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. Excellent convergence of harmonic frequencies and cubic force constants is provided by these explicitly correlated methods with R12-suited basis irrespective of the used standard approximation and/or the correlation factor. The Slater type geminal, however, outperforms the linear r(12) for quartic force constants and vibrational anharmonicity constants. The converged force constants from explicitly correlated CCSD(T) calculations succeed in reproducing the fundamental frequencies of water molecule with spectroscopic accuracy after corrections for post-CCSD(T) effects are made.

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. It is found that truncated correlation consistent basis sets that lack certain higher angular momentum functions on hydrogen atoms offer accuracy similar to traditional Dunning's basis sets for conformational analysis. Combination of such basis sets with the basis set extrapolation technique to estimate Hartree-Fock and Møller-Plesset second order energies provides composite extrapolation model chemistries that are significantly more accurate and faster than analogous single point calculations with traditional correlation consistent basis sets. Root mean square errors of best composite extrapolation model chemistries on the used set of molecules are within 0.03 kcal/mol of traditional focal point conformational energies. The applicability of composite extrapolation methods is illustrated by performing conformational analysis of tert-butanol and cyclohexanol. For comparison, conformational energies calculated with popular molecular mechanics force fields are also given.

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. Specifically, second- and third-order correlation effects strongly stabilize structures in which the hydroxylic hydrogen eclipses with the adjacent carbon; a lesser stabilization is present in structures where the CC-OH moiety is in the gauche form. Fourth-order correlation effects to the CC-OH rotation are small due to a partial cancellation of the singles, doubles, and quadruples contribution by the triples contribution. Electron correlation significantly lowers barriers for methyl-group rotations in ethanol and isopropanol, and in these cases the fourth-order correlation effects are noticeable. The relatively large overall importance of third-order correlation energy contributions raises a concern that the inability to accurately estimate this slowly converging contribution may become a limiting factor when highly accurate conformational energies in larger molecules are sought.

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.S385) solvated in the TIP3P water box using the CHARMM force field to address the question of the structural change of the Enzyme. Substrate complex with temperature. The population of the reactive Enzyme. Substrate conformers (near attack conformers or NACs) increases by approximately 1100-fold in going from room temperature (E.S298) to high temperature (E.S385). This increased population of NAC conformers in the Michaelis complex correlates well with the increase in rate in going from 298 to 385 K. The positioning of the two active site residues Lys53 and Lys110 controls binding of the substrate in the favorable orientation for general acid-catalyzed intramolecular ring formation reaction. It can be concluded that the NAC formation allowing general acid catalysis has much to do with the temperature dependence of the free energy of reaction.

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. The details of the mechanism have been highly controversial despite several experimental and computational studies of this enzyme. The general acid-base catalysis has been proposed to involve either a catalytic diad or a cooperative hydrogen bond mechanism. In this paper, we report our results from the 1.5 nanosecond molecular dynamics (MD) simulation of enzyme bound natural substrate (E.S) and enzyme bound intermediate (E. In) solvated in a TIP3P water box. The final coordinates from our MD simulation strongly support the cooperative hydrogen bond mechanism. The MD simulation of E.S and E. In shows that both Tyr14 and Asp99 are hydrogen bonded to the O3 of the substrate or intermediate. The average hydrogen bonding distance between Tyr14-OH and O3 becomes shorter and exhibits less fluctuation on E.S --> E. In. We also observe dynamic motions of water moving in and out of the active site in the E.S structures. This free movement of water disappears in the E. In structures. The active site is shielded by hydrophobic residues, which come together and squeeze out the waters from the active site in the E. In complex.

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(-)...CH(2)(Cl)CH(2)Cl) family and are formed in the sequence II-->III-->IV-->NAC. The NAC subclass is defined by the COO(-)...CCl contact distance of < or = 3.41 A and the COO(-)...CCl angle of 157-180 degrees. The mole percentage of NACs is 0.16%, based on the 1 M standard state. This result may be compared with 13.4 mole percentage of NACs in the Michaelis complex in the enzyme. It follows that NAC formation in the enzyme is favored by 2.6 kcal/mol. Because reaction coordinates from S to TS, both in water and in the enzyme, pass via NAC (i.e., S --> NAC --> TS), the reduction in the S --> NAC barrier by 2.6 kcal/mol accounts for approximately 25% of the reduction of total barrier in the S --> TS (10.7 kcal/mol). The remaining 75% of the advantage of the enzymatic reaction revolves around the efficiency of NAC --> TS step. This process, based on previous studies, is discussed briefly.

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.I complex was undertaken as a reference. The ion pair between protonated His159 and thiolate of Cys25 is coplanar, and the hydrogen bonding interaction S(-)(25).HD1-ND1(159) is observed throughout MD simulation of the mutant enzyme.I complex. Such a sustained hydrogen bond is absent in nitrile-bound wild-type papain due to the flexibility of the imidazole ring of His159. The nature of the residue at position 19 plays a critical role in the hydrolysis of the covalent thioimidate intermediate. When position 19 represents Glu, the imidazolium ion of His159-ND1(+).Cys25-S(-) ion pair is distant, on average, from the nitrile nitrogen of substrate I. Near attack conformers (NACs) have been identified in which His159-ImH(+) is positioned to initiate a general acid-catalyzed addition of Cys-S(-) to nitrile. Though Glu19-CO(2)H is distant from nitrile nitrogen in the mutant.I structure, MD simulations of the mutant.II covalent adduct finds Glu19-CO(2)H hydrogen bonded to the thioimide nitrogen of II. This hydrogen bonded species is much less stable than the hydrogen bonded Glu19-CO(2)(-) with mutant-bound protonated thioimidate (III). This observation supports Glu19-CO(2)H general acid catalysis of the formation of mutant.III. This is the commitment step in the Gln19Glu mutant catalysis of nitrile hydrolysis.

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. The cyclic amine function of the iminoribitol ring can be either protonated (pAPIRH(+)) or unprotonated (pAPIR). pAPIRH(+) resembles the charge and geometry of the ribooxocarbenium ion transition state and can be looked upon as a transition-state analogue inhibitor; however, it is known that the pAPIR species is initially bound to the enzyme. We have characterized the pAPIRH(+) species as resident of the active site using ab initio calculations and molecular dynamics simulations. This is a novel use of molecular dynamics to investigate the protonation state of the bound ligand to the active site. Nanosecond molecular dynamics simulations reveal a short hydrogen-bonding network between pAPIRH(+)-O2'-Asp14-His241 triad, which is not seen in the crystal structure. Other features discussed are: hydrogen bonding between pAPIRH(+) and Asn168, unusual geometry of the iminoribitol ring, and hydrophobic interactions.

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. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.