Theoretical methodology for prediction of tropospheric oxidation of dimethyl phosphonate and dimethyl methylphosphonate.

Rate constants for the reactions of OH radicals with dimethyl phosphonate [DMHP, (CH(3)O)(2)P(O)H] and dimethyl methylphosphonate [DMMP, (CH(3)O)(2)P(O)CH(3)] have been calculated by ab initio structural methods and semiclassical dynamics modeling and compared with experimental measurements over the temperature range 250-350 K. The structure and energetics of reactants and transition structures are determined for all hydrogen atom abstraction pathways that initiate the atmospheric oxidation mechanism. Structures are obtained at the CCSD/6-31++G** level of chemical theory, and the height of the activation barrier is determined by a variant of the G2MP2 method. A Transfer Hamiltonian is used to compute the minimum energy path in the neighborhood of the transition state (TS). This calculation provides information about the curvature of the potential energy surface in the neighborhood of the TS, as well as the internal forces that are needed by the semiclassical flux-flux autocorrelation function (SCFFAF) dynamics model used to compute the temperature-dependent reaction rate constants for the various possible abstraction pathways. The computed temperature-dependent rate curves frequently lie within the experimental error bars.

A pseudoatom approach to molecular truncation: application in ab initio MBPT methods.

In this paper, we test the performance of the molecular truncation method of Mallik et al., which was originally applied at the semiempirical NDDO level, in ab initio MBPT methods. Pseudoatoms developed for the replacement of -OCH(3) and -OCH(2)CH(3) functional groups are used in optimizations of selected clusters, and the resulting geometries are compared to reference values taken from the full molecules. It is shown that the pseudoatoms, which consist of parametrized effective core potentials for the nearest neighbor interactions and an external charge field for long-range Coulomb effects, perform well at the MP2 and CCSD levels of theory for the suite of molecules to which they were applied. Representative timings for some of the pseudoatom-terminated clusters are presented, and it is seen that there is a significant reduction in computational time, yet the geometric configurations and deprotonation energies of the pseudoatom-terminated clusters are comparable to the more computationally expensive all-atom molecules.

Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein.

Cavity complementation has been observed in many proteins, where an appropriate small molecule binds to a cavity-forming mutant. Here, the binding of compounds to the W191G cavity mutant of cytochrome c peroxidase is characterized by X-ray crystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, the W191G cavity does not bind neutral or hydrophobic compounds, but displays a strong specificity for heterocyclic cations, consistent with the role of the protein to stabilize a tryptophan radical at this site. Ligand dissociation constants for the protonated cationic state ranged from 6 microM for 2-amino-5-methylthiazole to 1 mM for neutral ligands, and binding was associated with a large enthalpy-entropy compensation. X-ray structures show that each of 18 compounds with binding behavior bind specifically within the artificial cavity and not elsewhere in the protein. The compounds make multiple hydrogen bonds to the cavity walls using a subset of the interactions seen between the protein and solvent in the absence of ligand. For all ligands, every atom that is capable of making a hydrogen bond does so with either protein or solvent. The most often seen interaction is to Asp235, and most compounds bind with a specific orientation that is defined by their ability to interact with this residue. Four of the ligands do not have conventional hydrogen bonding atoms, but were nevertheless observed to orient their most polar CH bond towards Asp235. Two of the larger ligands induce disorder in a surface loop between Pro190 and Asn195 that has been identified as a mobile gate to cavity access. Despite the predominance of hydrogen bonding and electrostatic interactions, the small variation in observed binding free energies were not correlated readily with the strength, type or number of hydrogen bonds or with calculated electrostatic energies alone. Thus, as with naturally occurring binding sites, affinities to W191G are likely to be due to a subtle balance of polar, non-polar, and solvation terms. These studies demonstrate how cavity complementation and judicious choice of site can be used to produce a protein template with an unusual ligand-binding specificity.