Resume

• 2009

  Doctor of Philosophy (PhD)

  Theoretical Chemistry

  Imperial College London

• 2004

  MChem

  Chemistry

  Southampton University

• 264

  Single-site photocatalysts are a class of materials in which single-site and small cluster molecules are embedded onto and within scaffolds such as zeolites

  MOFs

  graphene and bulk semiconductors. Experimental findings demonstrated the ability of a VO4 cluster embedded on MCM-41 mesoporous structure to effect partial oxidation of methane to methanol with high activity and selectivity (Hu

  Y.; Anpo

  M.; Wei

  C. Journal of Photochemistry and Photobiology A: Chemistry 2013

  48–55). Photoluminescence spectra indicated that the photoexcited state is localized to the cluster. This work aims to examine the nature of the VO4/MCM-41 photoexcited state theoretically to i) determine if the experimentally observed localization of the excited state electronic structure can be confirmed

  ii) understand the electronic structure of low-lying excited states to rationalize the initial step of the photocatalytic cycle

  and iii) establish agreement between theory and experiment to determine if the truncated cluster model of VO4/MCM-41 used in this study is sufficient for further studies into the photoreaction mechanism.

  Excited State Electronic Structure of Single-Site Vanadium Oxide Photocatalysts Supported on Mesoporous Silica

  Attempts to reconcile simulated photoelectron spectra of MoVO−4 clusters are complicated by the presence of very low energy barriers in the potential energy surfaces (PESs) of the lowest energy spin states and isomers. Transition state structures associated with the inversion of terminal oxygen ligands are found to lie below

  or close to

  the zero point energy of associated modes

  which themselves are found to be of low frequency and thus likely to be significantly populated in the experimental characterization. Our simulations make use of Boltzmann averaging over low-energy coordinates and full mapping of the PES to obtain simulations in good agreement with experimental spectra. Furthermore

  molecular orbital analysis of accessible final spin states reveals the existence of low energy two-electron transitions in which the final state is obtained from a finite excitation of an electron along with the main photodetachment event. Two-electron transitions are then used to justify the large difference in intensity between different bands present in the photoelectron spectrum. Owing to the general presence of terminal ligands in metal oxide clusters

  this study identifies and proposes a solution to issues that are generally encountered when attempting to simulate transition metal cluster photoelectron spectroscopy.

  Explaining the MoVO4− Photoelectron Spectrum: Rationalization of Geometric and Electronic Structure

  A compact orbital representation of ionization processes is described utilizing the difference of calculated one-particle density matrices. Natural orbital analysis involving this difference density matrix simplifies interpretation of electronic detachment processes and allows differentiation between one-electron transitions and shake-up/shake-off transitions

  in which one-electron processes are accompanied by excitation of a second electron into the virtual orbital space.

  Natural ionization orbitals for interpreting electron detachment processes

  A spin projected double-hybrid density functional theory is presented that accounts for different scaling of opposite and same spin terms in the second order correction. This method is applied to three dissociation reactions which in the unprojected formalism exhibit significant spin contamination with higher spin states. This gives rise to a distorted potential surface and can lead to poor geometries and energies. The projected method presented is shown to improve the description of the potential over unprojected double hybrid density functional theory. Comparison is made with the reference states of the two double hybrid functionals considered here (B2PLYP and mPW2PLYP) in which the projected potential surface is degraded by an imbalance in the description of dynamic and static correlation.

  Spin Projection with Double Hybrid Density Functional Theory

  Approximate projection (AP) schemes are widely used in computational studies of diradicals and transition metal systems to remove spin contamination in unrestricted density functional theory and Hartree–Fock results. Spin contamination results from an inability of single-reference descriptions to correctly model orbital degeneracies. Spin projection methods

  including AP

  avoid more expensive approaches using multi-reference wave functions to rectify the spin contamination error. Efficient derivations of the AP derivatives have allowed the computation of improved geometries and properties. In this work

  we establish a connection between AP and formulations developed using Löwdin's projection operator to obtain an understanding of where the method will work and highlight situations in which caution should be exercised.

  On approximate projection models

  Reliable global elucidation of (subsets of) self-consistent field solutions is required for continued development and application of computational approaches that utilize these solutions as reference wavefunctions. We report the derivation and implementation of a stochastic approach to perform global elucidation of self-consistent field solutions by exploiting the connection between global optimization and global elucidation problems. We discuss the design of the algorithm through combining basin-hopping search algorithms with a Lie algebraic approach to linearize self-consistent field solution space

  while also allowing preservation of desired spin-symmetry properties of the wavefunction. The performance of the algorithm is demonstrated on minimal basis C2v H4 due to its use as a model system for global self-consistent field solution exploration algorithms. Subsequently

  we show that the model is capable of successfully identifying low-lying self-consistent solutions of benzene and NO2 with polarized double-zeta and triple-zeta basis sets and examine the properties of these solutions.

  Global Elucidation of Self-Consistent Field Solution Space Using Basin Hopping

  Developments in biochemistry and materials sciences have led to increasing interest in the reactivity of large chemical systems

  presenting theoretical and computational challenges that can be addressed with hybrid methods such as ONIOM. Here

  we show that the diagonalized ONIOM Hessian can be partitioned/deconstructed into contributions from the individual subcalculations—indicating the curvature of their potential energy surfaces (PESs)—without increasing the computational cost. The resulting pseudofrequencies have particular application in the study of transition structures and higher-order saddle points with ONIOM

  where we find that an imaginary frequency may result from combining subcalculations for which the corresponding vibrational frequencies are all real. Two cycloaddition reactions

  including functionalization of a 150 atom (5

  5) single-walled carbon nanotube

  demonstrate how this analysis of pseudofrequencies allows identification of critical points where further exploratory work should be carried out to ensure that the ONIOM PES correctly approximates the target.

  Deconstructing the ONIOM Hessian: Investigating Method Combinations for Transition Structures

  Azobenzene is a prototype molecule with potential applications in molecular switches

  solar thermal batteries

  sensors

  photoresponsive membranes

  molecular electronics

  data storage

  and nonlinear optics. Photo and thermal isomerization pathways exhibit different charge-transfer character and dipole moments

  implying that the use of electric fields can be used to modulate the reactivity of azobenzene. This article examines the differential effect of orientated electric fields on the rotation and inversion thermal and photoisomerization pathways of azobenzene to explore the feasibility of using electric fields in the design of azobenzene-based molecular devices. Our findings demonstrate that the application of orientated electric fields modifies the accessibility of the S0/S1 seam of electronic degeneracy

  as well as changes the energetically favored relaxation pathway in the branching space to yield different photoproducts. In addition

  we observed strong-field dipole-inversion effects that cause a topographical change in the response of the potential energy surface to the applied field and can result in geometric minima that do not exist under field-free conditions. On the S0 surface

  transition barriers can be modified on the order of ±10 kcal mol–1

  enabling control of thermal isomerization rates.

  Effect of Oriented External Electric Fields on the Photo and Thermal Isomerization of Azobenzene

  Spin contamination in density functional studies has been identified as a cause of discrepancies between theoretical and experimental spectra of metal oxide clusters such as MoNbO2. We perform calculations to simulate the photoelectron spectra of the MoNbO2 anion using broken-symmetry density functional theory incorporating recently developed approximate projection methods. These calculations are able to account for the presence of contaminating spin states at single-reference computational cost. Results using these new tools demonstrate the significant effect of spin-contamination on geometries and force constants and show that the related errors in simulated spectra may be largely overcome by using an approximate projection model.

  Modeling the Photoelectron Spectra of MoNbO2– Accounting for Spin Contamination in Density Functional Theory

  This work evaluates the quality of exchange coupling constant and spin crossover gap calculations using density functional theory corrected by the approximate projection model. Results show that improvements using the approximate projection model range from modest to significant. This study demonstrates that

  at least for the class of systems examined here

  spin projection generally improves the quality of density functional theory calculations of J-coupling constants and spin crossover gaps. Furthermore

  it is shown that spin projection can be important for both geometry optimization and energy evaluations. The approximate projection model provides an affordable and practical approach for effectively correcting spin-contamination errors in such calculations.

  Assessing the Calculation of Exchange Coupling Constants and Spin Crossover Gaps Using the Approximate Projection Model To Improve Density Functional Calculations

  Broken symmetry solutions—solutions to the independent particle model that do not obey all symmetries required by the Hamiltonian—have attracted significant interest for capturing multireference properties with mean-field scaling. However

  identification and optimization of broken-symmetry solutions is difficult owing to the non-linear nature of the self-consistent field (SCF) equations

  particularly for solutions belonging to low-symmetry subgroups and where multiple broken symmetry solutions are sought. Linearization of SCF solution space results in the Lie algebra

  which this work utilizes as a framework for elucidation of the set of solutions that exist at the desired symmetry. To demonstrate that searches constructed in the Lie algebra yield the set of broken symmetry solutions

  a grid-based search of real-restricted

  real-unrestricted

  complex-restricted

  paired-unrestricted

  and real-general solutions of the C2v (nearly D4h) H4 molecule is performed.

  Global elucidation of broken symmetry solutions to the independent particle model through a Lie algebraic approach

  A systematic comparison of different environmental effects on the vibrational modes of the 4-hydroxybenzylidene-2

  3-dimethylimidazolinone (HBDI) chromophore using the ONIOM method allows us to model how the molecule’s spectroscopic transitions are modified in the Green Fluorescent Protein (GFP). ONIOM(QM:MM) reduces the expense of normal mode calculations when computing the majority of second derivatives only at the MM level. New developments described here for the efficient solution of the CPHF equations

  including contributions from electrostatic interactions with environment charges

  mean that QM model systems of ∼100 atoms can be embedded within a much larger MM environment of ∼5000 atoms. The resulting vibrational normal modes

  their associated frequencies

  and dipole derivative vectors have been used to interpret experimental difference spectra (GFPI2-GFPA)

  chromophore vibrational Stark shifts

  and changes in the difference between electronic and vibrational transition dipoles (mode angles) in the protein environment.

  Analytical Harmonic Vibrational Frequencies for the Green Fluorescent Protein Computed with ONIOM: Chromophore Mode Character and Its Response to Environment

  UC Merced

  University of Louisville

  Imperial College London

  Development and application of quantum chemistry software. Research in Computational Photochemistry

  particularly the study of photoactive proteins using QM/MM hybrid methods.

  Postgraduate Student

  London

  United Kingdom

  Imperial College London

  Louisville

  Kentucky Area

  Assistant Professor

  University of Louisville

  Merced

  California Area

  Postdoctoral Scholar

  UC Merced

• Bowling

  Molecular Dynamics

  Scientific Writing

  Quantum Chemistry

  Physical Chemistry

  Molecular Biology

  Materials Science

  Photochemistry

  Scientific Computing

  LaTeX

  The Influence of β‐Ammonium Substitution on the Reaction Kinetics of Aminooxy Condensations with Aldehydes and Ketones

  The click‐chemistry capture of volatile aldehydes and ketones by ammonium aminooxy compounds has proven to be an efficient means of analyzing the carbonyl subset in complex mixtures

  such as exhaled breath or environmental air. In this work

  we examine the carbonyl condensation reaction kinetics of three aminooxy compounds with varying β‐ammonium ion substitution using Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS). We determined the activation energies for the reactions of the aminooxy compounds ATM

  ADMH and AMAH with a panel of ketones and aldehydes that included acrolein and crotonaldehyde. The measurements indicate that the activation energies for the oximation reactions are quite low

  less than 75 kJ/mol. ADMH is observed to react the fastest with the carbonyls studied. We postulate this result may be attributed to the ADMH ammonium proton effecting a Brønsted‐Lowry acid‐catalyzed elimination of water during the rate‐determining step of oxime ether formation. A theoretical study of oxime ether formation is presented to explain the enhanced reactivity of ADMH relative to the tetraalkylammonium analog ATM.

  The Influence of β‐Ammonium Substitution on the Reaction Kinetics of Aminooxy Condensations with Aldehydes and Ketones

  We present a brief review of the current understanding and analysis of the photocycle of the Green Fluorescent Protein (GFP). GFP is unique to show directed excited state proton transfer (ESPT) in a protein environment

  which provides a directional coordinate for the ultrafast proton transfer reactions in contrast with disordered liquids. ESPT proceeds on a picosecond time scale and we consider details of the vibrational response of the chromophore and the protein environment during the course of this reaction. In addition we discuss both experimental and computational methodology and corrections that measure and model vibrational dichroism from polarised pump-probe infrared measurements. For the GFP photocycle

  a direct relationship between equilibrium protein side-chain conformation of glutamate 222 and reaction kinetics has been established for the ultrafast ESPT in the fluorescence photocycle. We have resolved the infrared spectral differences between heterogeneous ESPT reaction dynamics that were assigned to the carboxylate of the Glutamate 222 side chain. We additionally discuss photoselection measurements for the molecular interpretation of the vibrational transition dipole moments placed in the X-ray frame as a sensitive probe of the mode character and assess the assignments based on frequency calculations from the analytical second derivative for the isolated chromophore. Dipole gradients can be calculated analytically

  or numerically by finite difference. An older software release that displays analytical dipole gradients incorrectly is identified.

  Ultrafast vibrational dynamics of parallel excited state proton transfer reactions in the Green Fluorescent Protein

  The use of broken-symmetry electronic structure methods is required in order to obtain correct behavior of electronically strained open-shell systems

  such as transition states

  biradicals

  and transition metals. This approach often has issues with spin contamination

  which can lead to significant errors in predicted energies

  geometries

  and properties. Approximate projection schemes are able to correct for spin contamination and can often yield improved results. To fully make use of these methods and to carry out exploration of the potential energy surface

  it is desirable to develop an efficient second energy derivative theory. In this paper

  we formulate the analytical second derivatives for the Yamaguchi approximate projection scheme

  building on recent work that has yielded an efficient implementation of the analytical first derivatives.

  Second derivatives for approximate spin projection methods

  Enantioselective substrate directed Heck reactions are desirable for the stereoselective synthesis of complex molecules. However

  due to the coordination requirements of both chiral ligands and directing groups

  such methodologies are underdeveloped. We report herein the desymmetrization of meso (1R

  2S)‐cyclohex‐4‐ene‐1

  2‐diol in an enantioselective and substrate directed fashion. The method provides all cis substituted highly functionalized chiral allylic alcohols in a complementary fashion to other Heck protocols.The products were obtained in high enantioselectivities (higher than 95% ee) and moderate to high yields (38–87%). The noncovalent interactions responsible for the directing effect were elucidated through computational examination of relevant minima and transition structures.

  Non-covalent substrate directed enantioselective Heck desymmetrization of cis-cyclohex-4-ene-1

  2-diol: Synthesis of all cis chiral 5-Aryl-cyclohex-3-ene-1

  2-diols and mechanistic investigation

  Lanthanide hydroxides are key species in a variety of catalytic processes and in the preparation of corresponding oxides. This work explores the fundamental structure and bonding of the simplest lanthanide hydroxide

  LnOH (Ln = La–Lu)

  using density functional theory calculations. Interestingly

  the calculations predict that all structures of this series will be linear. Furthermore

  these results indicate a valence electron configuration of σ2π4 for all LnOH compounds

  suggesting that the lanthanide-hydroxide bond is best characterized as a covalent triple bond.

  On the linear geometry of lanthanide hydroxide (Ln-OH

  Ln = La–Lu)

  The use of projection-after-variation double-hybrid density functional theory is proposed and examined as a difference method for the calculation of excited states. The strengths and weaknesses of the proposed method are discussed with particular reference to connections with linear response coupled-cluster theory. Vertical excitation energies are computed for the 28 molecule benchmark of Schreiber and co-workers in order to compare how the model performs with linear response coupled-cluster theories and multireference perturbation theory. The findings of this study show that the proposed method can achieve standard deviations in the error of computed vertical excitation energies compared to complete active space second-order perturbation theory of similar size to linear response coupled-cluster theories.

  Difference projection-after-variation double-hybrid density functional theory applied to the calculation of vertical excitation energies

  An experimental and computational investigation is conducted into the role of substituents in retro Diels–Alder extrusion of CO2 from 2-oxa-bicyclo[2.2.2]oct-5-en-3-ones. We provide the first experimental evidence that loss of CO2 from the cycloadducts significantly depends on the nature and position of the substituents. For example

  we show that whilst 5-carboethoxy-2-pyrone undergoes a more facile cycloaddition that 3-carboethoxy-2-pyrone

  the cycloadduct from the latter pyrone undergoes a more facile loss of CO2 than the cycloadduct from the former pyrone.

  The Role of Substituents in Retro Diels-Alder Extrusion of CO 2 from 2(H)- pyrone Cycloadducts