties of Nanoelectrodes
Publisher: American Chemical Society (ACS)
Date: 10-08-2001
DOI: 10.1021/JP011023I
Evidence of the three main clonal Toxoplasma gondii lineages from wild mammalian carnivores in the UK.
Publisher: Cambridge University Press (CUP)
Date: 19-08-2013
DOI: 10.1017/S0031182013001169
Abstract: Toxoplasma gondii is a zoonotic pathogen defined by three main clonal lineages (types I, II, III), of which type II is most common in Europe. Very few data exist on the prevalence and genotypes of T. gondii in the UK. Wildlife can act as sentinel species for T. gondii genotypes present in the environment, which may subsequently be transmitted to livestock and humans. DNA was extracted from tissue s les of wild British carnivores, including 99 ferrets, 83 red foxes, 70 polecats, 65 mink, 64 badgers and 9 stoats. Parasite DNA was detected using a nested ITS1 PCR specific for T. gondii , PCR positive s les were subsequently genotyped using five PCR–RFLP markers. Toxoplasma gondii DNA was detected within all these mammal species and prevalence varied from 6·0 to 44·4% depending on the host. PCR–RFLP genotyping identified type II as the predominant lineage, but type III and type I alleles were also identified. No atypical or mixed genotypes were identified within these animals. This study demonstrates the presence of alleles for all three clonal lineages with potential for transmission to cats and livestock. This is the first DNA-based study of T. gondii prevalence and genotypes across a broad range of wild British carnivores.
Formalism for Electron Transfer and Energy Transfer in Bridged Systems
Publisher: American Chemical Society
Date: 05-05-1989
Intermixed Adatom and Surface‐Bound Adsorbates in Regular Self‐Assembled Monolayers of Racemic 2‐Butanethiol on Au(111)
Publisher: Wiley
Date: 03-02-2015
Abstract: In situ scanning tunneling microscopy combined with density functional theory molecular dynamics simulations reveal a complex structure for the self-assembled monolayer (SAM) of racemic 2-butanethiol on Au(111) in aqueous solution. Six adsorbate molecules occupy a (10×√3)R30° cell organized as two RSAuSR adatom-bound motifs plus two RS species bound directly to face-centered-cubic and hexagonally close-packed sites. This is the first time that these competing head-group arrangements have been observed in the same ordered SAM. Such unusual packing is favored as it facilitates SAMs with anomalously high coverage (30%), much larger than that for enantiomerically resolved 2-butanethiol or secondary-branched butanethiol (25%) and near that for linear-chain 1-butanethiol (33%).
An allelic discrimination SNP assay for distinguishing the mitochondrial lineages of European wildcats and domestic cats
Publisher: Springer Science and Business Media LLC
Date: 10-12-2012
Atomic-Resolution Kinked Structure Of An Alkylporphyrin On Highly Ordered Pyrolytic Graphite
Publisher: American Chemical Society (ACS)
Date: 22-12-2011
DOI: 10.1021/JZ101529T
Abstract: The atomic structure of the chains of an alkyl porphyrin (5,10,15,20-tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for porphyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible. A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and, of the many possible atomic structures modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains.
The Solvation of Acetonitrile
Publisher: American Chemical Society (ACS)
Date: 04-1999
DOI: 10.1021/JA983878N
Frequency-based Quantum Computers from a Chemist's Perspective
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/CH12053
Abstract: Quantum computer elements are often designed and tested using molecular or nanoscopic components that form registers of qubits in which memory is stored and information processed. Often such registers are probed and manipulated using frequency-based techniques such as nuclear-magnetic resonance spectroscopy. A major challenge is to design molecules to act as these registers. We provide a basis for rational molecular design through consideration of the generic spectroscopic properties required for quantum computing, bypassing the need for intricate knowledge of the way these molecules are used spectroscopically. Designs in which two-qubit gate times scale similarly to those for one-qubit gates are presented. The specified spectroscopic requirements are largely independent of the type of spectroscopy used (e.g. magnetic resonance or vibrational) and are often independent of technical details of the application (e.g. broadband or high-resolution spectroscopy). This should allow the design of much larger quantum registers than have currently been demonstrated.
Photoluminescence, photophysics, and photochemistry of the v B- defect in hexagonal boron nitride
Publisher: American Physical Society (APS)
Date: 12-10-2020
Understanding the inelastic electron-tunneling spectra of alkanedithiols on gold
Publisher: AIP Publishing
Date: 07-03-2006
DOI: 10.1063/1.2166362
Abstract: We present results for a simulated inelastic electron-tunneling spectra (IETS) from calculations using the “gDFTB” code. The geometric and electronic structure is obtained from calculations using a local-basis density-functional scheme, and a nonequilibrium Green’s function formalism is employed to deal with the transport aspects of the problem. The calculated spectrum of octanedithiol on gold(111) shows good agreement with experimental results and suggests further details in the assignment of such spectra. We show that some low-energy peaks, unassigned in the experimental spectrum, occur in a region where a number of molecular modes are predicted to be active, suggesting that these modes are the cause of the peaks rather than a matrix signal, as previously postulated. The simulations also reveal the qualitative nature of the processes dominating IETS. It is highly sensitive only to the vibrational motions that occur in the regions of the molecule where there is electron density in the low-voltage conduction channel. This result is illustrated with an examination of the predicted variation of IETS with binding site and alkane chain length.
Chain-Branching Control Of The Atomic Structure Of Alkanethiol-Based Gold-Sulfur Interfaces
Publisher: American Chemical Society (ACS)
Date: 06-09-2011
DOI: 10.1021/JA204958H
Abstract: Density functional theory structure calculations at 0 K and simulations at 300 K of observed high-resolution in situ scanning tunneling microscopy (STM) images reveal three different atomic-interface structures for the self-assembled monolayers (SAMs) of three isomeric butanethiols on Au(111): direct binding to the Au(111) surface without pitting, binding to adatoms above a regular surface with extensive pitting, and binding to adatoms with local surface vacancies and some pitting. Thermal motions are shown to produce some observed STM features, with a very tight energy balance controlling the observed structures. Variation of the degree of substitution on the α carbon is found to significantly change the relative energies for interaction of the different types of adatom structures with the surface, while the nature of the surface cell, controlled primarily by inter-adsorbate steric interactions, controls substrate reorganization energies and adsorbate distortion energies. Most significantly, by manipulating these features, chemical control of the adsorbate can produce stable interfaces with surface pitting eliminated, providing new perspectives for technological applications of SAMs.
Quinoxalino[2,3-b′]porphyrins behave as π-expanded porphyrins upon one-electron reduction: Broad control of the degree of derealization through substitution at the macrocycle periphery
Publisher: American Chemical Society (ACS)
Date: 04-07-2007
DOI: 10.1021/JP0726743
Abstract: The synthesis and redox properties of a series of free-base and metal(II) quinoxalino[2,3-b']porphyrins and their use in an investigation of the substituent effects on the degree of communication between the porphyrin and its beta,beta'-fused quinoxalino component are reported. ESR, thin-layer spectroelectrochemistry, and quantum chemical calculations of the resultant radical anions from one-electron reduction indicate that localization of the unpaired electron across both the porphyrin and the fused quinoxalino group can be controlled, the system as a whole behaving as a highly polarizable pi-expanded porphyrin radical anion. ESR studies on the radical anions of zinc(II) quinoxalino[2,3-b']porphyrin derivatives indicate that nitrogen-atom spin distribution changes as a function of chemical substitution: 27% quinoxaline character when the porphyrin ring bears a 7-nitro substituent, 34% quinoxaline character in the unsubstituted parent, and 51-61% nitroquinoxaline character when the quinoxalino unit has one or more nitro groups. Close analogies are found between the calculated and observed nitrogen-atom spin distributions, indicating that the calculations embody the key chemical effects. The calculations also indicate that the nitrogen-atom spin distributions closely parallel the important total porphyrin, quinoxaline, and nitro spin distributions, indicating that the observed quantities realistically depict the change in the nature of the delocalization of the radical anion as a function of chemical substitution. The profound effects observed indicate long-range communication of the type that is essential in molecular electronics applications.
The First Singlet (n,π*) and (π,π*) Excited States of the Hydrogen-Bonded Complex between Water and Pyridine
Publisher: American Chemical Society (ACS)
Date: 15-08-2002
DOI: 10.1021/JP020552Z
The Spectroscopy Of The Low-Lying Bands In The Special-Pair Radical-Cations Of Photosynthetic Reaction Centres
Publisher: Springer Science and Business Media LLC
Date: 1998
CNDO-calculation of second order vibronic coupling in the 1B2u-1A1g transition of benzene
Publisher: Elsevier BV
Date: 11-1981
Free energies for the coordination of ligands to the magnesium of chlorophyll-a in solvents
Publisher: Informa UK Limited
Date: 28-01-2015
On the relationship between the classical, semiclassical, and quantum dynamics of a Morse oscillator
Publisher: American Chemical Society (ACS)
Date: 06-1988
DOI: 10.1021/J100322A034
Differential Gene Expression To Investigate the Effect of ( 5Z )-4-Bromo- 5-(Bromomethylene)-3-Butyl-2( 5H )-Furanone on Ba
Publisher: American Society for Microbiology
Date: 08-2004
DOI: 10.1128/AEM.70.8.4941-4949.2004
Abstract: ( 5Z )-4-Bromo-5-(bromomethylene)-3-butyl-2( 5H )-furanone (furanone) from the red marine alga Delisea pulchra was found previously to inhibit the growth, swarming, and biofilm formation of gram-positive bacteria. Using the gram-positive bacterium Bacillus subtilis as a test organism, we observed cell killing by 20 μg of furanone per ml, while 5 μg of furanone per ml inhibited growth approximately twofold without killing the cells. To discover the mechanism of this inhibition on a genetic level and to investigate furanone as a novel antibiotic, full-genome DNA microarrays were used to analyze the gene expression profiles of B. subtilis grown with and without 5 μg of furanone per ml. This agent induced 92 genes more than fivefold ( P 0.05) and repressed 15 genes more than fivefold ( P 0.05). The induced genes include genes involved in stress responses (such as the class III heat shock genes clpC , clpE , and ctsR and the class I heat shock genes groES , but no class II or IV heat shock genes), fatty acid biosynthesis, lichenan degradation, transport, and metabolism, as well as 59 genes with unknown functions. The microarray results for four genes were confirmed by RNA dot blotting. Mutation of a stress response gene, clpC , caused B. subtilis to be much more sensitive to 5 μg of furanone per ml (there was no growth in 8 h, while the wild-type strain grew to the stationary phase in 8 h) and confirmed the importance of the induction of this gene as identified by the microarray analysis.
Adsorption Of Benzene On Copper, Silver, And Gold Surfaces
Publisher: American Chemical Society (ACS)
Date: 10-05-2006
DOI: 10.1021/CT050237R
Abstract: The adsorption of benzene on the Cu(111), Ag(111), Au(111), and Cu(110) surfaces at low coverage is modeled using density-functional theory (DFT) using periodic-slab models of the surfaces as well as using both DFT and complete-active-space self-consistent field theory with second-order Møller-Plesset perturbation corrections (CASPT2) for the interaction of benzene with a Cu13 cluster model for the Cu(110) surface. For the binding to the (111) surfaces, key qualitative features of the results such as weak physisorption, the relative orientation of the adsorbate on the surface, and surface potential changes are in good agreement with experimental findings. Also, the binding to Cu(110) is predicted to be much stronger than that to Cu(111) and much weaker than that seen in previous calculations for Ni(110), as observed. However, a range of physisorptive-like and chemisorptive-like structures are found for benzene on Cu(110) that are roughly consistent with observed spectroscopic data, with these structures differing dramatically in geometry but trivially in energy. For all systems, the bonding is found to be purely dispersive in nature with minimal covalent character. As dispersive energies are reproduced very poorly by DFT, the calculated binding energies are found to dramatically underestimate the observed ones, while CASPT2 calculations indicate that there is no binding at the Hartree-Fock level and demonstrate that the expected intermolecular correlation (dispersive) energy is of the correct order to explain the experimental binding-energy data. DFT calculations performed for benzene on Cu(110) and for benzene on the model cluster indicate that this cluster is actually too reactive and provides a poor chemical model for the system.
The Structure, Energetics, And Nature Of The Chemical Bonding Of Phenylthiol Adsorbed On The Au(111) Surface: Implications For Density-Functional Calculations Of Molecular-Electronic Conduction 1.1850455G
Publisher: AIP Publishing
Date: 25-02-2005
DOI: 10.1063/1.1850455
Abstract: The adsorption of phenylthiol on the Au(111) surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S–H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag(111) this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8kcalmol−1, indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31kcalmol−1. No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%–30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3–4eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.
Peptide ligations accelerated by N-terminal aspartate and glutamate residues
Publisher: American Chemical Society (ACS)
Date: 10-08-2011
DOI: 10.1021/OL2017356
Abstract: A novel application of intramolecular base catalysis confers enhanced reaction rates for aminolysis ligations between peptide thioesters and peptides bearing N-terminal aspartate or glutamate residues. The broad scope of this process and its application in the total synthesis of the diabetes drug exenatide is demonstrated.
Controlling piezoresistance in single molecules through the isomerisation of bullvalenes
Publisher: Springer Science and Business Media LLC
Date: 21-09-0008
Binding to gold(0): Accurate computational methods with application to AuNH3
Publisher: AIP Publishing
Date: 30-05-2002
DOI: 10.1063/1.1473197
Abstract: The nature of the bonding of molecules to neutral gold atoms or surfaces is of wide interest, particularly with regard to recent molecular electronics experiments involving molecules linked to gold electrodes and nanoclusters. Here, the fundamental problem of accurate calculation of gold atom–ligand interactions is addressed, and a best-possible estimate for the binding energy of AuNH3 is obtained via coupled-cluster and density-functional calculations using series of Gaussian, Slater, and plane-wave basis sets. Poor convergence of both coupled-cluster and density-functional calculations toward the infinite basis-set limit is obtained from the Gaussian basis sets using Slater basis sets, convergence is more rapid while plane-wave basis sets easily reached convergence. A total of 24 Gaussian basis sets are examined, and a method is introduced for determining if a particular basis set is sufficiently balanced in its treatment of the metal and its ligand. For balanced basis sets, better estimates of the binding energy are obtained neglecting corrections for basis-set superposition error. Various treatment of relativistic effects are examined including the use of relativistic effective core potentials (RECPs), ultrasoft pseudopotentials, and all electron scalar and full spin–orbit zero-order regular approximation calculations. While the use of RECPs has minimal affect, use of ultrasoft pseudopotentials and neglect of spin–orbit coupling both result in underestimation of the binding energy by 2–3 kcal mol−1 (15%–20%), as does the neglect of triples excitations in coupled-cluster theory. The PW91, B3LYP, BLYP, and LDA density functionals were investigated and of these only PW91 predicted binding energies and geometries in qualitative agreement with the coupled-cluster results. The AuNH3 complex is found to be a realistic model for the bonding of NH3 to a gold (111) surface, the primary differences being the prediction of charge transfer within the complex and associated significantly stronger binding. This may have profound implications for molecular electronics applications in which small gold clusters are used to represent macroscopic electrodes.
The Importance of Motions that Accompany Those Occurring Along the Reaction Coordinate
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/CH15313
Abstract: The reaction coordinate is a well known quantity used to define the motions critical to chemical reactions, but many other motions always accompany it. These other motions are typically ignored but this is not always possible. Sometimes it is not even clear as to which motions comprise the reaction coordinate: spectral measurements that one may assume are dominated by the reaction coordinate could instead be dominated by the accompanying modes. Ex les of different scenarios are considered. The assignment of the visible absorption spectrum of chlorophyll-a was debated for 50 years, with profound consequences for the understanding of how light energy is transported and harvested in natural and artificial solar-energy devices. We recently introduced a new, comprehensive, assignment, the centrepiece of which was determination of the reaction coordinate for an unrecognized photochemical process. The notion that spectroscopy and reactivity are so closely connected comes directly from Hush’s adiabatic theory of electron-transfer reactions. Its basic ideas are reviewed, similarities to traditional chemical theories drawn, key analytical results described, and the importance of the accompanying modes stressed. Also highlighted are recent advances that allow this theory to be applied to general transformations including isomerization processes, hybridization, aromaticity, hydrogen bonding, and understanding why the properties of first-row molecules such as NH3 (bond angle 108°) are so different to those of PH3–BiH3 (bond angles 90–93°). Historically, the question of what is the reaction coordinate and what is just an accompanying motion has not commonly been at the forefront of attention. In our new approach in which all chemical processes are described using the same core theory, this question becomes thrust forward as always being the most important qualitative feature to determine.
Monte Carlo simulation of the OH stretching spectrum of solutions of KCl, KF, LiCl and LiF in water
Publisher: Informa UK Limited
Date: 03-1986
Relating transition-state spectroscopy to standard chemical spectroscopic processes
Publisher: Elsevier BV
Date: 09-2017
The symmetry of single-molecule conduction
Publisher: AIP Publishing
Date: 08-11-2006
DOI: 10.1063/1.2363976
Abstract: We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green’s function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an ex le system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research.
Application of the Computationally Efficient Self-Consistent-Charge Density-Functional Tight-Binding Method to Magnesium-Containing Molecules
Publisher: American Chemical Society (ACS)
Date: 08-06-2007
DOI: 10.1021/JP071701M
Abstract: The geometric properties, ionization potentials, heats of formation, incremental binding energies, and protonation energies for up to 75 magnesium-containing compounds have been studied using the self-consistent-charge density-functional tight-binding method (SCC-DFTB), the complete-basis set (CBS-QB3) method, traditional B3LYP density-functional theory, and a number of modern semiempirical methods such as Austin Model 1 (AM1), modified neglect of diatomic overlap without and with inclusion of d functions (MNDO, MNDO/d), and the Parametric Method 3 (PM3) and its modification (PM5). The test set contains some widely varying chemical motifs including ionic or covalent, closed-shell or radical compounds, and many biologically relevant complexes. Geometric data are compared to experiment, if available, and otherwise to previous high-level ab initio calculations or the present B3LYP results. SCC-DFTB is found to predict bond lengths to high accuracy, with the root-mean-square (RMS) error being less than half that found for the other semiempirical methods. However, SCC-DFTB performs very poorly for absolute heats of formation, giving an RMS error of 29 kcal mol(-1), but for this property B3LYP and the other semiempirical methods also yield poor but useful results with errors of 12-22 kcal mol(-1). Nevertheless, SCC-DFTB does provide useful results for biologically relevant chemical-process energies such as protonation energies (RMS error 10 kcal mol(-1), with the range 6-19 kcal mol(-1) found for the other semiempirical methods) and ligation energies (RMS error 9 kcal mol(-1), less than the errors of 12-23 kcal mol(-1) found for the other semiempirical methods). SCC-DFTB is shown to provide a computationally expedient means of calculating properties of magnesium compounds, providing results with at most double the inaccuracy of the high-quality but dramatically more-expensive B3LYP method.
The Effect Of Alkylation Of N- And O-Donor Atoms On Their Strength Of Coordination To Silver(I)
Publisher: American Chemical Society (ACS)
Date: 09-06-2001
DOI: 10.1021/JP010687P
Towards efficient molecular wires and switches: the Brooker ions
Publisher: Elsevier BV
Date: 1995
DOI: 10.1016/0303-2647(94)01495-S
Abstract: In search of materials which may function as molecular wires or switches, analytical models have suggested that the Brooker ions should be particularly interesting. We study them in detail using ab initio, semi-empirical and specially-designed empirical techniques, predicting molecular geometries, charge distributions, and conductivities. Provided molecular symmetry is maintained, odd polyenes and Brooker ions NH2-(CH)+ 2n - 1 - NH2 are shown to conduct significantly better than even polyenes, but the advantage becomes a simple multiplicative factor once solitons form (chains of length ca 20 A). Symmetry lowering is predicted to dramatically decrease the conductivity but introduces the possibility that the Brooker ions may function as molecular switches, having greatly enhanced, switchable, non-linear optical properties.
Sulfur ligand mediated electrochemistry of gold surfaces and nanoparticles: What, how, and why
Publisher: Elsevier BV
Date: 02-2017
Hole, electron and energy transfer through bridged systems. VIII. Soliton molecular switching in symmetry-broken Brooker (polymethinecyanine) cations
Publisher: Elsevier BV
Date: 10-1993
Control Of The Site And Potential Of Reduction And Oxidation Processes In Pi-Expanded Quinoxalinoporphyrins
Publisher: Royal Society of Chemistry (RSC)
Date: 2008
DOI: 10.1039/B711320J
Abstract: Quinoxalino[2,3-b']porphyrins are pi-expanded porphyrins, having a quinoxaline fused to a beta,beta'-pyrrolic position of the porphyrin. They are used as components in systems proposed as 'molecular wires'. Knowledge of their redox properties is of value in the design of electron- or hole-conduction systems. In particular, the location of the charge density in the radical anions of quinoxalinoporphyrins can be modulated by peripheral functionalization. New theoretical treatments of electrochemical potentials are developed that identify the site of reduction in both the anions and the dianions of 33 quinoxalinoporphyrins. These molecules include free-base and metallated macrocycles substituted on the quinoxaline with electron-withdrawing groups (NO2, Cl, Br) and/or electron-donating groups (NH2, OCH3). Spectroelectrochemistry, density-functional theory calculations, and substituent-parameter models are used to verify the analysis. Five distinct patterns are observed for the locations of the first and second reductions some of these patterns involve delocalized charges. Nitroquinoxalinoporphyrins with the nitro groups at the 5- and 6-quinoxaline positions are found to have quite different properties owing to distortions caused by peri interactions that force the nitro group of the 5-nitro regioisomer out of conjugation. Charge localization on the nitroquinoxaline fragment is found for some molecules, and this is attributed to ion-pairing with the 0.1 M tetrabutylammonium perchlorate electrolyte used, leading to the verified prediction that electron-paramagnetic resonance spectra of these molecules taken without the electrolyte yield delocalized anions. These properties enable the control of conduction through molecular wires synthesised from quinoxalinoporphyrins.
Theoretical spectroscopy of the VNNB defect in hexagonal boron nitride
Publisher: American Physical Society (APS)
Date: 12-10-2020
Modeling the bacterial photosynthetic reaction center. VII. Full simulation of the intervalence hole–transfer absorption spectrum of the special-pair radical cation
Publisher: AIP Publishing
Date: 24-07-2003
DOI: 10.1063/1.1589742
Abstract: ENDOR data suggests that the special-pair radical cation P+ from Rhodobacter sphaeroides is 68% localized on PL while simple interpretations of FTIR difference spectra based primarily on intensity information, but to some extent also bandwidths, suggest near-complete charge localization. We provide a complete a priori spectral simulation of the spectrum of P+ in the range 0–5000 cm−1, including explicit treatment of the high-resolution vibrational transitions, the low-resolution hole–transfer absorption centered at 2700 cm−1, and the resonance with the SHOMO to HOMO transition at 2200 cm−1 that resolve the issues concerning the nature of P+. The description of the vibrational aspects of the problem were taken from results of previous density-functional calculations, and a qualitatively realistic large number of vibrational modes (50 antisymmetric and 18–20 symmetric) were included. To facilitate the calculations, a new representation of the vibronic-coupling Hamiltonian for intervalence hole–transfer or electron–transfer problems is introduced, allowing the spectrum to be simulated efficiently using only up to 4×109 vibronic basis functions and leading also to new general analytical relationships. Observed spectra are fitted using seven adjustable chemical parameters describing the interactions between the four electronic states involved. The resulting fits provide unique descriptions of the parameters that are insensitive to the source of the observed spectrum or the nature of the symmetric modes used in the model, and all fitted parameters are found to be close in value to those from independent estimates. We determine the electronic coupling, antisymmetric-mode reorganization energy, and redox asymmetry to be J=0.126±0.002 eV, λ=0.139±0.003 eV, and E0=0.069±0.002 eV, respectively. Our description forms the basis of understanding for a wide range of other properties observed for Rhodobacter sphaeroides mutants, as well as the properties of the reaction centers from photosystems I, II, etc., facilitating a deeper understanding of the role of the special pair in initiating primary charge separation during photosynthesis.
Conceptual Understanding of Mixed‐Valence Compounds and Its Extension to General Stereoisomerism
Publisher: Wiley
Date: 14-12-2306
Reaction Force and Its Link to Diabatic Analysis: A Unifying Approach to Analyzing Chemical Reactions
Publisher: American Chemical Society (ACS)
Date: 14-09-2010
DOI: 10.1021/JZ101135Y
Relation between predicted soliton charge-density wave structure of odd polyene anions and 13C NMR chemical shifts
Publisher: American Chemical Society (ACS)
Date: 03-1993
DOI: 10.1021/J100113A048
Electron and Energy Transfer through Bridged Systems. 9. Toward a Priori Evaluation of the Intermetallic Coupling in Bis-metal Complexes
Publisher: American Chemical Society (ACS)
Date: 04-1999
DOI: 10.1021/JP984598X
Solitons in finite- and infinite-length negative-defect trans-polyacetylene and the corresponding Brooker (polymethinecyanine) cations. II. Charge density wave
Publisher: Elsevier BV
Date: 11-1992
Accurate prediction of the properties of materials using the CAM‐B3LYP density functional
Publisher: Wiley
Date: 19-05-2021
DOI: 10.1002/JCC.26558
Abstract: Density functionals with asymptotic corrections to the long‐range potential provide entry‐level methods for calculations on molecules that can sustain charge transfer, but similar applications in materials science are rare. We describe an implementation of the CAM‐B3LYP range‐separated functional within the Vienna Ab‐initio Simulation Package (VASP) framework, together with its analytical functional derivatives. Results obtained for eight representative materials: aluminum, diamond, graphene, silicon, NaCl, MgO, 2D h‐BN, and 3D h‐BN, indicate that CAM‐B3LYP predictions embody mean‐absolute deviations (MAD) compared to HSE06 that are reduced by a factor of six for lattice parameters, four for quasiparticle band gaps, three for the lowest optical excitation energies, and six for exciton binding energies. Further, CAM‐B3LYP appears competitive compared to ab initio G 0 W 0 and Bethe‐Salpeter equation approaches. The CAM‐B3LYP implementation in VASP was verified by comparison of optimized geometries and reaction energies for isolated molecules taken from the ACCDB database, evaluated in large periodic unit cells, to analogous results obtained using Gaussian basis sets. Using standard GW pseudopotentials and energy cutoffs for the plane‐wave calculations and the aug‐cc‐pV5Z basis set for the atomic‐basis ones, the MAD in energy for 1738 chemical reactions was 0.34 kcal mol −1 , while for 480 unique bond lengths this was 0.0036 Å these values reduced to 0.28 kcal mol −1 (largest error 0.94 kcal mol −1 ) and 0.0009 Å by increasing the plane‐wave cutoff energy to 850 eV.
Finding efficient Methods For The Quantum Chemical Treatment Of Protein Structures: The Effects Of London-Dispersion And Basis-Set Incompleteness On Peptide And Water-Cluster Geometries
Publisher: American Chemical Society (ACS)
Date: 14-06-2013
DOI: 10.1021/CT400321M
Abstract: We demonstrate how quantum chemical Hartree-Fock (HF) or density functional theory (DFT) optimizations with small basis sets of peptide and water cluster structures are decisively improved if London-dispersion effects, the basis-set-superposition error (BSSE), and other basis-set incompleteness errors are addressed. We concentrate on three empirical corrections to these problems advanced by Grimme and co-workers that lead to computational strategies that are both accurate and efficient. Our analysis encompasses a reoptimized version of Hobza's P26 set of tripeptide structures, a new test set of conformers of cysteine dimers, and isomers of the water hexamer. These systems reflect features commonly found in protein crystal structures. In all cases, we recommend Grimme's DFT-D3 correction for London-dispersion. We recommend usage of large basis sets such as cc-pVTZ whenever possible to reduce any BSSE effects and, if this is not possible, to use Grimme's gCP correction to account for BSSE when small basis sets are used. We demonstrate that S-S and C-S bond lengths are very prone to basis-set incompleteness and that polarization functions should always be used on S atoms. At the double-ζ level, the PW6B95-D3-gCP DFT method combined with the SVP and 6-31G* basis sets yields accurate results. Alternatively, the HF-D3-gCP/SV method is recommended, with inclusion of polarization functions for S atoms only. Minimal basis sets offer an intriguing route to highly efficient calculations, but due to significant basis-set incompleteness effects, calculated bond lengths are seriously overestimated, making applications to large proteins very difficult, but we show that Grimme's newest HF-3c correction overcomes this problem and so makes this computational strategy very attractive. Our results provide a useful guideline for future applications to the optimization, quantum refinement, and dynamics of large proteins.
Solvent Effects on the Electronic Spectra of Transition Metal Complexes
Publisher: American Chemical Society (ACS)
Date: 05-01-2000
DOI: 10.1021/CR980409V
Examination of the Photophysical Processes of Chlorophyll d Leading to a Clarification of Proposed Uphill Energy Transfer Processes in Cells of Acaryochloris marina¶
Publisher: Wiley
Date: 2003
DOI: 10.1562/0031-8655(2003)077<0628:EOTPPO>2.0.CO;2
Abstract: A comprehensive study of the photophysical properties of chlorophyll (Chl) d in 1:40 acetonitrile-methanol solution is performed over the temperature range 170-295 K. From comparison of absorption and emission spectra, time-dependent density-functional calculations and homologies with those of Chl a, we assign the key features of the absorption and fluorescence spectra. Possible photophysical energy relaxation mechanisms are summarized, and thermal equilibration processes are studied in detail by monitoring the observed emission profiles and quantum yields as a function of excitation energy. In particular, we concentrate on emission subsequent to excitation in the extreme far-red tail of the Qy absorption spectrum, with this emission partitioned into contributions from hot-band absorptions as well as uphill energy transfer processes that occur subsequent to absorption. No unusual photophysical processes are detected for Chl d it appears that all intramolecular relaxation processes reach thermal equilibration on shorter timescales than the fluorescence lifetime even at 170 K. The results from these studies are used to reinterpret a previous study of photochemical processes observed in intact cells and their acetone extracts of the photosynthetic system of Acaryochloris marina. In the study of Mimuro et al., light absorbed by Chl d at 736 nm is found to give rise to emission by another species, believed to also be Chl d, at 703 nm this uphill energy transfer process is easily rationalized in terms of the thermal equilibration processes that we deduced for Chl d. However, no evidence is found in the experimental results of Mimuro et al. to support claims that (nonequilibrium) uphill energy transfer is additionally observed to Chl a species that emit at 670-680 nm. This finding is relevant to broader issues concerning the nature of the special pair in photosystem II of A. marina because suggestions that it is comprised of Chl a can only be correct if nonthermal uphill energy transfer processes from Chl d are operative.
Solvent Effects on Molecular and Ionic Spectra. VIII. The 1(n,π*) Excited States of Pyridazine in Water
Publisher: American Chemical Society (ACS)
Date: 1996
DOI: 10.1021/JP960175O
Density Functional Theory For Charge Transfer: The Nature Of The N-Bands Of Porphyrins And Chlorophylls Revealed Through Cam-B3Lyp, Caspt2, And Sac-Ci Calculations
Publisher: American Chemical Society (ACS)
Date: 18-07-2006
DOI: 10.1021/JP063376T
Abstract: While density functional theory (DFT) has been proven to be extremely useful for the prediction of thermodynamic and spectroscopic properties of molecules, to date most functionals used in common implementations of DFT display a systematic failure to predict the properties of charge-transfer processes. While this is explicitly manifest in Rydberg transitions of atoms and molecules and in molecular charge-transfer spectroscopy, it also becomes critical for systems containing extended conjugation such as polyenes and other conducting polymers, porphyrins, chlorophylls, etc. A new density functional, a Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP), has recently been developed specifically to overcome these limitations, and it has been shown to properly predict molecular charge-transfer spectra. Here, we demonstrate that it predicts qualitatively reasonable spectra for porphyrin, some oligoporphyrins, and chlorophyll. However, alternate density functionals developed to overcome the same limitations such as current-density functional theory are shown, in their present implementation, to remain inadequate. The CAM-B3LYP results are shown to be in excellent agreement with complete-active-space plus second-order Møller-Plesset perturbation theory and symmetry-adapted cluster configuration interaction calculations: These depict the N and higher bands of porphyrins and chlorophylls as being charge-transfer bands associated with localization of molecular orbitals on in idual pyrrole rings. The validity of the basic Gouterman model for the spectra of porphyrins and chlorophylls is confirmed, rejecting modern suggestions that non-Gouterman transitions lie close in energy to the Q-bands of chlorophylls. As porphyrins and chlorophylls provide useful paradigms for problems involving extended conjugation, the results obtained suggest that many significant areas of nanotechnology and biotechnology may now be realistically treated by cost-effective density-functional-based computational methods.
Competition between charge migration and charge transfer induced by nuclear motion following core ionization: Model systems and application to Li2.
Publisher: AIP Publishing
Date: 26-09-2019
DOI: 10.1063/1.5117246
Abstract: Attosecond and femtosecond spectroscopies present opportunities for the control of chemical reaction dynamics and products, as well as for quantum information processing we address the somewhat unique situation of core-ionization spectroscopy which, for dimeric chromophores, leads to strong valence charge localization and hence tightly paired potential-energy surfaces of very similar shape. Application is made to the quantum dynamics of core-ionized Li2+. This system is chosen as Li2 is the simplest stable molecule facilitating both core ionization and valence ionization. First, the quantum dynamics of some model surfaces are considered, with the surprising result that subtle differences in shape between core-ionization paired surfaces can lead to dramatic differences in the interplay between electronic charge migration and charge transfer induced by nuclear motion. Then, equation-of-motion coupled-cluster calculations are applied to determine potential-energy surfaces for 8 core-excited state pairs, calculations believed to be the first of their type for other than the lowest-energy core-ionized molecular pair. While known results for the lowest-energy pair suggest that Li2+ is unsuitable for studying charge migration, higher-energy pairs are predicted to yield results showing competition between charge migration and charge transfer. Central is a focus on the application of Hush’s 1975 theory for core-ionized X-ray photoelectron spectroscopy to understand the shapes of the potential-energy surfaces and hence predict key features of charge migration.
Complex time dependent wave packet technique for thermal equilibrium systems: Electronic spectra
Publisher: AIP Publishing
Date: 15-11-1983
DOI: 10.1063/1.445618
Abstract: A time dependent wave packet method is presented for the rapid calculation of the properties of systems in thermal equilibrium and is applied, as an illustration, to electronic spectra. The thawed Gaussian approximation to quantum wave packet dynamics combined with evaluation of the density matrix operator by imaginary time propagation is shown to give exact electronic spectra for harmonic potentials and excellent results for both a Morse potential and for the band contours of the three transitions of the visible electronic absorption spectrum of the iodine molecule. The method, in principle, can be extended to many atoms (e.g., condensed phases) and to other properties (e.g., infrared and Raman spectra and thermodynamic variables).
Polarization effect within a protein crystal: A molecular dynamics simulation study
Publisher: Elsevier BV
Date: 08-2018
The vaccinia virus kelch-like protein C2L affects calcium-independent adhesion to the extracellular matrix and inflammation in a murine intradermal model
Publisher: Microbiology Society
Date: 09-2003
Abstract: Chordate poxviruses encode several uncharacterized POZ-kelch proteins and three of these are present in Vaccinia virus (VV) strain Western Reserve. VV gene C2L is predicted to encode a protein of 512 amino acid residues with a POZ/BTB domain in the N-terminal region and three kelch motifs in the C-terminal half of the protein. We have identified the C2L gene product as an intracellular protein of 56 kDa and constructed and characterized a VV mutant lacking the C2L gene (v Delta C2L). Compared to wild-type and revertant viruses, v Delta C2L had unaltered growth in vitro, but had a different plaque morphology due to an altered cytopathic effect (CPE) of infected cells. Deleting C2L had no effect on VV-induced formation of actin tails or enhanced cell motility, but affected the development of VV-induced cellular projections and the Ca(2+)-independent cell/extracellular matrix adhesion late during infection. In an intranasal mouse model, C2L did not contribute to virus virulence. However, in an intradermal mouse model, infection with v Delta C2L resulted in larger lesions and more cell infiltration into the infected ears during recovery from infection. Thus, in this model, C2L protein inhibits inflammation and reduces immunopathology. In summary, we found that C2L is not required for virus replication in vitro but contributes to aspects of VV-induced CPE and reduces immunopathology in vivo.
Modeling The Adsorption Of Norbornadiene On The Si(001) Surface: The Predominance Of Non-[2+2]-Cycloaddition Products
Publisher: AIP Publishing
Date: 26-06-2003
DOI: 10.1063/1.1577539
Abstract: Norbornadiene (NBE) chemisorbs to a Si(001) surface in a flagpolelike structure that has potential as an anchor point for nanoscale molecular devices to the surface. Its bindings to the reconstructed Si(001)-(2×1) surface and a partially depassivated Si(001)-(2×1)-H surfaces are modeled by slab-based density functional theory using the PW91 density functional. This method is shown to quantitatively and qualitatively reproduce many known properties of bulk silicon, the silicon surface reconstruction, and the gas-phase NBE molecule. Four strongly bound adsorbate configurations are found, with the C–C bonds located either above a Si–Si dimer row or trough, oriented either parallel or perpendicular to each other. The calculated binding energies are 96, 85, 81, and 72 kcal mol−1 for the perpendicular row, perpendicular trough, parallel row, and parallel trough configurations, respectively, evaluated at quarter-monolayer coverage on the bare surface, with hydrogen passivation of the surrounding sites having little influence. These results indicate that the observed structural disorder for NBE adsorption on the bare surface at very high coverage results from kinetic rather than thermodynamic control of the reaction products. Such kinetic control is shown to be associated with large barriers in excess of 40 kcal mol−1 for possible adsorbate annealing processes, with desorption into a (partially or fully) physisorbed precursor state being required. Enhanced disorder is also predicted arising from the strong partial binding of NBE through one alkene linkage only, with the analogous four structural motifs being calculated to be very similar in energy. The lowest-energy single-alkene-bonded structure is predicted to be of the parallel–above-row type, consistent with the observed structures for most monoalkene adducts. Preference for the uncommon perpendicular binding of NBE is predicted to arise from unfavorable interactions within the silicon lattice when parallel binding occurs on adjacent rows, a binding motif that is observed for only the simplest monoalkene, ethylene, and only at high coverage. The primary reaction products of NBE are not those predicted by a [2+2] cycloaddition reaction between C=C and Si=Si double bonds, suggesting that, in general, this is not the mechanism for chemisorption of alkenes on Si(001). Rather, the reaction products are those expected on the basis that the silicon dimer bond is biradical in nature. Careful structural, polarization, and band-structure analyses of the reconstructed surface are also shown to provide no evidence for the existence for a doubly bonded silicon dimer.
Recommending Hartree-Fock theory with London-dispersion and basis-set-superposition corrections for the optimization or quantum refinement of protein structures.
Publisher: American Chemical Society (ACS)
Date: 03-12-2014
DOI: 10.1021/JP510148H
Abstract: We demonstrate the importance of properly accounting for London dispersion and basis-set-superposition error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serve as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but also, for the first time, demonstrate how London dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme's recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density functional theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also the convergence behavior is much better. In particular, we show that the BP86/6-31G* approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. Using HF-D3-gCP is technically straightforward, and we therefore encourage users of quantum-chemical methods to adopt this approach in future applications.
Formalism, analytical model, and a priori Green’s-function-based calculations of the current–voltage characteristics of molecular wires
Publisher: AIP Publishing
Date: 15-01-2000
DOI: 10.1063/1.480696
Abstract: Various Green’s-function-based formalisms which express the current I as a function of applied voltage V for an electrode–molecule–electrode assembly are compared and contrasted. The analytical solution for conduction through a Hückel (tight binding) chain molecule is examined and only one of these formalisms is shown to predict the known conductivity of a one-dimensional metallic wire. Also, from this solution we extract the counter-intuitive result that the imaginary component of the self-energy produces a shift in the voltage at which molecular resonances occur, and complete analytical descriptions are provided of the conductivity through one-atom and two-atom bridges. A method is presented by which a priori calculations could be performed, and this is examined using extended-Hückel calculations for two gold electrodes spanned by the dithioquinone dianion. A key feature of this is the use of known bulk-electrode properties to model the electrode surface rather than the variety of more approximate schemes which are in current use. These other schemes are shown to be qualitatively realistic but not sufficiently reliable for use in quantitative calculations. We show that in such calculations it is very important to obtain accurate estimates of both the molecule–electrode coupling strength and the location of the electrode’s Fermi energies with respect to the molecular state energies.
Formalism for Electron Transfer and Energy Transfer in Bridged Systems
Publisher: American Chemical Society
Date: 05-05-1989
Domestic cat neutering to preserve the Scottish wildcat
Publisher: Wiley
Date: 07-2018
DOI: 10.1136/VR.K2905
From chaos to order: Chain-length dependence of the free energy of formation of meso-tetraalkylporphyrin self-assembled monolayer polymorphs
Publisher: American Chemical Society (ACS)
Date: 20-01-2016
Toward ab initio refinement of protein X-ray crystal structures: interpreting and correlating structural fluctuations
Publisher: Springer Science and Business Media LLC
Date: 2012
Bond angle variations in XH3[X = N, P, As, Sb, Bi]: the critical role of Rydberg orbitals exposed using a diabatic state model
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5CP02237A
Abstract: The origins of the observed bond angles in XH 3 and XH 3 + are explained using high-level calculations and a simple diabatic model.
Hamiltonian operators including both symmetric and antisymmetric vibrational modes for vibronic coupling and intervalence charge-transfer applications
Publisher: Elsevier BV
Date: 03-2004
Synchronous diversification of sulawesi’s iconic artiodactyls driven by recent geological events
Publisher: The Royal Society
Date: 11-04-2018
Abstract: The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted ersification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2–3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
Challenges facing an understanding of the nature of low-energy excited states in photosynthesis
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.BBABIO.2016.06.010
Abstract: While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.
The Lowest Singlet (n,π*) and (π,π*) Excited States of the Hydrogen-Bonded Complex between Water and Pyrazine
Publisher: American Chemical Society (ACS)
Date: 12-01-2007
DOI: 10.1021/JP0658142
Abstract: The hydrogen bonding between water and pyrazine in its ground, lowest (n,pi*), and lowest (pi,pi*) states is investigated using density-functional theory (DFT), time-dependent density function theory (TD-DFT), coupled-cluster singles and doubles (CCSD) theory and equation-of-motion coupled cluster (EOM-CCSD) theory. For all states, the minimum-energy configuration is found to be an orthodox linear hydrogen-bonded species, with the bond strength increasing by 0.4 kcal mol-1 upon formation of the (pi,pi*) state and decreasing by 1.0 kcal mol-1 upon formation of the (n,pi*) state. The calculated solvent shifts for the complexes match experimental data and provide a basis for the understanding of the aqueous solvation of pyrazine, and the excited-state complexes are predicted to be only short-lived, explaining the failure of molecular beam experiments to observe them. Quite a different scenario for hydrogen bonding to the (n,pi*) excited state is found compared to those of H2O:pyridine and H2O:pyrimidine: for pyridine linear hydrogen bonds are unstable and hydrogen bonds to the electron-enriched pi cloud are strong, whereas for pyrimidine the excitation localizes on the nonbonded nitrogen leaving the hydrogen-bonding unaffected. For H2O:pyrazine, the (n,pi*) excitation remains largely delocalized, providing a distinct intermediary scenario.
Q|R: quantum-based refinement
Publisher: International Union of Crystallography (IUCr)
Date: 2017
DOI: 10.1107/S2059798316019847
Abstract: Quantum-based refinement utilizes chemical restraints derived from quantum-chemical methods instead of the standard parameterized library-based restraints used in refinement packages. The motivation is twofold: firstly, the restraints have the potential to be more accurate, and secondly, the restraints can be more easily applied to new molecules such as drugs or novel cofactors. Here, a new project called Q|R aimed at developing quantum-based refinement of biomacromolecules is under active development by researchers at Shanghai University together with PHENIX developers. The central focus of this long-term project is to develop software that is built on top of open-source components. A development version of Q|R was used to compare quantum-based refinements with standard refinement using a small model system.
Defect states in hexagonal boron nitride: Assignments of observed properties and prediction of properties relevant to quantum computation
Publisher: American Physical Society (APS)
Date: 02-2018
The Role of High-Level Calculations in the Assignment of the Q-Band Spectra of Chlorophyll
Publisher: AIP Publishing LLC
Date: 2014
DOI: 10.1063/1.4897663
Gold surfaces and nanoparticles are protected by Au(0)–thiyl species and are destroyed when Au(I)–thiolates form
Publisher: Proceedings of the National Academy of Sciences
Date: 29-02-2016
Abstract: Synthetic design strategies for gold surface protection and nanoparticle formation require knowledge of how protectant ligands bind. Sulfur compounds may protect gold surfaces using a weakly bound (physisorbed) form or a strongly bound (chemisorbed) one often assumed to be Au(I)–thiolate. However, chemical reaction conditions optimized for Au(I)–thiolate protection instead etch surfaces to produce molecular thin films. All experimental and calculated evidence indicates that chemisorbed surface species are actually bound mainly by strong van der Waals (aurophilic-like) forces. This understanding unifies gold–sulfur surface chemistry with that of all other ligands and also with that of gold compounds, forming the basis for future methodological developments. It is applied to predict intermediate species during the Brust–Schiffrin nanoparticle synthesis that are subsequently observed spectroscopically.
Electronic Couplings and Energy Transfer Dynamics in the Oxidized Primary Electron Donor of the Bacterial Reaction Center
Publisher: American Chemical Society (ACS)
Date: 10-01-2004
DOI: 10.1021/JP036516X
First steps towards quantum refinement of protein X-ray structures
Publisher: Springer Netherlands
Date: 2012
Electron transfer and energy transfer through bridged systems. 4. Intermetallic coupling and electronic spectra of the bis(pentaammineruthenium) complexes of .alpha.,.omega.-dipyridyl trans-polyenes i
Publisher: American Chemical Society (ACS)
Date: 09-1990
DOI: 10.1021/IC00344A013
Lattice strain and band overlap of the thermoelectric composite Mg2Si1-xSnx
Publisher: American Physical Society (APS)
Date: 13-09-2022
The Basics of Covalent Bonding
Publisher: American Chemical Society (ACS)
Date: 12-1997
DOI: 10.1021/ED074P1503.1
Noel S. Hush.
Publisher: American Chemical Society (ACS)
Date: 09-05-2019
A unified diabatic description for electron transfer reactions, isomerization reactions, proton transfer reactions, and aromaticity
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5CP02236C
Abstract: A way is found for describing general chemical reactions using diabatic multi-state and “twin-state” models. (Image adapted with permission from hotos/cybaea/64638988/).
Spectroscopic evidence for electronically forbidden but vibronically allowed long-range electron transfer in norbornylog-bridged naphthalene-diacyanoethylene systems
Publisher: Elsevier BV
Date: 09-1990
Modeling the Bacterial Photosynthetic Reaction Center. 1. Magnesium Parameters for the Semiempirical AM1 Method Developed Using a Genetic Algorithm
Publisher: American Chemical Society (ACS)
Date: 19-09-1998
DOI: 10.1021/JP9805205
Dynamics of the A + BC reaction in solution
Publisher: Elsevier BV
Date: 1986
Noel S. Hush.
Publisher: American Chemical Society (ACS)
Date: 09-05-2019
Absorption-emission symmetry breaking and the different origins of vibrational structures of the 1Qy and 1Qx electronic transitions of pheophytin a.
Publisher: AIP Publishing
Date: 28-10-2019
DOI: 10.1063/1.5116265
Abstract: The vibrational structure of the optical absorption and fluorescence spectra of the two lowest-energy singlet electronic states (Qy and Qx) of pheophytin a were carefully studied by combining low-resolution and high-resolution spectroscopy with quantum chemical analysis and spectral modeling. Large asymmetry was revealed between the vibrational structures of the Qy absorption and fluorescence spectra, integrally characterized by the total Huang-Rhys factor and reorganization energy in absorption of SvibA = 0.43 ± 0.06, λA = 395 cm−1 and in emission of SvibE = 0.35 ± 0.06, λE = 317 cm−1. Time-dependent density-functional theory using the CAM-B3LYP, ωB97XD, and MN15 functionals could predict and interpret this asymmetry, with the exception of one vibrational mode per model, which was badly misrepresented in predicted absorption spectra for CAM-B3LYP and ωB97XD, this mode was a Kekulé-type mode depicting aromaticity. Other computational methods were also considered but performed very poorly. The Qx absorption spectrum is broad and could not be interpreted in terms of a single set of Huang-Rhys factors depicting Franck-Condon allowed absorption, with Herzberg-Teller contributions to the intensity being critical. For it, CAM-B3LYP calculations predict that SvibA (for modes & cm−1) = 0.87 and λA = 780 cm−1, with effective x and y polarized Herzberg-Teller reorganization energies of 460 cm−1 and 210 cm−1, respectively, delivering 15% y-polarized intensity. However, no method was found to quantitatively determine the observed y-polarized contribution, with contributions of up to 50% being feasible.
Vibrational Stark Spectroscopy. 1. Basic Theory and Application to the CO Stretch
Publisher: American Chemical Society (ACS)
Date: 10-1995
DOI: 10.1021/J100043A018
Solitons in finite- and infinite-length negative-defect trans-polyacetylene and the corresponding Brooker (polymethinecyanine) cations. I. Geometry
Publisher: Elsevier BV
Date: 11-1992
The effects of couplings to symmetric and antisymmetric modes and minor asymmetry on the spectral properties of mixed-valence and related charge-transfer systems
Publisher: Elsevier BV
Date: 08-1996
Simulating optical linear absorption for mesoscale molecular aggregates: An adaptive hierarchy of pure states approach.
Publisher: AIP Publishing
Date: 05-2023
DOI: 10.1063/5.0141882
Abstract: In this paper, we present dyadic adaptive HOPS (DadHOPS), a new method for calculating linear absorption spectra for large molecular aggregates. This method combines the adaptive HOPS (adHOPS) framework, which uses locality to improve computational scaling, with the dyadic HOPS method previously developed to calculate linear and nonlinear spectroscopic signals. To construct a local representation of dyadic HOPS, we introduce an initial state decomposition that reconstructs the linear absorption spectra from a sum over locally excited initial conditions. We demonstrate the sum over initial conditions can be efficiently Monte Carlo s led and that the corresponding calculations achieve size-invariant [i.e., O(1)] scaling for sufficiently large aggregates while trivially incorporating static disorder in the Hamiltonian. We present calculations on the photosystem I core complex to explore the behavior of the initial state decomposition in complex molecular aggregates as well as proof-of-concept DadHOPS calculations on an artificial molecular aggregate inspired by perylene bis-imide to demonstrate the size-invariance of the method.
The exact eigenfunctions and eigenvalues of a two-dimensional rigid rotor obtained using Gaussian wave packet dynamics
Publisher: AIP Publishing
Date: 15-07-1985
DOI: 10.1063/1.449514
Abstract: Exact eigenfunctions for a two-dimensional rigid rotor are obtained using Gaussian wave packet dynamics. The wave functions are obtained by propagating, without approximation, an infinite set of Gaussian wave packets that collectively have the correct periodicity, being coherent states appropriate to this rotational problem. This result leads to a numerical method for the semiclassical calculation of rovibrational, molecular eignestates. Also, a simple, almost classical, approximation to full wave packet dynamics is shown to give exact results: this leads to an a posteriori justification of the De Leon–Heller spectral quantization method.
Two-dimensional, phenanthroline-based, extended π-conjugated molecules for single-molecule conduction
Publisher: IOP Publishing
Date: 26-06-2008
The exact thermal rotational spectrum of a two-dimensional rigid rotor obtained using Gaussian wave packet dynamics
Publisher: AIP Publishing
Date: 15-07-1985
DOI: 10.1063/1.449515
Abstract: The exact thermal rotational spectrum of a two-dimensional rigid rotor is obtained using Gaussian wave packet dynamics. The spectrum is obtained by propagating, without approximation, infinite sets of Gaussian wave packets. These sets are constructed so that collectively they have the correct periodicity, and indeed, are coherent states appropriate to this problem. Also, simple, almost classical, approximations to full wave packet dynamics are shown to give results which are either exact or very nearly exact. Advantages of the use of Gaussian wave packet dynamics over conventional linear response theory are discussed.
The Mechanism of Covalent Bonding
Publisher: American Chemical Society (ACS)
Date: 12-1997
DOI: 10.1021/ED074P1494
The Primary Process in Photooxidation of Fe2+(H2O)6 in Water
Publisher: American Chemical Society
Date: 17-04-0006
Asymmetry in the Qy Fluorescence and Absorption Spectra of Chlorophyll a Pertaining to Exciton Dynamics
Publisher: Frontiers Media SA
Date: 02-12-2020
DOI: 10.3389/FCHEM.2020.588289
Abstract: Significant asymmetry found between the high-resolution Q y emission and absorption spectra of chlorophyll-a is herein explained, providing basic information needed to understand photosynthetic exciton transport and photochemical reactions. The Q y spectral asymmetry in chlorophyll has previously been masked by interference in absorption from the nearby Q x transition, but this effect has recently been removed using extensive quantum spectral simulations or else by analytical inversion of absorption and magnetic circular dichroism data, allowing high-resolution absorption information to be accurately determined from fluorescence-excitation spectra. To compliment this, here, we measure and thoroughly analyze the high-resolution differential fluorescence line narrowing spectra of chlorophyll-a in trimethylamine and in 1-propanol. The results show that vibrational frequencies often change little between absorption and emission, yet large changes in line intensities are found, this effect also being strongly solvent dependent. Among other effects, the analysis in terms of four basic patterns of Duschinsky-rotation matrix elements, obtained using CAM-B3LYP calculations, predicts that a chlorophyll-a molecule excited into a specific vibrational level, may, without phase loss or energy relaxation, reemit the light over a spectral bandwidth exceeding 1,000 cm −1 (0.13 eV) to influence exciton-transport dynamics.
Vibrational Stark Spectroscopy 3. Accurate Benchmark ab Initio and Density Functional Calculations for CO and CN-
Publisher: American Chemical Society (ACS)
Date: 18-11-1999
DOI: 10.1021/JP992218H
Weak, Strong, And Coherent Regimes Of Frohlich Condensation And Their Applications To Terahertz Medicine And Quantum Consciousness
Publisher: Proceedings of the National Academy of Sciences
Date: 17-03-2009
Abstract: In 1968, Fröhlich showed that a driven set of oscillators can condense with nearly all of the supplied energy activating the vibrational mode of lowest frequency. This is a remarkable property usually compared with Bose–Einstein condensation, superconductivity, lasing, and other unique phenomena involving macroscopic quantum coherence. However, despite intense research, no unambiguous ex le has been documented. We determine the most likely experimental signatures of Fröhlich condensation and show that they are significant features remote from the extraordinary properties normally envisaged. Fröhlich condensates are classified into 3 types: weak condensates in which profound effects on chemical kinetics are possible, strong condensates in which an extremely large amount of energy is channeled into 1 vibrational mode, and coherent condensates in which this energy is placed in a single quantum state. Coherent condensates are shown to involve extremely large energies, to not be produced by the Wu–Austin dynamical Hamiltonian that provides the simplest depiction of Fröhlich condensates formed using mechanically supplied energy, and to be extremely fragile. They are inaccessible in a biological environment. Hence the Penrose–Hameroff orchestrated objective-reduction model and related theories for cognitive function that embody coherent Fröhlich condensation as an essential element are untenable. Weak condensates, however, may have profound effects on chemical and enzyme kinetics, and may be produced from biochemical energy or from radio frequency, microwave, or terahertz radiation. Pokorný's observed 8.085-MHz microtubulin resonance is identified as a possible candidate, with microwave reactors (green chemistry) and terahertz medicine appearing as other feasible sources.
Crystal deposition triggers tubule dilation that accelerates cystogenesis in polycystic kidney disease.
Publisher: American Society for Clinical Investigation
Date: 16-09-2019
DOI: 10.1172/JCI128503
Prediction of Entanglement Detection by I-V Characteristics
Publisher: Springer Berlin Heidelberg
Date: 2006
Nature of the ground and first excited states of the radical cations of photosynthetic bacterial reaction centres
Publisher: Elsevier BV
Date: 08-1995
Electron–vibration entanglement in the Born–Oppenheimer description of chemical reactions and spectroscopy
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5CP02239H
Abstract: Entanglement in the diabatic basis produces useful quantum information whilst that in the adiabatic basis tells how good is the Born–Oppenheimer approximation.
Molecular Electronic Properties Of Fused Rigid Porphyrin-Oligomer Molecular Wires
Publisher: Elsevier BV
Date: 07-1996
Coexistence Of Multiple Conformations In Cysteamine Monolayers On Au(111)
Publisher: American Chemical Society (ACS)
Date: 21-07-2005
DOI: 10.1021/JP050797M
Abstract: The structural organization, catalytic function, and electronic properties of cysteamine monolayers on Au(111) have been addressed comprehensively by voltammetry, in situ scanning tunneling microscopy (STM) in anaerobic environment, and a priori molecular dynamics (MD) simulation and STM image simulation. Two sets of voltammetric signals are observed. One peak at -(0.65-0.70) V (SCE) is caused by reductive desorption of cysteamine. The other signal, at -(0.25-0.40) V consists of a peak doublet. The pH dependence of the latter suggests that the origin is catalytic dihydrogen evolution. The doublet feature is indicative of two distinct cysteamine configurations. Cysteamine monolayer formation from initial nucleation to a highly ordered phase has been successfully observed in real time using oxygen-free in situ STM. Random cellular patterns, disordered adlayer formation accompanied by high step edge mobility, and ultimately a highly ordered (square root 3 x 4) R30 degrees lattice are observed sequentially. Pits are formed due to enclosure of the mobile edges during the adsorption process. In the highly ordered cysteamine layer, each unit has two spots with apparent 0.6 A height difference in STM images. The coverage 5.7 +/- 0.1 x 10(-10) mol cm(-2) determined by voltammetry supports that the spots represent two in idual cysteamine molecules. A priori MD and density functional simulations hold other clues to the image interpretation and indicate that the NH(3)(+) groups dominate the tunneling contrast. A wide range of interface structures, showing variations in the sulfur binding site and orientation, gauche and trans conformers, and especially hydrogen-bonding interactions, are examined, from which it is concluded that the adsorbate structure is controlled by interactions with the solvent rather than with the substrate.
Adsorption Of Ammonia On The Gold(111) Surface
Publisher: AIP Publishing
Date: 06-05-2002
DOI: 10.1063/1.1471245
Abstract: We have modeled the adsorption of ammonia on the Au(111) surface at coverages of 1/4 and 1/9 of a monolayer using density-functional theory employing the pseudopotential method, periodic imaging, a plane-wave basis set, and the PW91 density functional. The geometries of the adsorbate and the surface are fully optimized. The adsorption is found to be highly favored on top of a surface atom. Adsorption energies of 26 and 32 kJ mol−1 are obtained for the 1/4 and 1/9 of a monolayer coverage, respectively, extrapolating to 34 kJ mol−1 at zero coverage the experimental estimate is 32–42 kJ mol−1. Small changes in the work function are predicted and interpreted as arising from a surface layer whose effective dipole moment is 2.15 D, 0.77 D larger than the calculated value of isolated ammonia. Examination of the calculated charge density and the local electric field strengths indicate that the change in dipole moment is due to polarization effects and that ammonia to gold charge transfer is minimal, at most 0.01 e in magnitude. Qualitatively, the local densities of states and the charge distribution provide little indication of covalent bonding between the gold and ammonia, and quantitatively the adsorption is interpreted as arising from dispersive interactions with some contribution from polarization. This picture is in contrast with common notions of gold to ammonia binding which depict weak chemisorption rather than physisorption, but the usefulness of PW91 in distinguishing between these processes is questioned through examination of the calculated potential energy surface of Ne2. PW91 is shown only to mimic dispersive interactions using modified covalent terms.
Molecular Electronic Properties Of Fused Rigid Porphyrin-Oligomer Molecular Wires
Publisher: IOP Publishing
Date: 12-1996
Analytic solutions to resonant and non-resonant through-bridge electronic coupling
Publisher: IOP Publishing
Date: 12-1996
Assignment Of The Q-Bands Of The Chlorophylls: Coherence Loss Via Q(X) - Q(Y) Mixing
Publisher: Springer Science and Business Media LLC
Date: 26-09-2013
DOI: 10.1038/SREP02761
Abstract: We provide a new and definitive spectral assignment for the absorption, emission, high-resolution fluorescence excitation, linear dichroism, and/or magnetic circular dichroism spectra of 32 chlorophyllides in various environments. This encompases all data used to justify previous assignments and provides a simple interpretation of unexplained complex decoherence phenomena associated with Q x → Q y relaxation. Whilst most chlorophylls conform to the Gouterman model and display two independent transitions Q x (S 2 ) and Q y (S 1 ), strong vibronic coupling inseparably mixes these states in chlorophyll-a. This spreads x -polarized absorption intensity over the entire Q -band system to influence all exciton-transport, relaxation and coherence properties of chlorophyll-based photosystems. The fraction of the total absorption intensity attributed to Q x ranges between 7% and 33%, depending on chlorophyllide and coordination and is between 10% and 25% for chlorophyll-a. CAM-B3LYP density-functional-theory calculations of the band origins, relative intensities, vibrational Huang-Rhys factors and vibronic coupling strengths fully support this new assignment.
Solvent Effects on Molecular and Ionic Spectra. 5. Development of a Method for Simulation of the Liquid Structure and Solvatochromic Shift of Inorganic Complexes such as Pentaaminopyridylruthenium(II)
Publisher: American Chemical Society (ACS)
Date: 06-1995
DOI: 10.1021/J100026A007
Solvent Effects on Molecular and Ionic Spectra. 6. Hydrogen Bonding and the Delocalized Nature of the First 1(n,.pi.*) Excited State of Pyrazine
Publisher: American Chemical Society (ACS)
Date: 08-1995
DOI: 10.1021/JA00138A018
The Appropriateness Of Density-Functional Theory For The Calculation Of Molecular Electronics Properties
Publisher: Wiley
Date: 12-2003
Abstract: As molecular electronics advances, efficient and reliable computation procedures are required for the simulation of the atomic structures of actual devices, as well as for the prediction of their electronic properties. Density-functional theory (DFT) has had widespread success throughout chemistry and solid-state physics, and it offers the possibility of fulfilling these roles. In its modern form it is an empirically parameterized approach that cannot be extended toward exact solutions in a prescribed way, ab initio. Thus, it is essential that the weaknesses of the method be identified and likely shortcomings anticipated in advance. We consider four known systematic failures of modern DFT: dispersion, charge transfer, extended pi conjugation, and bond cleavage. Their ramifications for molecular electronics applications are outlined and we suggest that great care is required when using modern DFT to partition charge flow across electrode-molecule junctions, screen applied electric fields, position molecular orbitals with respect to electrode Fermi energies, and in evaluating the distance dependence of through-molecule conductivity. The causes of these difficulties are traced to errors inherent in the types of density functionals in common use, associated with their inability to treat very long-range electron correlation effects. Heuristic enhancements of modern DFT designed to eliminate in idual problems are outlined, as are three new schemes that each represent significant departures from modern DFT implementations designed to provide a priori improvements in at least one and possible all problem areas. Finally, fully semiempirical schemes based on both Hartree-Fock and Kohn-Sham theory are described that, in the short term, offer the means to avoid the inherent problems of modern DFT and, in the long term, offer competitive accuracy at dramatically reduced computational costs.
A local mode potential function for the water molecule
Publisher: Informa UK Limited
Date: 10-06-1984
Electronic spectrum of 1,5-naphthyridine: Theoretical treatment of vibronic coupling
Publisher: Elsevier BV
Date: 06-1981
Hydrogen bonding and reactivity of water to azines in their S1 (n,π*) electronic excited states in the gas phase and in solution
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2CP24040H
Abstract: A unified picture is presented of water interacting with pyridine, pyridazine, pyrimidine, and pyrazine on the S(1) manifold in both gas-phase dimers and in aqueous solution. As (n,π*) excitation to the S(1) state removes electrons from the ground-state hydrogen bond, this analysis provides fundamental understanding of excited-state hydrogen bonding. Traditional interpretations view the excitation as simply breaking hydrogen bonds to form dissociated molecular products, but reactive processes such as photohydrolysis and excited-state proton coupled electron transfer (PCET) are also possible. Here we review studies performed using equations-of-motion coupled-cluster theory (EOM-CCSD), multireference perturbation theory (CASPT2), time-dependent density-functional theory (TD-DFT), and excited-state Monte Carlo liquid simulations, adding new results from symmetry-adapted-cluster configuration interaction (SAC-CI) and TD-DFT calculations. Invariably, gas-phase molecular dimers are identified as stable local minima on the S(1) surface with energies less than those for dissociated molecular products. Lower-energy biradical PCET minima are also identified that could lead to ground-state recombination and hence molecular dissociation, dissociation into radicals or ions, or hydration reactions leading to ring cleavage. For pyridine.water, the calculated barriers to PCET are low, suggesting that this mechanism is responsible for fluorescence quenching of pyridine.water at low energies rather than accepted higher-energy Dewar-benzene based "channel three" process. Owing to (n,π*) excitation localization, much higher reaction barriers are predicted for the diazines, facilitating fluorescence in aqueous solution and predicting that the as yet unobserved fluorescence from pyridazine.water and pyrimidine.water should be observable. Liquid simulations based on the assumption that the solvent equilibrates on the fluorescence timescale quantitatively reproduce the observed spectral properties, with the degree of (n,π*) delocalization providing a critical controlling factor.
The Green'S Function Density Functional Tight-Binding (Gdftb) Method For Molecular Electronic Conduction
Publisher: American Chemical Society (ACS)
Date: 27-05-2007
DOI: 10.1021/JP070598Y
Abstract: A review is presented of the nonequilibrium Green's function (NEGF) method "gDFTB" for evaluating elastic and inelastic conduction through single molecules employing the density functional tight-binding (DFTB) electronic structure method. This focuses on the possible advantages that DFTB implementations of NEGF have over conventional methods based on density functional theory, including not only the ability to treat large irregular metal-molecule junctions with high nonequilibrium thermal distributions but perhaps also the ability to treat dispersive forces, bond breakage, and open-shell systems and to avoid large band lineup errors. New results are presented indicating that DFTB provides a useful depiction of simple gold-thiol interactions. Symmetry is implemented in DFTB, and the advantages it brings in terms of large savings of computational resources with significant increase in numerical stability are described. The power of DFTB is then harnessed to allow the use of gDFTB as a real-time tool to discover the nature of the forces that control inelastic charge transport through molecules and the role of molecular symmetry in determining both elastic and inelastic transport. Future directions for the development of the method are discussed.
The structure, thermodynamic properties and infrared spectra of liquid water and ice
Publisher: Elsevier BV
Date: 12-1984
Overcoming computational uncertainties to reveal chemical sensitivity in single molecule conduction calculations
Publisher: AIP Publishing
Date: 08-06-2005
DOI: 10.1063/1.1926280
Abstract: In the calculation of conduction through single molecule’s approximations about the geometry and electronic structure of the system are usually made in order to simplify the problem. Previously [G. C. Solomon, J. R. Reimers, and N. S. Hush, J. Chem. Phys. 121, 6615 (2004)], we have shown that, in calculations employing cluster models for the electrodes, proper treatment of the open-shell nature of the clusters is the most important computational feature required to make the results sensitive to variations in the structural and chemical features of the system. Here, we expand this and establish a general hierarchy of requirements involving treatment of geometrical approximations. These approximations are categorized into two classes: those associated with finite-dimensional methods for representing the semi-infinite electrodes, and those associated with the chemisorption topology. We show that ca. 100 unique atoms are required in order to properly characterize each electrode: using fewer atoms leads to nonsystematic variations in conductivity that can overwhelm the subtler changes. The choice of binding site is shown to be the next most important feature, while some effects that are difficult to control experimentally concerning the orientations at each binding site are actually shown to be insignificant. Verification of this result provides a general test for the precision of computational procedures for molecular conductivity. Predictions concerning the dependence of conduction on substituent and other effects on the central molecule are found to be meaningful only when they exceed the uncertainties of the effects associated with binding-site variation.
Electron transfer and energy transfer through bridged systems. II. Tight binding linkages with zero asymptotic band gap
Publisher: Elsevier BV
Date: 09-1990
Non-adiabatic effects in thermochemistry, spectroscopy and kinetics: the general importance of all three Born–Oppenheimer breakdown corrections
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5CP02238J
Abstract: Analytical and numerical solutions describing Born–Oppenheimer breakdown in a simple, widely applicable, model depict shortcomings in modern computational methods.
Understanding The Chemisorption Of 2-Methyl-2-Propanethiol On Au(111)
Publisher: American Chemical Society (ACS)
Date: 29-06-2007
DOI: 10.1021/JP068833K
Electron transfer and energy transfer through bridged systems. I. Formalism
Publisher: Elsevier BV
Date: 07-1989
Solvent effects on metal to ligand charge transfer excitations
Publisher: Elsevier BV
Date: 10-1998
Bioferroelectric Properties of Glycine Crystals.
Publisher: American Chemical Society (ACS)
Date: 18-02-2019
DOI: 10.1021/ACS.JPCLETT.8B03837
Abstract: Biological ferroelectric materials have great potential in biosensing and disease diagnosis and treatment. Glycine crystals form the simplest bioferroelectric materials, and here we investigate the polarizations of its β- and γ-phases. Using density functional theory, we predict that glycine crystals can develop polarizations even larger than those of conventional inorganic ferroelectrics. Further, using systematic molecular dynamics simulations utilizing polarized crystal charges, we predict the Curie temperature of γ-glycine to be 630 K, with a required coercive field to switch its polarization states of 1 V·nm
Identifying carbon as the source of visible single-photon emission from hexagonal boron nitride
Publisher: Springer Science and Business Media LLC
Date: 02-11-2020
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