Charge reversal mass spectrum of CC13CCC.

The chemistry of silylene, SiH₂, and to a lesser extent germylene, GeH₂, has been the focus of a considerable amount of attention over the last 2 decades due to the importance of these group IV electron-deficient radicals in chemical vapor deposition, semiconductor manufacture, and the photonics and aerospace industries.  In particular, the oxidation chemistry of silylene has received considerable attention, both experimental and theoretical, in recent years.  For example, silylene is well known to insert into O-H bonds via a zwitterionic donor-acceptor intermediate.  Nonetheless, there remains a paucity of experimental data characterizing the energetics and kinetics of silylene oxidation chemistry.  Even less experimental data are available to characterize the oxidation chemistry of germylene.  Ab initio quantum chemistry has proven to be a valuable tool in developing a more detailed understanding of the chemistry of the silicon-oxy-hydrides, Si_xH_yO_z.  At The University of Adelaide molecular orbital calculations have been performed to explore the reaction potential energy surfaces of singlet silylene and germylene with water, methanol, ethanol, dimethyl ether, and trifluoromethanol.  Two new reaction channels have been identified on the reaction surfaces.  The previously unknown reaction channels involve H₂ elimination following the initial formation of an association complex. For reactions involving singlet silylene and water (see the figure below), a simple activated complex theory (ACT) analysis predicts that these newly identified reaction channels are equally likely to be accessed as the previously identified 1,2 hydrogen atom shift channels.  For reactions involving singlet germylene and water, a similar ACT analysis predicts that the H₂-elimination channels will occur in preference to the 1,2 hydrogen shift.  Indeed, the room-temperature rate constants for H₂ elimination from the germanium complex are predicted to be approximately 5 orders of magnitude greater than for the H atom migration channel.

MP2/6-311++G(d,p) stationary points determined on the silylene-plus-water reaction potential energy surface. Note that the pathways leading to the formation of syn- and anti-hydroxysilylene are hitherto unknown.  Stationary point energies are given in kJ mol-1.

Van der Waals complexes provide insights into intermolecular bonding in condensed phases and for this reason are the subject of intense scrutiny, both theoretically and experimentally, from the international chemical physics community.  Researchers at The University of Adelaide and Flinders University are using ab initio theory to explore the potential energy surfaces of van der Waals complexes involving one or more atoms (typically argon) or small polyatomic molecules (eg. nitrogen or acetylene) bound to an aromatic molecule (benzene or p-difluorobenzene).  These studies are at the cutting edge of international work in the field.  In particular, ab initio interrogation of trimer complexes are providing insights into 3-body effects in intermolecular interactions, improving our understanding of intermolecular interactions in model systems of relevance as targets for improving our ability to model chemistry in condensed phases.

Stationary Points on the potential energy surfaces for the Benzene-Acetylene and Benzene-(Acetylene)2 Complexes.

Metal-molecule interactions play an important role in heterogeneous catalysis, however, the subtle interplay between the metal surface and the reacting molecules that drive these chemical reactions is often poorly understood.  Improvements to catalytic processes can be achieved by developing a better understanding of the crucial steps at the metal-molecule interface, including characterisation of key reaction intermediates in the catalytic cycle.  Researchers in the Laser Chemistry Laboratory at the University of Adelaide are exploring the chemical and physical properties of interfacial metal-molecule bonds via a combined experimental and computational investigation of model chemical systems in which a molecule is adsorbed onto a small metal cluster.  Over the last few years, these workers have developed extensive experience using DFT methods to calculate reaction pathways and energies associated with physisorption, associative chemisorption and dissociative chemisorption.  For example, calculations for the Nb3 + CO reaction indicate that interaction of CO spontaneously leads to dissociation, consistent with the latest experimental findings.  Recent work on the other 4d transition metal trimers (e.g. Rh3, Ag3) indicate that the most thermodynamically favourable pathway can be predicted in terms of the energies of the molecular orbitals of the CO molecule and the electron density of the metal cluster.  Future consideration will be given towards adding or withdrawing electron density from the metal cluster moiety.  What happens if a positive or negative charge is added?  Alternatively, what if an electron-donating atom, or an electron-withdrawing atom, is added to the metal cluster (i.e. carbon c.f fluorine)?  Are these effects analogous to the surface additives effects (i.e. poisons and promoters) observed on bulk surfaces reactions?  DFT calculations can provide insight into these answers in a way that experiment alone cannot.  Furthermore, in this manner, it may be possible to create an ideal cluster that has specific bonding characteristics that allow the production of finely tuned nano-catalysts.

The reaction potential energy surface for Nb3 + CO.  Stationary point energies are given in eV.

Molecular dynamics is a now standard tool for exploring reactivity and time-dependent relaxation (folding) as well as equilibrium properties. The tool is used for fully converged rate predictions in smaller molecular systems as well as for gaining qualitative understanding of structural and dynamical features in complex materials or biopolymer systems. A topical issue, and a major direction for future advances in this field, is the question of how to effectively integrate intrinsically quantum phenomena into the broadly classical MD treatment of large molecular systems. For example, photosynthesis involves generation of a charge separation via electron transfer after initial absorption of light. The electron transfer is fundamentally a quantum phenomenon, not described adequately by classical mechanics, yet much of the structural and relaxational aspects of the surrounding protein are adequately described by a classical MD treatment. A related question is to determine accurately the energetics of reactions such as electron transfer, bond cleavage and rearrangement or proton transfer – this implies the need for accurate solutions of the electronic Schrödinger equation in the vicinity of the reaction, while more distant parts of the protein can in principle be dealt with at a lower level of electronic structure theory. The Molecular Electronics Group in Sydney are world leaders in quantum/classical modelling of the photosynthetic reaction centre, and also other molecular electronics applications where the kinetics and reversibility of electron transport is an important issue (shown at left is a DFT simulation of the dynamics of device interfaces at high temperature).

Groups at the Australian National University (ANU Supercomputing Facility and the John Curtin School of Medical Research) are working on new computational approaches for solving the electronic Schrödinger equation in very large systems that will give superior scaling properties as the size of the enzyme or protein increases. The Centre for Computational Molecular Science (CCMS) at UQ is exploring pathways for complex multi-step proton transfer in proteins and developing models to describe the time-dependent quantum dynamics of this phenomenon.

Geminal to experimental studies of the optical spectra of gas phase species of astrophysical interest is the prediction of excited state energies by ab initio methods. Ab initio support is crucial in assigning spectra to their isomeric structure.  In order to predict accurate excited state energies of large molecules, accurate ab initio methods are required which scale favourably with system size.  Dr Tim Schmidt at the University of Sydney is developing a way to localize electrons for a Diffusion Monte Carlo calculation.  Taking an initial guiding function from CASSCF (converged with respect to nodes), a Diffusion Monte Carlo is performed to retrieve the dynamic correlation energy.  Proper exploitation of localized orbitals and therefore sparse Slater Determinant coupled with a technique for keeping electrons "in their place" yields a linearly scaling calculation resulting in accurate excitation energies for comparison with laboratory spectra.  These methods are being applied to carbon-chain molecules as large as HC₂₆H and smaller exotic species such as C₉H₃.

CCMS signature graphic profiled in the international journal PCCP, in association with an invited review article.

The Lanczos-recursion-based scattering methods developed at UQ, while significantly more efficient, have many properties similar to the more well known wavepacket methods. In particular, a single recursion (analogous to a wavepacket propagation in real time) yields a single column of the scattering matrix for all energies. The most recent breakthrough in the application of the Lanczos methods finally breaks this paradigm. In a recent development the UQ group have shown that the Lanczos approach is capable of generating the entire S-matrix, for all energies, from a single recursion. This is a landmark development in the design of quantum scattering algorithms.

The dynamics group at the ANU have developed a powerful collaboration with the Singapore quantum scattering group. This development recognizes the important contribution of the ANU group's potential energy surface construction approach for the subsequent accurate quantum predictions of reaction rates.

Another important quantum methodology, which allows the prediction of ground state properties and also thermal equilibrium properties, is quantum monte carlo. A group at Sydney have developed considerable expertise in this area and are applying it to the prediction of ground state properties of hydrogen bonded systems. This is an important extension of much exploratory quantum chemical study of such systems which the group has pursued in recent years, and certainly places them near the leading edge of the field in this area.

Probing the pathways of molecular reactions is an essential first step to the computational characterization of processes as diverse as simple chemical reactions, biosynthetic pathways, and hydrogen storage in new materials.  Such pathways are often complex, with fleeting intermediate species occurring along the way.

Researchers in the School of Chemistry, University of Sydney, are interested in using quantum mechanics to explore the photochemical reactivity of halocarbons and aldehydes, both classes of molecules being of significant atmospheric importance. Halogenated species have been released to the atmosphere in significant amounts over the past few decades. The group has been established, for the first time, that irradiation of some of these compounds in the UV can lead to triple fragmentation, producing a carbene and 2 halogen atoms. Further experiments on the carbene intermediates have explained why some carbenes undergo bond cleavage under UV exposure and others do not. However, the explanation of the experimental data was enabled only by a high level ab initio investigation of the electronic structure of these carbenes. Other experiments on photodissociation reactions of aldehydes have led to the first exploration of how the 3-dimensional rotation of a fragment provides information on the transition state of a reaction, and how the 3-dimensional rotation of a molecule affects the reaction outcome. There have been only 8 reactions for which the full 3-dimensional rotation of the products has been measured, half of which have been measured by the Sydney group. To date, it appears that one of the quantum numbers in these reactions (the Kc quantum number) is a robust indicator of reaction dynamics, even for quite large molecules. Various theoretical approaches are now being applied to predict these experimental outcomes.  

Australia has several active groups in the general area of computational simulation of different types of molecular spectroscopy.  The interpretation of X-ray spectra to derive structural and, as time-dependent data becomes an achievable reality with the intense light available from synchrotron sources, ultimately also dynamical properties is an area of active research at UNE and at UWA.  Electron momentum spectroscopy provides unique avenues to determine information about the nature of external molecular orbitals.  The theoretical treatment of this type of experiment proceeds via a dual space (i.e., configuration and momentum space) analysis.  A number of groups are active in the simulation of high resolution spectra for rovibrationally excited molecules and also weakly bound clusters.

Results of calculations at Swinburne on the highest-occupied molecular orbital of norbornadiene.

Researchers in the School of Biological and Chemical Sciences  at Deakin University use a variety of theoretical and computational methods to probe the fundamental chemistry of reactions and processes at the molecular level.  In particular, quantum chemical methods are being used to predict and interpret the energetics, structure, NMR and UV spectra of short-lived molecules that are produced and reacted during a reaction.  These quantum chemical methods will be combined with kinetic modelling to better understand the reaction mechanism of chemiluminescence systems.  The understanding of the mechanism of chemiluminescence reactions will enable identification of the reactive centre and the role (if any) of the side groups around that centre. This information will be used to design chemiluminescent reagents with improved solubility, sensitivity or selectivity, by substitution of the side groups.  This will enable assessment of the compositions of complex mixtures with minimal separation.

The Deakin team also collaborates with the Dynamics Group at the ANU to predict and understand the collisional energy transfer step that is the precursor to combustion and other gas-phase chemistries.

At The University of Adelaide, studies of host defence secretions of Australian anurans has, to date, resulted in the identification of over 200 bioactive peptides.   Mass spectrometry is used to sequence the peptides, but a combination of 2D nuclear magnetic resonance spectroscopy and molecular modelling is used to identify the 3D structure of the active molecule.  As an example, the 25 residue peptide caerin 1.1 is a peptide with multifaceted activity.  It is a wide-spectrum antibiotic and a fungicide, it is active against all types of human cancers, and it inhibits the formation of nitric oxide by neuronal nitric oxide synthase.  The 3D structure (below) identifies it as a peptide with two helical regions separated by a central flexible hinge.

The 3D structure of caerin 1.1.

Researchers at The University of Melbourne are seeking to develop a microscopic understanding of ion-neutral solvent interactions through theoretical ab initio electronic structure calculations of simple charged complexes and clusters, and experimentally by forming and spectroscopically characterizing charged complexes and clusters in the gas phase to yield information on vibrational frequencies, rotational constants, and more generally on the intermolecular potential energy surface.  The two approaches are complementary.  The computational studies guide spectroscopic searches, and assist in interpreting the infrared spectra, while in turn, spectroscopic data serve to test the efficacy of modern computational approaches for describing charged molecules, complexes and clusters.  During the past 5 years the Melbourne group has characterized, using experimental and computational techniques, a series of anion complexes and clusters including Cl^--(C₂H₂)_n, Br^--(C₂H₂)_n, Cl^–-C₆H₆, I^--(C₂H₂)_n, F^–-CH₄, Cl^–-CH₄, Cl^--NH₃, Cl^--H₂, Cl^--D₂, Br^--H₂, Br^--D₂ and I^--H₂.

Accurate predictions for the rovibrational energy levels of the complexes require going beyond the familiar harmonic oscillator/rigid rotor approximation.  For example, in theoretical studies of the Cl^--H₂ complex, the rovibrational energy levels were calculated variationally using a potential energy surface fitted to ab initio points. The Melbourne researchers collaborate with computational chemists in Russia, Switzerland and the USA.

The conformation of flexible biomolecules can change dramatically depending on the degree of solvation.  For example, it is known that in solution many amino acids exist in their zwitterionic (charge-separated) state due to interactions with the surrounding water molecules, yet when isolated in the gas phase the same amino acids exist in their non-zwitterionic form.

(Left) Intramolecular hydrogen bonding within the ethanolamine side chain of the neurotransmitter dopamine is disrupted by insertion of a single water molecule. (Right) The onset of a ‘3D’ network of hydrogen bonding occurs with four water molecules bound to the neurotransmitter side chain.

Theoretical calculations are used to provide the range of structural possibilities, whether they be molecular conformers or complexes in which molecules are attached to the host in different ways. The calculated properties of each one are then compared to experiment to determine the ones actually observed. The fine details of energetics, local H-bonded interactions, and the factors that determine conformation are revealed by this combined approach.

Researchers at The University of Adelaide’s Laser Chemistry Laboratory and Monash University’s Centre for Biospectroscopy are involved in experimental and computational investigations into the spectroscopy of biological molecules and their clusters, with a focus on structural and energetic aspects of hydrogen-bonding interactions and how they affect other properties of the molecules.