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Transforming olefins to chiral amino alcohols is a useful approach to synthesize biologically active natural products and numerous drugs. A recent study has demonstrated a promising and synthetic value of an engineered hemoprotein for catalyzing olefins to chiral amino alcohols with 2500 total turnover numbers and 90% ee. Density functional theory (DFT) calculation has been used to systematically investigate the detailed mechanisms of the aforementioned process. One electron transfers from Fe atom to HN–nitrene in the iron–nitrene intermediate formation. Subsequently, styrene aziridination, singlet state is characterized by a nonradical, concerted nonsynchronous mechanism, while a radical and stepwise mechanism for triplet. Through hydrolysis reaction forming amino alcohol enantiomers, radical intermediate in triplet state without ring‐opening process is obviously more feasible than singlet aziridine, where the energy barrier difference between triplet and singlet approaches to 20.00 kcal/mol. Moreover, due to the hydrogen bond effect, the water dimer‐assisted hydrolysis reaction is effective to reduce the energy barrier by about 7.00 kcal/mol compared with one water assisted in triplet; however, the energy barrier difference in singlet is unapparent with only 0.18 kcal/mol accompanied with ring‐opening process. Further, homology modeling shows that the reactivity and enantioselectivity can be attributed to the structure of the enzyme active pocket. This study sheds light on the mechanism of engineered hemoprotein‐mediated amino alcohols synthesis and shows the development of biological catalysts. [ABSTRACT FROM AUTHOR]

Continuum solvent models have shown to be very efficient for calculating solvation energy of biomolecules in solution. However, in order to produce accurate results, besides atomic radii or volumes, an appropriate set of partial charges of the molecule is needed. Here, a set of partial charges produced by a fluctuating charge model-the atom-bond electronegativity equalization method model (ABEEMσπ) fused into molecular mechanics is used to fit for the analytical continuum electrostatics model of generalized-Born calculations. Because the partial atomic charges provided by the ABEEMσπ model can well reflect the polarization effect of the solute induced by the continuum solvent in solution, accurate and rapid calculations of the solvation energies have been performed for series of compounds involving 105 small neutral molecules, twenty kinds of dipeptides and several protein fragments. The solvation energies of small neutral molecules computed with the combination of the GB model with the fluctuating charge protocol (ABEEMσπ/GB) show remarkable agreement with the experimental results, with a correlation coefficient of 0.97, a slope of 0.95, and a bias of 0.34 kcal/mol. Furthermore, for twenty kinds of dipeptides and several protein fragments, the results obtained from the analytical ABEEMσπ/GB model calculations correlate well with those from ab initio and Poisson-Boltzmann calculations. The remarkable agreement between the solvation energies computed with the ABEEMσπ/GB model and PB model provides strong motivation for the use of ABEEMσπ/GB solvent model in the simulation of biochemical systems. [ABSTRACT FROM AUTHOR]

N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters klpO==,H and klpO–,HN–, respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H2O)n (n=1–3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H2O)n (n=4–6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations. [ABSTRACT FROM AUTHOR]

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces “the hydrogen bond interaction region” in which a new parameter k[sub lp,H](R[sub lp,H]) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom–atom interaction, i.e., oxygen–oxygen, hydrogen–hydrogen, oxygen–hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H[sub 2]O)[sub n] (n=2–6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Nitrosylation reaction mechanisms of the hydrolysates of NAMI‐A and hydrolysis reactions of ruthenium nitrosyl complexes were investigated in the triplet state and the singlet state. Activation free energies were calculated by combining the QM/MM(ABEEM) method with free energy perturbation theory, and the explicit solvent environment was simulated by an ABEEMσπ polarizable force field. Our results demonstrate that nitrosylation reactions of the hydrolysates of NAMI‐A occur in both the triplet and the singlet states. The Ru‐N‐O angle of the triplet ruthenium nitrosyl complexes is in the range of 132.0°–138.2°. However, all the ruthenium nitrosyl complexes at the singlet state show an almost linear Ru‐N‐O angle. The nitrosylation reaction happens prior to the hydrolysis reaction for the first‐step hydrolysates. The activation free energies of the nitrosylation reactions show that the H2O‐NO exchange reaction of [RuCl4(Im)(H2O)] in the singlet spin sate is the most likely one. Comparing with the activation free energies of the hydrolysis reactions of the ruthenium nitrosyl complexes, the results indicate that the rate of the DMSO–H2O exchange reaction of [RuCl3(NO)(Im)(DMSO)] is faster than that of [RuCl3(H2O)(Im)(DMSO)] in both the triplet spin state and the singlet spin state. © 2018 Wiley Periodicals, Inc. Ab initio method and ABEEM/MM‐FEP method have been combined to investigate reaction mechanism of the interactions of NO with NAMI‐A hydrolysates in both the triplet and singlet spin states. The combined QM/MM(ABEEM polarizable force field) method with MD‐FEP was employed to calculate the activation free energies. The rates of nitrosylation reactions are faster than those of further hydrolysis reactions for the first step hydrolysates of NAMI‐A. The activation free energies of the nitrosylation reactions show that the H2O‐NO exchange reaction of [RuCl4(Im)(H2O)] in the singlet spin sate is the most likely one. [ABSTRACT FROM AUTHOR]

Based on the concept of the intrinsic characteristic atomic and ionic radii and an ab initio study, we present a new criterion of defining ionic or covalent character of AB-type crystals, showing that the ions in an ionic crystal do not necessarily contact each other in the classical meaning. The criterion states that an AB-type crystal is sorted as a primarily ionic in bonding nature if there exists a separation region which is the classically forbidden region for the electronic motion between a pair of adjacent cation A+ and anion B− anion, and if there is no such a separation region for a pair of adjacent cation A+ and anion B− cations in an AB-type crystal it is sorted as a primarily covalent one. This provides a fundamental understanding of the nature of ionic and covalent crystals. A comparison between the judging results of this criterion with that issued from the widely accepted Pauling's electronegativity criterion has been given, which demonstrates that in most cases both criteria give same judge results of the ionic or covalent character and the new criterion gives suitable judge results for a few cases when there are discrepancy between the two criterion judge rules. [ABSTRACT FROM AUTHOR]

The dioxygen formation mechanism of biological water oxidation in nature has long been the focus of argument; many diverse mechanistic hypotheses have been proposed. Based on a recent breakthrough in the resolution of the electronic and structural properties of the oxygen-evolving complex in the S3 state, our density functional theory (DFT) calculations reveal that the open-cubane oxo–oxyl coupling mechanism, whose substrates preferably originate from W2 and O5 in the S2 state, emerges as the best candidate for O–O bond formation in the S4 state. This is justified by the overwhelming energetic superiority of this mechanism over alternative mechanisms in both the isomeric open and closed-cubane forms of the Mn4CaO5 cluster; spin-dependent reactivity rooted in variable magnetic couplings was found to play an essential role. Importantly, this oxygen evolution mechanism is supported by the recent discovery of femtosecond X-ray free electron lasers (XFEL), and the origin of the observed structural changes from the S1 to S3 state has been analyzed. In this view, we corroborate the proposed water binding mechanism during S2–S3 transition and correlate the theoretical models with experimental findings from aspects of substrate selectivity according to water exchange kinetics. This theoretical consequence for native metalloenzymes may serve as a significant guide for improving the design and synthesis of biomimetic materials in the field of photocatalytic water splitting. [ABSTRACT FROM AUTHOR]