Proton molecular dynamics

It seems that surface hopping (also called Molecular Dynamics with Quantum Transitions, MDQT) is a rather heavy tool to simulate proton dynamics. A recent and promising development is path integral centroid dynamics [123] that provides approximate dynamics of the centroid of the wavefunctions. Several improvements and applications have been published [123, 124, 125, 126, 127, 128). 

Bala, P., Lesyng, B., McCammon, J.A. Application of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes. Chem. Phys. 180 (1994) 271-285. 

Mavri, J., Berendsen, H.J.C., Van Gunsteren, W.F. Influence of solvent on intramolecular proton transfer in hydrogen malonate. Molecular dynamics study of tunneling by density matrix evolution and nonequilibrium solvation. J. Phys. Chem. 97 (1993) 13469-13476. 

Hammes-Schiffer, S., Tully, J.C. Proton transfer in solution Molecular dynamics with quantum transitions. J. Chem. Phys. 101 (1994) 4657 667. 

Van der Spoel,D., Berendsen, H.J.C. Determination of proton transfer rate constants using ab initio, molecular dynamics and density matrix evolution calculations. Pacific Symposium on Biocomputing, World Scientific, Singapore (1996) 1-14. 

Marrink, S.J., Jahnig, F., Berendsen, H.J.C. Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophys. J. 71 (1996) 632-647. 

In molecular mechanics and molecular dynamics studies of proteins, assig-ment of standard, non-dynamical ionization states of protein titratable groups is a common practice. This assumption seems to be well justified because proton exchange times between protein and solution usually far exceed the time range of the MD simulations. We investigated to what extent the assumed protonation state of a protein influences its molecular dynamics trajectory, and how often our titration algorithm predicted ionization states identical to those imposed on the groups, when applied to a set of structures derived from a molecular dynamics trajectory [34]. As a model we took the bovine... 

Another principal difficulty is that the precise effect of local dynamics on the NOE intensity cannot be determined from the data. The dynamic correction factor [85] describes the ratio of the effects of distance and angular fluctuations. Theoretical studies based on NOE intensities extracted from molecular dynamics trajectories [86,87] are helpful to understand the detailed relationship between NMR parameters and local dynamics and may lead to structure-dependent corrections. In an implicit way, an estimate of the dynamic correction factor has been used in an ensemble relaxation matrix refinement by including order parameters for proton-proton vectors derived from molecular dynamics calculations [72]. One remaining challenge is to incorporate data describing the local dynamics of the molecule directly into the refinement, in such a way that an order parameter calculated from the calculated ensemble is similar to the measured order parameter. 

If the amount of the sample is sufficient, then the carbon skeleton is best traced out from the two-dimensional INADEQUATE experiment. If the absolute configuration of particular C atoms is needed, the empirical applications of diastereotopism and chiral shift reagents are useful (Section 2.4). Anisotropic and ring current effects supply information about conformation and aromaticity (Section 2.5), and pH effects can indicate the site of protonation (problem 24). Temperature-dependent NMR spectra and C spin-lattice relaxation times (Section 2.6) provide insight into molecular dynamics (problems 13 and 14). 

DFT molecular dynamics simulations were used to investigate the kinetics of the chemical reactions that occur during the induction phase of acid-catalyzed polymerization of 205 [97JA7218]. These calculations support the experimental finding that the induction phase is characterized by the protolysis of 205 followed by a rapid decomposition into two formaldehyde molecules plus a methylenic carbocation (Scheme 135). For the second phase of the polymerization process, a reaction of the protonated 1,3,5-trioxane 208 with formaldehyde yielding 1,3,5,7-tetroxane 209 is discussed (Scheme 136). 

For the 1,3-dithiane-1-oxide (R=H) case molecular dynamics simulations at the experimental temperature revealed that the R-hydroxysulfoniiun cation was considerably more stable than the more weakly adsorbed 1,3-dithiane molecule We consider that the hydroxydithiane cation may act as a proton transfer agent and this may account for the enhanced reactivity of this system. 

Besides these generalities, little is known about proton transfer towards an electrode surface. Based on classical molecular dynamics, it has been suggested that the ratedetermining step is the orientation of the HsO with one proton towards the surface [Pecina and Schmickler, 1998] this would be in line with proton transport in bulk water, where the proton transfer itself occurs without a barrier, once the participating molecules have a suitable orientation. This is also supported by a recent quantum chemical study of hydrogen evolution on a Pt(lll) surface [Skulason et al., 2007], in which the barrier for proton transfer to the surface was found to be lower than 0.15 eV. This extensive study used a highly idealized model for the solution—a bilayer of water with a few protons added—and it is not clear how this simplification affects the result. However, a fully quantum chemical model must necessarily limit the number of particles, and this study is probably among the best that one can do at present. 

In addition to enhancing surface reactions, water can also facilitate surface transport processes. First-principles ab initio molecular dynamics simulations of the aqueous/ metal interface for Rh(l 11) [Vassilev et al., 2002] and PtRu(OOOl) alloy [Desai et al., 2003b] surfaces showed that the aqueous interface enhanced the apparent transport or diffusion of OH intermediates across the metal surface. Adsorbed OH and H2O molecules engage in fast proton transfer, such that OH appears to diffuse across the surface. The oxygen atoms, however, remained fixed at the same positions, and it is only the proton that transfers. Transport occurs via the symmetric reaction... 

Wang YX, Balbuena PB. 2004 Roles of proton and electric field in the electroreduction of O2 on Pt(lll) surfaces Results of an ab-initio molecular dynamics study. J Phys Chem B 108 4376-4384. 

Wei, D., Salahub, D. R., 1997, Hydrated Proton Clusters Ab Initio Molecular Dynamics Simulation and Simulated Annealing , J. Chem. Phys., 106, 6086. 

Constant pH Molecular Dynamics Based on Discrete Protonation States... 

In recent years, a class of methods has been developed for molecular dynamics simulations to be performed with an external pH parameter, like temperature or pressure [18, 43, 44, 70], These methods treat the solution as an infinite proton bath, and are thus referred to as constant pH molecular dynamics (PHMD). In PHMD, conformational dynamics of a protein is sampled simultaneously with the protonation states as a function of pH. As a result, protein dielectric response to the... 

Dlugosz M, Antosiewicz JM (2005) Effects of solute-solvent proton exchange on polypeptide chain dynamics A constant-pH molecular dynamics study. J Phys Chem B 109 13777-13784. 

Dlugosz M, Antosiewicz JM, Robertson AD (2004) Constant-pH molecular dynamics study of protonation-structure relationship in a heptapeptide derived from ovomucoid third domain. Phys RevE 69 021915. 

Khandogin J, Brooks CL III (2005) Constant pH molecular dynamics with proton tautomerism. Biophys J 89 141-157. 

Machuqueiro M, Baptista AM (2006) Constant-pH molecular dynamics with ionic strength effects Protonation-conformation coupling in decalysine. J Phys Chem B 110 2927—2933. 

Coe JD, Martinez TJ (2006) Ab initio molecular dynamics of excited-state intramolecular proton transfer around a three-state conical intersection in malonaldehyde. J Phys Chem A 110 618-630... 

Borgis D, Hynes JT (1991) Molecular-dynamics simulation for a model nonadiabatic proton transfer reaction in solution. J Chem Phys 94 3619-3628... 

Curioni et al.148 studied the protonation of 1,3-dioxane and 1,3,5-trioxane by means of CP molecular dynamics similations. The dynamics of both molecules was continued for few ps following protonation. The simulation provided a detailed picture the evolution of both the geometry and the electronic structure, which helped to rationalize some experimental observations. CP molecular dynamics simulations were applied by Tuckerman et al.149,150 to study the dynamics of hydronium (H30+) and hydroxyl (OH-) ions in liquid water. These ions are involved in charge transfer processes in liquid water H20 H+. .. OH2 - H20. .. H+-OH2, and HOH. . . OH- -> HO-. . . HOH. For the solvatetd H30+ ion, a picture consistent with experiment emerged from the simulation. The simulation showed that the HsO+ ion forms a complex with water molecules, the structure of which oscillates between the ones of H502 and I L/ij clusters as a result of frequent proton transfers. During a consid-... 

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