The First Chemically Accurate Tools in Theoretical Materials Research. Non-metallic materials are widely used in catalytic, separation and sensing applications. This project will create a new, accurate, general and systematic approach to the computational study of non-metallic materials and will provide an enormous step forward in our ability to design these materials for specific applications. With ever increasing demand, growing world population and shrinking natural resources, the benefits of ....The First Chemically Accurate Tools in Theoretical Materials Research. Non-metallic materials are widely used in catalytic, separation and sensing applications. This project will create a new, accurate, general and systematic approach to the computational study of non-metallic materials and will provide an enormous step forward in our ability to design these materials for specific applications. With ever increasing demand, growing world population and shrinking natural resources, the benefits of such rational materials design impact on the development of new, safer, more efficient, reusable materials in chemical, engineering, electronic and biological applications. Read moreRead less
TOWARDS A COMPLETE DESCRIPTION OF HOW ENZYMES WORK: development of simulation methods and protocols, blind test predictions, and experimental validation. Enzymes catalyze quite fantastic chemistry under mild physiological conditions. Many special chemical concepts (such as "transition-state stabilization" and "entropy-enthalpy compensation") proposed to explain these powers are unnecessary. Uniquely for a catalyst, these powers are integral to the structure, properties and dynamics of the protei ....TOWARDS A COMPLETE DESCRIPTION OF HOW ENZYMES WORK: development of simulation methods and protocols, blind test predictions, and experimental validation. Enzymes catalyze quite fantastic chemistry under mild physiological conditions. Many special chemical concepts (such as "transition-state stabilization" and "entropy-enthalpy compensation") proposed to explain these powers are unnecessary. Uniquely for a catalyst, these powers are integral to the structure, properties and dynamics of the protein, as constrained and selected by evolution. The question is how do they work? Answering this requires energetic and thermodynamic analysis beyond current experimental techniques, but accessible by computer simulation. We aim to develop a robust toolkit of simulation methods and protocols, blind test them by predicting the mechanism of a new enzyme, with followup experimental validation.
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Quantum chemical methods: From wavefunction to density functional theory. This project aims to address a major challenge in quantum chemistry - how to extend the applicability of high-level quantum chemical methods to larger molecules. High-level quantum chemical methods can consistently obtain reliable thermochemical and kinetic data, but due to their steep computational cost, they are only applicable to relatively small molecules. The project expects to introduce new concepts and methodologies ....Quantum chemical methods: From wavefunction to density functional theory. This project aims to address a major challenge in quantum chemistry - how to extend the applicability of high-level quantum chemical methods to larger molecules. High-level quantum chemical methods can consistently obtain reliable thermochemical and kinetic data, but due to their steep computational cost, they are only applicable to relatively small molecules. The project expects to introduce new concepts and methodologies that build on recent breakthrough research in the field of ab initio computational chemistry. The new methods should be capable of energetic predictions of unprecedented accuracy for relatively large systems across the Periodic Table and will be used for the development of better density functional theory procedures.Read moreRead less
Importance of conformational and electrostatic contributions in simulations of enzyme reaction mechanisms. The research will contribute to the development of biomolecular simulation in Australia by demonstrating its potential to complement experiment, and also promote the effective use of APAC (Australian national supercomputer facilities) resources by providing advanced programs and computational protocols for other researchers. It will assist the diffusion of computational biology technology i ....Importance of conformational and electrostatic contributions in simulations of enzyme reaction mechanisms. The research will contribute to the development of biomolecular simulation in Australia by demonstrating its potential to complement experiment, and also promote the effective use of APAC (Australian national supercomputer facilities) resources by providing advanced programs and computational protocols for other researchers. It will assist the diffusion of computational biology technology into industrial applications such as rational drug design and protein engineering, as, for example, in our associated Linkage project grant, and provide novel insights into protein engineering and other sorts of design, which transcend concepts currently used in biomimetic chemistry.Read moreRead less
Computer simulation of DNA biochips. The DNA biochip technology has been a major breakthrough in cell biology and clinical analysis. Companies in Australia and in the rest of the world are now developing biochips for genome sequencing and point-of-care diagnosis. DNA biochips have the potential to provide simple, fast and accurate clinical analysis, thus enhancing the efficiency of medical treatments and reducing the costs of health care.
The structural properties of the immobilized DNA are cri ....Computer simulation of DNA biochips. The DNA biochip technology has been a major breakthrough in cell biology and clinical analysis. Companies in Australia and in the rest of the world are now developing biochips for genome sequencing and point-of-care diagnosis. DNA biochips have the potential to provide simple, fast and accurate clinical analysis, thus enhancing the efficiency of medical treatments and reducing the costs of health care.
The structural properties of the immobilized DNA are critical for determining the DNA chip sensitivity and efficiency. A fundamental understanding of the molecular interactions at the surface of a biochip is therefore not only relevant for the scientific community, but can have direct implications for the design of improved DNA chips.Read moreRead less
A priori simulations of condensed-phase molecular spectroscopy. Molecular spectroscopy is used to probe phenomena in chemistry, biology, and nanoscience, but interpretation of the results often requires simulation of the spectra. While most applications involve condensed phases, until recently most accurate computations could only be performed for gas-phase molecules. Last year, a major advance has started to emerge, stemming from the production of analytical atomic forces for molecules in exc ....A priori simulations of condensed-phase molecular spectroscopy. Molecular spectroscopy is used to probe phenomena in chemistry, biology, and nanoscience, but interpretation of the results often requires simulation of the spectra. While most applications involve condensed phases, until recently most accurate computations could only be performed for gas-phase molecules. Last year, a major advance has started to emerge, stemming from the production of analytical atomic forces for molecules in excited states obtained using density-functional theory. We will adapt these methods to solve fundamental chemical problems involving the intermolecular interactions of molecules that have absorbed light- in particular, hydrogen-bonding interactions in water, studying, eg., chemical solvation and optical damage to DNA.Read moreRead less
Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of new metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of industrial and synthetic importance. These outcomes will have a significant impact on the development of both novel transition metal systems for synthetic chemistry and new industrial procedures for the activation and cleavage of multiply-bonded molecules su ....Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of new metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of industrial and synthetic importance. These outcomes will have a significant impact on the development of both novel transition metal systems for synthetic chemistry and new industrial procedures for the activation and cleavage of multiply-bonded molecules such as molecular nitrogen and carbon dioxide. They will lead to new consumer products, better methods of production, and potential downstream applications such as nitric oxide/nitrogen dioxide converters and carbon dioxide emission controls.Read moreRead less
Activation and Scission of Small Molecules using Three-Coordinate Metal Complexes. Chemists have long admired the ease with which such fundamental molecules as nitrogen, oxygen and carbon dioxide are processed in biological systems under mild conditions in contrast to existing industrial processes such as nitrogen 'fixation' which require drastic temperatures and pressures. Our project addresses this inbalance by using powerful computational methods to design highly-tuned chemical systems based ....Activation and Scission of Small Molecules using Three-Coordinate Metal Complexes. Chemists have long admired the ease with which such fundamental molecules as nitrogen, oxygen and carbon dioxide are processed in biological systems under mild conditions in contrast to existing industrial processes such as nitrogen 'fixation' which require drastic temperatures and pressures. Our project addresses this inbalance by using powerful computational methods to design highly-tuned chemical systems based on three-coordinate metal complexes which are specific for the activation and scission of important small molecules possessing multiple bonds.Read moreRead less
Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of chemical importance. This will have a significant impact on industry by providing cheaper and safer alternatives to currently expensive and hazardous processes for producing nitrogen and phosphorus containing compounds esential to the chemical and agricultural i ....Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of chemical importance. This will have a significant impact on industry by providing cheaper and safer alternatives to currently expensive and hazardous processes for producing nitrogen and phosphorus containing compounds esential to the chemical and agricultural industries. It will also greatly benefit the chemical community by providing novel routes to constructing metal complexes with unusual and exotic ligands. These outcomes will lead to new consumer products and potential downstream applications such as nitric oxide/nitrogen dioxide converters and carbon dioxide emission controls.Read moreRead less
Function, Mechanism and Dynamics in Fluorescent Proteins: a Computational Investigation. The rich reservoir of chromoproteins and fluorescent proteins in the ecosystem of the Great Barrier Reef offers Australia a unique natural advantage for the development of a niche biotechnology industry based on fluorescent markers for cellular biology and biomedical imaging. This project provides a crucial component of the science that is necessary for developing such an industry: a molecular-level knowledg ....Function, Mechanism and Dynamics in Fluorescent Proteins: a Computational Investigation. The rich reservoir of chromoproteins and fluorescent proteins in the ecosystem of the Great Barrier Reef offers Australia a unique natural advantage for the development of a niche biotechnology industry based on fluorescent markers for cellular biology and biomedical imaging. This project provides a crucial component of the science that is necessary for developing such an industry: a molecular-level knowledge of how these proteins function and how we can manipulate and enhance their properties as imaging agents. It will achieve fundamental advances in biomolecular modelling techniques, train graduates with exceedingly valuable skill sets as well as deriving knowledge that aids the development of Australia's biotech industries.Read moreRead less