New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.

Multiple molecular dynamics (MD) simulations of crambin with different initial atomic velocities are used to sample conformations in the vicinity of the native structure. Individual trajectories of length up to 5 ns sample only a fraction of the conformational distribution generated by ten independent 120 ps trajectories at 300 K. The backbone atom conformational space distribution is analyzed using principal components analysis (PCA). Four different major conformational regions are found. In general, a trajectory samples only one region and few transitions between the regions are observed. Consequently, the averages of structural and dynamic properties over the ten trajectories differ significantly from those obtained from individual trajectories. The nature of the conformational sampling has important consequences for the utilization of MD simulations for a wide range of problems, such as comparisons with X-ray or NMR data. The overall average structure is significantly closer to the X-ray structure than any of the individual trajectory average structures. The high frequency (less than 10 ps) atomic fluctuations from the ten trajectories tend to be similar, but the lower frequency (100 ps) motions are different. To improve conformational sampling in molecular dynamics simulations of proteins, as in nucleic acids, multiple trajectories with different initial conditions should be used rather than a single long trajectory.

Twenty-five years after the discovery of a vast class of organic reactions named "pericyclic reactions" by Woodward and Hoffmann, ab initio quantum mechanics provides a detailed analysis of the geometries, energies, and electronic characteristics of the transition structures of these reactions. Common features are found in all these reactions, and generalizations permit prediction of other transition-structure geometries and energies. At the same time, great diversity is observed-from strongly bonded, rigid, closed-shell entities to weakly interacting, flexible diradical structures.

The influence of the distal pocket conformation on the structure and vibrations of the heme-CO bond in carbonmonoxy myoglobin (MbCO) is investigated by means of hybrid QM/MM calculations based on density functional theory combined with a classical force field. It is shown that the heme-CO structure (QM treated) is quite rigid and not influenced by the distal pocket conformation (MM treated). This excludes any relation between FeCO distortions and the different CO absorptions observed in the infrared spectra of MbCO (A states). In contrast, both the CO stretch frequency and the strength of the CO...His64 interaction are very dependent on the orientation and tautomerization state of His64. Our calculations indicate that the CO...N(epsilon) type of approach does not contribute to the A states, whereas the CO...H-N(epsilon) interaction is the origin of the A(1) and A(3) states, the His64 residue being protonated at N(epsilon). The strength of the CO...His64 interaction is quantified, in comparison with the analogous O(2)...His64 interaction and with the observed changes in the CO stretch frequency. Additional aspects of the CO...His64 interaction and its biological implications are discussed.

The impact of acidic and basic ionic liquid 1-ethyl-3-methylimidazolium chloride (EMIC) melts upon cyclopentadiene and methyl acrylate Diels-Alder reaction rates has been investigated using QM/MM calculations. The ability of the ionic liquid to act as a hydrogen bond donor (cation effect), moderated by its hydrogen bond accepting ability (anion effect), has been proposed previously to explain observed endo/exo ratios. However, the molecular factors that endow ionic liquids with their rate enhancing potential remain unknown. New OPLS-AA force field parameters in conjunction with potentials of mean force (PMF) derived from free energy perturbation calculations in Monte Carlo simulations (MC/FEP) are used to compute activation energies. QM/MM simulations using a periodic box of ions reproduce relative rate enhancements for the EMIC melts compared to water and 1-chlorobutane that reproduce kinetic experiments. Solute-solvent interactions in acidic and basic ionic liquid melts have been analyzed at key stationary points along the reaction coordinate. The reaction rate was found to be greater in the acidic rather than the basic melt due to less-dominant ion-pairing in the acidic melt, enabling the EMI cation to better coordinate to the dienophile at the transition state. The simulations suggest that the hydrogen on C2 of the EMI cation does not contribute to stabilization of the transition state, as previously believed, and the interactions with the more sterically exposed hydrogens on C4 and C5 play a larger role. In addition, the relative stabilization of the transition state through electrostatic interactions with the EMI cation in the acidic melt is also greater than that afforded by the weaker Lewis-acid effect provided by hydrogen bonding with water molecules in aqueous solution.

The structural, dynamic, and electronic origin of the spectroscopically observed carbonmonoxy myoglobin (MbCO) A states has been investigated by using molecular dynamics to sample conformational space, multivariate analysis to aid in structural interpretations, and quantum mechanics to compute ligand stretch frequencies. Ten short (400 ps) and two longer time (1.2 ns) molecular dynamics simulations, starting from five different crystallographic and solution phase structures centered in a 37 Å radius sphere of water, were used to sample the native-fold of MbCO. Three discrete conformational substates resulted where the primary structural differences corresponded to a variable strength nonbond interaction between His64, Arg45, and the bound ligand. To correlate the structures from the computed substates with the experimentally observed ligand stretch frequencies, Hartree-Fock theory with the 6-31G(d) basis set was used to carry out constrained minimizations and vibrational analysis on representative model geometries from each conformational substate. The A 0 state (out conformation) was determined to have both Arg45 and His64 removed from the heme pocket with negligible electrostatic effect on the ligand. Alternatively, His64 was determined to induce the redshifted frequencies characteristic of the A states (A 1-3 ) by forming a weak hydrogen bond between its protonated N δ and the ligand (in/N δ conformation). The A 1,2 state was specifically assigned to the in/N δ conformation with Arg45 removed from His64 (∆ν comp ) -10.0 ( 1.8 cm -1 ). The second and faster translational motion engaged Arg45 in an additional and cooperative electrostatic interaction with His64 that distinguished between the A 1,2 and A 3 states. The strongest red-shifted ligand stretch frequency (A 3 state) was computed when Arg45 interacted with His64 in the in/N δ conformation. The polarizing effect of the distal histidine on the CO ligand (∆ν comp ) -19.0 ( 6.8 cm -1 ) was increased by the positive charge on Arg45. Consequently, a new A-state model, which rationalizes the A 3 state based upon the fluctuating electrostatic field generated by the gate-like dynamics of His64 and Arg45, is presented, which is consistent with previously reported time scales for substate interconversion.

The four stereospecific transition structures of the butadiene and acrolein Diels-Alder reaction have been studied using the Becke three-parameter density functional theory with the 6-31G(d) basis set. The effect of solvent on the activation energies and endo/exo selectivity has been approximated by the polarizable continuum model (PCM); explicit definition of one, two, and three waters; and the combined strategy of the discrete-continuum model. The full aqueous acceleration and enhanced endo/exo selectivity observed by experiment is computed only when solvation forces are approximated by the discrete-continuum model. Consistent with previous ideas, two explicit waters are used to satisfy localized hydrogen bonding of acrolein and induce a charge polarization of the endo s-cis transition structure. Smaller enforced hydrophobic interactions result. Significant bulk-phase effects beyond hydrogen bonding and enforced hydrophobic interactions are computed for the first time. The gas-phase activation energy is lowered to 11.5 kcal/mol, in excellent agreement with known experimental activation energies of similar Diels-Alder reactions in mixed methanol and water solutions. The computed endo preference is enhanced to 2.4 kcal/mol in aqueous solution, in agreement with experiment. Approximately 50% of the rate acceleration and endo/exo selectivity is attributed to hydrogen bonding, and the remainder to bulk-phase effects, which includes enforced hydrophobic interactions and antihydrophobic cosolvent effects. The local and bulk influence of solvent on the energetics, endo/exo selectivity, and transition structure asynchronicity is discussed and analyzed for this particular pericyclic reaction that has a well-known and strong solvent dependency. The catalytic and endo/exo selectivity results are consistent with the hypothesis of maximum accumulation of unsaturation and support the importance of antihydrophobic cosolvents in stabilizing hydrophobic regions of transition structures.

A natural bonding orbital (NBO) analysis of phosphate bonding and connection to experimental phosphotransfer potential is presented. Density functional calculations with the 6-311++G(d,p) basis set carried out on 10 model phosphoryl compounds verify that the wide variability of experimental standard free energies of hydrolysis (a phosphotransfer potential benchmark) is correlated with the instability of the scissile O-P bond through computed bond lengths. NBO analysis is used to analyze all delocalization interactions contributing to O-P bond weakening. Phosphoryl bond lengths are found to correlate strongest (R = 0.90) with the magnitude of the ground-state n(O) --> sigma*(O-P) anomeric effect. Electron-withdrawing interactions of the substituent upon the sigma(O-P) bonding orbital also correlate strongly with O-P bond lengths (R = 0.88). However, an analysis of sigma*(O-P) and sigma(O-P) populations show that the increase in sigma*(O-P) density is up to 6.5 times greater than the decrease in sigma(O-P) density. Consequently, the anomeric effect is more important than other delocalization interactions in impacting O-P bond lengths. Factors reducing anomeric power by diminishing either lone pair donor ability (solvent) or antibonding acceptor ability (substituent) are shown to result in shorter O-P bond lengths. The trends shown in this work suggest that the generalized anomeric effect provides a simple explanation for relating the sensitivity of the O-P bond to diverse environmental and substituent factors. The anomeric n(O) --> sigma*(O-P) interaction is also shown to correlate strongly with experimentally determined standard free energies of hydrolysis (R = -0.93). A causal mechanism cannot be inferred from correlation. Equally, a P-value of 1.2 x 10(-4) from an F-test indicates that it is unlikely that the ground-state anomeric effect and standard free energies of hydrolysis are coincidentally related. It is found that as the exothermicity of hydrolysis increases, the energy stabilization of the ground-state anomeric effect increases with selective destabilization of the high-energy O-P bond to be broken in hydrolysis. The anomeric effect therefore partially counteracts a larger resonance stabilization of products that makes hydrolysis exothermic and needs to be considered in achieving improved agreement between calculated and empirical energies of hydrolysis. The avenues relating the thermodynamic behavior of phosphates to underlying structural factors via the anomeric effect are discussed.