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Molecular Geometry (molecular + geometry)
Selected AbstractsDirect Spectroscopic Evidence that the Photochemical Outcome of Flutamide in a Protein Environment is Tuned by Modification of the Molecular Geometry: A Comparison with the Photobehavior in Cyclodextrin and VesiclesHELVETICA CHIMICA ACTA, Issue 2 2003Salvatore Sortino The photoreactivity of the phototoxic anticancer drug flutamide (FM) in the presence of bovine serum albumin (BSA) has been investigated. The presence of BSA induces a remarkable modification of the photochemical outcome of the drug with respect to that observed in aqueous solution. Induced circular dichroism (ICD) measurements combined with theoretical calculations provide strong evidence that the new photochemical scenario is tuned by changes of the molecular geometry of FM when incorporated in the protein microenvironment. This behavior presents close analogies to that found in the presence of either cyclodextrin or phospholipid vesicles, chosen as models for biological systems, and delineates a quite general photochemical picture that can be useful for a more appropriate understanding of the adverse phototoxic effects induced by this drug. [source] ChemInform Abstract: Millimeter-Wave Spectroscopy, High Resolution Infrared Spectrum, ab initio Calculations, and Molecular Geometry of FPO.CHEMINFORM, Issue 52 2001H. Beckers 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] Crystal structures and spectroscopic characterization of chiral and racemic 4-phenyl-1,3-oxazolidin-2-oneCRYSTAL RESEARCH AND TECHNOLOGY, Issue 4 2004S. Kitoh Abstract Crystal structures of (R)- and (rac)-4-phenyl-1,3-oxazolidin-2-one (4-POO) have been determined by X-ray diffraction and characterized by the solid state 13C NMR and IR spectra. Molecular geometries and intermolecular interactions in (R)- and (rac)-4-POO crystals are very similar to each other; 4-POO molecules are linked via the N-H,O intermolecular hydrogen bonds to form the chained structure. Chemical shifts of the solid state 13C NMR spectra are very similar to each other, whereas the 1H spin-lattice relaxation times (T1H) value for (R)-4-POO is five times as large as that for (rac)-4-POO, reflecting the more restricted mobility of the (R)-4-POO chain. Although both crystals contain an unique molecule in the asymmetric unit, a doublet feature is observed for the C=O stretching mode in the IR spectra of (R)- and (rac)-4-POO crystals. The frequency gap of the C=O bands are correlated with the strength of the dipole-dipole interactions between the neighboring C=O groups. © 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim [source] Quantum chemical studies on molecular structural conformations and hydrated forms of salicylamide and O-hydroxybenzoyl cyanideINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2005K. Anandan Abstract Ab initio and density functional theory (DFT) methods have been employed to study the molecular structural conformations and hydrated forms of both salicylamide (SAM) and O-hydroxybenzoyl cyanide (OHBC). Molecular geometries and energetics have been obtained in the gaseous phase by employing the Møller,Plesset type 2 MP2/6-311G(2d,2p) and B3LYP/6-311G(2d,2p) levels of theory. The presence of an electron-releasing group (SAM) leads to an increase in the energy of the molecular system, while the presence of an electron-withdrawing group (OHBC) drastically decreases the energy. Chemical reactivity parameters (, and ,) have been calculated using the energy values of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) obtained at the Hartree,Fock (HF)/6-311G(2d,2p) level of theory for all the conformers and the principle of maximum hardness (MHP) has been tested. The condensed Fukui functions have been calculated using the atomic charges obtained through the natural bond orbital (NBO) analysis scheme for all the optimized structures at the B3LYP/6-311G(2d,2p) level of theory, and the most reactive sites of the molecules have been identified. Nuclear magnetic resonance (NMR) studies have been carried out at the B3LYP/6-311G(2d,2p) level of theory for all the conformers in the gaseous phase on the basis of the method of Cheeseman and coworkers. The calculated chemical shift values have been used to discuss the delocalization activity of the electron clouds. The dimeric structures of the most stable conformers of both SAM and OHBC in the gaseous phase have been optimized at the B3LYP/6-311G(2d,2p) level of theory, and the interaction energies have been calculated. The most stable conformers of both compounds bear an intramolecular hydrogen bond, which gives rise to the formation of a pseudo-aromatic ring. These conformers have been allowed to interact with the water molecule. Special emphasis has been given to analysis of the intermolecular hydrogen bonds of the hydrated conformers. Self-consistent reaction field (SCRF) theory has been employed to optimize all the conformers in the aqueous phase (, = 78.39) at the B3LYP/6-311G(2d,2p) level of theory, and the solvent effect has been studied. Vibrational frequency analysis has been performed for all the optimized structures at MP2/6-311G(2d,2p) level of theory, and the stationary points corresponding to local minima without imaginary frequencies have been obtained for all the molecular structures. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] An ab initio theoretical study of electronic structure and properties of 2,-deoxyguanosine in gas phase and aqueous mediaJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2002S. K. Mishra Abstract Molecular geometries of two structural forms of 2,-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2,-endo and C3,-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2,-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2,-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water,air interface. Though the normal Watson,Crick-type base pairing would not be possible with the keto-N7R form of 2,-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti -conformation of 2,-deoxyguanosine including the dihedral angle ,CN agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2,-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H+ and OH, fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH, group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2,-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 530,540, 2002; DOI 10.1002/jcc.10046 [source] Relationship between substituent effect and aromaticity , Part III: naphthalene as a transmitting moiety for substituent effectJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 5 2007Tadeusz M. Krygowski Abstract Molecular geometry of 10 isomeric nitronaphtholate ions (excluding peri - and ortho -type substituted systems), 1- and 2-naphtholate ions, 1- and 2-nitronaphthalene, meta - and para -nitrophenolate, phenolate, and nitrobenzene were optimized at B3LYP/6-311G** level of approximation. Substituent effect stabilization energy (SESE), geometry-based aromaticity index HOMA, magnetism-based indices NICS, NICS(1), NICS(1)zz, and parameters characterizing Bond Critical Points (BCP) (,, ,2,, ellipticity, ion/cov) of the Bader AIM theory were used to characterize transmitting properties for substituent effect through the naphthalene moiety. It results from our study that the studied systems could be clearly divided into two groups, (i) a para -type group, where the intramolecular charge transfer between the , -electron donating and , -electron accepting substituents can be described by canonical forms with charge separation (as in the case of para -nitrophenolate) and (ii) a meta -type group, where this transfer requires using canonical forms with double charge separation (as in the case of meta -nitrophenolate). Copyright © 2007 John Wiley & Sons, Ltd. [source] The invariom model and its application: refinement of d,l -serine at different temperatures and resolutionACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2005B. Dittrich Three X-ray data sets of the same d,l -serine crystal were measured at temperatures of 298, 100 and 20,K. These data were then evaluated using invarioms and the Hansen & Coppens aspherical-atom model. Multipole populations for invarioms, which are pseudoatoms that remain approximately invariant in an intermolecular transfer, were theoretically predicted using different density functional theorem (DFT) basis sets. The invariom parameters were kept fixed and positional and thermal parameters were refined to compare the fitting against the multi-temperature data at different resolutions. The deconvolution of thermal motion and electron density with respect to data resolution was studied by application of the Hirshfeld test. Above a resolution of sin,/,,,,0.55,Å,1, or d,,,0.9,Å, this test was fulfilled. When the Hirshfeld test is fulfilled, a successful modeling of the aspherical electron density with invarioms is achieved, which was proven by Fourier methods. Molecular geometry improves, especially for H atoms, when using the invariom method compared to the independent-atom model, as a comparison with neutron data shows. Based on this example, the general applicability of the invariom concept to organic molecules is proven and the aspherical density modeling of a larger biomacromolecule is within reach. [source] V-Shaped Thiophene-Based Oligomers with Improved Electroluminescence Properties,ADVANCED FUNCTIONAL MATERIALS, Issue 4 2005G. Barbarella Abstract The synthesis via the Stille coupling of a new family of oligomers derived from benzo[b]thiophene is reported. Owing to their branched molecular structure lacking any symmetry element, these compounds display a low tendency to crystallization and better film-forming properties than their linear counterparts. Spin-coated films show photoluminescence efficiencies up to 50,%. Light-emitting diodes with spin-coated films as the active layers display markedly improved performance with respect to similar devices based on linear oligothiophenes, with luminance values up to more than 10,000,cd,m,2. Semiempirical PM3 and ZINDO/S calculations provide insight into the molecular geometries and electron distribution of the frontier orbitals of the new compounds. Cyclic voltammetry data indicates that the transformation of the thienyl sulfur of benzo[b]thiophene to the corresponding thienyl- S,S -dioxide leads an increase in electron affinity by 0.5,0.7,V, analogous to that of the corresponding linear oligomers. [source] A theoretical investigation on the structures, densities, detonation properties, and pyrolysis mechanism of the nitro derivatives of phenolsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2010Guixiang Wang Abstract The nitro derivatives of phenols are optimized to obtain their molecular geometries and electronic structures at the DFT-B3LYP/6-31G* level. Detonation properties are evaluated using the modified Kamlet,Jacobs equations based on the calculated densities and heats of formation. It is found that there are good linear relationships between density, detonation velocity, detonation pressure, and the number of nitro and hydroxy groups. Thermal stability and pyrolysis mechanism of the title compounds are investigated by calculating the bond dissociation energies (BDEs) at the unrestricted B3LYP/6-31G* level. The activation energies of H-transfer reaction is smaller than the BDEs of all bonds and this illustrates that the pyrolysis of the title compounds may be started from breaking OH bond followed by the isomerization reaction of H transfer. Moreover, the CNO2 bond with the smaller bond overlap population and the smaller BDE will also overlap may be before homolysis. According to the quantitative standard of energetics and stability as a high-energy density compound, pentanitrophenol essentially satisfies this requirement. In addition, we have discussed the effect of the nitro and hydroxy groups on the static electronic structural parameters and the kinetic parameter. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Soft Coulomb hole method applied to moleculesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2007J. Ortega-Castro Abstract The soft Coulomb hole method introduces a perturbation operator, defined by ,e/r12 to take into account electron correlation effects, where , represents the width of the Coulomb hole. A new parametrization for the soft Coulomb hole operator is presented with the purpose of obtaining better molecular geometries than those resulting from Hartree,Fock calculations, as well as correlation energies. The 12 parameters included in , were determined for a reference set of 12 molecules and applied to a large set of molecules (38 homo- and heteronuclear diatomic molecules, and 37 small and medium-size molecules). For these systems, the optimized geometries were compared with experimental values; correlation energies were compared with results of the MP2, B3LYP, and Gaussian 3 approach. On average, molecular geometries are better than the Hartree,Fock values, and correlation energies yield results halfway between MP2 and B3LYP. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Structures and properties of the hydrides of light elementsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2002Garry T. Smith Abstract Basic geometric and other properties for a number of neutral holovalent hydrides of light elements (M = Li , F)(MHn) are discussed. Their molecular geometries, energies, and vibrational frequencies have been determined from ab initio calculations of benchmark quality. We calculated harmonic vibrational frequencies, zero point vibrational energies, and atomization energies for the deuterides, tritiides, and combinations of them for these light elements. These isotopomers are of great interest for thermonuclear applications because they are often used as thermonuclear fuels or components of such fuels. In fact, only for these substances thermonuclear energy gain exceeds (at some densities and temperatures) the bremsstrahlung loss and other high-temperature losses, i.e., thermonuclear burn-up is possible. The vibrational frequencies are useful in determining the composition of mixed samples by means of spectroscopy. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolasesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2009Nikolaj Otte Abstract CHARMM force-field parameters are reported for the tetrahedral intermediate of serine hydrolases. The fitting follows the standard protocol proposed for CHARMM22. The reference data include ab initio (RHF/6-31G*) interaction energies of complexes between water and the model compound 1,1-dimethoxyethoxide, torsional profiles of related model compounds from correlated ab initio (MP2/6-311+G*//B3LYP/6-31+G*) calculations, as well as molecular geometries and vibrational frequencies from density functional theory (B3LYP/6-31+G*). The optimized parameters reproduce the target data well. Their utility is demonstrated by a QM/MM study of the tetrahedral intermediate in Bacillus subtilis lipase A, and by classical molecular modeling of enantioselectivity in Pseudomonas aeruginosa lipase and its mutants. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Prediction of experimentally unknown re distances of organic molecules from Dunning basis set extrapolations for ab initio post-HF calculationsJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 3 2006Alexander Neugebauer Abstract An approach to estimate equilibrium re bond lengths of organic molecules which contain standard bonding situations for CC, CH, CO and CN distances from only one equation is presented. For this, optimizations of molecular geometries using correlated post-Hartree,Fock and density functional methods have been performed. A selection scheme was developed to determine the most reliable methodology for prediction of equilibrium re distances of covalent bonds from a set of investigated theoretical methods. Consequently, distances computed in the CCSD(T) procedure via exponential extrapolation from a consecutive set of Dunning cc-pVXZ basis sets by use of Eqn (2) are accurate up to ±,0.0005,Å in comparison to experimentally available re distances. Applications for predictions of the experimentally unknown re distances of methanol, methylamine and methylenimine are presented. Additionally the estimation of re distances of larger, chemically more interesting molecules is possible by lower order calculations (e.g. DFT B3LYP/cc-pVDZ) via linear correlation statistics using the results from our re reference model system via Eqn (3). Copyright © 2006 John Wiley & Sons, Ltd. [source] Molecular Modeling and Receptor-Dependent (RD) 3D-QSAR Approach to a Set of Antituberculosis DerivativesMOLECULAR INFORMATICS, Issue 11-12 2009Fernanda, Kerly, Mesquita Pasqualoto Abstract In this study, receptor-dependent (RD) 3D-QSAR models were built for a set of thirty-seven isoniazid derivatives bound to the enoyl-acp reductase from M. tuberculosis, called InhA (PDB entry code 1zid). Ligand-receptor (L-R) molecular dynamics (MD) simulations [500,000 steps; the step size was 0.001,ps (1,fs)] were carried out at 310,K (biological assay temperature). The hypothesized active conformations resulting from a previously reported receptor-independent (IR) 4D-QSAR analysis were used as the molecular geometries of each ligand in this structure-based L-R binding research. The dependent variable is the reported MIC values against M. tuberculosis var. bovis. The independent variables (descriptors) are energy terms of a modified first-generation AMBER force field combined with a hydration shell aqueous solvation model. Genetic function approximation (GFA) formalism and partial least squares (PLS) regression were employed as the fitting functions to develop 3D-QSAR models. The bound ligand solvation energy, the sum of electrostatic and hydrogen bonding energies of the unbound ligand, the bending energy of the unbound ligand, the electrostatic intermolecular L-R energy, and the change in hydrogen bonding energy upon binding were found as important energy contributions to the binding process. The 3D-QSAR model at 310,K has good internal and external predictability and may be regarded as representative of the binding process of ligands to InhA. [source] From small structural modifications to adjustment of structurally dependent properties: 1-methyl-3,5-bis[(E)-2-thienylidene]-4-piperidone and 3,5-bis[(E)-5-bromo-2-thienylidene]-1-methyl-4-piperidoneACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2009Paul Tongwa The molecules of the title compounds, C16H15NOS2, (I), and C16H13Br2NOS2, (II), are E,E -isomers and consist of an extensive conjugated system, which determines their molecular geometries. Compound (I) crystallizes in the monoclinic space group P21/c. It has one thiophene ring disordered over two positions, with a minor component contribution of 0.100,(3). Compound (II) crystallizes in the noncentrosymmetric orthorhombic space group Pca21 with two independent molecules in the unit cell. These molecules are related by a noncrystallographic pseudo-inversion center and possess very similar geometries. The crystal packings of (I) and (II) have a topologically common structural motif, viz. stacks along the b axis, in which the molecules are bound by weak C,H...O hydrogen bonds. The noncentrosymmetric packing of (II) is governed by attractive intermolecular Br...Br and Br...N interactions, which are also responsible for the very high density of (II) (1.861,Mg,m,3). [source] Life-science applications of the Cambridge Structural DatabaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 6-1 2002Robin Taylor Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling of in vivo situations, although the influence of crystal packing is sometimes important and should always be borne in mind. Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of molecules with several rotatable bonds. The use of crystallographic data in this way is complementary to in vacuo theoretical calculations since it gives insights into conformational preferences in condensed-phase situations. Crystallographic data also underpin many molecular-fragment libraries and programs for generating three-dimensional models from two-dimensional chemical structures. The modelling of ligand binding to metalloenzymes is assisted by information in the CSD on preferred coordination numbers and geometries. CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein,ligand interaction is and what its geometry is likely to be. They can also be used to guide searches for bioisosteric replacements. Crystallographically derived information has contributed to many life-science software applications, including programs for locating binding `hot spots' on proteins, docking ligands into enzyme active sites, de novo ligand design, molecular superposition and three-dimensional QSAR. Overall, crystallographic data in general, and the CSD in particular, are very significant tools for the rational design of biologically active molecules. [source] Theoretical Study on the Vibrational Spectra and Thermodynamic Properties for Nitro Derivatives of Benzene and AnilinesCHINESE JOURNAL OF CHEMISTRY, Issue 8 2008Gui-Xiang WANG Abstract Nitro derivatives of benzene and anilines were optimized to obtain their molecular geometries and electronic structures at a DFT-B3LYP/6-31G, level. Their IR spectra were obtained and assigned by vibrational analysis. Comparing the calculated IR spectra with these of experiments known, all the IR data obtained in this paper were considered to be reliable. Based on the frequencies scaled by 0.96 and the principle of statistic thermodynamics, the thermodynamic properties were evaluated, which were linearly related with the number of nitro and amino groups as well as the temperature, obviously showing good group additivity. [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] Electrochemically Induced Modulation of the Catalytic Activity of a Reversible Redoxsensitive RiboswitchELECTROANALYSIS, Issue 9 2008Denise Strohbach Abstract Over the past decade, RNA conformation has been shown to respond to external stimuli. Thus, dependent on the presence of a high affinity ligand, specifically designed ribozymes can be regulated in a classical allosteric way. In this scenario, a binding event in one part of the RNA structure induces conformational changes in a separated part, which constitutes the catalytic centre. As a result activity is switched on (positive regulation) or off (negative regulation). We have developed a hairpin aptazyme responding to flavine mononucleotide (FMN). Ribozyme activity is dependent on binding of FMN and thus is switched on in the presence of FMN in its oxidized form. Under reducing conditions, however, FMN changes its molecular geometry, which is associated with loss of binding and consequently down-regulation of ribozyme activity. While in previous experiments sodium dithionite was used for reduction of FMN, we now present an assay for electrochemically induced activity switching. We have developed an electrochemical microcell that allows for iterative cycles of reduction/oxidation of FMN in an oxygen free atmosphere and thus for reversible switching of ribozyme activity. The reaction proceeds in droplets of 3 to 10,,L at micro- to nanomolar concentrations of the reaction components. [source] Synthesis, Solution-State and Solid-State Structural Characterization of Monocationic Nitrido Heterocomplexes [M(N)(DTC)(PNP)]+ (M = 99Tc, Re; DTC = Dithiocarbamate; PNP = Heterodiphosphane)EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 9 2004Cristina Bolzati Abstract Mono-cationic nitrido heterocomplexes of general formula [M(N)(DTC)(PNP)]+ (where M is 99Tc or Re, DTC is the mono-anionic form of a dithiocarbamate ligand, and PNP is a diphosphane ligand with a tertiary amine-containing five-membered spacer) were prepared by ligand-exchange reactions with the labile precursors [M(N)Cl2(PPh3)2] in dichloromethane/alcohol mixtures. The molecular structure of the representative rhenium complex [Re(N)(dedc)(pnp2)][PF6] (1) displays a distorted, square-pyramidal geometry with the dithiocarbamate sulfur and the diphosphane phosphorus atoms spanning the four coordination positions on the equatorial plane. If the additional interactions between the nitrido nitrogen and the weakly bonded transN -diphosphane heteroatom, the molecular geometry can be viewed as pseudo-octahedral. The structure in solution, as established by multinuclear NMR spectroscopy and ESI spectrometry, is monomeric, and identical to that shown in the solid state. Replacement of the phenyl groups on the phosphorous atoms in complexes 1, 2, 5, and 6 with alkyl groups modified neither the course of the reaction nor the composition of the resulting complexes. These results, together with the observation that no symmetrical complexes containing two identical bidentate ligands were produced in these reactions, strongly supports the conclusion that a mixed coordination sphere, composed by a combination of ,-donor and ,-acceptor atoms around the [M,N]2+ group, constitutes a highly stable system. Compounds containing dangling alkyl-substituted groups in the outer sphere (3, 4, 7, and 8) were fully characterized by multinuclear NMR spectroscopy and ESI mass spectrometry. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Functional role of fumarate site Glu59 involved in allosteric regulation and subunit,subunit interaction of human mitochondrial NAD(P)+ -dependent malic enzymeFEBS JOURNAL, Issue 4 2009Ju-Yi Hsieh Here we report on the role of Glu59 in the fumarate-mediated allosteric regulation of the human mitochondrial NAD(P)+ -dependent malic enzyme (m-NAD-ME). In the present study, Glu59 was substituted by Asp, Gln or Leu. Our kinetic data strongly indicated that the charge properties of this residue significantly affect the allosteric activation of the enzyme. The E59L enzyme shows nonallosteric kinetics and the E59Q enzyme displays a much higher threshold in enzyme activation with elevated activation constants, KA,Fum and ,KA,Fum. The E59D enzyme, although retaining the allosteric property, is quite different from the wild-type in enzyme activation. The KA,Fum and ,KA,Fum of E59D are also much greater than those of the wild-type, indicating that not only the negative charge of this residue but also the group specificity and side chain interactions are important for fumarate binding. Analytical ultracentrifugation analysis shows that both the wild-type and E59Q enzymes exist as a dimer,tetramer equilibrium. In contrast to the E59Q mutant, the E59D mutant displays predominantly a dimer form, indicating that the quaternary stability in the dimer interface is changed by shortening one carbon side chain of Glu59 to Asp59. The E59L enzyme also shows a dimer,tetramer model similar to that of the wild-type, but it displays more dimers as well as monomers and polymers. Malate cooperativity is not significantly notable in the E59 mutant enzymes, suggesting that the cooperativity might be related to the molecular geometry of the fumarate-binding site. Glu59 can precisely maintain the geometric specificity for the substrate cooperativity. According to the sequence alignment analysis and our experimental data, we suggest that charge effect and geometric specificity are both critical factors in enzyme regulation. Glu59 discriminates human m-NAD-ME from mitochondrial NADP+ -dependent malic enzyme and cytosolic NADP+ -dependent malic enzyme in fumarate activation and malate cooperativity. [source] Air-Stable n-Type Organic Field-Effect Transistors Based on Carbonyl-Bridged Bithiazole DerivativesADVANCED FUNCTIONAL MATERIALS, Issue 6 2010Yutaka Ie Abstract An electronegative conjugated compound composed of a newly designed carbonyl-bridged bithiazole unit and trifluoroacetyl terminal groups is synthesized as a candidate for air-stable n-type organic field-effect transistor (OFET) materials. Cyclic voltammetry measurements reveal that carbonyl-bridging contributes both to lowering the lowest unoccupied molecular orbital energy level and to stabilizing the anionic species. X-ray crystallographic analysis of the compound shows a planar molecular geometry and a dense molecular packing, which is advantageous to electron transport. Through these appropriate electrochemical properties and structures for n-type semiconductor materials, OFET devices based on this compound show electron mobilities as high as 0.06,cm2 V,1 s,1 with on/off ratios of 106 and threshold voltages of 20,V under vacuum conditions. Furthermore, these devices show the same order of electron mobility under ambient conditions. [source] Influence of Electric Field on Microstructures of Pentacene Thin-Films in Field-Effect Transistors,ADVANCED FUNCTIONAL MATERIALS, Issue 2 2008L. Cheng Abstract We report on electric-field-induced irreversible structural modifications in pentacene thin films after long-term operation of organic field-effect transistor (OFET) devices. Micro-Raman spectroscopy allows for the analysis of the microstructural modifications of pentacene in the small active channel of OFET during device operation. The results suggest that the herringbone packing of pentacene molecules in a solid film is affected by an external electric field, particularly the source-to-drain field that parallels the a,b lattice plane. The analysis of vibrational frequency and Davydov splitting in the Raman spectra reveals a singular behavior suggesting a reduced separation distance between pentacene molecules after long-term operations and, thus, large intermolecular interactions. These results provide evidence for improved OFET performance after long-term operation, related to the microstructures of organic semiconductors. It is known that the application of large electric fields alters the semiconductor properties of the material owing to the generation of defects and the trapping of charges. However, we first suggest that large electric fields may alter the molecular geometry and further induce structural phase transitions in the pentacene films. These results provide a basis for understanding the improved electronic properties in test devices after long-term operations, including enhanced field-effect mobility, improved on/off current ratio, sharp sub-threshold swing, and a slower decay rate in the output drain current. In addition, the effects of source-to-drain electric field, gate electric field, current and charge carriers, and thermal annealing on the pentacene films during OFET operations are discussed. [source] Photophysical Processes in ,Supramolecular Balls' Formed by Lanthanide Chloride with 2,2,-BipyridineHELVETICA CHIMICA ACTA, Issue 11 2009Abstract The europium complex [EuCl2(bpy)2(H2O)2]Cl,1.25,C2H6O,0.37,H2O, where bpy is 2,2,-bipyridine, was synthesized and investigated with the aim to relate its molecular geometry and crystal packing to the efficiency of energy-transfer processes. The presence of H-bonds between noncoordinated Cl, ions and coordinated H2O molecules leads to the formation of discrete trimers assembled by a number of CH,,,Cl and stacking interactions into ,supramolecular balls' which contain Cl, ions and solvate molecules (H2O and EtOH). The additional stabilization of the complex is due to intramolecular N,,,C interactions between two bpy ligands that causes some shortening of the EuN bonds. Deciphering the luminescence properties of the Eu complex was performed under consideration of both the composition of the inner coordination sphere and the peculiarities of the crystal packing. The influence of the latter and the bpy orientation on the energy of the ligand,Eu charge-transfer state (LMCT) was established, and an additional excited state induced by the , -stacking interaction (SICT) was identified. [source] Crystal Structure of Garciniaphenone and Evidences on the Relationship between Keto,Enol Tautomerism and ConfigurationHELVETICA CHIMICA ACTA, Issue 7 2008Felipe Abstract Garciniaphenone (=rel- (1R,5R,7R)-3-benzoyl-4-hydroxy-8,8-dimethyl-1,7-bis(3-methylbut-2-en-1-yl)bicyclo[3.3.1]non-3-ene-2,9-dione; 1), a novel natural product, was isolated from a hexane extract of Garcinia brasiliensis fruits. The crystal structure of 1 as well as the selected geometrical and configurational features were compared with those of known related polyprenylated benzophenones. Garciniaphenone is the first representative of polyprenylated benzophenones without a prenyl substituent at C(5). Notably, the absence of a 5-prenyl substituent has an impact on the molecular geometry. The tautomeric form of 1 in the solid state was readily established by a residual-electronic-density map generated by means of a difference Fourier analysis, and there is an entirely delocalized six-membered chelate ring encompassing the keto,enol moiety. The configuration at C(7) was used to rationalize the nature of the keto,enol tautomeric form within 1. The intermolecular array in the network is maintained by nonclassical intermolecular H-bonds. [source] Direct Spectroscopic Evidence that the Photochemical Outcome of Flutamide in a Protein Environment is Tuned by Modification of the Molecular Geometry: A Comparison with the Photobehavior in Cyclodextrin and VesiclesHELVETICA CHIMICA ACTA, Issue 2 2003Salvatore Sortino The photoreactivity of the phototoxic anticancer drug flutamide (FM) in the presence of bovine serum albumin (BSA) has been investigated. The presence of BSA induces a remarkable modification of the photochemical outcome of the drug with respect to that observed in aqueous solution. Induced circular dichroism (ICD) measurements combined with theoretical calculations provide strong evidence that the new photochemical scenario is tuned by changes of the molecular geometry of FM when incorporated in the protein microenvironment. This behavior presents close analogies to that found in the presence of either cyclodextrin or phospholipid vesicles, chosen as models for biological systems, and delineates a quite general photochemical picture that can be useful for a more appropriate understanding of the adverse phototoxic effects induced by this drug. [source] Thermally Induced Reversible Phase Transformations Accompanied by Emission Switching Between Different Colors of Two Aromatic-Amine CompoundsADVANCED MATERIALS, Issue 31 2009Yunfeng Zhao Thermally driven reversible emission switching between different colors and solid-phase transformation are investigated for two aromatic-amine compounds bearing trifluoromethyl (CF3) groups. The phase-dependent emission properties are attributed to the different molecular packing properties and changeable molecular geometry for different solid phases (see figure). [source] Identification and thermodynamic treatment of several types of large-amplitude motionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2005Gernot Katzer Abstract We present a partially automated method for the thermodynamic treatment of large-amplitude motions. Starting from the molecular geometry and the Hessian matrix, we evaluate anharmonic partition functions for selected vibrational degrees of freedom. Supported anharmonic vibration types are internal rotation and inversion (oscillation in a double-well potential). By heuristic algorithms, we identify internal rotations in most cases automatically from the Hessian eigenvectors, and we also estimate the parameters of anharmonic partition functions (e.g., potential barrier, periodicity, and symmetry number) with thermodynamically sufficient precision. We demonstrate the validity of our schemes by comparison to pointwise calculated ab initio potential curves. © 2005 Wiley Periodicals, Inc. J Comput Chem 14: 1438,1451, 2005 [source] Effect of pressure on the luminescence of a series of methoxy phenylacetylene dendrimers neat and in dilute solution in solid poly(tert -butyl methacrylate)JOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 16 2001A. Zhu Abstract The effect of pressure up to 60 kbar was measured on the luminescence peak location and efficiency for a series of methoxy phenylacetylene dendrimers (MeO). Dendrimers MeO-3, MeO-7, MeO-15, MeO-31, MeO-63, and MeO-127 were studied as neat polymers. MeO-3, MeO-15, MeO-63, and MeO-127 were also investigated in dilute solutions in poly(tert -butyl methacrylate). According to measurements of the dilute solutions, there is a charge-transfer (CT) state that, for the smaller dendrimers, lies well above the ,* state; for the larger dendrimers, it is the emitting state at 1 atm. With increasing pressure, the intramolecular CT state is rapidly stabilized, so that at high pressure the emission is from this state for all dendrimers. For the neat polymers, there is an initial redshift that reverses direction at a pressure that is higher for smaller dendrimers. This reversal is attributed to intermolecular CT. There may be changes in the molecular geometry and/or relative orientation of adjacent dendrimers that tend to stabilize the intermolecular CT in the solid state. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 2859,2865, 2001 [source] IR, Raman and SERS spectra of ethyl salicylateJOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2009C. Yohannan Panicker Abstract The IR and Raman spectra of ethyl salicylate were recorded and analyzed. The surface enhanced Raman scattering (SERS) spectrum was recorded in a silver colloid. The vibrational wavenumbers of the compound have been computed using the Hartree-Fock/6-31G* basis. The direction of charge transfer contribution to SERS has been discussed from the frontier orbital theory. The presence of methyl modes in the SERS spectrum indicates the nearness of the methyl group to the metal surface and the presence of ring vibrations and out-of-plane ring modes in the SERS spectrum suggests a flat orientation of the molecule on the silver surface. The first hyperpolarizability is calculated and the calculated molecular geometry has been compared with the reported similar structures. Copyright © 2009 John Wiley & Sons, Ltd. 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