High-accuracy computation of reaction barriers in enzymes.
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4-Hydroxybenzoate-3-Monooxygenase↗
Biomedical subjects
Frederick R Manby
Publications and source records attributed to Frederick R Manby.
Design of infrared laser pulses for the deexcitation of highly excited homonuclear diatomic molecules.
We explore the possibility of using shaped infrared laser pulses to deexcite a homonuclear diatomic molecule from its highest vibrational state down to its ground vibrational state. The motivation for this study arises from the need to deexcite alkali metal dimers in a similar way so as to stabilize molecular Bose-Einstein condensates. We demonstrate that for the case of the H(2) molecule, where it is possible to evaluate all the necessary high accuracy ab initio data on the interaction of the molecule with an electric field, we are able to successfully design a sequence of infrared laser pulses to accomplish the desired deexcitation process in a highly efficient manner.
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Analytical control of molecular excitations including strong field polarization effects.
An analytical scheme is presented for designing a laser pulse to excite H2 from one specified vibrational-rotational state to another. The scheme is based on an adiabatic two-state approximation in a Floquet picture. By continuously and smoothly changing the laser frequency, we explicitly harness the dynamic Stark shifts and maintain resonance between the dressed diabatic states during laser-molecule interaction. The explicit time-dependent solution of the Schrödinger equation confirms the validity and efficacy of the analytically designed laser pulses. The scheme depends on the molecular polarizability to achieve its control objectives.
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Explicitly correlated local second-order perturbation theory with a frozen geminal correlation factor.
The recently introduced MP2-R122*A(loc) and LMP2-R122*A(loc) methods are modified to use a short-range correlation factor expanded as a fixed linear combination of Gaussian geminals. Density fitting is used to reduce the effort for integral evaluation, and local approximations are introduced to improve the scaling of the computational resources with molecular size. The MP2-F122*A(loc) correlation energies converge very rapidly with respect to the atomic orbital basis set size. Already with the aug-cc-pVTZ basis the correlation energies computed for a set of 21 small molecules are found to be within 0.5% of the MP2 basis set limit. Furthermore the short-range correlation factor leads to an improved convergence of the resolution of the identity, and eliminates problems with long-range errors in density fitting caused by the linear r12 factor. The DF-LMP2-F122*A(loc) method is applied to compute second-order correlation energies for molecules with up to 49 atoms and more than 1600 basis functions.
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Explicitly correlated second-order perturbation theory using density fitting and local approximations.
Three major obstacles in electronic structure theory are the steep scalings of computer time with respect to system size and basis size and the slow convergence of correlation energies in orbital basis sets. Three solutions to these are, respectively, local methods, density fitting, and explicit correlation; in this work, we combine all three to produce a low-order scaling method that can achieve accurate MP2 energies for large systems. The errors introduced by the local approximations into the R12 treatment are analyzed for 16 chemical reactions involving 21 molecules. Weak pair approximations, as well as local resolution of the identity approximations, are tested for molecules with up to 49 atoms, over 100 correlated electrons, and over 1000 basis functions.
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Quantum control of molecular vibrational and rotational excitations in a homonuclear diatomic molecule: a full three-dimensional treatment with polarization forces.
The optimal control of the vibrational excitation of the hydrogen molecule [Balint-Kurti et al., J. Chem. Phys. 122, 084110 (2005)] utilizing polarization forces is extended to three dimensions. The polarizability of the molecule, to first and higher orders, is accounted for using explicit ab initio calculations of the molecular electronic energy in the presence of an electric field. Optimal control theory is then used to design infrared laser pulses that selectively excite the molecule to preselected vibrational-rotational states. The amplitude of the electric field of the optimized pulses is restricted so that there is no significant ionization during the process, and a new frequency sifting method is used to simplify the frequency spectrum of the pulse. The frequency spectra of the optimized laser pulses for processes involving rotational excitation are more complex than those relating to processes involving only vibrational excitation.
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Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization.
Multiple profiles for the reaction from chorismate to prephenate in the enzyme chorismate mutase calculated with hybrid density functional combined quantum mechanics/molecular mechanics methods (B3LYP/6-31G(d)-CHARMM27) agree well with experiment, and provide direct evidence of transition-state stabilization by this important enzyme, which is at the centre of current debates about the nature of enzyme catalysis.
Chorismate Mutase↗
Analysis of the errors in explicitly correlated electronic structure theory.
The explicitly correlated second order Møller-Plesset (MP2-R12) methods perform well in reproducing the last detail of the correlation cusp, allowing higher accuracy than can be accessed through conventional means. Nevertheless in basis sets that are practical for calculations on larger systems (i.e., around triple- or perhaps quadruple-zeta) MP2-R12 fails to bridge the divide between conventional MP2 and the MP2 basis set limit. In this contribution we analyse the sources of error in MP2-R12 calculations in such basis sets. We conclude that the main source of error is the choice of the correlation factor r12. Sources of error that must be avoided for accurate quantum chemistry include the neglect of exchange commutators and the extended Brillouin condition. The generalized Brillouin condition is found not to lead to significant errors.
Algorithms↗
The interpretation of molecular magnetic hyperfine interactions.
Investigations of the hyperfine structure in the excited electronic states of several free radical species have revealed shortcomings in the currently accepted values used for the theoretical interpretation of such interactions. We introduce updated reference atomic values from a combination of experimental observations and ab initio calculations. The latter are at Hartree-Fock and multireference configuration interaction levels of theory and several atomic test cases are discussed. Furthermore, ground and excited electronic state hyperfine coupling constants are calculated using both levels of theory for a range of first- and second-row diatomic hydride and nonhydride radicals. These results, together with a selection of other experimental measurements are then compared with experimental data where available, and the implications of the revised interpretation are discussed.
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Quantum control of molecular motion including electronic polarization effects with a two-stage toolkit.
A method for incorporating strong electric field polarization effects into optimal control calculations is presented. A Born-Oppenheimer-type separation, referred to as the electric-nuclear Born-Oppenheimer (ENBO) approximation, is introduced in which variations of both the nuclear geometry and the external electric field are assumed to be slow compared with the speed at which the electronic degrees of freedom respond to these changes. This assumption permits the generation of a potential energy surface that depends not only on the relative geometry of the nuclei but also on the electric field strength and on the orientation of the molecule with respect to the electric field. The range of validity of the ENBO approximation is discussed in the paper. A two-stage toolkit implementation is presented to incorporate the polarization effects and reduce the cost of the optimal control dynamics calculations. As an illustration of the method, it is applied to optimal control of vibrational excitation in a hydrogen molecule aligned along the field direction. Ab initio configuration interaction calculations with a large orbital basis set are used to compute the H-H interaction potential in the presence of the electric field. The significant computational cost reduction afforded by the toolkit implementation is demonstrated.
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An explicitly correlated second order Møller-Plesset theory using a frozen Gaussian geminal.
A variant of the MP2-R12 class of theories is introduced using an arbitrary geminal function in the place of r12. Integrals are derived for the case where the geminal is expanded in a basis of Gaussian functions in the interelectronic distance. Recurrence relations are derived that do not depend on the exponents of the Gaussian geminals, allowing much of the integration work to be performed after summations over the geminal expansion. Sample calculations at various levels of explicitly correlated MP2 theory are presented for He, Ne, and water.
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Analytical energy gradients for local second-order Møller-Plesset perturbation theory using density fitting approximations.
An efficient method to compute analytical energy derivatives for local second-order Møller-Plesset perturbation energy is presented. Density fitting approximations are employed for all 4-index integrals and their derivatives. Using local fitting approximations, quadratic scaling with molecular size and cubic scaling with basis set size for a given molecule is achieved. The density fitting approximations have a negligible effect on the accuracy of optimized equilibrium structures or computed energy differences. The method can be applied to much larger molecules and basis sets than any previous second-order Møller-Plesset gradient program. The efficiency and accuracy of the method is demonstrated for a number of organic molecules as well as for molecular clusters. Examples of geometry optimizations for molecules with 100 atoms and over 2000 basis functions without symmetry are presented.
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