New insights in the formation of thioxophosphine: a quantum chemical study

The investigation of the thioxophosphine (PS) formation from different reaction paths is successfully performed and presented in this paper. The PH(3)+SH(1) reaction is likely to yield the intermediates PH(2) (2)+H(2)S through an energy barrier of 2.8 kcal mol(-1). However, the next step is the H(2)PS(2) formation, which has a too high energy barrier, 52.6 kcal mol(-1). The PH(3)+S(1) reaction path is the likely source of the HPS(1) molecule. The other possibilities are the PH(1)+H(2)S, PH(2) (2)+SH(1), and PH(3)+H(2)S reactions, but they are spin forbidden and energetically unfavorable for the HPS(1) and PSH(1) formations. On the other hand, the PS(2) formation is more likely to happen by the PH(1)+SH(1) reaction. The PH(2) (2)+S(1), PH(3)+SH(1), P(2)+H(2)S, and P(4)+H(2)S reactions are also favorable in terms of energetics; however, these reactions are spin forbidden. The chemical mechanism for the PS(2) formation is now presented in more details, which is of great importance in the atmosphere of Jupiter and Saturn, and in interstellar medium.     

Inhibition of class A beta-lactamases by carbapenems: crystallographic observation of two conformations of meropenem in SHV-1

Carbapenem antibiotics are often the "last resort" in the treatment of infections caused by bacteria resistant to penicillins and cephalosporins. To understand why meropenem is resistant to hydrolysis by the SHV-1 class A beta-lactamase, the atomic structure of meropenem inactivated SHV-1 was solved to 1.05 A resolution. Two conformations of the Ser70 acylated intermediate are observed in the SHV-1-meropenem complex; the meropenem carbonyl oxygen atom of the acyl-enzyme is in the oxyanion hole in one conformation, while in the other conformation it is not. Although the structures of the SHV-1 apoenzyme and the SHV-1-meropenem complex are very similar (0.29 A rmsd for Calpha atoms), the orientation of the conserved Ser130 is different. Notably, the Ser130-OH group of the SHV-1-meropenem complex is directed toward Lys234Nz, while the Ser130-OH of the apo enzyme is oriented toward the Lys73 amino group. This altered position may affect proton transfer via Ser130 and the rate of hydrolysis. A most intriguing finding is the crystallographic detection of protonation of the Glu166 known to be involved in the deacylation mechanism. The critical deacylation water molecule has an additional hydrogen-bonding interaction with the OH group of meropenem's 6alpha-1 R-hydroxyethyl substituent. This interaction may weaken the nucleophilicity and/or change the direction of the lone pair of electrons of the water molecule and result in poor turnover of meropenem by the SHV-1 beta-lactamase. Using timed mass spectrometry, we further show that meropenem is covalently attached to SHV-1 beta-lactamase for at least 60 min. These observations explain key properties of meropenem's ability to resist hydrolysis by SHV-1 and lead to important insights regarding future carbapenem and beta-lactamase inhibitor design.     

Structure determination of the 4d metal diborides: a quantum mechanical study

Metal diborides (MB(2)) often have interesting thermal, mechanical, and superconducting properties. MgB(2) was put into focus some years ago for its high transition temperature (39 K) in combination with its simple AlB(2) structure. The boron structure in MB(2) is assumed to be dependent on the electron transfer from the nearby positioned metal atoms. An electronic and structural comparison has been performed here for various initially planar and puckered transition-metal borides, using quantum mechanical density functional theory (DFT) calculations under periodic boundary conditions. In comparison to MgB(2), the experimentally planar transition-metal diborides (ZrB(2), NbB(2), and MoB(2)) and the experimentally puckered ones (TcB(2), RuB(2), RhB(2), and PdB(2)) have been examined. The results indicate that the energetic stability generally follows the experimentally obtained results. The metals that are less electronegative than boron donate electrons to boron, which in turn induce planar boron structures (graphitic-like). The metals that prefer to be planar donate more than one electron, while the trend for metals which favor puckered B structures is that they donate less than one electron per metal atom. Two donated electrons per metal atom (or very close to) will result in the most stable AlB(2) structure.     

A solid state 13C NMR, crystallographic, and quantum chemical investigation of chemical shifts and hydrogen bonding in histidine dipeptides

We report the first solid-state NMR, crystallographic, and quantum chemical investigation of the origins of the 13C NMR chemical shifts of the imidazole group in histidine-containing dipeptides. The chemical shift ranges for Cgamma and Cdelta2 seen in eight crystalline dipeptides were very large (12.7-13.8 ppm); the shifts were highly correlated (R2= 0.90) and were dominated by ring tautomer effects and intermolecular interactions. A similar correlation was found in proteins, but only for buried residues. The imidazole 13C NMR chemical shifts were predicted with an overall rms error of 1.6-1.9 ppm over a 26 ppm range, by using quantum chemical methods. Incorporation of hydrogen bond partner molecules was found to be essential in order to reproduce the chemical shifts seen experimentally. Using AIM (atoms in molecules) theory we found that essentially all interactions were of a closed shell nature and the hydrogen bond critical point properties were highly correlated with the N...H...O (average R2= 0.93) and Nepsilon2...H...N (average R2= 0.98) hydrogen bond lengths. For Cepsilon1, the 13C chemical shifts were also highly correlated with each of these properties (at the Nepsilon2 site), indicating the dominance of intermolecular interactions for Cepsilon1. These results open up the way to analyzing 13C NMR chemical shifts, tautomer states (from Cdelta2, Cepsilon1 shifts), and hydrogen bond properties (from Cepsilon1 shifts) of histidine residue in proteins and should be applicable to imidazole-containing drug molecules bound to proteins, as well.     

Catalysis in glycerol: a survey of recent advances

There is currently a significant increase in the use of glycerol as a renewable solvent for catalytic reactions. Glycerol has often been the solvent of choice in both homogeneous and heterogeneous catalyses, despite its high viscosity at ambient temperature and the low solubility of highly hydrophobic reagents found in glycerol. Its biodegradability and non-toxicity have led to reports of improved reaction performance and selectivity, as well as easier product separation and effective catalyst recycling. All relevant advances in this emerging field of “green” catalysis are thoroughly reviewed below.     

Prebiotic routes to nucleosides: a quantum chemical insight into the energetics of the multistep reaction pathways

One of the most controversial questions of the RNA world theory is the formation of nucleosides through the reaction of nucleobases with ribose. The study presented herein discusses the thermodynamics of nucleoside formation under prebiotic conditions through the classical reaction route, which involves ribose and cytosine, as well as through the novel pathway suggested by Powner et al. [Nature 2009 , 459, 239–242]. Our computations show that, in contrast to the classical pathway, the route proposed by Powner et al. perfectly satisfies all conditions of a typical metabolic pathway that occurs in living organisms. In addition, we reveal the reasons that render the reaction of ribose with nucleobases endothermic and, thereby, less plausible under prebiotic conditions. We show that phosphates may play an indispensable role in the glycosylation of nucleobases by making this endothermic reaction step exothermic. In addition, we describe the catalytic role of phosphate anions in the formation of 2‐aminooxazole, which is one of the key steps of the synthetic route reported by Powner et al.     

Quantum chemical insights into the aggregation induced emission phenomena: A QM/MM study for pyrazine derivatives

There have been intensive studies on the newly discovered phenomena called aggregation induced emission (AIE), in contrast to the conventional aggregation quenching. Through combined quantum mechanics and molecular mechanics computations, we have investigated the aggregation effects on the excited state decays, both via radiative and nonradiative routes, for pyrazine derivatives 2,3‐dicyano‐5,6‐diphenylpyrazine ( DCDPP ) and 2,3‐dicyanopyrazino phenanthrene ( DCPP ) in condensed phase. We show that for DCDPP there appear AIE for all the temperature, because the phenyl ring torsional motions in gas phase can efficiently dissipate the electronic excited state energy, and get hindered in aggregate; while for its “locked”‐phenyl counterpart, DCPP , theoretical calculation can only give the normal aggregation quenching. These first‐principles based findings are consistent with recent experiment. The primary origin of the exotic AIE phenomena is due to the nonradiative decay effects. This is the first time that AIE is understood based on theoretical chemistry calculations for aggregates, which helps to resolve the present disputes over the mechanism. © 2012 Wiley Periodicals, Inc.     

Silver clusters in the cages of zeolites: A quantum chemical study

The electronic structure of zeolite A is developed in a step by step procedure from the simple O_hH₈Si₈O₁₂ molecule, to the _∞ ¹ [(-O)₂H₄[Si₈O₁₂)] chain, to the _∞ ² [(-O₄)(Si₈O₁₂)] layer, and finally to the silica zeolite A framework _∞ ³ [Si₂₄O₄₈]. It is remarkable how well the calculated band structures of both, _∞ ² [(-O)₄(Si₈O₁₂)] and _∞ ³ [Si₂₄O₄₈] correspond to the experimentally determined band structure of α-quartz with a Fermi level of -10.55 eV. The HOMO region consists in each case of nonbonding 2p-oxygen bands which in a localized language can be denoted as oxygen lone pairs ( | O<). We observe in each case the typical behaviour of an insulator with saturated valencies whose electronic structure can be described as being localized and is already present in the starting O_h-H₈Si₈O₁₂ molecule. The double-8-rings D8R of the _∞ ² [(-O)₄(Si₈O₁₂)] layer have a pore diameter of 4.1 Å, the same as the pore opening of zeolite A. It is large enough to accept up to four Ag, forming _∞ ² [(-O)₄(Si₈O₁₂)Ag_n], n = 1, 2, 3, 4, layers, suitable for modelling the electronic interactions between the zeolite cavity embedded silver clusters and between the clusters and the zeolite framework. With one Ag per D8R the band structure is simply a superposition of the 4d, 5s and 5p levels of a layer of nearly noninteracting Ag and the silicon dioxide layer. The Ag-d band lies below the oxygen lone pairs, the Ag-s band lies about 3 eV above the oxygen lone pairs, and the Ag-5p bands are in the antibonding silicon dioxide region. The first electronic transition is of oxygen lone pair to Ag-5s LMCT type. Increasing silver content results in progressive splitting of the 5σ Ag bands and shifts the first (Ag^m+ _n)? ← (| O<) charge transfer transition to lower energies. The filled Ag 4d-bands lie always significantly below the (| O<) HOCOs (highest occupied crystal orbitals) but their band width increases with increasing silver content. In all cases the zeolite environment separates the Ag clusters through antibonding Ag-(← O<) interactions so that the coupling remains weak and it makes sense to describe the Ag clusters in the D8R as quantum dots weakly interacting with each other.     

Hydrogen bonds formed upon encapsulation of doxorubicin into amphiphilic N-vinylpyrrolidone copolymer: a quantum chemical study

Russian Chemical Bulletin - The structures of H-complexes of the anthracycline antibiotic doxorubicin with poly-N-vinylpyrrolidone segments in an aqueous medium were examined using the density...     

Structural and spectral properties of 4-bromo-1-naphthyl chalcones: a quantum chemical study

The structural and optical properties of 4-bromo-1-naphthyl chalcones (BNC) have been studied by using quantum chemical methods. The density functional theory (DFT) and the singly excited configuration interaction (CIS) methods were employed to optimize the ground and excited state geometries of unsubstituted and substituted BNC with different electron withdrawing and donating groups in both gas and solvent phases. Based on the ground and excited state geometries, the absorption and emission spectra of BNC molecules were calculated using the time-dependent density functional theory (TDDFT) method. The solvent phase calculations were performed using the polarizable continuum model (PCM). The geometrical parameters, vibrational frequencies, and relative stability of cis- and trans-isomers of unsubstituted and substituted BNC molecules have been studied. The results from the TDDFT calculations reveal that the substitution of electron withdrawing and electron donating groups affects the absorption and emission spectra of BNC.     

A quantum chemical study of reactions of DNA bases with sulphur mustard: a chemical warfare agent

Reactions of the sulphonium ion of sulphur mustard (SM⁺¹) at the N7, N3 and O6 sites of guanine, N7, N3 and N1 sites of adenine, O2 and N3 sites of cytosine and O2 and O4 sites of thymine were studied theoretically in gas phase and aqueous media employing density functional theory (DFT) and second order Møller–Plesset perturbation (MP2) theory. The B3LYP, B3PW91 and B1B95 functionals of DFT and the 6-31+G* and AUG-cc-pVDZ basis sets were used in the calculations. Basis set superposition error was treated using the counterpoise method by single point energy calculations at the B3LYP/6-31+G* level in gas phase. The present study explains the mechanism of alkylation of the DNA bases and shows that SM⁺¹ would form stable adducts at the endocyclic nitrogen sites of the DNA bases, and at the O6 site of guanine and the O2 site of cytosine. Formation of adducts at the N7 site of guanine and N3 site of adenine are found to be most favored and next most favored respectively, which agrees with experimental observations.     

A quantum chemical study of the reaction mechanism of acetyl-coenzyme a synthase

Recent experimental and theoretical studies have focused on the mechanism of the A-cluster active site of acetyl-CoA synthase that produces acetyl-CoA from a methyl group, carbon monoxide, and CoA. Several proposals have been made concerning the redox states of the (Ni-Ni) bimetallic center and the iron-sulfur cluster connected to one of the metals. Using hybrid density functional theory, we have investigated putative intermediate states from the catalytic cycle. Among our conclusions are the following: (i) the zerovalent state proposed for the proximal metal is unlikely if the charge on the iron-sulfur cluster is +2; (ii) a mononuclear mechanism in which both CO and CH(3) bind the proximal nickel is favored over the binuclear mechanism in which CO and CH(3) bind the proximal and distal nickel ions, respectively; (iii) the formation of a disulfide bond in the active site could provide the two electrons necessary for the reaction but only if methylation occurs simultaneously; and (iv) the crystallographic closed form of the active site needs to open to accommodate ligands in the equatorial site.     

Dense gas extraction on a laboratory scale: A survey of some recent results

Dense gas extraction followed by thin-layer chromatography (DGE-TLC) gives a first fast survey of various parameters influencing this separation technique. As an example, the effect of pressure on the extraction of castor beans is illustrated. Applying the coupling procedure to steroids allows to establish relations between the structure of such compounds and their solubility. The quantitative determination of solubility is described and the behaviour of soybean oil up to 2600 bar is discussed. The solubilities of limonene and eugenol in the subcritical pressure range serve to demonstrate that the recovery of volatile compounds requires carefully chosen separation parameters. The detoxification of wormwood leaves on a preparative scale is described.     

Ab initio chemical kinetics for the hydrolysis of N2O4 isomers in the gas phase

The mechanism and kinetics for the gas-phase hydrolysis of N(2)O(4) isomers have been investigated at the CCSD(T)/6-311++G(3df,2p)//B3LYP/6-311++G(3df,2p) level of theory in conjunction with statistical rate constant calculations. Calculated results show that the contribution from the commonly assumed redox reaction of sym-N(2)O(4) to the homogeneous gas-phase hydrolysis of NO(2) can be unequivocally ruled out due to the high barrier (37.6 kcal/mol) involved; instead, t-ONONO(2) directly formed by the association of 2NO(2), was found to play the key role in the hydrolysis process. The kinetics for the hydrolysis reaction, 2NO(2) + H(2)O ? HONO + HNO(3) (A) can be quatitatively interpreted by the two step mechanism: 2NO(2) → t-ONONO(2), t-ONONO(2) + H(2)O → HONO + HNO(3). The predicted total forward and reverse rate constants for reaction (A), k(tf) = 5.36 × 10(-50)T(3.95) exp(1825/T) cm(6) molecule(-2) s(-1) and k(tr) = 3.31 × 10(-19)T(2.478) exp(-3199/T) cm(3) molecule(-1) s(-1), respectively, in the temperature range 200-2500 K, are in good agreement with the available experimental data.     

Molecular parameterization and determination of the electrode potentials of anticoagulant derivatives: Electrochemical and quantum chemical study

This research presents calculations and computation of two anticoagulant derivatives electrode potentials in methanol. For this purpose, the ab initio molecular orbital calculations (HF) and density functional theory (DFT) together with the 6-31G(d) basis set were utilized. The calculated values were compared with the experimental values obtained by linear sweep voltammetry. The observed and the calculated changes in the reduction potential of the anticoagulant derivatives differed from those of the reference compound (catechol), being less than 20 mV. In this way, a method was provided, by which the reduction potentials of the related molecules could be predicted very accurately. Actually, the resulting data illustrated that the method was likely to be useful for the prediction of biomolecules electrode potentials in different aprotic solvents. The bond lengths, bond angles and dipole moment of the studied compounds were calculated in two different solvents and the solvent effects were discussed.     

Orientation of amide-nitrogen-15 chemical shift tensors in peptides: a quantum chemical study.

Knowledge of the orientation of the nitrogen-15 chemical shift anisotropy (CSA) tensor is critical for a variety of experiments that provide information on protein structure and dynamics in the solid and solution states. Unfortunately, the methods available for determining the orientation of the CSA tensor experimentally have inherent limitations. Rotation studies of a single crystal provide complete information but are tedious and limited in applicability. Solid-state NMR studies on powder samples can be applied to a greater range of samples but suffer from ambiguities in the results obtained. Density functional gauge-including-atomic-orbitals (GIAO) calculations of the orientations of (15)N CSA tensors in peptides are presented here as an independent source of confirmation for these studies. A comparison of the calculated (15)N CSA orientations with the available experimental values from single-crystal and powder studies shows excellent agreement after a partial, constrained optimization of some of the crystal structures used in the calculation. The results from this study suggest that the orientation as well as the magnitudes of (15)N CSA tensors may vary from molecule to molecule. The calculated alpha(N) angle varies from 0 degrees to 24 degrees with the majority in the 10 degrees to 20 degrees range and the beta(N) angle varies from 17 degrees to 24 degrees in good agreement with most of the solid-state NMR experimental results. Hydrogen bonding is shown to have negligible effect on the orientation of (15)N CSA tensor in accordance with recent theoretical predictions. Furthermore, it is demonstrated that the orientation of the (15)N CSA can be calculated accurately with much smaller basis sets than is needed to calculate the chemical shift, suggesting that the routine application of ab initio calculations to the determination of (15)N CSA tensor orientations in large biomolecules might be possible.