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Quantum-chemical Calculations (quantum-chemical + calculation)
Selected AbstractsGas-Phase Electron-Diffraction Investigation and Quantum-Chemical Calculations of the Structure of 1,5-Dimethylsemibullvalene-2,4,6,8-tetracarboxylic DianhydrideHELVETICA CHIMICA ACTA, Issue 5 2003Svein Samdal The bridged homotropilidines have been of interest for decades because their molecules offer the potential for homoaromaticity. Although many of these have been shown not to be homoaromatic, the energy differences of the delocalized (homoaromatic) forms and the localized (nonhomoaromatic) ones, and the barriers to the interconversion of the localized forms via a Cope rearrangement, have been found to vary greatly. The title compound is a strong candidate for homoaromaticity, and, since the structures of the possible localized and delocalized forms could differ significantly, we have carried out an electron-diffraction investigation of it augmented by quantum-mechanical calculations with different basis sets at several levels of theory. Three models were explored: one representing a localized form of Cs symmetry, one a delocalized form of C2v symmetry, and one a 2,:,1 mixture of the localized/delocalized forms. Although none of the models could be ruled out, the experimental evidence slightly favors the Cs form. These results are consistent with those from the DFT B3PW91 calculations with basis sets ranging from 6-31G(d) to cc-pVTZ, which, surprisingly, predict essentially equal thermally corrected free energies for each. The results are discussed. [source] ChemInform Abstract: Characterization of cis- and trans-HSSOH via Rotational Spectroscopy and Quantum-Chemical Calculations.CHEMINFORM, Issue 22 2009Monika Koerber 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] Quasilinear Molecule par Excellence, SrCl2: Structure from High-Temperature Gas-Phase Electron Diffraction and Quantum-Chemical Calculations,Computed Structures of SrCl2×Argon Complexes.CHEMINFORM, Issue 3 2007Zoltan Varga 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] Unexpected Structural Diversity in Alkali Metal Azide-Crown Ether Complexes: Syntheses, X-ray Structures, and Quantum-Chemical CalculationsCHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2006Michael D. Brown Abstract A series of alkali metal azide-crown ether complexes, [Li([12]crown-4)(N3)], [Na([15]crown-5)(N3)], [Na([15]crown-5)(H2O)2]N3, [K([18]crown-6)(N3)(H2O)], [Rb([18]crown-6)(N3)(H2O)], [Cs([18]crown-6)(N3)]2, and [Cs([18]crown-6)(N3)(H2O)(MeOH)], has been synthesised. In most cases, single crystals were obtained, which allowed X-ray crystal structures to be derived. The structures obtained have been compared with molecular structures computed by density functional theory (DFT) calculations. This has allowed the effects of the crystal lattice on the structures to be investigated. Also, a study of the MNterminal metal,azide bond length and charge densities on the metal (M) and terminal nitrogen centre (Nterminal) in these complexes has allowed the nature of the metal,azide bond to be probed in each case. The bonding in these complexes is believed to be predominantly ionic or ion-dipole in character, with the differences in geometries reflecting the balance between maximising the coordination number of the metal centre and minimising ligand-ligand repulsions. The structures of the crown ether complexes determined in this work show the subtle interplay of such factors. The significant role of hydrogen bonding is also demonstrated, most clearly in the structures of the K and Rb dimers, but also in the chain structure of the hydrated Cs complex. [source] Structure-hepatoprotective activity relationship study of sesquiterpene lactones: A QSAR analysisINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2009Yuliya Paukku Abstract This study has been carried out using quantitative structure-activity relationship analysis (QSAR) for 22 sesquiterpene lactones to correlate and predict their hepatoprotective activity. Sesquiterpenoids, the largest class of terpenoids, are a widespread group of substances occurring in various plant organisms. QSAR analysis was carried out using methods such as genetic algorithm for variables selection among generated and calculated descriptors and multiple linear regression analysis. Quantum-chemical calculations have been performed by density functional theory at B3LYP/6-311G(d, p) level for evaluation of electronic properties using reference geometries optimized by semi-empirical AM1 approach. Three models describing hepatoprotective activity values for series of sesquiterpene lactones are proposed. The obtained models are useful for description of sesquiterpene lactones hepatoprotective activity and can be used to estimate the hepatoprotective activity of new substituted sesquiterpene lactones. The models obtained in our study show not only statistical significance, but also good predictive ability. The estimated predictive ability (r) of these models lies within 0.942,0.969. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Possible Pathways of CVD Processes Leading to III,V Semiconductors via a Two-Dimensional Growth,CHEMPHYSCHEM, Issue 4 2005Hans-Jörg Himmel Priv.-Doz. Abstract Quantum-chemical calculations were carried out to shed more light upon possible first intermediates formed during chemical vapour deposition (CVD) processes leading to III,V semiconductors. Information about possible structures of intermediates and about thermodynamic properties in dependence of the temperature were collected. Because some of the systems calculated herein contain a substantial number of atoms (up to 144), it is limited to intermediates on the way to solid AlN. According to our suggestion, the first intermediates are species with the overall formula AlNH2, Al2N2H4, Al3N3H6, Al5N5H8, Al7N7H, and Al9N9H, Al12N12H12. In further calculations the growth of a second layer, on top of the first layer, which is modelled by the Al12N12H12 cluster, is simulated. The Al12N12H12 "surface" offers two places for the attachment of an Al3N3H6 ring. At temperatures of 1000 K, the ,G value for this attachment is only slightly negative, which suggests that the molecules can move relatively freely on the surface. This might be of importance for a defect-free growth process. Up to four layers are built on top of the first Al12N12H12 layer leading to Al24N24H24 (two layers), Al36N36H36 (three layers) and Al48N48H48 (four layers). The structures are compared with that of solid AlN in its most stable Wurzit-type structure. [source] Calculated on 1H and 13C NMR chemical shifts of 2,4-difluorobenzaldehyde isonicotinoylhydrazone and 2,3-dichlorobenzaldehyde isonicotinoylhydrazone with GIAO, IGAIM, and CSGT modelsCONCEPTS IN MAGNETIC RESONANCE, Issue 5 2009N. Günay Abstract The 1H and 13C NMR chemical shifts of the 2,4-difluorobenzaldehyde isonicotinoylhydrazone (I) and 2,3-dichlorobenzaldehyde isonicotinoylhydrazone (II) were determined with the help of full spectral analysis. The geometry and electronic structure of the title compounds were investigated at both the ab initio Hartree-Fock and the B3LYP levels with 6-31+G(d,p) basis set. The NMR data were calculated by means of the GIAO, CSGT, and IGAIM methods. All quantum-chemical calculations, including those of NMR data, were performed by ab initio level HF and DFT methods. Excellent agreement between the theoretical and experimental results was found for the HF level 1H and 13C chemical shifts. The parameters of molecular geometry and 1H and 13C chemical shift values of the title compounds (I, II) in the ground state have been calculated and and compared with corresponding experimental result. © 2009 Wiley Periodicals, Inc. Concepts Magn Reson Part A 34A: 297,304, 2009. [source] Aliphatic Thiocarbonyl Ylides and Thiobenzophenone: Experimental Study of Regiochemistry and Methylene Transfer in CycloadditionsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 8 2005Rolf Huisgen Abstract 1,3-Dipolar cycloadditions of aliphatic or alicyclic thiocarbonyl ylides 3A-D , sterically hindered at least at one terminus , with thiobenzophenone produce both regioisomeric 1,3-dithiolanes 4 and 5. According to quantum-chemical calculations (preceding paper), a concerted cycloaddition furnishing 2,4-substituted dithiolanes 4 competes with the formation of an intermediate C,C -biradical 9 which cyclizes to the more crowded 4,5-substituted dithiolanes 5. When steric hindrance of 3 increases, the cycloaddition is superseded by ,methylene transfer', i.e., the transfer of the less hindered terminus of 3E-J to the S-atom of thiobenzophenone. The thiobenzophenone S -alkylide 11, thus formed, rapidly reacts with a second molecule ofthiobenzophenone to generate the 4,4,5,5-tetraphenyl-1,3-dithiolane 12 via the highly stabilized C,C -biradical 10. Methylene transfer occurs when the cyclization of the mixed C,C -biradical 9 requires a higher activation barrier than its dissociation to aliphatic thioketone + 11; the threshold is surprisingly well reproduced by calculations. The structural assignment of sixteen 1,3-dithiolanes is based on their formation from corresponding reactant pairs as well as on 1H and 13C chemical shifts. X-ray diffraction analyses of three spiro-1,3-dithiolanes reveal the van der Waals strain in non-bonded interactions, folding angles, shearing forces, and bond lengths. Comparison of the mass spectra of many 1,3-dithiolanes allows the reconstruction of major fragmentation pathways. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Modeling Polymer Dielectric/Pentacene Interfaces: On the Role of Electrostatic Energy Disorder on Charge Carrier MobilityADVANCED FUNCTIONAL MATERIALS, Issue 20 2009Nicolas G. Martinelli Abstract Force-field and quantum-chemical calculations are combined to model the packing of pentacene molecules at the atomic level on two polymer dielectric layers (poly(methyl methacrylate) (PMMA) versus polystyrene (PS)) widely used in field-effect transistors and to assess the impact of electrostatic interactions at the interface on the charge mobility values in the pentacene layers. The results show unambiguously that the electrostatic interactions introduce a significant energetic disorder in the pentacene layer in contact with the polymer chains; a drop in the hole mobility by a factor of 5 is predicted with PS chains while a factor of 60 is obtained for PMMA due to the presence of polar carbonyl groups. [source] Quantum-Chemical Characterization of the Origin of Dipole Formation at Molecular Organic/Organic InterfacesADVANCED FUNCTIONAL MATERIALS, Issue 4 2009Igor Avilov Abstract Recent experiments have reported a vacuum level shift at the interface between organic materials due to the formation of an interface dipole layer. On the basis of quantum-chemical calculations, this paper sheds light on the factors contributing to the formation of an interface dipole between an electron donor and an electron acceptor, considering as model system a complex made of tetrathiafulvalene (TTF) as a donor and tetracyanoquinodimethane (TCNQ) as an acceptor. The results indicate that the interface dipole is governed both by charge-transfer and polarization effects and allow for disentangling of their respective contributions. Two regimes of charge transfer can be distinguished depending on the strength of the electronic coupling: a fractional charge transfer occurs in the strong coupling regime while only integer charges are transferred when the coupling is weak. The polarization contribution can be significant, even in the presence of a pronounced charge transfer between the donor and acceptor molecules. The values of ionization potential and electron affinity of the donor and acceptor molecules may experience shifts as large as several tenths of an eV at the interface with respect to the isolated compounds. [source] Oligophenylenevinylenes in Spatially Confined Nanochannels: Monitoring Intermolecular Interactions by UV/Vis and Raman Spectroscopy,ADVANCED FUNCTIONAL MATERIALS, Issue 6 2008Mariya Aloshyna Abstract Perhydrotriphenylene-based channel-forming inclusion compounds (ICs) and thin films made of polyphenylenevinylene (PPV)-type oligomers with terminal alkoxy groups are investigated and compared in a combined experimental and theoretical approach. Interchromophore interactions and host-guest interactions are elucidated by UV/Vis and Raman spectroscopy. The impact of the local environment of the chromophore on the optical and photophysical properties is discussed in light of quantum-chemical calculations. In stark contrast to thin films where preferential side-by-side orientation leads to quenching of photoluminescence (PL) via non-emissive traps, the ICs are found to be attractive materials for opto-electronic applications: they offer high chromophore concentrations, but at the same time behave as quasi-isolated entities of tightly packed, well-oriented objects with high PL quantum yields and the possibility of color tuning. [source] NMR Conformational Analysis and Theoretical Calculations for 2-Aryl- 1,3-dihydroxy-4,4,5,5-tetramethylimidazolidinesHELVETICA CHIMICA ACTA, Issue 2 2004Antônio Conformational studies of 1,3-dihydroxy-4,4,5,5-tetramethyl-2-(pyridin-1-yl)imidazolidine (1a) and 1,3-dihydroxy-4,4,5,5-tetramethyl-2-(pyridin-3-yl)imidazolidine (1b), carried out by using 1D 1H- and 13C-NMR and 2D HMQC, HMBC, and NOESY experiments and with the aid of theoretical calculations, indicate that the OH groups are trans to the pyridinyl substituent. Because the two 1H-NMR signals of the Me groups are distinguishable and do not change between 290 and 380,K, it is proposed that 1a and 1b have each only one conformation in this temperature range. This behavior was not found with 1,3-dihydroxy-4,4,5,5-tetramethyl-2-(pyridin-2-yl)imidazolidine (1c) because its Me 1H-NMR signals cross over at 300,K. Hence, more than one conformation must be present, beyond those produced by simple inversions. Theoretical calculations including temperature and solvent effects were performed to provide further information on the conformational analysis and to help to assign the NMR data. The combination of NMR measurements and quantum-chemical calculations is shown to be a very promising strategy for conformational analysis studies in solution. [source] A molecular mechanics force field for biologically important sterolsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005Zoe Cournia Abstract A parameterization has been performed of the biologically important sterols cholesterol, ergosterol, and lanosterol for the CHARMM27 all-atom molecular mechanics force field. An automated parameterization method was used that involves fitting the potential to vibrational frequencies and eigenvectors derived from quantum-chemical calculations. The partial charges were derived by fitting point charges to quantum-chemically calculated electrostatic potentials. To model the dynamics of the hydroxyl groups of the sterols correctly, the parameter set was refined to reproduce the energy barrier for the rotation of the hydroxyl group around the carbon connected to the hydroxyl of each sterol. The frequency-matching plots show good agreement between the CHARMM and quantum chemical normal modes. The parameters are tested in a molecular dynamics simulation of the cholesterol crystal structure. The experimental geometry and cell dimensions are well reproduced. The force field derived here is also useful for simulating other sterols such as the phytosterols sigmasterol, and campesterol, and a variety of steroids. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1383,1399, 2005 [source] Exploring the Active-Site of a Rationally Redesigned Lipase for Catalysis of Michael-Type AdditionsCHEMBIOCHEM, Issue 2 2005Peter Carlqvist Abstract Michael-type additions of various thiols and ,,,-unsaturated carbonyl compounds were performed in organic solvent catalyzed by wild-type and a rationally redesigned mutant of Candida antarctica lipase B. The mutant lacks the nucleophilic serine 105 in the active-site; this results in a changed catalytic mechanism of the enzyme. The possibility of utilizing this mutant for Michael-type additions was initially explored by quantum-chemical calculations on the reaction between acrolein and methanethiol in a model system. The model system was constructed on the basis of docking and molecular-dynamics simulations and was designed to simulate the catalytic properties of the active site. The catalytic system was explored experimentally with a range of different substrates. The kcatvalues were found to be in the range of 10,3to 4 min,1, similar to the values obtained with aldolase antibodies. The enzyme proficiency was 107. Furthermore, the Michael-type reactions followed saturation kinetics and were confirmed to take place in the enzyme active site. [source] Neutral and Oxidized Triisopropylsilyl End-Capped Oligothienoacenes: A Combined Electrochemical, Spectroscopic, and Theoretical StudyCHEMISTRY - A EUROPEAN JOURNAL, Issue 18 2010Juan Aragó Abstract This work presents an analysis of the structural, electrochemical, and optical properties of a family of triisopropylsilyl end-capped oligothienoacenes (TIPS- Tn -TIPS, n=4,8) by combining cyclic voltammetry, spectroscopic techniques, and quantum-chemical calculations. TIPS- Tn -TIPS compounds form stable radical cations, and dications are only obtained for the longest oligomers (n=7 and 8). Oxidation leads to the quinoidization of the conjugated backbone, from which electrons are mainly extracted. The absorption and fluorescence spectra show partially resolved vibronic structures even at room temperature, due to the rigid molecular geometry. Two well-resolved vibronic progressions are observed at low temperatures due to the vibronic coupling, with normal modes showing wavenumbers of ,1525 and ,480,cm,1. Optical absorption bands display remarkable bathochromic dispersion with the oligomer length, indicative of the extent of , conjugation. The optical properties of the oxidized compounds are characterized by in situ UV/Vis/NIR spectroelectrochemistry. The radical cation species show two intense absorption bands emerging at energies lower than in the neutral compounds. The formation of the dication is only detected for the heptamer and the octamer, and shows a new band at intermediate energies. Optical data are interpreted with the help of density functional theory calculations performed at the B3LYP/6-31G** level, both for the neutral and the oxidized compounds. [source] Asymmetric Allylation of Methyl Ketones by Using Chiral Phenyl CarbinolsCHEMISTRY - A EUROPEAN JOURNAL, Issue 25 2009Abstract To methyl or to alkyl? High induced facial selectivities and excellent yields are obtained in the allylation of aliphatic methyl ketones by using a structurally simple phenylbenzyl auxiliary to give the corresponding homoallylic ethers (see scheme). The transferred auxiliary has a very good protecting quality and can easily be removed. Novel chiral auxiliaries for the stereoselective allylation of aliphatic methyl ketones with allyltrimethylsilane and their use in the synthesis of homoallylic ethers are described. In a multicomponent domino process catalyzed by trifluoromethanesulfonic acid, the allyl moiety and the auxiliary are transferred onto the substrate to yield tertiary homoallylic ethers. The most useful auxiliary for a general application turned out to be the trimethylsilyl ether of phenyl benzyl carbinol with an induced diastereoselectivity of 90:10 using ethyl methyl ketone and 94:6 using isopropyl methyl ketone as substrates. The transferred substituted benzyl moiety has good protecting properties in subsequent transformations and can easily be removed under reductive conditions to provide the corresponding homoallylic alcohol. The origin of the high selectivity could be elucidated by identifying the relevant transition states using quantum-chemical calculations. An excellent agreement between calculated and experimentally observed selectivities was obtained assuming an oxocarbenium ion as intermediate. [source] Self-Assembly of an Alkylated Guanosine Derivative into Ordered Supramolecular Nanoribbons in Solution and on Solid SurfacesCHEMISTRY - A EUROPEAN JOURNAL, Issue 13 2007Stefano Lena Dr. Abstract We report on the synthesis and self-assembly of a guanosine derivative bearing an alkyloxy side group under different environmental conditions. This derivative was found to spontaneously form ordered supramolecular nanoribbons in which the individual nucleobases are interacting through H-bonds. In toluene and chloroform solutions the formation of gel-like liquid-crystalline phases was observed. Sub-molecularly resolved scanning tunneling microscopic imaging of monolayers physisorbed at the graphite,solution interface revealed highly ordered two-dimensional networks. The recorded intramolecular contrast can be ascribed to the electronic properties of the different moieties composing the molecule, as proven by quantum-chemical calculations. This self-assembly behavior is in excellent agreement with that of 5,- O -acylated guanosines, which are also characterized by a self-assembled motif of guanosines that resembles parallel ribbons. Therefore, for guanosine derivatives (without sterically demanding groups on the guanine base) the formation of supramolecular nanoribbons in solution, in the solid state, and on flat surfaces is universal. This result is truly important in view of the electronic properties of these supramolecular anisotropic architectures and thus for potential applications in the fields of nano- and opto-electronics. [source] A New Class of Binuclear Gallium Hydrides: Synthesis and Properties of [{GaCl(hpp)H}2] (hpp=1,3,4,6,7,8-Hexahydro-2H -pyrimido[1,2- a]pyrimidate)CHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2007George Robinson Abstract Herein we report on the synthesis and characterization of the first representative of a new class of gallium hydrides, namely [{GaCl(hpp)H}2] (hpp=1,3,4,6,7,8-hexahydro-2H -pyrimido[1,2- a]pyrimidate). Our X-ray diffraction data suggest the presence of weak HH contacts between adjacent [{GaCl(hpp)H}2] molecules in the crystal. With the aid of quantum-chemical calculations, the pathway of its formation starting with the adduct H2ClGa,NMe3 and the pyrimidine hppH were analyzed. [{GaCl(hpp)H}2] slowly decomposes at 25,°C, a process which presumably leads under H2 elimination to [{GaCl(hpp)}2]. Although we were not yet able to characterize [{GaCl(hpp)}2] experimentally, DFT calculations provide information about its likely structure. According to these calculations, the molecule features a GaGa single bond. [source] Interaction Energies for the Purine Inhibitor Roscovitine with Cyclin-Dependent Kinase 2: Correlated Ab Initio Quantum-Chemical, DFT and Empirical CalculationsCHEMISTRY - A EUROPEAN JOURNAL, Issue 16 2006Petr Dobe Abstract The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein,inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution. [source] Fluorophores as Optical Sensors for Local Forces,CHEMPHYSCHEM, Issue 12 2009Stefan Marawske Abstract The main aim of this study is to investigate correlations between the impact of an external mechanical force on the molecular framework of fluorophores and the resultant changes in their fluorescence properties. Taking into account previous theoretical studies, we designed a suitable custom-tailored oligoparaphenylenevinylene derivative (OPV5) with a twisted molecular backbone. Thin foils made of PVC doped with 100 nM OPV were prepared. By applying uniaxial force, the foils were stretched and three major optical effects were observed simultaneously. First, the fluorescence anisotropy increased, which indicates a reorientation of the fluorophores within the matrix. Second, the fluorescence lifetime decreased by approximately 2.5,% (25 ps). Finally, we observed an increase in the emission energy of about 0.2,% (corresponding to a blue-shift of 1.2 nm). In addition, analogous measurements with Rhodamine 123 as an inert reference dye showed only minor effects, which can be attributed to matrix effects due to refractive index changes. To relate the observed spectroscopic changes to the underlying changes in molecular properties, quantum-chemical calculations were also performed. Semiempirical methods had to be used because of the size of the OPV5 chromophore. Two conformers of OPV5 (C2 and Cisymmetry) were considered and both gave very similar results. Both the observed blue-shift of fluorescence and the reduced lifetime of OPV5 under tensile stress are consistent with the results of the semiempirical calculations. Our study proves the feasibility of fluorescence-based local force probes for polymers under tension. Improved optical sensors of this type should in principle be able to monitor local mechanical stress in transparent samples down to the single-molecule level, which harbors promising applications in polymer science and nanotechnology. [source] | ||||||||||||||||||||||