Computational tests of quantum chemical models for structures, vibrational frequencies, and heats of formation of molecules with phosphorus and sulfur atoms

Efficient Ab Initio Estimation of Formation Enthalpies for Organic Compounds: Extension to Sulfur and Critical Evaluation of Experimental Data

The efficient protocol for the estimation of gas-phase enthalpies of formation developed previously for C, H, O, N, and F elements was extended to sulfur. The protocol is based on a local coupled cluster with single, double, and perturbative triple excitation [CCSD(T)] approximation and allows rapid evaluation of compounds with sizes computationally prohibitive to canonical CCSD(T) using quadruple zeta basis sets. As a part of model development, a comprehensive review and critical evaluation of experimental data were performed for 87 sulfur-containing organic and inorganic compounds. A compact model with only three empirical parameters for sulfur introduced to address the effects beyond frozen core CCSD(T) was developed. The model exhibits approximately 2 kJ·mol-1 standard deviation over a set of experimental values for a diverse collection of sulfur-containing compounds. The complete basis set version of the model demonstrates a similar performance and requires only one empirical parameter. Multiple problems with the existing experimental data were identified and discussed. In addition, a lack of reliable data for certain important classes of sulfur compounds was found to impede the model generalization and confident performance assessment.

The alkaline hydrolysis of sulfonate esters: challenges in interpreting experimental and theoretical data

Sulfonate ester hydrolysis has been the subject of recent debate, with experimental evidence interpreted in terms of both stepwise and concerted mechanisms. In particular, a recent study of the alkaline hydrolysis of a series of benzene arylsulfonates (Babtie et al., Org. Biomol. Chem. 10, 2012, 8095) presented a nonlinear Brønsted plot, which was explained in terms of a change from a stepwise mechanism involving a pentavalent intermediate for poorer leaving groups to a fully concerted mechanism for good leaving groups and supported by a theoretical study. In the present work, we have performed a detailed computational study of the hydrolysis of these compounds and find no computational evidence for a thermodynamically stable intermediate for any of these compounds. Additionally, we have extended the experimental data to include pyridine-3-yl benzene sulfonate and its N-oxide and N-methylpyridinium derivatives. Inclusion of these compounds converts the Brønsted plot to a moderately scattered but linear correlation and gives a very good Hammett correlation. These data suggest a concerted pathway for this reaction that proceeds via an early transition state with little bond cleavage to the leaving group, highlighting the care that needs to be taken with the interpretation of experimental and especially theoretical data.

Modeling catalytic promiscuity in the alkaline phosphatase superfamily

In recent years, it has become increasingly clear that promiscuity plays a key role in the evolution of new enzyme function. This finding has helped to elucidate fundamental aspects of molecular evolution. While there has been extensive experimental work on enzyme promiscuity, computational modeling of the chemical details of such promiscuity has traditionally fallen behind the advances in experimental studies, not least due to the nearly prohibitive computational cost involved in examining multiple substrates with multiple potential mechanisms and binding modes in atomic detail with a reasonable degree of accuracy. However, recent advances in both computational methodologies and power have allowed us to reach a stage in the field where we can start to overcome this problem, and molecular simulations can now provide accurate and efficient descriptions of complex biological systems with substantially less computational cost. This has led to significant advances in our understanding of enzyme function and evolution in a broader sense. Here, we will discuss currently available computational approaches that can allow us to probe the underlying molecular basis for enzyme specificity and selectivity, discussing the inherent strengths and weaknesses of each approach. As a case study, we will discuss recent computational work on different members of the alkaline phosphatase superfamily (AP) using a range of different approaches, showing the complementary insights they have provided. We have selected this particular superfamily, as it poses a number of significant challenges for theory, ranging from the complexity of the actual reaction mechanisms involved to the reliable modeling of the catalytic metal centers, as well as the very large system sizes. We will demonstrate that, through current advances in methodologies, computational tools can provide significant insight into the molecular basis for catalytic promiscuity, and, therefore, in turn, the mechanisms of protein functional evolution.

Computational tests of models for kinetic parameters of unimolecular reactions of organophosphorus and organosulfur compounds

A computational study of the kinetics of isomerization and elimination reactions of organophosphorus and organosulfur reactions is presented with a view to characterizing the predictive capabilities of widely applied techniques for processes that pertain to the destruction of chemical warfare agents. A set of 22 reactions has been studied, and the results have been compared to experimentally derived data. The BMK functional and the MG3S basis set have been used to compute minimum energy paths. Corrections have been added from CBS-QB3, CASSCF, and CASMP2 calculations. Thermal rate constants at experimental temperatures have been calculated with canonical variational transition state theory and small-curvature tunneling theory. The quality of these results may depend on recrossing of the variational transition state, the amount of radical or diradical character found in the minimum energy paths, or the accuracy of barrier heights.