<i>Ab initio</i> molecular dynamics: Propagating the density matrix with Gaussian orbitals

Schlegel, H. Bernhard; Millam, John M.; Iyengar, Srinivasan S.; Voth, Gregory A.; Daniels, Andrew D.; Scuseria, Gustavo E.; Frisch, Michael J.

doi:10.1063/1.1372182

Cited by 1,205 publications

(1,298 citation statements)

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“…The N-representability 50,57 of the density matrix is retained through the constraint term Tr[Λ(PP -P)], and additional harmonic constraints are enforced through the last term in the Hamiltonian above. The quantity N C represents the number of constrained atoms, and the quantity k i, j represents the harmonic constraint on the jth coordinate of the ith atom.…”

Section: Computational Detailsmentioning

confidence: 99%

Hydrogen Tunneling in an Enzyme Active Site: A Quantum Wavepacket Dynamical Perspective

2008

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We study the hydrogen tunneling problem in a model system that represents the active site of the biological enzyme, soybean lipoxygenase-1. Toward this, we utilize quantum wavepacket dynamics performed on potential surfaces obtained by using hybrid density functional theory under the influence of a dynamical active site. The kinetic isotope effect is computed by using the transmission amplitude of the wavepacket, and the experimental value is reproduced. By computing the hydrogen nuclear orbitals (eigenstates) along the reaction coordinate, we note that tunneling for both hydrogen and deuterium occurs through the existence of distorted, spherical s-type proton wave functions and p-type polarized proton wave functions for transfer along the donor-acceptor axis. In addition, there is also a significant population transfer through distorted p-type proton wave functions directed perpendicular to the donor-acceptor axis (via intervening π-type proton eigenstate interactions) which underlines the three-dimensional nature of the tunneling process. The quantum dynamical evolution indicates a significant contribution from tunneling processes both along the donor-acceptor axis and along directions perpendicular to the donor-acceptor axis. Furthermore, the tunneling process is facilitated by the occurrence of curve crossings and avoided crossings along the proton eigenstate adiabats.

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Section: Computational Detailsmentioning

confidence: 99%

Hydrogen Tunneling in an Enzyme Active Site: A Quantum Wavepacket Dynamical Perspective

2008

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“…We include the bulk of the nuclear and electronic degrees of freedom within subsystems B and C. Ab initio molecular dynamics (AIMD) 63,[79][80][81][82][83]85 is used to treat the evolution of these subsystems, where the nuclei in subsystem B are treated using classical mechanics. Both extended Lagrangian 81, 83,84,[107][108][109][110][111] and Born-Oppenheimer treatment 82,85,86 options are available. We have derived and tested a scheme [97][98][99] that allows simultaneous dynamics of all three subsystems coupled through a time-dependent procedure.…”

Section: Introductionmentioning

confidence: 99%

Quantum Wavepacket Ab Initio Molecular Dynamics: An Approach for Computing Dynamically Averaged Vibrational Spectra Including Critical Nuclear Quantum Effects

2007

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We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantumclassical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl] -, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

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“…Finally, an extended Lagrangian MD method can be derived from the PCM free energy functional, 6,25 in which the polarization charges become dynamical variables with their own fictitious mass. Such an approach could be further extended by coupling it with methods like Car-Parrinello 26 or atom-centered density matrix propagation 27 where also the electronic degrees of freedom are propagated as dynamical variables with a suitable fictitious mass.…”

Section: Introductionmentioning

confidence: 99%

A variational formulation of the polarizable continuum model

Lipparini¹,

Scalmani²,

Mennucci³

et al. 2010

The Journal of Chemical Physics

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139

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Articles you may be interested inContinuum solvation models are widely used to accurately estimate solvent effects on energy, structural and spectroscopic properties of complex molecular systems. The polarizable continuum model ͑PCM͒ is one of the most versatile among the continuum models because of the variety of properties that can be computed and the diversity of methods that can be used to describe the solute from molecular mechanics ͑MM͒ to sophisticated quantum mechanical ͑QM͒ post-self-consistent field methods or even hybrid QM/MM methods. In this contribution, we present a new formulation of PCM in terms of a free energy functional whose variational parameters include the continuum polarization ͑represented by the apparent surface charges͒, the solute's atomic coordinates andpossibly-its electronic density. The problem of finding the optimized geometry of the ͑polarized͒ solute, with the corresponding self-consistent reaction field, is recast as the minimization of this free energy functional, simultaneously with respect to all its variables. The numerous potential applications of this variational formulation of PCM are discussed, including simultaneous optimization of solute's geometry and polarization charges and extended Lagrangian dynamics. In particular, we describe in details the simultaneous optimization procedure and we include several numerical examples.

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Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals

Cited by 1,205 publications

References 41 publications

Hydrogen Tunneling in an Enzyme Active Site: A Quantum Wavepacket Dynamical Perspective

Hydrogen Tunneling in an Enzyme Active Site: A Quantum Wavepacket Dynamical Perspective

Quantum Wavepacket Ab Initio Molecular Dynamics: An Approach for Computing Dynamically Averaged Vibrational Spectra Including Critical Nuclear Quantum Effects

A variational formulation of the polarizable continuum model

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