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Chemical Calculations (chemical + calculation)
Kinds of Chemical Calculations Selected AbstractsStructures of the Chromophore Binding Sites in BLUF Domains as Studied by Molecular Dynamics and Quantum Chemical Calculations,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Kazuya Obanayama BLUF (blue-light sensing using FAD) domains constitute a new family of flavin-based blue light photoreceptors. The photocycle of BLUF is unique in the sense that a few hydrogen bond rearrangements are accompanied by only slight structural changes in the bound chromophore. The hydrogen bond rearrangements upon illumination have been inferred from spectral changes in the chromophore: ,10 nm redshift of the absorption maximum and ,16 cm,1 downshift of the C4=O stretching frequency. However, the exact features of the hydrogen bond network around the active site are still the subject of some controversy. In particular, the orientation of a conserved Gln (Gln63 in AppA) is presently one of the most questioned topics in the field. Here we perform molecular dynamics simulations for the wild-type AppA, AppA1-124C20S, BlrB and T110078 and furthermore quantum chemical calculations to investigate their spectroscopic properties in the dark and signaling states. On the basis of these results, we reveal the dynamic aspect of hydrogen bonding networks at the active site and propose theoretically reasonable models for the dark and signaling states of the BLUF domains. [source] ChemInform Abstract: Quantum Chemical Calculations on a Selection of Iodine-Containing Species (IO, OIO, INO3, (IO)2, I2O3, I2O4 and I2O5) of Importance in the Atmosphere.CHEMINFORM, Issue 29 2008Nikolas Kaltsoyannis Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Quantum Chemical Calculations of Reduction Potentials of AnO2+2/AnO+2 (An: U, Np, Pu, Am) and Fe3+/Fe2+ Couples.CHEMINFORM, Issue 40 2006Satoru Tsushima Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] Structure of Silicate Glasses and Melts at High Pressure: Quantum Chemical Calculations and Solid-State NMR.CHEMINFORM, Issue 28 2004Sung Keun Lee No abstract is available for this article. [source] Thermodynamic Properties of PaCl5 and PaF5 Based on Quantum Chemical Calculations.CHEMINFORM, Issue 23 2003A. Kovacs No abstract is available for this article. [source] ChemInform Abstract: Structure and Bonding in the Aluminum Radical Species Al×NH3, HAlNH2, HAlNH2×NH3, and Al(NH2)2 Studied by Means of Matrix IR Spectroscopy and Quantum Chemical Calculations.CHEMINFORM, Issue 28 2002Benjamin Gaertner Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] The Reaction of Ozone with the Hydroxide Ion: Mechanistic Considerations Based on Thermokinetic and Quantum Chemical Calculations and the Role of HO4, in Superoxide DismutationCHEMISTRY - A EUROPEAN JOURNAL, Issue 4 2010Gábor Merényi Prof. Abstract The reaction of OH, with O3 eventually leads to the formation of . OH radicals. In the original mechanistic concept (J. Staehelin, J. Hoigné, Environ. Sci. Technol.1982, 16, 676,681), it was suggested that the first step occurred by O transfer: OH,+O3,HO2,+O2 and that . OH was generated in the subsequent reaction(s) of HO2, with O3 (the peroxone process). This mechanistic concept has now been revised on the basis of thermokinetic and quantum chemical calculations. A one-step O transfer such as that mentioned above would require the release of O2 in its excited singlet state (1O2, O2(1,g)); this state lies 95.5,kJ,mol,1 above the triplet ground state (3O2, O2(3,g,)). The low experimental rate constant of 70,M,1,s,1 is not incompatible with such a reaction. However, according to our calculations, the reaction of OH, with O3 to form an adduct (OH,+O3,HO4,; ,G=3.5,kJ,mol,1) is a much better candidate for the rate-determining step as compared with the significantly more endergonic O transfer (,G=26.7,kJ,mol,1). Hence, we favor this reaction; all the more so as numerous precedents of similar ozone adduct formation are known in the literature. Three potential decay routes of the adduct HO4, have been probed: HO4,,HO2,+1O2 is spin allowed, but markedly endergonic (,G=23.2,kJ,mol,1). HO4,,HO2,+3O2 is spin forbidden (,G=,73.3,kJ,mol,1). The decay into radicals, HO4,,HO2.+O2.,, is spin allowed and less endergonic (,G=14.8,kJ,mol,1) than HO4,,HO2,+1O2. It is thus HO4,,HO2.+O2., by which HO4, decays. It is noted that a large contribution of the reverse of this reaction, HO2.+O2.,,HO4,, followed by HO4,,HO2,+3O2, now explains why the measured rate of the bimolecular decay of HO2. and O2., into HO2,+O2 (k=1×108,M,1,s,1) is below diffusion controlled. Because k for the process HO4,,HO2.+O2., is much larger than k for the reverse of OH,+O3,HO4,, the forward reaction OH,+O3,HO4, is practically irreversible. [source] Unexpected Conformational Properties of 1-Trifluoromethyl-1-Silacyclohexane, C5H10SiHCF3: Gas Electron Diffraction, Low-Temperature NMR Spectropic Studies, and Quantum Chemical Calculations,CHEMISTRY - A EUROPEAN JOURNAL, Issue 6 2007Georgiy Abstract The molecular structure of axial and equatorial conformers of 1-trifluoromethyl-1-silacyclohexane, (C5H10SiHCF3), as well as the thermodynamic equilibrium between these species was investigated by means of gas electron diffraction (GED), dynamic nuclear magnetic resonance (DNMR) spectroscopy, and quantum chemical calculations (B3LYP, MP2, and CBS-QB3). According to GED, the compound exists as a mixture of two Cs symmetry conformers possessing the chair conformation of the six-membered ring and differing in the axial or equatorial position of the CF3 group (axial=58(12) mol,%/equatorial=42(12) mol,%) at T=293,K. This result is in a good agreement with the theoretical prediction. This is, however, in sharp contrast to the conformational properties of the cyclohexane analogue. The main structural feature for both conformers is the unusually long exocyclic bond length SiC 1.934(10),Å. A low-temperature 19F,NMR experiment results in an axial/equatorial ratio of 17(2) mol,%:83(2) mol,% at 113,K and a ,G,, of 5.5(2),kcal,mol,1. CBS-QB3 calculations in the gas-phase and solvation effect calculations using the PCM(B3LYP/6-311G*) and IPCM(B3LYP/6-311G*) models were applied to estimate the axial/equatorial ratio in the 100,300,K temperature range, which showed excellent agreement with the experimental results. The minimum energy pathways for the chair-to-chair inversion of trifluoromethylsilacyclohexane and methylsilacyclohexane were also calculated using the STQN(Path) method. [source] Theoretical Elucidation of DPPH Radical-Scavenging Activity Difference of Antioxidant XanthonesMOLECULAR INFORMATICS, Issue 7 2005Hong-Fang Ji Abstract As naturally occurring polyphenols, xanthones are rather active in scavenging 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical. By means of quantum chemical calculation, we reveal that the activity difference of xanthones can be elucidated by their different OH bond dissociation enthalpies (BDEs) and can be further explained in terms of electronic effect and intramolecular hydrogen bond effect of substituents. The unique structure of xanthones enables them to be promising antioxidants with advantages of rather low OH BDE and relatively high ionization potential. [source] Nuclear magnetic moments from NMR spectra,Experimental gas phase studies and nuclear shielding calculationsCONCEPTS IN MAGNETIC RESONANCE, Issue 5 2007Karol Jackowski Abstract NMR spectra of gaseous compounds and quantum chemical calculations are combined to determine new accurate values of magnetic dipole moments for a series of nuclei. We have analyzed shielding constants, resonance frequencies, and nuclear magnetic moments for a group of simple molecules. The chemical shifts and resonance frequencies are measured at 300 K and extrapolated to the zero-density limit in order to remove all the intermolecular effects from the experimental parameters. The absolute shielding constants in the studied molecules are obtained from ab initio calculations. Assuming the proton magnetic moment as the reference, we determine the nuclear magnetic moments of 13C, 14N, 15N, 17O, 19F, 29Si, 31P, 33S, and 73Ge. The new nuclear magnetic moments are consistent with the experimental NMR parameters, and using these new values one can for the first time predict successfully the shielding constant of a nucleus in a molecule when the corresponding resonance frequency is known. © 2007 Wiley Periodicals, Inc. Concepts Magn Reson Part A 30A: 246,260, 2007. [source] An experimental and computational study on the epimeric contribution to the infrared spectrum of budesonideDRUG TESTING AND ANALYSIS, Issue 9 2010H. R. H. Ali Abstract Budesonide is a mixture of 22R and 22S epimers. The epimeric content of budesonide was reported in both British and European pharmacopoeias to be within the range of 60,49/40,51 for R and S epimers, respectively. In this work, contribution of the two epimers to the overall infrared spectrum of budesonide has been investigated by quantum chemical calculations. Copyright © 2010 John Wiley & Sons, Ltd. [source] Thermal Behavior of Tetrahydropyran-Intercalated VOPO4: Structural and Dynamics StudyEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 3 2007Klára Melánová Abstract The thermal behavior of tetrahydropyran-(THP-)intercalated VOPO4 was probed by an extensive combination of experimental methods (XRD, DSC, FTIR, solid-state NMR) and quantum chemical calculations. Two temperature-induced transitions were detected and all polymorphs exhibit a high degree of molecular order and tight packing of THP in VOPO4. The first reversible thermal transition at around 100 °C was attributed to boat/chair conformation changes of the THP molecules. Most probably, a low-temperature boat conformation of the guest molecules present in the interlayer space of VOPO4 changes to a high-temperature chair conformation. This rearrangement of the THP molecules was confirmed by variable-temperature 13C CP/MAS NMR spectroscopy. Quantum chemical calculations using a B3LYP functional and 6-31G(d) basis set also support this idea. The second change at around 140 °C is probably caused by a weakening of the donor,acceptor bond between the oxygen molecule of THP and the vanadium atom of the host and the formation of a disorder in packing of the THP molecules. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Electronic Structure of Binary Phosphoric and Arsenic TriazidesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2 2006Zeng Xiaoqing Abstract Two highly explosive binary triazides of the group 15 elements P(N3)3 and As(N3)3 have been obtained in the gas phase through the heterogeneous reaction of PCl3 and AsCl3, respectively with AgN3 at room temperature. The electronic structures of both triazides have been characterized by photoelectron spectroscopy, combined with quantum chemical calculations. This represents the first electronic study of covalent triazides. The first experimental vertical ionization potentials for P(N3)3 and As(N3)3 are 9.74 and 9.98 eV, with the contribution primarily from the lone pairs of the azido moiety and the arsenic atom, respectively. The results indicate the relative "isolation" of azido moieties in triazides and less stability of these highly explosive compounds in comparison to monoazides and diazides. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Density Functional Study of the Complexation Reaction of Sn(CH3)3X (X = F, Cl, Br and I) with Halide AnionsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 20 2003Frank De Proft Abstract The Lewis acid-base reaction between Sn(CH3)3X and Y, (with X, Y = F, Cl, Br and I) has been studied using quantum chemical calculations. Complexation energies were calculated at the Density Functional Theory (DFT) level and rationalized on the basis of a local application of the hard and soft acids and bases principle. It was observed that smaller differences in the local softness of the interacting sites in the Lewis acid and base correspond to stronger interactions. Moreover, the calculated sequences in complexation energies can be reproduced using equations containing chemical concepts introduced within the framework of conceptual density functional theory and rooted in the hard and soft acids and bases principle and referring only to the reactants. A method of treating the electronegativity and softness of the halide anions is presented based on a Taylor expansion of the electronegativity of the neutral halogens and the softness-polarizability proportionality. Experimental evidence for the calculated sequences was gathered from measured 117Sn chemical shifts and 1J (13C- 119/117Sn) coupling constant changes upon complexation. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Intercalates of Vanadyl Phosphate with Benzonitrile and TolunitrileEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 19 2003Ludvík Bene Abstract Intercalates of vanadyl phosphate with benzonitrile and p -tolunitrile were prepared and characterized by X-ray powder diffraction, TG analysis, IR and Raman spectroscopy. Both intercalates contain one nitrile molecule per formula unit. The intercalates prepared are moisture sensitive and guest molecules are easily replaced by water molecules. The nitrile molecules are anchored to the host layers by an N,V donor-acceptor bond. Local structures and interactions appearing in the intercalates were suggested on the base of quantum chemical calculations. These calculations support the results of the IR and Raman spectroscopy, indicating the formation of a C,N,V bond in the intercalates. The calculated basal spacings (11.32 Å for the benzonitrile and 13.00 Å for the tolunitrile intercalates) are in good agreement with the experimental values (11.22 and 13.19 Å, respectively). (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] 2H -Pyrrole Derivatives from an Aza-Nazarov Reaction Cascade Involving Indole as the Neutral Leaving GroupEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 21 2008Nugzar Ghavtadze Abstract Trifluoromethyl-substituted N -indolinyl-1-aza-1,4-dien-3-ones 4, which are accessible in good yields from indolinylimino esters 6 in a two-step procedure, undergo a novel type of aza-Nazarov cyclization if treated with strong acids to give the hitherto unknown 3-hydroxy-5H -pyrrole derivatives 8a,p. The solvent-free polyphosphoric acid/acyl anhydride system as the acidic reaction medium is especially efficient and requires only short reaction times. According to quantum chemical calculations the key step in the reaction cascade is the cleavage of the N,N bond of the hydrazone fragment of a protonated N -(indolin-1-yl)-1-aza-1,4-dien-3-one intermediate such as 10. This intermediate releases 3H -indole as an unusual, but very efficient neutral leaving group. Several 1-aza-1,4-dien-3-ones 4 and some 3-hydroxy-5H -pyrrole derivatives 8 were characterized by X-ray diffraction.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Design, Synthesis, and Spectral Luminescent Properties of a Novel Polycarbocyanine Series Based on the 2,2-Difluoro-1,3,2-dioxaborine NucleusEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 9 2008Konstantin Zyabrev Abstract The natures of the chromophores in symmetric polymethine dyes derived from 2,2-difluoro-1,3,2-dioxaborine have been investigated. Ab initio quantum chemical calculations demonstrated that the presence of dioxaborine end residues stabilizes the frontier levels of the corresponding polymethine dye and makes electron-density distribution over the oxygen atoms in the chelate ring more even than in the analogous dye structure with boron-free acyclic end groups. A series of novel symmetric polycarbocyanines and a tricarbocyanine series with variously bridged polymethine chromophores have been synthesized from hitherto unknown pyrimidino-annelated dioxaborines. The absorption, fluorescence and 13C NMR spectroscopic data point to the polymethinic type of electron-density distribution in the 2,2-difluoro-1,3,2-dioxaborine polymethine dye molecules. The fundamental options for controlling the spectral properties of these dyes by modification of their polymethine chains have been evaluated. One of the new compounds synthesized is remarkable among the known open-chain polymethine dyes for its record high fluorescence quantum yield. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] N -Acetylation as a Means to Activate Polyfluoroarylamines for Selective ortho -Hydrodefluorination by Zinc in Aqueous Ammonia: A Concise Route to Polyfluorobenzo Azaheterocycles,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 2 2007Sergey S. Laev Abstract N -Acetylation of polyfluoroarylamines is proposed as a meansto remove the amino group blocking effect of their hydrodefluorination by zinc in aqueous ammonia. With pentafluoroacetanilide, the Zn ion specific effect has been demonstrated to be responsible for ortho hydrodefluorination. This regiochemistry is accompanied by the removal of a fluorine atom from the para position, which occurs predominantly in the initial phase of the process in the absence of deliberately added zinc salt. The CuCl2 additive has been found to accelerate the reaction and to propel it to double defluorination. Quantum chemical calculations suggest a diminished electron affinity of pentafluoroaniline, which is responsible for its inertness in relation to the hydrodefluorination reaction. The pentafluoroaniline radical anion, which essentially has a nonplanar structure, is prone to easy fragmentation to give an aminotetrafluorophenyl radical. For pentafluoroacetanilide, CVA experiments and quantum chemical calculations predict that the pentafluorophenyl moiety serves as the electron receptor and that the acetamido group is twisted out of coplanarity with the benzene ring; thus, together with the electron-withdrawing effect of the acetyl group, the amino group blocking effect is suppressed. On this ground, the selective ortho hydrodefluorination of polyfluoroacetanilides is developed as an important protocol for the expeditious and general synthesis of polyfluorobenzo azaheterocycles via readily accessible polyfluoroarylamines from base polyfluoroarenes. Its applicability has been illustrated by preparing quinolines that possess a polyfluorinated benzene moiety by the Skraup synthesis utilizing crude polyfluoroacetanilide hydrodefluorination products as starting materials. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] The 15N-CPMAS spectra of simazine and its metabolites: measurements and quantum chemical calculationsEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 4 2007A. E. Berns Summary DFT calculations are a powerful tool to support NMR studies of xenobiotics such as decomposition studies in soil. They can help interpret spectra of bound residues, for example, by predicting shifts for possible model bonds. The described bound-residue models supported the hypothesis of a free amino side chain already suspected by comparison with the experimental data of the standards. No match was found between the calculated shifts of amide bondings of the amino side chains (free or substituted) and the experimental NMR shifts of a previous study. In the present paper, first-principles quantum chemical calculations were used to support and check the interpretation of the 15N cross polarization-magic angle spinning nuclear magnetic resonance (15N-CPMAS NMR) spectra of simazine and its metabolites. Density functional theory (DFT) calculations were performed using Gaussian 03 and the nuclear magnetic shielding tensors were calculated using the Gauge-Independent Atomic Orbital (GIAO) method and B3LYP/6,311+G(2d,p) model chemistry. Good agreement was reached between the calculated and measured chemical shifts of the core nitrogens and the lactam and lactim forms of the hydroxylated metabolites could be clearly distinguished. The calculated spectra showed that these metabolites exist preferentially in the lactam form, an important fact when considering the possible interactions of such hydroxylated metabolites with the soil matrix. Although the calculated bound-residue models in the present study only partly matched the experimental data, they were nevertheless useful in helping to interpret the experimental NMR results of a previous study. To get a better match between the calculated and the measured shifts of the side-chain nitrogens the calculations need to be further developed, taking into account the influence of neighbouring molecules in the solid state. Altogether, quantum chemical calculations are very helpful in the interpretation of NMR spectra. In the future, they can also be very useful for the prediction of NMR shifts, in particular when it is not possible to measure the metabolites due to a lack of material or in cases where practical experiments cannot be conducted. [source] Computational studies on the reactions of 3-butenyl and 3-butenylperoxy radicalsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 5 2010Akira MiyoshiArticle first published online: 11 MAR 2010 The reactions of 3-butenyl (,CH2CH2CHCH2) radicals,unimolecular decomposition, isomerization, as well as reaction with O2,and the subsequent unimolecular rearrangement reactions of the 3-butenylperoxy radicals have been investigated and are compared to the analogous reactions of butyl (,CH2CH2CH2CH3) and butylperoxy radicals using transition-state theory based on the quantum chemical calculations at the CBS-QB3 level. For alkyl-analogue processes, the reactions of 3-butenyl and 3-butenylperoxy radicals can be well characterized by the decreased and increased bond dissociation energies at the allylic and vinylic sites, respectively. The intramolecular addition reactions of the radical center atoms to the double bonds were found to be important non-alkyl-analogue reactions of 3-butenyl and 3-butenylperoxy radicals. As a consequence, the thermal decomposition of 3-butenyl radicals was found to be slower than that of butyl radicals by one order of magnitude at temperature near 1000 K. Intramolecular addition reactions are suggested to be the predominant unimolecular rearrangement processes of 3-butenylperoxy radicals over the entire temperature range investigated (500,1200 K). The intramolecular addition reactions of the alkenyl peroxy radicals, which have not been included in combustion kinetic models, and their implications for the autoignition of alkenes are discussed. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 273,288, 2010 [source] Comparative study on the nonadditivity of methyl group in lithium bonding and hydrogen bondingINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2009Qingzhong Li Abstract Quantum chemical calculations at the second-order Moeller,Plesset (MP2) level with 6-311++G(d,p) basis set have been performed on the lithium-bonded and hydrogen-bonded systems. The interaction energy, binding distance, bond length, and stretch frequency in these systems have been analyzed to study the nonadditivity of methyl group in the lithium bonding and hydrogen bonding. In the complexes involving with NH3, the introduction of one methyl group into NH3 molecule results in an increase of the strength of lithium bonding and hydrogen bonding. The insertion of two methyl groups into NH3 molecule also leads to an increase of the hydrogen bonding strength but a decrease of the lithium bonding strength relative to that of the first methyl group. The addition of three methyl groups into NH3 molecule causes the strongest hydrogen bonding and the weakest lithium bonding. Although the presence of methyl group has a different influence on the lithium bonding and hydrogen bonding, a negative nonadditivity of methyl group is found in both interactions. The effect of methyl group on the lithium bonding and hydrogen bonding has also been investigated with the natural bond orbital and atoms in molecule analyses. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Periodicity in proton conduction along a H-bonded chain.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2008Application to biomolecules Abstract Molecular complexes are constructed to simulate proton transfer channels of the influenza A virus and of the active site of carbonic anhydrase. These complexes consist of proton donor and acceptor groups connected by a chain of water molecules. Quantum chemical calculations on the methylimidazole(H+)H2OCH3COO, model of the M2 virus channel indicate free translational motion of the water molecule between donor and acceptor, as well as concerted transfer of both H-bond protons. The proton transfer barrier does not depend on the position of the bridged water molecule and varies linearly with the difference of electrostatic potentials between the donor and acceptor. When the water chain is elongated, and with various donor and acceptor models, periodicity appears in the H-bond lengths and the progression of proton transfer in each link. This "wave" is shown to propagate along the chain, as it is driven by the displacement of a single proton. One can thereby estimate the velocity of the proton wave and proton conduction time. Computations are performed to examine the influence of immersing the system within a polarizable medium. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Geometries, vibrational frequencies, and electron affinities of X2Cl (X=C,Si,Ge) clustersINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2007Feng-You Hao Abstract Ab initio quantum chemical calculations have been performed on X2Cl, and X2Cl (X = C, Si, Ge) clusters. The geometrical structures, vibrational frequencies, electronic properties and dissociation energies are investigated at the Hartree,Fock (HF), Møller,Plesset second- and fourth-order (MP2, MP4), CCSD(T) level with the 6-311+G(d) basis set. The X2Cl (X = C, Si, Ge) and X2Cl, (X = Si, Ge) take a bent shape obtained at the ground state, while C2Cl, has a linear structure. The impact on internal electron transfer between the X2Cl and the corresponding anional clusters is studied. The three different types of electron affinities (EAs) at the CCSD(T) are reported. The most reliable adiabatic electronic affinities, obtained at the CCSD(T)/cc-pvqz level of theory, are predicted to be 3.30, 2.62, and 1.98 eV for C2Cl, Si2Cl, and Ge2Cl, respectively. The calculated EAs of C2Cl and Ge2Cl are in good agreement with theoretical results reported. The correlation effects and basis sets effects on the geometrical structures and dissociation energies are discussed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Structure of charge-transfer reaction complexes in anionic polymerization of isoprene: Quantum chemical calculationsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2005K. K. Kalninsh Abstract A new mechanism of isoprene anionic polymerization is proposed. Its central moment is thermal electronic excitation of a living polyisoprene,isoprene complex into the quasi-degenerate electronically excited state (S · T)1, which is of the charge (electron) transfer character. It is asserted that the probability of chemical bond formation is determined by the free valence index on carbon atoms and by the geometry of reacting complex in the excited state (S · T)1. Semi-empirical AM1 and ab initio 6-31G* quantum chemical calculations revealed low energies of triplet excited levels (<10 kcal/mole). Comparison of isoprene polymerization on free anions and on solvated ion pairs shows that both types of active centers produce vinyl 1,2 (4,3)-units. Free anions generate predominantly 1,2-units, whereas solvated ion pairs tend to form units with the 4,3-structure. Analysis of energies of excited isoprenyl lithium + isoprene complexes shows that the formation of 1,4 (4,1)- cis -polyisoprene in an inert media is most preferable. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Chemical bonding in ternary magnesium hydridesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2003Emilio Orgaz Abstract The electronic structure of various alkali and alkaline,earth magnesium-based hydrides was investigated in detail. These types of crystalline compounds show MgH4 or MgH6 units ordered within a light-metal framework. We investigated the nature of the chemical bonding in these units by means of quantum chemical calculations of several related clusters. The properties of the charge density of the clusters, within the framework of the theory of atoms in molecules, was analyzed. A further set of computations of the band structure of the solid hydrides was conducted using a state-of the-art density functional-based method and the mechanism of stabilization of the MgH units is discussed. It was found that the properties obtained at the molecular level correlate well with those of the solid crystals, indicating the molecular nature of the extended systems in which the units MgHx, x = 4, 6, are stabilized by means of MgH closed-shell interactions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 150,164, 2003 [source] Development of the force field parameters for phosphoimidazole and phosphohistidineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2004Yuri A. Kosinsky Abstract Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule,a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1313,1321, 2004 [source] Evaluation of the reduction of imidazophenazine dye derivatives under fast-atom-bombardment mass-spectrometric conditions,JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2006Marina V. Kosevich Abstract Satellite [M + 2]+, and [M + 3]+ peaks accompanying the common peak of the protonated molecule [M + H]+ that are known to indicate the occurrence of a reduction process were observed in the fast atom bombardment (FAB) mass spectra of imidazophenazine dye derivatives in glycerol matrix. The distribution of the abundances in the [M + nH]+ peak group varied noticeably for different derivatives. This indicated different levels of the reduction depending on the different structure variations of the studied molecules. In the search for correlations between the mass spectral pattern and the structural features of the dyes, ab initio HF/6-31++G** quantum chemical calculations were performed. They revealed that the abundances of the [M + 2]+, and [M + 3]+ ions show growth proportional to the decrease of the energy of the lowest unoccupied molecular orbital, i.e. proportional to the increase of the electron affinity of the dye molecule. A method for rapid screening of reductive properties of sets of dye derivatives on the basis of the FAB mass spectral data is discussed. Copyright © 2005 John Wiley & Sons, Ltd. [source] Gas-phase tautomers of protonated 1-methylcytosine.JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 11 2005Preparation, dissociation mechanisms, energetics Abstract Tautomers of 1-methylcytosine that are protonated at N-3 (1+) and C-5 (2+) have been specifically synthesized in the gas phase and characterized by tandem mass spectrometry and quantum chemical calculations. Ion 1+ is the most stable tautomer in aqueous and methanol solution and is likely to be formed by electrospray ionization of 1-methylcytosine and transferred in the gas phase. Gas-phase protonation of 1-methylcytosine produces a mixture of 1+ and the O-2-protonated tautomer (3+), which are nearly isoenergetic. Dissociative ionization of 6-ethyl-5,6-dihydro-1-methylcytosine selectively forms isomer 2+. Upon collisional activation, ions 1+ and 3+ dissociate by loss of ammonia and [C,H,N,O], whose mechanisms have been established by deuterium labeling and ab initio calculations. The main dissociations of 2+ following collisional activation are losses of CH2CNH and HNCO. The mechanisms of these dissociations have been elucidated by deuterium labeling and theoretical calculations. Copyright © 2005 John Wiley & Sons, Ltd. [source] Computational study of the cooperative effects of nitrogen and silicon atoms on the singlet,triplet energy spacing in 1,3-diradicals and the reactivity of their singlet statesJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 4 2010Takeshi Nakamura Abstract Quantum chemical calculations were performed to investigate the cooperative effect of the nitrogen and silicon atoms on the singlet,triplet energy spacing and the reactivity of the singlet state in 1,2-diazacyclopentane-3,5-diyls and 1,2-diaza-4-silacyclopentane-3,5-diyls. The largest singlet,triplet energy gap (,=,,36.1,kcal/mol) found so far in localized 1,3-diradicals was in the C2v symmetry of 4,4-difluoro-1,2-diaza-4-silacyclopentane-3,5-diyl at the UB3LYP/6-31G(d) level of theory. The cooperative effect was also found in the energy differences of singlet diradicals with the corresponding ring-closing compounds, bicyclo[2.1.0]pentane derivatives. The singlet state of the 1,2-diaza-4-silacyclopentane-3,5-diyls was calculated to be energetically more stable than the ring-closing compound. The notable finding on the stability of the singlet diradicals may be attributed to the resonance structures that specifically stabilize the singlet state of diradicals. The computational studies predict that the singlet 1,2-diaza-4-silacyclopentane-3,5-diyl is a persistent molecule under conditions without intermolecular-trapping reagents. Copyright © 2010 John Wiley & Sons, Ltd. [source] Comparative DFT study on the role of conformers in the ruthenium alkylidene-catalyzed ROMP of norborn-2-eneJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 11 2008Sergej Naumov Abstract Comparative quantum chemical calculations on the reaction pathways for the formation of ruthena(IV)cyclobutanes from both 1st - and 2nd -generation Grubbs catalysts of the general formula RuX2(L)(L,)(CH2) (L,=,PCy3 or 1,3-dimesityl-4,5-dihydroimidazolin-2-ylidene, L,,=,PCy3) and norborn-2-ene (NBE) were carried out on the B3LYP/LACVP** level in dependence on the ligand X,=,I, Br, Cl, and F. The mechanism proposed by Straub for the formation of (one) active and (three) inactive NBE,Ru,carbene complexes for non-cyclic alkenes was applied to the cyclic alkene NBE. In RuX2(PCy3)2(CH2), the inactive NBE,Ru,carbene complex is energetically more stable than the active one; however, in RuX2(IMesH2)(PCy3)(CH2), the active NBE,Ru,carbene complex is more stable than the inactive one. In due consequence, the possible rate limiting barrier for the conversion of the NBE,Ru,carbene complex into the corresponding metallocyclobutane (MCB) is systematically larger in the case of 1st -generation Grubbs catalysts than of 2nd -generation Grubbs catalysts due to an additional re-arrangement for the formation of an active , -complex from the more stable (inactive) conformer. This correlates with the observed reactivity of both types of initiators. There is a strong influence of the ligands L and X on the conformational properties and relative stabilities of the 14-electron intermediates, which has a direct effect on the distribution of the inactive and active conformations of the corresponding Ru,carbene,NBE complexes. A direct correlation between the conformational properties of the 14-electron intermediates and the relative stabilities of the active Ru,carbene,NBE complexes was observed. Copyright © 2008 John Wiley & Sons, Ltd. [source] | ||||||||||||||||||||||||||||||||||