Biomedical subjects

Michael V Pak

Publications and source records attributed to Michael V Pak.

5 recordsLinked to original sources

PubMed2006

Explicit dynamical electron-proton correlation in the nuclear-electronic orbital framework.

A method that includes explicit electron-proton correlation directly into the nuclear-electronic orbital self-consistent-field framework is presented. This nuclear-electronic orbital explicitly correlated Hartree-Fock (NEO-XCHF) scheme is formulated using Gaussian basis functions for the electrons and the quantum nuclei in conjunction with Gaussian-type geminal functions. The NEO approach is designed for the quantum treatment of a relatively small number of nuclei, such as the hydrogen nuclei involved in key hydrogen bonding interactions or hydrogen transfer reactions. The conventional nuclear-electronic-orbital-based methods produce nuclear wave functions that are too localized, leading to severe overestimations of hydrogen vibrational frequencies, as well as inaccuracies in geometries, isotope effects, couplings, and tunneling splittings. The application of the NEO-XCHF approach to a model system illustrates that the description of the nuclear wave function is significantly improved by the inclusion of explicit electron-proton correlation. In contrast to the NEO-HF method, the NEO-XCHF method leads to hydrogen vibrational stretch frequencies that are in excellent agreement with those calculated from grid-based methods. This approach is computationally practical for many-electron systems because only a relatively small number of nuclei are treated quantum mechanically and only electron-proton correlation is treated explicitly. Electron-electron dynamical correlation can be included with density functional theory or perturbation theory methods.

Letter↗

PubMed2005

Nuclear-electronic orbital nonorthogonal configuration interaction approach.

The nuclear-electronic orbital nonorthogonal configuration interaction (NEO-NOCI) approach is presented. In this framework, the hydrogen nuclei are treated quantum mechanically on the same level as the electrons, and a mixed nuclear-electronic time-independent Schrodinger equation is solved with molecular orbital techniques. For hydrogen transfer systems, the transferring hydrogen is represented by two basis function centers to allow delocalization of the nuclear wave function. In the two-state NEO-NOCI approach, the ground and excited state delocalized nuclear-electronic wave functions are expressed as linear combinations of two nonorthogonal localized nuclear-electronic wave functions obtained at the NEO-Hartree-Fock level. The advantages of the NEO-NOCI approach are the removal of the adiabatic separation between the electrons and the quantum nuclei, the computational efficiency, the potential for systematic improvement by enhancing the basis sets and number of configurations, and the applicability to a broad range of chemical systems. The tunneling splitting is determined by the energy difference between the two delocalized vibronic states. The hydrogen tunneling splittings calculated with the NEO-NOCI approach for the [He-H-He]+ model system with a range of fixed He-He distances are in excellent agreement with NEO-full CI and Fourier grid calculations. These benchmarking calculations indicate that NEO-NOCI is a promising approach for the calculation of delocalized, bilobal hydrogen wave functions and the corresponding hydrogen tunneling splittings.

Chemical Phenomena↗

PubMed2005

Investigation of isotope effects with the nuclear-electronic orbital approach.

This paper addresses fundamental issues that arise in the application of the nuclear-electronic orbital (NEO) approach to systems with equivalent quantum nuclei. Our analysis illustrates that Hartree-Fock nuclear wave functions do not provide physically reasonable descriptions of systems comprised of equivalent low-spin fermions or equivalent bosons. The physical basis for this breakdown is that the ionic terms dominate due to the localized nature of the nuclear orbitals. Multi-configurational wave functions that include only covalent terms provide physically reasonable descriptions of these types of systems. The application of the NEO approach to a variety of chemical systems is presented to elucidate the isotope effects on the geometries and electronic wave functions. Deuteration of hydrogen halides, water, ammonia, and hydronium ion decreases the bond length and the magnitude of negative partial atomic charge on the heavy atom. These results are consistent with experimental spectroscopic data. Deuteration at the beta position for formate anion and a series of amines increases the magnitude of negative partial atomic charge on the protonation site for the unprotonated species. This observation is consistent with the experimentally observed increase in basicity upon deuteration at the beta position for carboxylic acids and amines.

Amines↗

PubMed2005

Analysis of the nuclear-electronic orbital method for model hydrogen transfer systems.

Fundamental issues associated with the application of the nuclear-electronic orbital (NEO) approach to hydrogen transfer systems are addressed. In the NEO approach, specified nuclei are treated quantum mechanically on the same level as the electrons, and mixed nuclear-electronic wavefunctions are calculated with molecular orbital methods. The positions of the nuclear basis function centers are optimized variationally. In the application of the NEO approach to hydrogen transfer systems, the hydrogen nuclei and all electrons are treated quantum mechanically. Within the NEO framework, the transferring hydrogen atom can be represented by two basis function centers to allow delocalization of the proton vibrational wavefunction. In this paper, the NEO approach is applied to the [He-H-He]+ and [He-H-He]++ model systems. Analyses of technical issues pertaining to flexibility of the basis set to describe both single and double well proton potential energy surfaces, linear dependency of the hydrogen basis functions, multiple minima in the basis function center optimization, convergence of the number of hydrogen basis function centers, and basis set superposition error are presented. The accuracy of the NEO approach is tested by comparison to grid calculations for these model systems.

Chemistry, Physical↗

PubMed2004

Electron-proton correlation for hydrogen tunneling systems.

Hydrogen tunneling is important for numerous chemical and biological processes. We study this phenomenon with a multiconfigurational nuclear-electronic orbital approach. Our results demonstrate that a single configuration nuclear-electronic wave function is inadequate to describe hydrogen tunneling systems because such wave functions do not include the essential electron-proton correlation. A state-averaged multiconfigurational approach is proposed as a practical method for potentially including sufficient electron-proton correlation to obtain delocalized nuclear-electronic wave functions for these systems.

Journal Article↗