Communication: convergence of anharmonic infrared intensities of hydrogen fluoride in traditional and explicitly correlated coupled cluster calculations.

It is shown that the convergence of anharmonic infrared spectral intensities with respect to the basis set size is much enhanced in explicitly correlated calculations as compared to traditional configuration interaction type wave function expansion. Explicitly correlated coupled cluster (CC) calculations using Slater-type geminal correlation factor (CC-F12) yield well-converged dipole derivatives and vibrational intensities for hydrogen fluoride with basis set involving f functions on the heavy atom. Combination of CC-F12 with singles, doubles, and non-iterative triples (CCSD(T)-F12) with small corrections due to quadruple excitations, core-electron correlation, and relativistic effects yields vibrational line positions, dipole moments, and transition dipole matrix elements in good agreement with the best experimental values.

Anharmonic vibrational analysis of water with traditional and explicitly correlated coupled cluster methods.

It is well known that the convergence of harmonic frequencies with respect to the basis set size in traditional correlated calculations is slow. We now report that the convergence of cubic and quartic force constants in traditional CCSD(T) calculations on H(2)O with Dunning's cc-pVXZ family of basis sets is also frustratingly slow. As an alternative, we explore the performance of R12-based explicitly correlated methods at the CCSD(T) level.

Improved efficiency of focal point conformational analysis with truncated correlation consistent basis sets.

It has been suggested that the computational cost of correlated ab initio calculations could be reduced efficiently by using truncated basis sets on hydrogen atoms (Mintz et al., J Chem Phys 2004, 121, 5629). We now explore this proposal in the context of conformational analysis of small molecules, such as hydrogen peroxide, dimethyl ether, ethyl methyl ether, formic acid, methyl formate, and several small alcohols.

Convergence of third order correlation energy in atoms and molecules.

We have investigated the convergence of third order correlation energy within the hierarchies of correlation consistent basis sets for helium, neon, and water, and for three stationary points of hydrogen peroxide. This analysis confirms that singlet pair energies converge much slower than triplet pair energies. In addition, singlet pair energies with (aug)-cc-pVDZ and (aug)-cc-pVTZ basis sets do not follow a converging trend and energies with three basis sets larger than aug-cc-pVTZ are generally required for reliable extrapolations of third order correlation energies, making so the explicitly correlated R12 calculations preferable.

Focal-point conformational analysis of ethanol, propanol, and isopropanol.

Conformational analysis of three small alcohols--ethanol, propanol, and isopropanol--was carried out by systematically improving the basis set and the level of electron correlation. Correlation energy contributions to conformational energies are strongly basis-set-dependent but accurate energy contributions can be obtained by extrapolation to the basis-set limit. At the basis-set limit, second- and third-order electron correlation effects play a significant role for rotations around the CC-OH, HC-CO, and CC-CO bonds.

Computational study of the ground state of thermophilic indole glycerol phosphate synthase: structural alterations at the active site with temperature.

Hyperthermophlic indole-3-glycerol phosphate synthase (IGPS) catalyzes the terminal ring-closure step in tryptophan biosynthesis. In this paper, we compare the results from the molecular dynamics (MD) simulation of enzyme-bound substrate at 298 K (E.S298) and 385 K (E.

Computational study of ketosteroid isomerase: insights from molecular dynamics simulation of enzyme bound substrate and intermediate.

Delta(5)-3-Ketosteroid Isomerase (KSI) catalyzes the isomerization of 5,6-unsaturated ketosteroids to their 4,5-unsaturated isomers at a rate approaching the diffusion limit. The isomerization reaction follows a two-step general acid-base mechanism starting with Asp38-CO(2)(-) mediated proton abstraction from a sp(3)-hybridized carbon atom, alpha to carbonyl group, providing a dienolate intermediate. In the second step, Asp38-CO(2)H protonates the C6 of the intermediate providing a 4,5-unsaturated ketosteroid.

Comparison of formation of reactive conformers for the SN2 displacements by CH3CO2- in water and by Asp124-CO2- in a haloalkane dehalogenase.

The S(N)2 displacement of Cl(-) from 1,2-dichloroethane by acetate (CH(3)CO(2)(-)) in water and by the carboxylate of the active site aspartate in the haloalkane dehalogenase of Xanthobacter autothropicus have been compared by using molecular dynamics simulations. In aqueous solution, six families of contact-pair structures (I-VI) were identified, and their relative concentrations and dissociation rate constants were determined. The near attack conformers (NACs) required for the S(N)2 displacement reaction are members of the IV (CH(3)COO(-).

Protein engineering of nitrile hydratase activity of papain: molecular dynamics study of a mutant and wild-type enzyme.

The mechanism of hydrolysis of the nitrile (N-acetyl-phenylalanyl-2-amino-propionitrile, I) catalyzed by Gln19Glu mutant of papain has been studied by nanosecond molecular dynamics (MD) simulations. MD simulations of the complex of mutant enzyme with I and of mutant enzyme covalently attached to both neutral (II) and protonated (III) thioimidate intermediates were performed. An MD simulation with the wild-type enzyme.

Computer simulations of trypanosomal nucleoside hydrolase: determination of the protonation state of the bound transition-state analogue.

Inosine-uridine nucleoside hydrolase (IU-NH) catalyzes the hydrolysis of nucleosides into base and ribose moieties via a ribooxocarbenium ion transition state, which has been characterized using kinetic isotope effects. Protozoan parasites lack de novo purine and pyrimidine biosynthesis and depend on the purine salvage from the host. Vern Schramm and co-workers characterized p-aminophenyliminoribitol (pAPIR) to be a potent inhibitor of IU-NH from Crithidia fasciculata with K(d) of 30 nM.

Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides.

The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids.