Electrostatic energies and forces computed without explicit interparticle interactions: a linear time complexity formulation

A rapid method for the calculation of the electrostatic energy of a system without a cutoff is described in which the computational time grows linearly with the number of particles or charges. The inverse of the distance is approximated as a polynomial, which is then transformed into a function whose terms involve individual particles, instead of particle pairs, by a partitioning of the double sum. In this way, the electrostatic energy that is determined by the interparticle interactions is obtained without explicit calculation of these interactions. For systems of positive charges positioned on a face-centered cubic lattice, the calculation of the energy by the new method is shown to be faster than the calculation of the exact energy, in many cases by an order of magnitude, and to be accurate to within 1-2%. The application of this method to increase the accuracy of conventional truncation-based calculations in condensed-phase systems is also demonstrated by combining the approximated long-range electrostatic interactions with the exact short-range interactions in a "hybrid" calculation. For a 20-A sphere of water molecules, the forces are shown to be six times as accurate using this hybrid method as those calculated with conventional truncation of the electrostatic energy function at 12 A. This is accomplished with a slight increase in speed, and with a sevenfold increase in speed relative to the exact all-pair calculation. Structures minimized with the hybrid function are shown to be closer to structures minimized with an exact all-pair electrostatic energy function than are those minimized with a conventional 13-A cutoff-based electrostatic energy function. Comparison of the energies and forces calculated with the exact method illustrate that the absolute errors obtained with standard truncation can be very large. The extension of the current method to other pairwise functions as well as to multibody functions, is described.     

A differential fluctuation theorem

We derive a nonequilibrium thermodynamics identity (the "differential fluctuation theorem") that connects forward and reverse joint probabilities of nonequilibrium work and of arbitrary generalized coordinates corresponding to states of interest. This identity allows us to estimate the free energy difference between domains of these states. Our results follow from a general symmetry relation between averages over nonequilibrium forward and backward path functions derived by Crooks [Crooks, G. E. Phys. Rev. E 2000, 61, 2361-2366]. We show how several existing nonequilibrium thermodynamic identities can be obtained directly from the differential fluctuation theorem. We devise an approach for measuring conformational free energy differences, and we demonstrate its applicability to the analysis of molecular dynamics simulations by estimating the free energy difference between two conformers of the alanine dipeptide model system. We anticipate that these developments can be applied to the analysis of laboratory experiments.     

Asymmetric synthesis of pochonin E and F, revision of their proposed structure, and their conversion to potent Hsp90 inhibitors

A concise and modular synthesis of pochonin?E and F, and their epimers at C-6 established the correct stereochemistry of these two natural products. Several members of the pochonin family have been shown to bind the heat shock protein?90 (Hsp90), which has been the focus of intense drug discovery efforts. Pochonin?E and F as well as their epimers were derivatized into the corresponding pochoximes and further modified at the C-6 position. Molecular dynamics simulations, docking studies, and Hsp90 affinity measurements were performed to evaluate the impact of these modifications.     

Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

A density functional study of the hydrolysis reaction of phosphodiesters with a series of attacking nucleophiles in the gas phase and in solution is presented. The nucleophiles HOH, HO-, CH3OH, and CH3O- were studied in reactions with ethylene phosphate, 2'3'-ribose cyclic phosphate and in their neutral (protonated) and monoanionic forms. Stationary-point geometries for the reactions were determined at the density functional B3LYP/6-31++G(d,p) level followed by energy refinement at the B3LYP/6-311++G(3df,2p) level. Solvation effects were estimated by using a dielectric approximation with the polarizable continuum model (PCM) at the gas-phase optimized geometries. This series of reactions characterizes factors that influence the intrinsic reactivity of the model phosphate compounds, including the effect of nucleophile, protonation state, cyclic structure, and solvent. The present study of the in-line mechanism for phosphodiester hydrolysis, a reaction of considerable biological importance, has implications for enzymatic mechanisms. The analysis generally supports the associative mechanism for phosphate ester hydrolysis. The results highlight the importance for the reaction barrier of charge neutralization resulting from the protonation of the nonbridging phosphoryl oxygens and the role of internal hydrogen transfer in the gas-phase mechanism. It also shows that solvent stabilization has a profound influence on the relative barrier heights for the dianionic, monoanionic, and neutral reactions. The calculations provide a comprehensive data set for the in-line hydrolysis mechanisms that can be used for the development of improved semiempirical quantum models for phosphate hydrolysis reactions.     

EFFECT OF COMPOSITION AND PROCESSING CONDITION ON MICROSTRUCTURAL PROPERTIES AND DURABILITY OF FLUOROPOLYMER/ACRYLIC BLENDS

Fluoropolymer blends have been widely used as binders for exterior coatings because of their excellent resistance to ultra-violet (UV) radiation as well as to many corrosive chemical agents.It is known that the fluorinated component usually has a lower glass transition temperature and easily crystallizes in the final structure depending upon the blend composition and sample annealing condition.We investigated the effect of blend composition and annealing process (slow and fast cooling) on the surface mor...     

Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

A method is proposed for improving the accuracy and efficiency of free energy simulations. The essential idea is that the convergence of the relevant measure (e.g., the free energy derivative in thermodynamic integration) is monitored in the reverse direction starting from the last frame of the trajectory, instead of the usual approach, which begins with the first frame and goes in the forward direction. This simple change in the use of the simulation data makes it straightforward to eliminate the contamination of the averages by contributions from the equilibrating region. A statistical criterion is introduced for distinguishing the equilibrated (production) region from the equilibrating region. The proposed method, called reverse cumulative averaging, is illustrated by its application to the well-studied case of the alchemical free energy simulation of ethane to methanol.     

Decoherence via the dynamical casimir effect

We derive a master equation for a mirror interacting with the vacuum field via radiation pressure. The dynamical Casimir effect leads to decoherence of a superposition state in a time scale that depends on the degree of "macroscopicity" of the state components, and which may be much shorter than the relaxation time scale. Coherent states are selected by the interaction as pointer states.