7 research outputs found
VPT2+K Spectroscopic Constants and Matrix Elements of the Transformed Vibrational Hamiltonian of a Polyatomic Molecule with Resonances Using Van Vleck Perturbation Theory
Vibrational levels of polyatomic molecules are analysed with Van Vleck perturbation theory to connect experimental energy levels to computed molecular potential energy surfaces. Vibrational matrix elements are calculated from a quartic potential function via second-order Van Vleck perturbation theory, a procedure that treats both weak and strong interactions among vibrational states by approximately block-diagonalising the vibrational Hamiltonian. A clear and complete derivation of anharmonic and resonance constants as well as general expressions for both on- and off-diagonal matrix elements of the transformed Hamiltonian is presented. The equations are written in partial fraction form and as a constant multiplied by a harmonic oscillator matrix element to facilitate removing the effect of strongly interacting resonant states both in analytical formulae and in computer code. The derived equations are validated numerically, and results for the isotopomers of formaldehyde (H2CO, HDCO, D2CO) are included. The implications of the equations on zero-point energy calculations and experimental fits are discussed. The VPT2+K method is defined by these results for use in fitting and calculating vibrational energy levels
Theoretical characterization of the spectral density of the water-soluble chlorophyll-binding protein from combined quantum mechanics/molecular mechanics molecular dynamics simulations
Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042â4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called 'geometry mismatch' problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis
Remembering the work of Phillip L. Geissler: A coda to his scientific trajectory
Phillip L. Geissler made important contributions to the statistical mechanics
of biological polymers, heterogeneous materials, and chemical dynamics in
aqueous environments. He devised analytical and computational methods that
revealed the underlying organization of complex systems at the frontiers of
biology, chemistry, and materials science. In this retrospective, we celebrate
his work at these frontiers
Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations
Over
the past decade, both experimentalists and theorists have
worked to develop methods to describe pigmentâprotein coupling
in photosynthetic light-harvesting complexes in order to understand
the molecular basis of quantum coherence effects observed in photosynthesis.
Here we present an improved strategy based on the combination of quantum
mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations
and excited-state calculations to predict the spectral density of
electronic-vibrational coupling. We study the water-soluble chlorophyll-binding
protein (WSCP) reconstituted with <i>Chl a</i> or <i>Chl b</i> pigments as the system of interest and compare our
work with data obtained by Pieper and co-workers from differential
fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042â4052). Our results demonstrate that the use of
QM/MM MD simulations where the nuclear positions are still propagated
at the classical level leads to a striking improvement of the predicted
spectral densities in the middle- and high-frequency regions, where
they nearly reach quantitative accuracy. This demonstrates that the
so-called âgeometry mismatchâ problem related to the
use of low-quality structures in QM calculations, not the quantum
features of pigments high-frequency motions, causes the failure of
previous studies relying on similar protocols. Thus, this work paves
the way toward quantitative predictions of pigmentâprotein
coupling and the comprehension of quantum coherence effects in photosynthesis
Recommended from our members
Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory.
Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers.Royal Society (URF\R1\211144
Recommended from our members
Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory.
Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers