[PDF][PDF] Implicit solvation models: equilibria, structure, spectra, and dynamics

CJ Cramer, DG Truhlar - Chemical Reviews, 1999 - Citeseer
The present review is concerned with continuum and other implicit models of solvation
effects. We will concentrate on the elements required to make such models successful and …

Electrostatic basis for enzyme catalysis

A Warshel, PK Sharma, M Kato, Y Xiang, H Liu… - Chemical …, 2006 - ACS Publications
Enzymatic reactions play a fundamentally important role in controlling and performing most
life processes. 1-3 Thus, understanding how enzymes work has both fundamental and …

Why nature really chose phosphate

SCL Kamerlin, PK Sharma, RB Prasad… - Quarterly reviews of …, 2013 - cambridge.org
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and
maintaining the integrity of the genetic material. On the surface, it would appear to be a …

Theoretical methods for the description of the solvent effect in biomolecular systems

M Orozco, FJ Luque - Chemical Reviews, 2000 - ACS Publications
The environment plays a key role in the determination of the properties and reactivity of
substances in condensed phases. The complexity of chemical phenomena in solution has …

Protein kinase biochemistry and drug discovery

PA Schwartz, BW Murray - Bioorganic chemistry, 2011 - Elsevier
Protein kinases are fascinating biological catalysts with a rapidly expanding knowledge
base, a growing appreciation in cell regulatory control, and an ascendant role in successful …

Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation …

SCL Kamerlin, M Haranczyk… - The journal of physical …, 2009 - ACS Publications
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used
to provide a general scheme for chemical reactions in proteins. However, such approaches …

An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations

K Nam, J Gao, DM York - Journal of Chemical Theory and …, 2005 - ACS Publications
A method is presented for the efficient evaluation of long-range electrostatic forces in
combined quantum mechanical and molecular mechanical (QM/MM) calculations of periodic …

Phosphate ester hydrolysis in aqueous solution: associative versus dissociative mechanisms

J Florián, A Warshel - The Journal of Physical Chemistry B, 1998 - ACS Publications
Phosphate hydrolysis plays a major role in many biological processes. To fully understand
such processes, it is essential to obtain a quantitative description of the corresponding …

Langevin dipoles model for ab initio calculations of chemical processes in solution: Parametrization and application to hydration free energies of neutral and ionic …

J Florián, A Warshel - The Journal of Physical Chemistry B, 1997 - ACS Publications
A new parametrization of the Langevin dipole (LD) model is developed for ab initio
calculations of chemical processes in aqueous solution. This parametrization is …

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins

M Klähn, E Rosta, A Warshel - Journal of the American Chemical …, 2006 - ACS Publications
The nature of the hydrolysis of phosphate monoester dianions in solutions and in proteins is
a problem of significant current interest. The present work explores this problem by …