ORCID Profile
0000-0002-7731-605X
Current Organisations
Dalhousie University
,
University of California Santa Cruz
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Publisher: American Chemical Society (ACS)
Date: 07-07-2021
Publisher: AIP Publishing
Date: 27-02-2020
DOI: 10.1063/1.5139446
Abstract: The photochemical dynamics of double-bond-containing hydrocarbons is exemplified by the smallest alkenes, ethylene and butadiene. Chemical substituents can alter both decay timescales and photoproducts through a combination of inertial effects due to substituent mass, steric effects due to substituent size, and electronic (or potential) effects due to perturbative changes to the electronic potential energy surface. Here, we demonstrate the interplay of different substituent effects on 1,3-butadiene and its methylated derivatives using a combination of ab initio simulation of nonadiabatic dynamics and time-resolved photoelectron spectroscopy. The purely inertial effects of methyl substitution are simulated through the use of mass 15 “heavy-hydrogen” atoms. As expected from both inertial and electronic influences, the excited-state dynamics is dominated by pyramidalization at the unsubstituted carbon sites. Although the electronic effects of methyl group substitution are weak, they alter both decay timescales and branching ratios by influencing the initial path taken by the excited wavepacket following photoexcitation.
Publisher: American Chemical Society (ACS)
Date: 11-01-2022
Abstract: Partial atomic charges are a useful and intuitive concept for understanding molecular properties and chemical reaction mechanisms, showing how changes in molecular geometry can affect the flow of electronic charge within a molecule. However, the use of partial atomic charges remains relatively uncommon in the characterization of excited-state electronic structure. Here, we show how well-established partial atomic charge methods perform for interatomic, intermolecular, and interbond electron transfer in electronically excited states. Our results demonstrate the utility of real-space partial atomic charges for interpreting the electronic structures that arise in excited-state processes. Furthermore, we show how this analysis can be used to demonstrate that analogous electronic structures arise near photochemically relevant conical intersection regions for several conjugated polyenes. On the basis of our analysis, we find that charges computed using the iterative Hirshfeld approach provide results which are consistent with chemical intuition and are transferable between homologous molecular systems.
Publisher: Canadian Science Publishing
Date: 04-2018
Abstract: The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish species and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic ersity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus, but overall, there is a low rate of outcrossing and, therefore, low heterozygosity. In this study, we used whole-genome data to assess the levels of heterozygosity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages. We sequenced whole genomes from 15 lineages that were completely homozygous at microsatellite loci and used single nucleotide polymorphisms (SNPs) to determine heterozygosity levels. More variation was uncovered than in studies using microsatellite data because of the resolution of full genome sequencing data. Moreover, missense polymorphisms were found most often in genes associated with immune function and reproduction. Inferred phylogenetic relationships suggest that lineages largely group by their geographic distribution. The use of whole-genome data provided further insight into genetic ersity in this unique species. Although this study was limited by the number of lineages that were available, these data suggest that there is previously undescribed variation within lineages of K. marmoratus that could have functional consequences and (or) inform us about the limits to selfing (e.g., genetic load, accumulation of deleterious mutations) and selection that might favor the maintenance of heterozygosity. These results highlight the need to sequence additional in iduals within and among lineages.
Publisher: Springer Science and Business Media LLC
Date: 23-01-2013
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D1CP05085K
Abstract: Time-resolved X-ray absorption spectroscopy is a particularly sensitive probe of nonadiabatic molecular wave packet dynamics.
Publisher: Springer Science and Business Media LLC
Date: 28-08-2023
Publisher: American Chemical Society (ACS)
Date: 24-09-2014
DOI: 10.1021/ES502113P
Abstract: Ambient fine particulate matter (PM2.5) is a leading environmental risk factor for premature mortality. We use aerosol optical depth (AOD) retrieved from two satellite instruments, MISR and SeaWiFS, to produce a unified 15-year global time series (1998-2012) of ground-level PM2.5 concentration at a resolution of 1° x 1°. The GEOS-Chem chemical transport model (CTM) is used to relate each in idual AOD retrieval to ground-level PM2.5. Four broad areas showing significant, spatially coherent, annual trends are examined in detail: the Eastern U.S. (-0.39 ± 0.10 μg m(-3) yr(-1)), the Arabian Peninsula (0.81 ± 0.21 μg m(-3) yr(-1)), South Asia (0.93 ± 0.22 μg m(-3) yr(-1)) and East Asia (0.79 ± 0.27 μg m(-3) yr(-1)). Over the period of dense in situ observation (1999-2012), the linear tendency for the Eastern U.S. (-0.37 ± 0.13 μg m(-3) yr(-1)) agrees well with that from in situ measurements (-0.38 ± 0.06 μg m(-3) yr(-1)). A GEOS-Chem simulation reveals that secondary inorganic aerosols largely explain the observed PM2.5 trend over the Eastern U.S., South Asia, and East Asia, while mineral dust largely explains the observed trend over the Arabian Peninsula.
Publisher: MDPI AG
Date: 12-10-2019
Abstract: In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing ergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression in the Tasmanian devil (Sarcophilus harrisii), a critically endangered species that occupies a heterogeneous environment. We performed RNA-sequencing on ear tissue biopsies from adult male and female devils from three populations at the extremes of their geographic range. There were no transcriptome-wide patterns of differential gene expression that would be suggestive of significant, environmentally-driven transcriptomic responses. The general lack of transcriptome-wide variation in gene expression levels across the devil’s geographic range is consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation to abiotic environment in devils were enriched for differentially expressed genes. Additionally, three modules of co-expressed genes were significantly associated with either population of origin or sex.
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1SC02142G
Abstract: Dynamics governing ultrafast chemical reactions can be efficiently simulated using analog quantum simulators composed of a coupled system of qudits and bosonic modes.
Publisher: Wiley
Date: 06-06-2022
DOI: 10.1111/MEC.16501
Abstract: Long‐read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long‐read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long‐read sequencing data to generate a high‐quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis , the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences ( Cebidichthys violaceus ) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage‐specific loss of this cluster. Beyond polar fishes, our results highlight the power of long‐read sequencing to understand genome evolution.
Publisher: American Chemical Society (ACS)
Date: 03-05-2019
Abstract: The photochemistry of organic chromophores generally involves the co-evolution of the electronic and nuclear degrees of freedom. To obtain a specific and predetermined photochemical reaction outcome, chemical substitution can be used to selectively alter the underlying electronic potential energy surfaces to favor a particular reaction pathway. We show using ab initio simulation that the substitution of s- trans-1,3-butadiene with a cyano group can effectively "direct" a molecular wavepacket to particular regions of the seam of conical intersection and either favor or inhibit the photoinitiated cis-trans isomerization. The substituent is able to effect this control due to the formation of transient charge-separated electronic structures that arise during the nonadiabatic dynamical process. The atomic site at which this charge develops can be selectively stabilized (or destabilized) depending on the location of the cyano substituent and gives rise to a single dominant decay pathway. This work aims to demonstrate how the application of known electron density effects to ultrafast dynamics may be used to obtain desired photochemical reactions and properties.
Publisher: Cold Spring Harbor Laboratory
Date: 22-09-2023
Publisher: AIP Publishing
Date: 28-12-2020
DOI: 10.1063/5.0031689
Abstract: Functional group substituents are a ubiquitous tool in ground-state organic chemistry often employed to fine-tune chemical properties and obtain desired chemical reaction outcomes. Their effect on photoexcited electronic states, however, remains poorly understood. To help build an intuition for these effects, we have studied ethylene, substituted with electron acceptor (cyano) and/or electron donor (methoxy) substituents, both theoretically and experimentally: using ab initio quantum molecular dynamics and time-resolved photoelectron spectroscopy. Our results show the consistent trend that photo-induced ethylenic dynamics is primarily localized to the carbon with the greater electron density. For doubly substituted ethylenes, the trend is additive when both substituents are located on opposite carbons, whereas the methoxy group (in concert with steric effects) dominates when both substituents are located on a single carbon atom. These results point to the development of rules for structure–dynamics correlations in this case, a novel mechanistic ultrafast photochemistry for conjugated carbon chains employing long-established chemical concepts.
Publisher: AIP Publishing
Date: 20-09-2016
DOI: 10.1063/1.4962170
Abstract: We report a joint experimental and theoretical study on the photoinitiated ultrafast dynamics of acrylonitrile (AN) and two methylated analogs: crotonitrile (CrN) and methacrylonitrile (MeAN). Time-resolved photoelectron spectroscopy (TRPES) and ab initio simulation are employed to discern the conical intersection mediated vibronic dynamics leading to relaxation to the ground electronic state. Each molecule is pumped with a femtosecond pulse at 200 nm and the ensuing wavepackets are probed by means of one and two photon ionization at 267 nm. The predominant vibrational motions involved in the de-excitation process, determined by ab initio trajectory simulations, are an initial twisting about the C=C axis followed by pyramidalization at a carbon atom. The decay of the time-resolved photoelectron signal for each molecule is characterized by exponential decay lifetimes for the passage back to the ground state of 60 ± 10, 86 ± 11, and 97 ± 9 fs for AN, CrN, and MeAN, respectively. As these results show, the excited state dynamics are sensitive to the choice of methylation site and the explanation for the observed trend may be found in the trajectory simulations. Specifically, since the pyramidalization motion leading to the conical intersection with the ground state is accompanied by the development of a partial negative charge at the central atom of the pyramidal group, the electron donation of the cyano group ensures that this occurs exclusively at the medial carbon atom. In this way, the donated electron density from the cyano group “directs” the wavepacket to a particular region of the intersection seam. The excellent agreement between the experimental and simulated TRPES spectra, the latter determined by employing trajectory simulations, demonstrates that this mechanistic picture is consistent with the spectroscopic results.
Publisher: Elsevier BV
Date: 11-2018
Publisher: Wiley
Date: 06-11-2020
DOI: 10.1111/MEC.15702
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D3SC02453A
Abstract: Analog quantum computers can calculate molecular vibronic spectra using time-domain simulation, with exponentially greater scalability than previous, frequency-domain approaches. An accurate, trapped-ion simulation of SO 2 validates the approach.
Publisher: American Chemical Society (ACS)
Date: 26-06-2020
Publisher: Wiley
Date: 19-08-2015
Abstract: In this joint experimental and theoretical study we characterize the complete dynamical "life cycle" associated with the photoexcitation of the singlet carbene cyclopropenylidene to the lowest lying optically bright excited electronic state: from the initial creation of an excited-state wavepacket to the ultimate fragmentation of the molecule on the vibrationally hot ground electronic state. Cyclopropenylidene is prepared in this work using an improved synthetic pathway for the preparation of the precursor quadricyclane, thereby greatly simplifying the assignment of the molecular origin of the measured photofragments. The excitation process and subsequent non-adiabatic dynamics have been previously investigated employing time-resolved photoelectron spectroscopy and are now complemented with high-level ab initio trajectory simulations that elucidate the specific vibronic relaxation pathways. Lastly, the fragmentation channels accessed by the molecule following internal conversion are probed using velocity map imaging (VMI) so that the identity of the fragmentation products and their corresponding energy distributions can be definitively assigned.
Publisher: Elsevier BV
Date: 04-2020
Location: United States of America
No related grants have been discovered for Joanna Kelley.