We present here a cell model for evaluating Gibbs energy barriers corresponding to bimolecular reactions (or processes of larger molecularity) in which a loss of translational degrees of freedom takes place along the reaction coordinate. With this model, we have studied the Walden inversion processes: Xa- + H3CXb --> XaCH3 + Xb- (X = F, Cl, Br, and I). In these processes, our model yields an increase of about 2.3-3.4 kcal/mol in Gibbs energy in solution corresponding to the loss of the translational degrees of freedom when passing from separate reactants to the TS in good agreement with experimental data. The corresponding value in the gas phase is about 6.7-7.1 kcal/mol. When the difference between these two figures is used to correct the results obtained by the standard UAHF implementation of the continuum model, the theoretical results are brought significantly closer to the experimental ones. This seems to indicate that for these reactions the parametrization used does not adequately introduce the increase in Gibbs energy corresponding to the constriction of the translational motion of the species along the reaction coordinate when passing from the gas phase to solution. Therefore, we believe that continuum models could perform much better if we released the parametrization process from the task of taking into account the constriction in translation motion in solution, which could be more adequately evaluated using the cell model proposed here, thus allowing it to focus on better reproducing all the remaining solvation effects.

Herein, we present results from molecular dynamics MD simulations ( approximately 1 ns) of the TEM-1 beta-lactamase in aqueous solution. Both the free form of the enzyme and its complex with benzylpenicillin were studied. During the simulation of the free enzyme, the conformation of the Omega loop and the interresidue contacts defining the complex H-bond network in the active site were quite stable. Most interestingly, the water molecule connecting Glu166 and Ser70 does not exchange with bulk solvent, emphasizing its structural and catalytic relevance. In the presence of the substrate, Ser130, Ser235, and Arg244 directly interact with the beta-lactam carboxylate via H-bonds, whereas the Lys234 ammonium group has only an electrostatic influence. These interactions together with other specific contacts result in a very short distance ( approximately 3 A) between the attacking hydroxyl group of Ser70 and the beta-lactam ring carbonyl group, which is a favorable orientation for nucleophilic attack. Our simulations also gave insight into the possible pathways for proton abstraction from the Ser70 hydroxyl group. We propose that either the Glu166 carboxylate-Wat1 or the substrate carboxylate-Ser130 moieties could abstract a proton from the nucleophilic Ser70.

The IIA binding site of human serum albumin (HSA) preferentially binds hydrophobic organic anions of medium size (e.g., aspirin, benzylpenicillin, warfarin, etc.) and bilirubin. This binding ability is particularly important for the distribution, metabolism, and efficacy of drugs. In addition, HSA can also covalently link to different IIA substrates owing to the presence of a highly reactive residue, Lys199, which is strategically located in the IIA site. Herein, we present results of three restrained molecular dynamics (MD) simulations of the IIA binding site on the HSA protein. From these simulations, we have determined the influence that the ionization state of the key residue, Lys199, and the nearby Lys195 has on the structure and dynamics of the IIA binding site. When Lys199 is neutral the computed average distances for the most significant interresidue contacts are in good agreement with those estimated from the X-ray coordinates. The analysis of the solvent structure and dynamics indicates that the basic form of Lys199 is likely connected to the acid form of Lys195 through a network of H-bonding water molecules with a donor --> acceptor character. The presence of these water bridges can be important for stabilizing the configuration of the IIA binding site and/or promoting a potential Lys195 --> Lys199 proton-transfer process. These results suggest that both lysine residues located in the IIA binding site of HSA, Lys195 and Lys199, could play a combined and comparable chemical role. Our simulations also give insight into the binding of bilirubin to HSA.

The use of the counterpoise method for the mitigation of basis set superposition error at the correlated level is discussed. Evidence is presented to show that the ghost basis plays a dual role in the counterpoise method: The orbitals of the system are improved by the ghost basis but at the expense of a nonphysical increase in the dimension of the virtual space. This second factor has no effect on application of the counterpoise method at the SCF level but it makes the use of the counterpoise method at the correlated level much less straightforward.

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Herein we present results of a computational study on the benzylpenicillin acylation of the class A TEM1 β-lactamase via hydroxyl-only and hydroxyl and carboxylate assisted processes. These mechanisms correspond to a one-step Ser130-assisted process and a second route in which the β-lactam carboxylate and the Ser130 hydroxyl group help the proton transfer from the hydroxyl group of Ser70 to the β-lactam leaving N atom. The internal geometry of the reactive part of the TEM1-benzylpenicillin system is taken from a B3LYP/6-31+G* computational study on the methanol-assisted methanolysis reaction of a penicillin model compound (3R-carboxypenam). The 6-acylamino side chain and the 2-methyl groups of benzylpenicillin, together with the closer residues around the essential Ser70, are relaxed by carrying out geometry optimizations with a hybrid QM/MM method. The corresponding relative energies in the protein combine the B3LYP/6-31+G* electronic energies of the reactive subsystem with semiempirical PM3 energies of the TEM1-benzylpenicillin systems both in vacuo and in solution. The PM3 calculations on the TEM1-benzylpenicillin systems are performed with a Divide and Conquer linear-scaling method. The hydroxyl and carboxylate assisted pathway, which is the most favored one, is in agreement with the experimentally observed kinetic isotope effects and is also compatible with the effects of mutagenesis experiments on the Ser130 residue. These results suggest that a similar mechanism for the formation of acylenzyme intermediates could be relevant to other active-site serine penicillin-recognizing enzymes.

The ring opening of 2-azetidinone via a neutral H 2 O-assisted aminolysis process is studied using different quantum chemical methods (MP2/6-31G**, B3LYP/6-31G**, and G2(MP2,SVP) levels of theory) as a further step to the theoretical investigation of the aminolysis reaction of β-lactam antibiotics (Dı ´az, N.;

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