The ab initio multiple spawning (AIMS) method is a time-dependent formulation of quantum chemistry, whereby the nuclear dynamics and electronic structure problems are solved simultaneously. Quantum mechanical effects in the nuclear dynamics are included, especially the nonadiabatic effects which are crucial in modeling dynamics on multiple electronic states. The AIMS method makes it possible to describe photochemistry from first principles molecular dynamics, with no empirical parameters. We describe the method and present the application to two molecules of interest in organic photochemistrysethylene and cyclobutene. We show that the photodynamics of ethylene involves both covalent and ionic electronic excited states and the return to the ground state proceeds through a pyramidalized geometry. For the photoinduced ring opening of cyclobutene, we show that the disrotatory motion predicted by the Woodward-Hoffmann rules is established within the first 50 fs after optical excitation.

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The photochemistry of stilbene is investigated using ab initio quantum chemistry with complete active space self-consistent field (CASSCF) and multireference perturbation theory (CASPT2) methods. We characterize photoisomerization pathways from both the cis and trans isomers, including a minimal energy conical intersection. Similarities to photoisomerization in ethylene are found and emphasized. In contrast to traditional one-dimensional models of stilbene photoisomerization, torsion and pyramidalization are required to reach the minimal energy conical intersection which is expected to dominate in quenching to the ground electronic state. This intersection is characterized as an interaction between charge transfer and covalent states. The present results suggest that the qualitative features of the photoisomerization dynamics elucidated for ethylene can also be expected to apply to stilbene, and call for reconsideration and refinement of the photoisomerization mechanism in stilbene.

We apply multireference ab initio quantum chemistry and microcanonical transition state (RRKM) theory with quantum energy flow corrections from local random matrix theory (LRMT) to determine the kinetics of trans-stilbene photoisomerization. With a single ab initio potential energy surface and no adjustable parameters, simultaneous agreement with experiment of the microcanonical isomerization rates for the d 0 , d 2 , d 10 , and d 12 isotopomers is obtained. We are also able to reproduce the pressure dependence of the thermal rate. Laser cooling effects on the isomerization rate are calculated and found to be quite small. The S 1 /S 2 energy gap at the transition state is found to be quite large (0.86 eV), suggesting that nonadiabatic effects are negligible. Using the ab initio results in a simple RRKM theory without corrections for finite quantum energy flow does not lead to agreement with experiment. We conclude that non-RRKM effects are essential to understand photoisomerization of trans-stilbene and that these can be predicted using LRMT.

Cytochrome c oxidase is a redox-driven proton pump which converts atmospheric oxygen to water and couples the oxygen reduction reaction to the creation of a membrane proton gradient. The structure of the enzyme has been solved; however, the mechanism of proton pumping is still poorly understood. Recent calculations from this group indicate that one of the histidine ligands of enzyme's CuB center, His291, may play the role of the pumping element. In this paper, we report on the results of calculations that combined first principles DFT and continuum electrostatics to evaluate the energetics of the key energy generating step of the model-the transfer of the chemical proton to the binuclear center of the enzyme, where the hydroxyl group is converted to water, and the concerted expulsion of the proton from delta-nitrogen of His291 ligand of CuB center. We show that the energy generated in this step is sufficient to push a proton against an electrochemical membrane gradient of about 200 mV. We have also re-calculated the pKa of His291 for an extended model in which the whole Fe(a3)-CuB center with their ligands is treated by DFT. Two different DFT functionals (B3LYP and PBE0), and various dielectric models of the protein have been used in an attempt to estimate potential errors of the calculations. Although current methods of calculations do not allow unambiguous predictions of energetics in proteins within few pKa units, as required in this case, the present calculation provides further support for the proposed His291 model of CcO pump and makes a specific prediction that could be targeted in the experimental test.

Using classical electrostatic calculations, earlier we examined the dependence of the protonation state of bovine cytochrome c oxidase (CcO) on its redox state. Based on these calculations, we have proposed a model of CcO proton pumping that involves His291, one of the Cu(B) histidine ligands, which was found to respond to redox changes of the enzyme Fe(a)(3)-Cu(B) catalytic center. In this work, we employ combined density functional and continuum electrostatic calculations to evaluate the pK(a)() values of His291 and Glu242, two key residues of the model. The pK(a) values are calculated for different redox states of the enzyme, and the influence of different factors on the pK(a)'s is analyzed in detail. The calculated pK(a)() values of Glu242 are between 9.4 and 12.0, depending on the redox state of the protein, which is in excellent agreement with recent experimental measurements. Assuming the reduced state of heme a(3), His291 of the oxidized Cu(B) center possesses a pK(a)() between 2.1 and 4.0, while His291 of the reduced Cu(B) center has a pK(a) above 17. The obtained results support the proposal that the His291 ligand of the Cu(B) center in CcO is a proton pump element.

By using molecular dynamics (MD) computer simulations in conjunction with the ReaxFF reactive force fields, the interaction of dimethyl methylphosphonate (DMMP) with amorphous silica as a function of surface hydration was examined. Surface hydroxylation densities of 2.0, 3.0, 4.0, and 4.5 hydroxyl/nm2 were modeled. The amorphous silica surface used in our simulations is quantified structurally and compares well to experimental findings. At the higher OH densities, binding of DMMP to the hydroxylated silica was found to occur through a combination of van der Waals interactions and hydrogen bonding. In addition to these types of interactions, at the lower OH surface coverages, strong covalent bonding between the phosphonyl (PO) oxygen of DMMP and 3-coordinate Si defects on the surface was observed. Finally, at extremely low hydroxyl coverages (2.0 nm−2), DMMP fragmentation was found to occur. The binding energy of DMMP on amorphous silica with a hydroxyl density of 4.5 OH/nm2 was calculated to be −4.7 kcal/mol. Addition of a water layer to the silica-supported DMMP system showed that water can displace and/or hydrolyze the adsorbed DMMP molecules. To validate the ReaxFF/MD findings, we performed MP2 and DFT quantum chemical studies of reactions predicted by the MD/ReaxFF by using small silica clusters. The quantum chemistry results support the MD/ReaxFF results, providing further verification of our findings and indicating the viability of ReaxFF/MD to study complex surface chemistry.