PH-coupled molecular dynamics

PDDG/PM3, 2, 263-265, 267, 268, 273-275 PDF inhibitor, 2, 288 periodic boundary conditions, 3, 181 permeability, intestinal, 1,134,135,161 perturbation theory (PT), 1,10, 51, 52 3,156 PES see potential energy surface pH-coupled molecular dynamics, 3, 4 pH-modulated helix-coil transitions, 3, 9 pharmaceutical chemicals... 

This report is mainly concerned with the recent development of a pH-coupled molecular dynamics technique, continuous constant pH molecular dynamics (CPHMD), [12,13] and its applications to first principles pK calculations [14] and pH-coupled biological phenomena [15]. To put this into context, we will also briefly survey other existing methods for pK predictions and pH-coupled conformational dynamics, but we refer interested readers to a recent preliminary review of this area for further details [9]. Finally, we will discuss opportunities for further development of the CPHMD method and our ongoing application studies. 

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. 

Barboiu M, Lehn JM (2002) Dynamic chemical devices modulation of contraction/extension molecular motion by coupled-ion binding/pH change-induced structural switching. Proc Natl Acad Sci USA 99 5201-5206... 

Let X be the ring-puckering coordinate and y the PH inversion coordinate in 3-phospholene (see Fig. 33). The dynamics of isomerization in this molecule is assumed to be adequately described by these coupled two DOF s without need for consideration of other DOFs. Under this assumption, the Harthcock-Laane potential energy surface consists of a fourth-order polynomial in x, a fourth-order polynomial in y, and a sixth-order polynomial coupling x and y. With molecular rotation neglected, the model Hamiltonian for 3-phospholene is given by... 

M. Barboiu, J.-M. Lehn, Dynamic Chemical Devices Modulation of Contrac-tion/Extension Molecular Motion by Coupled-Ion Binding/pH Change-Induced Structural Switching , Proc. Natl. Acad. Sci. USA, 99, 5201 (2002)... 

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