Two New Methods To Generate Internal Coordinates for Molecular Wave Packet Dynamics in Reduced Dimensions.

The curse of dimensionality still remains as the central challenge of molecular quantum dynamical calculations. Either compromises on the accuracy of the potential landscape have to be made or methods must be used that reduce the dimensionality of the configuration space of molecular systems to a low dimensional one. For dynamic approaches such as grid-based wave packet dynamics that are confined to a small number of degrees of freedom this dimensionality reduction can become a major part of the overall problem. A common strategy to reduce the configuration space is by selection of a set of internal coordinates using chemical intuition. We devised two methods that increase the degree of automation of the dimensionality reduction as well as replace chemical intuition by more quantifiable criteria. Both methods reduce the dimensionality linearly and use the intrinsic reaction coordinate as guidance. The first one solely relies on the intrinsic reaction coordinate (IRC), whereas the second one uses semiclassical trajectories to identify the important degrees of freedom.

[1]  D. Keefer,et al.  A multi target approach to control chemical reactions in their inhomogeneous solvent environment , 2015 .

[2]  M Nilges,et al.  Efficient sampling in collective coordinate space , 2000, Proteins.

[3]  R. Vivie-Riedle,et al.  Quantum dynamics of photoexcited cyclohexadiene introducing reactive coordinates , 2000 .

[4]  G. Worth,et al.  Quantum molecular dynamics: propagating wavepackets and density operators using the multiconfiguration time-dependent Hartree method , 2003 .

[5]  H. Schlegel.  A comparison of geometry optimization with internal, cartesian, and mixed coordinates , 1992 .

[6]  Irene Burghardt,et al.  Full quantum mechanical molecular dynamics using Gaussian wavepackets , 2003 .

[7]  J. M. Bofill,et al.  The reaction path intrinsic reaction coordinate method and the Hamilton-Jacobi theory. , 2005, The Journal of chemical physics.

[8]  Carl Eckart,et al.  Some Studies Concerning Rotating Axes and Polyatomic Molecules , 1935 .

[9]  R. de Vivie-Riedle,et al.  Molecular features in complex environment: Cooperative team players during excited state bond cleavage , 2016, Structural dynamics.

[10]  R. Kosloff,et al.  Time‐dependent photodissociation of methyl iodide with five active modes , 1994 .

[11]  R. Vivie-Riedle,et al.  Ground state normal mode analysis: Linking excited state dynamics and experimental observables , 2001 .

[12]  U. Manthe,et al.  The multi-configurational time-dependent Hartree approach , 1990 .

[13]  H. Bernhard Schlegel,et al.  Improved algorithms for reaction path following: Higher‐order implicit algorithms , 1991 .

[14]  H. Meyer,et al.  The multigrid POTFIT (MGPF) method: grid representations of potentials for quantum dynamics of large systems. , 2013, The Journal of chemical physics.

[15]  García,et al.  Large-amplitude nonlinear motions in proteins. , 1992, Physical review letters.

[16]  R. de Vivie-Riedle,et al.  Design of specially adapted reactive coordinates to economically compute potential and kinetic energy operators including geometry relaxation. , 2016, The Journal of chemical physics.

[17]  K. Hirao,et al.  Generation of full-dimensional potential energy surface of intramolecular hydrogen atom transfer in malonaldehyde and tunneling dynamics , 2001 .

[18]  Joel M. Bowman,et al.  High-dimensional ab initio potential energy surfaces for reaction dynamics calculations. , 2011, Physical chemistry chemical physics : PCCP.

[19]  G. Worth,et al.  Molecular dynamics of pyrazine after excitation to the S2 electronic state using a realistic 24-mode model Hamiltonian , 1999 .

[20]  B. R. Johnson,et al.  Generalized approximation to the reaction path: the formic acid dimer case. , 2008, The Journal of chemical physics.

[21]  Yu Xie,et al.  Full-dimensional multilayer multiconfigurational time-dependent Hartree study of electron transfer dynamics in the anthracene/C60 complex. , 2015, The Journal of chemical physics.

[22]  John E. Adams,et al.  Reaction path Hamiltonian for polyatomic molecules , 1980 .

[23]  J. Tully,et al.  Trajectory Surface Hopping Approach to Nonadiabatic Molecular Collisions: The Reaction of H+ with D2 , 1971 .

[24]  B. Roos,et al.  Intramolecular hydrogen bond. Ab initio MO calculations on the enol tautomer of malondialdehyde , 1975 .

[25]  K. Fukui.  Formulation of the reaction coordinate , 1970 .

[26]  R. de Vivie-Riedle,et al.  Nucleophilic substitution dynamics: comparing wave packet calculations with experiment. , 2014, The journal of physical chemistry. A.

[27]  K. Morokuma,et al.  Molecular orbital studies of hydrogen bonds. VIII. Malonaldehyde and symmetric hydrogen bonding in neutral species , 1975 .

[28]  K. Kudin,et al.  Computation of the pseudorotation matrix to satisfy the Eckart axis conditions. , 2005, The Journal of chemical physics.

[29]  R. de Vivie-Riedle,et al.  Chemoselective quantum control of carbonyl bonds in Grignard reactions using shaped laser pulses. , 2010, Physical chemistry chemical physics : PCCP.

[30]  R. Kosloff,et al.  A fourier method solution for the time dependent Schrödinger equation as a tool in molecular dynamics , 1983 .

[31]  W. Miller,et al.  A new (cartesian) reaction-path model for dynamics in polyatomic systems, with application to H-atom transfer in malonaldehyde , 1988 .

[32]  O. Kühn,et al.  The all-Cartesian reaction plane Hamiltonian: formulation and application to the H-atom transfer in tropolone. , 2005, The Journal of chemical physics.

[33]  Charles C. David,et al.  Principal component analysis: a method for determining the essential dynamics of proteins. , 2014, Methods in molecular biology.