A Theoretical Study on the Mechanisms Involved in Catalytic Dehydrogenation and Dehydration of Isopropanol on SrTiO.

The dehydrogenation and dehydration of isopropanol on the SrO and TiO terminated surfaces, of the SrTiO perovskite, is addressed by periodic DFT calculations in order to shed light on the involved mechanisms. The results show that the dehydrogenation occurs through a mechanism involving the dissociative adsorption of the alcohol on the SrO terminated surface, followed the nucleophilic attack of a hydride species on the previously adsorbed hydrogen atom to form molecular hydrogen and the corresponding carbonyl compound. The dehydration instead occurs by the molecular adsorption of the alcohol on the TiO terminated surface, followed by various possible E1 elimination pathways leading to the formation of the corresponding alkene and a water molecule.

A rationale for the unlike potency of avibactam and ETX2514 against OXA-24 β-lactamase.

Diazabicyclooctanone inhibitors such as ETX2514 and avibactam have shown enhanced inhibitory performance to fight the antibiotic resistance developed by pathogens. However, avibactam is ineffective against Acinetobacter baumannii infections, unlike ETX2514. The molecular basis for this difference has not been tackled from a molecular approach, precluding the knowledge of relevant information.

A theoretical approach for the acylation/deacylation mechanisms of avibactam in the reversible inhibition of KPC-2.

Klebsiella pneumoniae carbapenemase (KPC-2) is the most commonly encountered class A β-lactamase variant worldwide, which confer high-level resistance to most available antibiotics. In this article we address the issue by a combined approach involving molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations. The study contributes to improve the understanding, at molecular level, of the acylation and deacylation stages of avibactam involved in the inhibition of KPC-2.

Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations.

The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the C atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH) form. The calculated activation free energy for this step is 17.

Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations.

The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the C atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH) form. The calculated activation free energy for this step is 17.

Black Trumpet Mushroom-like ZnS incorporated with CuP: Noble metal free photocatalyst for superior photocatalytic H production.

The development of the efficient photocatalysts with improved photoexcited charge separation and transfer is an essential for the effective photocatalytic H generation using light energy. So far, owing to the unique properties and characteristics, the transition metal phosphides (TMPs) have been proven to be high performance co-catalysts to replace some of the classic precious metal materials in the photocatalytic water splitting. In the present work, we report a novel copper phosphide (CuP) as a co-catalyst to form a well-designed fabricated photocatalyst with blacktrumpet mushroom-like ZnS semiconductor for the first time.

Theoretical Evidence for the Nonoccurrence of Tetrahedral Intermediates in the Deacylation Pathway of the Oxacillinase-24/Avibactam Complex.

Oxacillinases (OXAs) β-lactamases are of special interest because of their capacity to hydrolyze antibacterial drugs such as cephalosporins and carbapenems, which are frequently used as the last option for the treatment of multidrug-resistant bacteria. Although the comprehension of the involved mechanisms at the atomic level is crucial for the rational design of new inhibitors and antibiotics, currently there is no study on the acylation/deacylation mechanisms of the OXA-24/avibactam complex from first principles; therefore, mechanistic details such as activation barriers, characterization of intermediates, and transition states are still uncertain. In this article, we address the deacylation of the OXA-24/avibactam complex by molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics computations.

Molecular Insights on the Release of Avibactam from the Acyl-Enzyme Complex.

Avibactam is a non-β-lactam β-lactamase inhibitor for treating complicated urinary tract and respiratory infections caused by multidrug-resistant bacterial pathogens, a serious public health threat. Despite its importance, the release mechanism of avibactam from the enzyme-inhibitor complex has been scarcely studied from first principles, considering the total protein environment. This information at the molecular level is essential for the rational design of new antibiotics and inhibitors.

Theoretical insights on the inhibition mechanism of a class A Serine Hydrolase by avibactam.

The inhibition mechanism of CTX-M-15 class A serine hydrolase by the inhibitor avibactam is addressed by a combined molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach postulating that the residue Ser70 is the sole reacting residue, that is, itself may play the role of the acid-base species required for the enzyme inhibition. Other residues located in the active site have key participation in the positioning of the inhibitor in the right conformation to favor the attack of Ser70, in addition to the stabilization of the transition state by electrostatic interactions with avibactam. The results validate the hypothesis and show that the reaction follows an asynchronous concerted mechanism, in which the nucleophilic attack of the hydroxyl oxygen of Ser70 precedes the protonation of the amidic nitrogen and ring opening.

A QM/MM study on the enzymatic inactivation of cefotaxime.

The reaction between the antibiotic cefotaxime and the CTX-M-14 class A serine hydrolase is addressed from a theoretical point of view, by means of hybrid quantum mechanics/molecular mechanical (QM/MM) calculations, adopting a new approach that postulates that the residue Ser70 itself should play the role of the acid-base species required for the cefotaxime acylation. The proposed mechanism differs from earlier proposals existing in literature for other class A β-lactamases. The results confirm the hypothesis, and show that the reaction should occur via a concerted mechanism in which the acylation of the lactam carbonyl carbon, protonation of the N lactam atom, and opening of the β-lactam ring occurs simultaneously.

New Insights on the Reaction Pathway Leading to Lactyl-ThDP: A Theoretical Approach.

In all ThDP-dependent enzymes, the catalytic cycle is initiated with the attack of the C2 atom of the ylide intermediate on the Cα atom of a pyruvate molecule to form the lactyl-ThDP (L-ThDP) intermediate. In this study, the reaction between the ylide intermediate and pyruvate leading to the formation of L-ThDP is addressed from a theoretical point of view. The study includes molecular dynamics, exploration of the potential energy surface by means of QM/MM calculations, and reactivity analysis on key centers.

How important is the synclinal conformation of sulfonylureas to explain the inhibition of AHAS: a theoretical study.

The inhibitory activity of 15 sulfonylureas on acetohydroxyacid synthase (AHAS) is addressed theoretically in order to stress how important the conformation is to explain their differences as AHAS inhibitors. The study includes calculations in gas phase, solution, and in the enzymatic environment. The results suggest that both the activation Gibbs free energy and Gibbs free energy change associated with the conformational change in solution allow for determining if sulfonylureas should have high or low inhibition activity.

A QM/MM study on the reaction pathway leading to 2-aceto-2-hydroxybutyrate in the catalytic cycle of AHAS.

The reaction between the intermediate 2-hydroxyethyl-thiamin diphosphate (HEThDP(-) ) and 2-ketobutyrate, in the third step of the catalytic cycle of acetodydroxy acid synthase, is addressed from a theoretical point of view by means of hybrid quantum/molecular mechanical calculations. The QM region includes one molecule of 2-ketobutyrate, the HEThDP(-) intermediate, and the residues Arg 380 y Glu 139; whereas the MM region includes the rest of the protein. The study includes potential energy surface scans to identify and characterize critical points on it, transition state search and activation barrier calculations.

Electron density reactivity indexes of the tautomeric/ionization forms of thiamin diphosphate.

The generation of the highly reactive ylide in thiamin diphosphate catalysis is analyzed in terms of the nucleophilicity of key atoms, by means of density functional calculations at X3LYP/6-31++G(d,p) level of theory. The Fukui functions of all tautomeric/ionization forms are calculated in order to assess their reactivity. The results allow to conclude that the highly conserved glutamic residue does not protonate the N1' atom of the pyrimidyl ring, but it participates in a strong hydrogen bonding, stabilizing the eventual negative charge on the nitrogen, in all forms involved in the ylide generation.

Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl-ThDP.

In this study the formation of the lactyl-thiamin diphosphate intermediate (L-ThDP) is addressed using density functional theory calculations at X3LYP/6-31++G(d,p) level of theory. The study includes potential energy surface scans, transition state search, and intrinsic reaction coordinate calculations. Reactivity is analyzed in terms of Fukui functions.

Density-functional study on the equilibria in the ThDP activation.

The equilibria among the various ionization and tautomeric states involved in the activation of ThDP is addressed using high level density functional theory calculations, X3LYP/6-311++G(d,p)//X3LYP(PB)/6-31++G(d,p). This study provides the first theoretically derived thermodynamic data for the internal equilibria in the activation of ThDP. The role of the medium polarity on the geometry and thermodynamics of the diverse equilibria of ThDP is addressed.

Theoretical calculation of partition coefficients of dimethoxypyrimidinylsalicylic acids.

Despite their importance as herbicides, dimethoxypyrimidinylsalicylic acids has been poorly characterized from a physical-chemical point of view. This lack of information has prevented the assessment of their impact in the environment once they are released. In this study, environmentally important properties (free energy of solvation, Henry's law constant, octanol/air, and octanol/water partition coefficients) of 39 dimethoxypyrimidinylsalicylic derived compounds are calculated by density functional theory (DFT) methods at B3LYP/6-31G(d,p) level of theory using the Poisson-Boltzmann solvation model.

Quantitative prediction of solvation free energy in octanol of organic compounds.

The free energy of solvation, DeltaGS0, in octanol of organic compounds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a DeltaGS0 range from about -50 to 0 kJ.mol(-1).

Predicting infinite dilution activity coefficients of organic compounds in water by quantum-connectivity descriptors.

Quantitative structure-property relationship (QSPR) models are developed to predict the logarithm of infinite dilution activity coefficient of hydrocarbons, oxygen containing organic compounds and halogenated hydrocarbons in water at 298.15 K. The description of the molecular structure in terms of quantum-connectivity descriptors allows to obtain more simple QSPR models because of the quantum-chemical and topological information coded in this type of descriptors.

Quantum-connectivity descriptors in modeling solubility of environmentally important organic compounds.

Quantum-connectivity indices are topographic descriptors combining quantum-chemical and topological information. They are used to describe the water solubility of a noncongeneric data set of organic compounds. A QSPR model is obtained with two quantum-connectivity indices that accounts for more than 90% of the variance in the water solubility of these chemicals.

On the aggregation state and QSPR models. The solubility of herbicides as a case study.

The goal of this article is to stress the importance of considering the phase in QSPR studies. It is found that the phase plays a fundamental role in the QSPR models from both a statistical and a physical point of view. From a statistical point of view, it is observed that the predictive performance drops drastically when the QSPR model, obtained for a given phase, is used to predict the solubility of the same set of compounds but in another phase.

A simple QSPR model for predicting soil sorption coefficients of polar and nonpolar organic compounds from molecular formula.

A quantitative structure-property relationship (QSPR) model is developed to predict the logarithm of the soil sorption coefficient of 82 organic compounds. The data set contains polar and nonpolar, saturated, unsaturated, aliphatic, aromatic, and polycyclic aromatic compounds covering a log K(oc) range from about 1 to 6 log units. The best correlation equation, containing only five constitutional descriptors (number of benzene rings, molecular weight, number of N, O, and S atoms), predicts log K(oc) with a squared correlation coefficient of 0.

Prediction of Henry's law constants of triazine derived herbicides from quantum chemical continuum solvation models.

The Henry's law constants (H) for triazine derived herbicides are calculated using quantum chemical solvation models, SM2, SM3, PCM-DFT, and CPCM-DFT, and their performances are discussed. The results show considerable differences in performance among the different levels of theory. The values of H calculated by the semiempirical methods agree much better with the experimental values than those obtained at the DFT level.

Prediction of infinite dilution activity coefficients of chlorinated organic compounds in aqueous solution from quantum-chemical descriptors.

A quantitative structure-property relationship (QSPR) model is developed to correlate the natural logarithm of infinite dilution activity coefficients, ln (gamma(infinity)), of 45 chlorinated organic compounds in aqueous solution from quantum-chemical descriptors. The best correlation equation contains five theoretical molecular descriptors. All descriptors were obtained from the chemical structure of the compounds and have definite physical meaning corresponding to different intermolecular interactions.

On the calculation of Henry's law constants of chlorinated benzenes in water from semiempirical quantum chemical methods.

The Henry's law constants for all 12 polychlorinated benzene congeners were calculated using semiempirical quantum chemical solvation models (SM2, SM2.1, and SM3), and their performances are discussed. The values obtained by the SM3 method are underestimated compared with the experimental values and those calculated by SM2 and SM2.