Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly widely utilized in studies of reactions in enzymes and other large systems. Here, we apply a range of QM/MM methods to investigate the Claisen rearrangement of chorismate to prephenate, in solution, and in the enzyme chorismate mutase. Using projector-based embedding in a QM/MM framework, we apply treatments up to the CCSD(T) level. We test a range of density functional QM/MM methods and QM region sizes. The results show that the calculated reaction energetics are significantly more sensitive to the choice of density functional than they are to the size of the QM region in these systems. Projector-based embedding of a wavefunction method in DFT reduced the 13 kcal/mol spread in barrier heights calculated at the DFT/MM level to a spread of just 0.3 kcal/mol, essentially eliminating dependence on the functional. Projector-based embedding of correlated ab initio methods provides a practical method for achieving high accuracy for energy profiles derived from DFT and DFT/MM calculations for reactions in condensed phases.well with the CI-NEB path and indicates that the reaction coordinate used here performs well for this reaction.Structures were taken from the corresponding solution or enzyme SCCDFTB/CHARMM22 MD stochastic boundary simulations (120 ps) of the model systems for use in adiabatic mapping calculations. For this, Jaguar 68 and Tinker 69 , linked by the interface program QoMMMa 70 , were used for QM and MM calculations, with electronic coupling between the two regions treated by including MM charges in the QM Hamiltonian.CHARMM27 Lennard-Jones parameters (for standard CHARMM27 atom types, see Table S1) were used to describe QM/MM van der Waals interactions. The QM region was treated at the hybrid density functional B3LYP/6-31G(d) level of theory, which gives a reasonably good description of the reaction. 12 The enzyme model consisted of 7077 atoms and the solution model contained 7218 atoms. The MM region comprised an approximate 25 Å radius sphere of protein and/or solvent, treated with the CHARMM27 forcefield. 71 The outer 5 Å in each case was fixed (3324 atoms fixed in the enzyme model and 3535 fixed in the solution model),with all other atoms free to move. As there is no evidence for large-scale conformational changes during the reaction, this approach should give a representative sample of reactive conformations in the enzyme. 49,51, 53,54 Each initial structure was fully optimized at the B3LYP/6-31G(d)/CHARMM27 QM/MM level, while restraining the reaction coordinate (r) to -0.5 Å with a harmonic force constant of 500 kcal/mol/Å 2 , to generate starting structures.Reaction pathways were generated by restrained optimizations in both directions along the reaction coordinate, towards the reactant and the product, in steps of 0.2 Å (0.1 Å around the TS), with both the MM and QM systems fully and consistently optimized at each step. Energy profiles were calculated from r = −2.2 Å to 2.2 Å, to identify the reactant and product mini...
Characterizing the photochemical reactivity of transient volatile organic compounds (VOCs) in our atmosphere begins with a proper understanding of their abilities to absorb sunlight. Unfortunately, the photoabsorption cross-sections for a large number of transient VOCs remain unavailable experimentally due to their short lifetime or high reactivity. While structure–activity relationships (SARs) have been successfully employed to estimate the unknown photoabsorption cross-sections of VOCs, computational photochemistry offers another promising strategy to predict not only the vertical electronic transitions of a given molecule but also the width and shape of the bands forming its absorption spectrum. In this work, we focus on the use of the nuclear ensemble approach (NEA) to determine the photoabsorption cross-section of four exemplary VOCs, namely, acrolein, methylhydroperoxide, 2-hydroperoxy-propanal, and (microsolvated) pyruvic acid. More specifically, we analyze the influence that different strategies for sampling the ground-state nuclear density—Wigner sampling and ab initio molecular dynamics with a quantum thermostat—can have on the simulated absorption spectra. We highlight the potential shortcomings of using uncoupled harmonic modes within Wigner sampling of nuclear density to describe flexible or microsolvated VOCs and some limitations of SARs for multichromophoric VOCs. Our results suggest that the NEA could constitute a powerful tool for the atmospheric community to predict the photoabsorption cross-section for transient VOCs.
Here we outline and test an extension of the energy grained master equation (EGME) for treating nonadiabatic (NA) hopping between different potential energy surfaces, which enables us to model the competition between stepwise collisional relaxation and kinetic processes which transfer population between different potential energy surfaces of the same spin symmetry. By incorporating Zhu-Nakamura theory into the EGME, we are able to treat nonadiabatic passages beyond the simple Landau-Zener approximation, along with corresponding treatments of zero-point energy and tunnelling probability. To evaluate this NA-EGME approach, we carried out detailed studies of the UV photodynamics of the volatile organic compound C6-hydroperoxyaldehyde (C6-HPALD) using on-the-fly ab initio molecular dynamics and trajectory surface hopping. For this multi-chromophore molecule, we show that the EGME is able to quantitatively capture important aspects of the dynamics, including kinetic timescales, and diabatic trapping. Such an approach provides a promising and efficient strategy for treating the long-time dynamics of photo-excited molecules in regimes which are difficult to capture using atomistic on-the-fly molecular dynamics.
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