Molecular dynamics simulations of proton

To date, our reactive molecular dynamics simulations of proton transport have been limited to bulk water. However, the extension of Ae RMD algorithm to proton transport in PFSA membranes is analogous to what has been done in bulk water and simi-... 

Smondyrev, A.M. and Voth, G.A. (2002). Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane. Biophys. J. 82, 1460-1468... 

Quantum Molecular Dynamic Simulation of Proton Conducting Materials... 

Electro-osmotic drag phenomena are closely related to the distribution and mobility of protons in pores. The molecular contribution can be obtained by direct molecular dynamics simulations of protons and water in single ionomer pores, as reviewed in the sections Proton Transport in Water and Stimulating Proton Transport in a Pore. The hydrodynamic contribution to nd can be studied, at least qualitatively, using continuum dielectric approaches. The solution of the Poisson-Boltzmann equation... 

Spohr, E. 2004. Molecular dynamics simulations of proton transfer in a model Nafion pore. Mol Simul.. 30. 107-115. 

Pozuelo, J., Riande, E., Saiz, E., Compan, V., Molecular dynamics simulations of proton conduction in sulfonated poly(phenylsulfone)s. Macromolecules, 2006, 39, 8862-8866. 

Bala, P, Grochowski, R, Lesyng, B., McCammon, J. A. (1996). Quantum-classical molecular dynamics simulation of proton transfer processes in molecular complexes and in enzymes. J. Phys. Chem. 100,2535-2545. 

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. 

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... 

Ab initio molecular dynamics simulation of a triflic acid monohydrate crystal. The intermediate state (right) with two delocalized protons is 0.3 eV higher in energy than the ordered conformation of the native crystal (left). 

Fig. 14. Formation of metastable intermediate revealed in a classical molecular dynamics simulation of the decaniobate ion under basic conditions. Oxygen atoms are red, niobium atoms are green, and protons are white. The added hydroxide ion is represented by the yellow oxygen. Nbi is nucleophilically attacked by the hydroxide ion in (b), and the upper bond to the m3 and the bonds to the me oxygen atoms in the center of the ion are broken. The displaced niobium atom then proceeds to hydrate, with the waters represented by the blue oxygen atoms becoming progressively attached, and then hydrolyzing to release protons that can bind to other oxygen atoms on the decaniobate. Water molecules also hydrate the top Nb3 atoms as they become detached from the central m6 oxygen atoms after the Nb -m30 bond is ruptured.

Theoretical studies using the results of molecular dynamics simulation of A-methylazetidin-2-one in aqueous solution predicted a stepwise mechanism for the hydrolysis <1998JA2146>. In the alkaline hydrolysis, the first reaction step involved the formation of a tetrahedral intermediate, which required a desolvation of the hydroxyl anion, which is difficult to simulate by calculations. Afterwards, the reaction proceeded through either a concerted or stepwise mechanism for ring opening and proton transfer. 

Tapia and Eklund (1986) carried out a Monte Carlo simulation of the substrate channel of liver alcohol dehydrogenase, based on the X-ray diffraction structure for this enzyme. The addition of substrate and the associated conformation change induce an order—disorder transition for the solvent in the channel. A solvent network, connecting the active-site zinc ion and the protein surface, may provide the basis for a proton relay system. A molecular dynamics simulation of carbonic anhydrase showed two proton relay networks connecting the active-site zinc atom to the surrounding solvent (Vedani et ai, 1989). They remain intact when the substrate, HCOf, is bound. 

Since the dielectric continuum representation of the solvent has significant limitations, the molecular dynamics simulation of PCET with explicit solvent molecules is also an important direction. One approach is to utilize a multistate VB model with explicit solvent interactions [34-36] and to incorporate transitions among the adiabatic mixed electronic/proton vibrational states with the Molecular Dynamics with Quantum Transitions (MDQT) surface hopping method [39, 40]. The MDQT method has already been applied to a one-dimensional model PCET system [39]. The advantage of this approach for PCET reactions is that it is valid in the adiabatic and non-adiatic limits as well as in the intermediate regime. Furthermore, this approach is applicable to PCET in proteins as well as in solution. 

The multiple time step propagation scheme is expected to be useful whenever a mixed quantum-classical molecular simulation is performed where only a few degrees of freedom are necessarily described within quantum mechanics and the force calculations in the classical subsystem is the time-limiting step. These conditions hold, for example, in molecular dynamics simulations of electron-and/or proton-transfer processes in the complex photosynthetic centre or in liquid phase. Furthermore, since the RPS is time-reversible, it is possible to calculate quantum reaction rates by propagating mixed quantum-classical trajectories located on the transition state back and forward in time. This opens a wide range of applications. 

S. Izvekov and G. A. Voth (2005) Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited. J. Chem. Phys. 123, 044505... 

Ab initio molecular dynamics simulations of the interactions of a HC1 molecule in [CjinimlCl delivered the formation of a linear [Cl-H-Cl]- species, which may be interpreted as a highly solvated complex of the proton. In extension to this consideration, a reduced activity of the proton results [125, 126],... 

Schlegel, B., Sippl, W., Holtje, H.-D. Molecular dynamics simulations of bovine rhodopsin influence of protonation states and different membrane-mimicking environments. J. Mol. Model. 2005,12, 49-64. 

Ramachandran-type plots in which the t and (p dihedrals of the chromphore within the GFP protein matrix were systematically varied [50] showed that there are two minima for all protonation states, one at z = 60 30° and

protein environment of GFP allows the chromophore some rotational freedom, especially by a HT or in the (p dihedral angle (Fig. 5.7). There is a significant energy barrier for t = 180-270°, therefore a cis-trans photoisomerization cannot occur by a 180° rotation of the (p dihedral angle. The protein exerts some strain on the chromophore when it is planar, and the only reason planar chromophores are found in GFP is due to their delocalized -electrons. These results have been confirmed by molecular dynamics simulations of the chromophore with freely rotating t and cp dihedral... 

The above-described features are reproduced in a high level quantum-molecular-dynamics simulation of an excess proton in water [30, 31]. In accordance with results from several other groups, this finds the excess proton either as part of a dimer (H5O2+, Zundel -ion) or as part of a hydrated hydronium ion (H9O4+, Eigen -ion) (Fig. 23.3). 

Tunon I, Martins-Costa MTC, Millot C, Ruiz-Lopez MF. Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potential I. Proton transfer in strongly H-bonded complexes. J Chem Phys 1997 106 3633-3642. 

Molecular dynamics simulations of the RC of Rps. viridis have provided additional evidence supporting the movement of Qb between the distal site and the proximal site (23). This work showed that the equilibrium between the two binding sites is not displaced by the reduction of Qb to the semiquinone, by the preceding reduction of the primary quinone Qa and by accompanying protonation changes in the protein. 

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