Direct ab initio dynamics studies of proton transfer in hydrogen-bond systems

Bell, Robert L.; Truong, Thanh N.
December 1994
Journal of Chemical Physics;12/15/1994, Vol. 101 Issue 12, p10442
Academic Journal
We present systematic direct ab initio dynamics studies of proton transfer in hydrogen-bond systems using the tautomerization in gas phase formamidine and its monohydrated complex as model reactions. The thermal rate constants were calculated using a canonical variational transition state theory (CVT) with multidimensional semiclassical tunneling corrections within a small-curvature ground-state approximation. The reaction valleys were calculated at the second-order Mo\ller–Plesset (MP2) perturbation theory, Hartree–Fock (HF) and nonlocal Becke’s half-and-half exchange and Lee–Yang–Parr correlation (BH&H–LYP) density functional theory (DFT) levels of theory using the 6-31 G(d,p) basis set. For accurate rate constants, the potential energy along the minimum energy path was scaled to match the single-point coupled cluster calculations including single and double excitations plus correction for triple excitation [CCSD(T)] at the MP2/6-31 G(d,p) classical barrier for each reaction. In the HF rate calculations, the HF frequencies were also scaled by a factor of 0.9. We found that adding a water to assist the proton transfer significantly enhances the tautomerization rate. Tunneling contributions in both systems are quite substantial and cannot be corrected by the Wigner approximation. We found that vibrational excitation of the solvent symmetriclike stretching mode would significantly enhance the rate of proton transfer in the formamidine–water complex. We also found that nonlocal DFT methods, particular the BH&H–LYP functionals studied here, can provide accurate potential energy information for dynamical calculations. Due to the computational advantage of DFT methods, prospects for dynamical studies of large polyatomic chemical reactions are quite encouraging. © 1994 American Institute of Physics.


Related Articles

  • Proton transfer in hydrogen-bonded acid–base complexes in polar solvents. Staib, Arnulf; Borgis, Daniel; Hynes, James T. // Journal of Chemical Physics;2/8/1995, Vol. 102 Issue 6, p2487 

    A theoretical approach exploiting molecular dynamics simulations to treat adiabatic proton transfer between an acid AH and a base B in a polar, aprotic solvent is presented. The dynamics of the proton transfer, which occurs on the electronic ground state surface of the reactive hydrogen-bonded...

  • Electron transport phenomena in metallic hydrogen and dynamics of the proton subsystem. Shvets, V. T. // Physics of the Solid State;Jul2007, Vol. 49 Issue 7, p1229 

    The electrical conductivity and the electron contribution to the thermal conductivity of metallic hydrogen are calculated over wide ranges of temperatures and densities, including those corresponding to the core of Jupiter. Hydrogen is considered in the liquid and solid states. The applicability...

  • Concerted Motion of Protons in Hydrogen Bonds of DNA-Type Molecules. Golo, V. L.; Kats, E. I.; Peyrard, M. // JETP Letters;2/25/2001, Vol. 73 Issue 4, p202 

    We study the dynamical behavior of proton transfer in hydrogen bonds in the base pairs of double helices of the DNA type. Under the assumption that the elastic and tunnelling degrees of freedom may be coupled, we derive a nonlinear and nonlocal Schr�dinger equation (NLNLS) that describes...

  • The dynamics of proton transfer in H[sub 5]O[sup +, sub 2]. Hai-Ping Cheng; Krause, Jeffrey L. // Journal of Chemical Physics;11/22/1997, Vol. 107 Issue 20, p8461 

    Studies the quantum molecular dynamics simulations of proton transfer in the protonated water dimer. Calculation of the electronic structure of the system using the Born-Oppenheimer molecular dynamics plus density functional theory; Broadening of the electronic density of states; Thermal...

  • Concertedness and solvent effects in multiple proton transfer reactions: The formic acid dimer in solution. Kohanoff, J.; Koval, S.; Estrin, D. A.; Laria, D.; Abashkin, Y. // Journal of Chemical Physics;6/1/2000, Vol. 112 Issue 21, p9498 

    The issue of multiple proton transfer (PT) reactions in solution is addressed by performing molecular dynamics simulations for a formic acid dimer embedded in a water cluster. The reactant species is treated quantum mechanically, within a density functional approach, while the solvent is...

  • Molecular simulation with variable protonation states at constant pH. Stern, Harry A. // Journal of Chemical Physics;4/28/2007, Vol. 126 Issue 16, p164112 

    A new method is presented for performing molecular simulations at constant pH. The method is a Monte Carlo procedure where trial moves consist of relatively short molecular dynamics trajectories, using a time-dependent potential energy that interpolates between the old and new protonation...

  • Targeted molecular dynamics (TMD) of the full-length KcsA potassium channel: on the role of the cytoplasmic domain in the opening process. Li, Yan; Barbault, Florent; Delamar, Michel; Zhang, Ruisheng; Hu, Rongjing // Journal of Molecular Modeling;Apr2013, Vol. 19 Issue 4, p1651 

    Some recent papers clearly indicate that the cytoplasmic domain of KcsA plays a role in pH sensing. We have performed, for the first time, a targeted molecular dynamics (TMD) simulation of the opening of full-length KcsA at pH 4 and pH 7, with a special interest for the cytoplasmic domain....

  • Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the chloroacetic acid dimer system. Durlak, Piotr; Morrison, Carole A.; Middlemiss, Derek S.; Latajka, Zdzislaw // Journal of Chemical Physics;8/14/2007, Vol. 127 Issue 6, p064304 

    We have studied the double proton transfer (DPT) reaction in the cyclic dimer of chloroacetic acid using both classical and path integral Car-Parrinello molecular dynamics. We also attempt to quantify the errors in the potential energy surface that arise from the use of a pure density...

  • Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics. Markwick, Phineus R. L.; Doltsinis, Nikos L.; Schlitter, Jürgen // Journal of Chemical Physics;1/28/2007, Vol. 126 Issue 4, p045104 

    Photoinduced proton transfer in the Watson-Crick guanine (G)-cytosine (C) base pair has been studied using Car-Parrinello molecular dynamics (CP-MD). A flexible mechanical constraint acting on all three hydrogen bonds in an unbiased fashion has been devised to explore the free energy profile...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics