TY - JOUR

T1 - Path-integral calculations of nuclear quantum effects in model systems, small molecules, and enzymes via gradient-based forward corrector algorithms

AU - Azuri, Asaf

AU - Engel, Hamutal

AU - Doron, Dvir

AU - Major, Dan Thomas

PY - 2011/5/10

Y1 - 2011/5/10

N2 - A practical approach to treat nuclear quantum mechanical (QM) effects in simulations of condensed phases, such as enzymes, is via Feynman path integral (PI) formulations. Typically, the standard primitive approximation (PA) is employed in enzymatic PI simulations. Nonetheless, these PI simulations are computationally demanding due to the large number of discretizations, or beads, required to obtain converged results. The efficiency of PI simulations may be greatly improved if higher order factorizations of the density matrix operator are employed. Herein, we compare the results of model calculations obtained employing the standard PA, the improved operator of Takahashi and Imada (TI), and several gradient-based forward corrector algorithms due to Chin (CH). The quantum partition function is computed for the harmonic oscillator, Morse, symmetric, and asymmetric double well potentials. These potentials are simple models for nuclear quantum effects, such as zero-point energy and tunneling. It is shown that a unique set of CH parameters may be employed for a variety of systems. Additionally, the nuclear QM effects of a water molecule, treated with density functional theory, are computed. Finally, we derive a practical perturbation expression for efficient computation of isotope effects in chemical systems using the staging algorithm. This new isotope effect approach is tested in conjunction with the PA, TI, and CH methods to compute the equilibrium isotope effect in the Schiff base-oxyanion keto-enol tautomerism in the cofactor pyridoxal-5′-phosphate in the enzyme alanine racemase. The study of the different factorization methods reveals that the higher-order actions converge substantially faster than the PA approach, at a moderate computational cost.

AB - A practical approach to treat nuclear quantum mechanical (QM) effects in simulations of condensed phases, such as enzymes, is via Feynman path integral (PI) formulations. Typically, the standard primitive approximation (PA) is employed in enzymatic PI simulations. Nonetheless, these PI simulations are computationally demanding due to the large number of discretizations, or beads, required to obtain converged results. The efficiency of PI simulations may be greatly improved if higher order factorizations of the density matrix operator are employed. Herein, we compare the results of model calculations obtained employing the standard PA, the improved operator of Takahashi and Imada (TI), and several gradient-based forward corrector algorithms due to Chin (CH). The quantum partition function is computed for the harmonic oscillator, Morse, symmetric, and asymmetric double well potentials. These potentials are simple models for nuclear quantum effects, such as zero-point energy and tunneling. It is shown that a unique set of CH parameters may be employed for a variety of systems. Additionally, the nuclear QM effects of a water molecule, treated with density functional theory, are computed. Finally, we derive a practical perturbation expression for efficient computation of isotope effects in chemical systems using the staging algorithm. This new isotope effect approach is tested in conjunction with the PA, TI, and CH methods to compute the equilibrium isotope effect in the Schiff base-oxyanion keto-enol tautomerism in the cofactor pyridoxal-5′-phosphate in the enzyme alanine racemase. The study of the different factorization methods reveals that the higher-order actions converge substantially faster than the PA approach, at a moderate computational cost.

UR - http://www.scopus.com/inward/record.url?scp=79955886180&partnerID=8YFLogxK

U2 - 10.1021/ct100716c

DO - 10.1021/ct100716c

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 26610122

AN - SCOPUS:79955886180

SN - 1549-9618

VL - 7

SP - 1273

EP - 1286

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

IS - 5

ER -