Ureases: quantum chemical calculations on cluster models

Herein, we present results from a computational study of dinickel complexes that are relevant to the catalytic hydrolysis of urea exerted by the urease enzymes. The B3LYP density functional is used to characterize the equilibrium geometry, electronic and magnetic properties, and energies for a series of realistic complexes modeling the active site of ureases. The analysis of the theoretical results gives new insight into the structure, substrate binding, and catalytic mechanism. The water bridge between the two Ni(II) ions observed in the crystallographic structures of the ureases was assigned to a hydroxide bridge in agreement with the observed small antiferromagnetic coupling. Both monodentate and bidentate urea-bound complexes, in which urea had favorable orientations for catalysis, were characterized. Finally, two reaction mechanisms were investigated starting from the monodentate and bidentate urea-bound complexes, respectively. Both a Ni1...Ni2 bridging hydroxide and a Ni2-bound water molecule play crucial roles in the two mechanisms.     

Diethylamine-based ionic liquids: quantum chemical calculations and experiment

Russian Chemical Bulletin - The structural and energetic characteristics of the compounds formed by the reaction of diethylamine (DEA) with protic acids (sulfuric (H2SO4), methanesulfonic (MsOH),...     

Thermochemistry and quantum chemical calculations of two dibenzocycloalkane nitriles

The energies of combustion and fusion of 5-cyano-5H-dibenzo[a,d]cycloheptene (1) and (5E,11E)-dibenzo[a,e]cyclooctene-5,11-dicarbonitrile (2) were measured by means of microbomb calorimetry and DSC, respectively. The derived enthalpies of formation in solid state are 320 ± 18 for nitrile 1 and 470 ± 31 kJ mol⁻¹ for nitrile 2, respectively. The experimental enthalpies of formation are discussed in relationship with values calculated at the G3(MP2)//B3LYP level of quantum chemical theory, by means of group additivity and isodesmic reactions. The two nitriles are not stabilized by dibenzoannelation.     

Perfluoropoly-ether/peroxide compounds: spectroscopic studies and quantum chemical calculations

Perfluoropolyethers (PFPEs) are a class of high performance materials used in a wide range of applications (refrigeration, lubrication, semiconductor industry, etc.). PFPEs containing peroxidic units are intermediate materials for the preparation of commercial end products. In this work we study the spectroscopic properties of ether and peroxides linkages in this class of compounds; nuclear magnetic resonance (NMR) spectra are discussed, FT-Raman data presented. Quantum chemical calculations on model molecules were used as a tool for the interpretation of the Raman experimental data and physical-chemical properties.     

interaction of nitro compounds with radicals: a quantum chemical study

Photoreduction of nitro compounds is accompanied by formation of various radical products that can react with the starting nitro compound, thus causing deviation of the decomposition kinetics from the first-order kinetics with respect to the nitro compound. The results of quantum chemical modeling of the reactions of nitro compounds with radicals and the pathways of further transformations of radical adducts formed in the reactions are presented. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 202–206, February, 2006.     

Structure of low-lying electronic states of NdO: quantum chemical calculations

Low-lying states of the NdO molecule have been predicted from quantum mechanical complete active-space self-consistent field/multireference configuration interaction/spin-orbit calculations. 54 states labeled through the quantum number Omega(+/-) have been determined in the excitation energy range of approximately 1 eV. For each state molecular constants T(e), T(v), omega(e), deltaG(v), R(e), B(e), and B(v) have been calculated. All these states display nearly identical principal structural characteristics: equilibrium internuclear distance and vibrational frequency. Calculated values of T(v), deltaG(v), and B(v) agree satisfactorily with experimental values available for nine electronic states among the 54 considered. The feasibility of a statistical representation of the low-lying states of NdO is considered.     

Spin-trapping of oxygen free radicals in chemical and biological systems: new traps, radicals and possibilities

The choice of the spin-trap that is to be applied in any EPR study represents the crossroad between a comprehensive investigation and an "ordinary" quantification of production of radicals. So, the scope of our study was to compare the performance of different spin-traps for qualitative analysis of radical-generating systems, and their ability to recognize previously unnoticed radicals. In addition, we present a brief account of the difficulties involved in the detection of oxygen-centered radicals in chemical and biological systems accompanied by the rationale for using the EPR spin-trapping technique in quantitative studies of such reactive species. Certain technical aspects of EPR experiments related to efficient trapping of free radicals in biochemical systems are also discussed. As an example we present here results obtained using EPR spectroscopy and the spin-trap DEPMPO, which show that the Fenton reaction, as well as various biological systems generate a previously unappreciated hydrogen (*H) atom.     

Semiempirical quantum chemical calculations of molecular π- complexes

A method is suggested to calculate the geometrical and thermodynamical characteristics of organic π- complexes. The interaction energy is considered as a sum of two terms: the specific quantum chemical interaction of the π- electron systems depending essentially on the chemical nature of reactants, and the nonspecific atom-atom (van-der-Waals) interaction depending only on the kind of atoms belonging to the fragments of a complex. An attractive quantum chemical interaction is described in terms of the PPP-method; the van-der-Waals interaction is expressed in terms of the empirical exp-6-potential. The geometries of complexes are found by the complete energy minimization with respect to six parameters characterizing the mutual orientation of the complex fragments. Energies, entropies and equilibrium constants of several tetracyanoethylene π-complexes are calculated by this method. The results agree satisfactorily with experimental data.     

Molecular dynamics simulations and quantum chemical calculations on β-cyclodextrin spironolactone complex

Molecular dynamics simulations on β-cyclodextrin in vacuo, with water and complexed with spironolactone (SP) were performed at a temperature of 300 K over a period of 1 ns. Two different orientations of SP in the cavity were considered. Along with conformational parameters, the formation of hydrogen bonds has been monitored during the whole simulation time. Cyclodextrins have the capability to form hydrogen bonds with the surrounding water molecules or intramolecular ones. The incorporation of ligands into the hydrophobic interior of β-cyclodextrin changes the preference of hydrogen bonds significantly and results in a contribution to the decrease of flexibility. Quantum chemical calculations on SP β-CD inclusion complex were performed to determine the interaction energy and to prove the applicability of various methods. Although all applied methods describe reasonable geometries for the association complex, higher level methods (e.g., B3LYP/6-31G(d,p)) seem to be necessary to determine reliable interaction energies.     

Structural studies on ethyl isovalerate by microwave spectroscopy and quantum chemical calculations

We observed the microwave spectrum of ethyl isovalerate by molecular beam Fourier transform microwave spectroscopy. The rotational and centrifugal distortion constants of the most abundant conformer were determined. Its structure was investigated by comparison of the experimental rotational constants with those obtained by ab initio methods. In a first step, the rotational constants of various conformers were calculated at the MP2/6-311++G** level of theory. Surprisingly, no agreement with the experimental results was found. Therefore, we concluded that in the case of ethyl isovalerate more advanced quantum chemical methods are required to obtain a reliable molecular geometry. Ab initio calculations carried out at MP3/6-311++G**, MP4/6-311++G**, and CCSD/6-311++G** levels and also density functional theory calculations using the B3LYP/6-311++G** method gave similar results for the rotational constants, but they were clearly distinct from those obtained at the MP2/6-311++G** level. With use of these more advanced methods, the rotational constants of the lowest energy conformer were in good agreement with those obtained from the microwave spectrum.     

Predicting Michael-acceptor reactivity and toxicity through quantum chemical transition-state calculations

The electrophilic reactivity of Michael acceptors is an important determinant of their toxicity. For a set of 35 α,β-unsaturated aldehydes, ketones and esters with experimental rate constants of their reaction with glutathione (GSH), k(GSH), quantum chemical transition-state calculations of the corresponding Michael addition of the model nucleophile methane thiol (CH(3)SH) have been performed at the B3LYP/6-31G** level, focusing on the 1,2-olefin addition pathway without and with initial protonation. Inclusion of Boltzmann-weighting of conformational flexibility yields intrinsic reaction barriers ΔE(?) that for the case of initial protonation correctly reflect the structural variation of k(GSH) across all three compound classes, except that they fail to account for a systematic (essentially incremental) decrease in reactivity upon α-substitution. By contrast, the reduction in k(GSH) through β-substitution is well captured by ΔE(?). Empirical correction for the α-substitution effect yields a high squared correlation coefficient (r(2) = 0.96) for the quantum chemical prediction of log k(GSH), thus enabling an in silico screening of the toxicity-relevant electrophilicity of α,β-unsaturated carbonyls. The latter is demonstrated through application of the calculation scheme for a larger set of 46 Michael-acceptor aldehydes, ketones and esters with experimental values for their toxicity toward the ciliates Tetrahymena pyriformis in terms of 50% growth inhibition values after 48 h exposure (EC(50)). The developed approach may add in the predictive hazard evaluation of α,β-unsaturated carbonyls such as for the European REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) Directive, enabling in particular an early identification of toxicity-relevant Michael-acceptor reactivity.     

Molecular structure and conformations of benzenesulfonamide: gas electron diffraction and quantum chemical calculations

The molecular structure and conformational properties of benzenesulfonamide, C6H5SO2NH2, were studied by gas electron diffraction (GED) and quantum chemical methods (MP2 and B3LYP with different basis sets). The calculations predict the presence of two stable conformers with the NH2 group eclipsing or staggering the SO2 group. The eclipsed form is predicted to be favored by about 0.5 kcal/mol. According to GED, the saturated vapor over solid benzenesulfonamide at a temperature of 150(5) degrees C consists of the eclipsed conformer. The GED intensities, however, possess a very low sensitivity toward the vapor composition, and contributions of the anti conformer of up to 75% (at the 0.05 level of significance) or up to 55% (at the 0.25 level of significance) cannot be excluded. The molecule possesses C(sS) symmetry with the S-N bond perpendicular to the ring plane.     

Structure and energetics of water-silanol binding on the surface of silicalite-1: quantum chemical calculations

Quantum mechanical calculations have been carried out to investigate the structural properties and the interaction between water molecules and silanol groups on the surface of silicalite-1. The (010) surface, which is perpendicular to the straight channel, has been selected and represented by three fragments taken from different parts of the surface. Calculations have been performed using different levels of accuracy: HF/6-31G(d,p), B3LYP/6-31G(d,p), HF/6-31++G(d,p), and B3LYP/6-31++G(d,p). The basis set superposition error has been taken into account. The geometry of the silanol groups and that of the water molecules have been fully optimized. The results show that the most stable conformation takes place when a water molecule forms two hydrogen bonds with two silanols, with only one silanol lying on the opening of the pore of the straight channel. The corresponding binding energy is -48.82 kJ/mol. These areas are supposed to be the first binding sites which have to be covered when the water molecule approaches the surface. When the water loading increases, the next favorable silanols are those of the opening of the pore in which the four possible complex conformations yield a binding energy between -25.62 and -37.41 kJ/mol. It was also found that the calculated O-H bond length of the silanol in the free form was slightly shorter than that in the complex. In terms of the stretching frequency, the complexation leads to a red shift of the O-H stretching of the silanol group.     

Radical ions and radicals in electron-irradiated acrylates and N-isopropylacrylamide: a quantum chemical study

The semiempirical quantum chemical methods MNDO, AM1 and PM3 were used to investigate the performance of the single excited configuration interaction (SCI) approximation for calculating low energy excitation energies of open-shell systems. Systematic calculations were done for eight radicals formed by reactions of H√, OH√ and e⁻_aq with various acrylates and N-isopropylacrylamide. The calculated electronic spectra show a reasonable correlation with experimental data for both neutral radicals and radical ions. The AM1 as well as the PM3 formalism can be successfully applied to calculate the low energy excited states of these types of open shell systems. The best correlation between experimental and calculated excitation energies was obtained using the PM3 method (correlation coefficient 0.96, overall average error 0.16 eV).     

FT-IR, FT-Raman spectra and quantum chemical calculations of 3,4-dimethoxyaniline

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of 3,4-dimethoxyaniline (3,4-DMA). The Fourier transform infrared and Fourier transform Raman spectra of 3,4-DMA was recorded in the solid phase. The optimized geometry was calculated by HF and B3LYP methods using 6-31G(d,p) and 6-311++G(d,p) basis sets. The harmonic vibrational frequencies, infrared intensities, Raman scattering activities and the thermodynamic functions of the title compound were performed at and HF/B3LYP/6-311++G(d,p) level of theories. The scaled theoretical wavenumber showed very good agreement with the experimental values. A detailed interpretation of the infrared and Raman spectra of 3,4-DMA was reported. The theoretical spectrograms for IR and Raman spectra of the title molecule have been constructed.     

Vibrational spectra and quantum chemical calculations of 3,4-diaminobenzoic acid.

The Fourier Transform Raman and Fourier Transform infrared spectra of 3,4-diaminobenzoic acid (3,4-DABA) were recorded in the solid phase. Geometry optimizations were done without any constraint and harmonic-vibrational wave numbers and several thermodynamic parameters were calculated for the minimum energy conformer at ab initio and DFT levels invoking 6-311++G(d,p) basis set. The results were compared with the experimental values with the help of specific scaling procedures, the observed vibrational wavenumbers in FT-IR and FT-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range, the error obtained was in general very low. The appropriate theoretical spectrograms for the IR and Raman spectra of the title molecule were also constructed.     

Conformational properties of 1-methyl-1-germacyclohexane: low-temperature NMR and quantum chemical calculations

The conformational preference of the methyl group of 1-methyl-1-germacyclohexane was studied experimentally in solution (low-temperature ¹³C NMR) and by quantum chemical calculations (CCSD(T), MP2 and DFT methods). The NMR experiment resulted in an axial/equatorial ratio of 44/56 mol% at 114 K corresponding to an A value (A = G _ax ? G _eq) of 0.06 kcal mol^?1. An average value for ΔG _e→a ^#  = 5.0 ± 0.1 kcal mol^?1 was obtained for the temperature range 106–134 K. The experimental results are very well reproduced by the calculations. CCSD(T)/CBS calculations + thermal corrections resulted in an A value of 0.02 kcal mol^?1, whereas a ΔE value of ?0.01 kcal mol^?1 at 0 K was obtained.     

Application of quantum chemical calculations of C NMR chemical shifts to quinoxaline structure determination

Comparison of experimental and theoretical (GIAO DFT) ¹³C NMR chemical shifts allows the reliable assignment of isomeric structures of heteroaromatic compounds. This methodology was applied to establish the structures of isomeric quinoxalines. A modern 1D NOE technique permitted independent proof of the proposed structures.