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Molecular Orbital (molecular + orbital)
Kinds of Molecular Orbital Terms modified by Molecular Orbital Selected AbstractsStructural, electronic, bonding, magnetic, and optical properties of bimetallic [RunAum]0/+ (n + m , 3) clustersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Dimitrios N. Garbounis Abstract The structural, electronic, bonding, magnetic, and optical properties of bimetallic [RunAum]0/+ (n + m , 3; n, m = 0,3) clusters were computed in the framework of the density functional theory (DFT) and time-dependent DFT (TD-DFT) using the full-range PBE0 non local hybrid GGA functional combined with the Def2-QZVPP basis sets. Several low-lying states have been investigated and the stability of the ground state spinomers was estimated with respect to all possible fragmentation schemes. Molecular orbital and population analysis schemes along with computed electronic parameters illustrated the details of the bonding mechanisms in the [RunAum]0/+ clusters. The TD-DFT computed UV-visible absorption spectra of the bimetallic clusters have been fully analyzed and compared to those of pure gold and ruthenium clusters. Assignments of all principal electronic transitions are given and interpreted in terms of contribution from specific molecular orbital excitations. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010 [source] A Rigid Molecular Scaffold Affixing a (Polypyridine)ruthenium(II)- and a Nickel(II)-Containing Complex: Spectroscopic Evidence for a Weakly Coupled Bichromophoric SystemEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 10 2003Yann Pellegrin Abstract The synthesis of DppztBuSalH2 (7), a rigid conjugated ditopic ligand containing a Dppz (dipyrido[3,2- a:2,,3,- c]phenazine) skeleton and a salophen-type chelate, is reported. The complexes DppztBuSalNi (10), [Ru(bpy)2(DppztBuSalH2)]2+ (11), and [Ru(bpy)2(DppztBuSalNi)]2+ (12) have been prepared and characterised using common spectroscopic methods. Electrochemical, UV/Vis spectroelectrochemical and EPR studies were conducted on compounds 7, 10, 11, and 12. The singly reduced radical forms of 7 and 10 can be generated electrochemically, with the lone electron located on the low-lying phenazine ,*-molecular orbital. Complexes 11 and 12 show several reduction waves and electronic and EPR data obtained for the electrogenerated singly reduced species show them to be closely related to the radical species 7·, and 10·,, respectively. The presence of nickel(II) in compound 12 renders the addition of the second electron on the phenazine group reversible. Both 11 and 12 show common features on the cathodic side of their cyclic voltammograms, with reversible one-electron ruthenium-centred oxidation. An additional low-potential reversible-oxidation wave is observed for 12, and this is ascribed to oxidation of the nickel(II) ion. The combined spectroscopic data best describe the ruthenium-containing complexes as weakly coupled bichromophoric systems. Photophysical studies attest to the formation of a charge-separated state for 11, whereas a strong quenching is detected for 12. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Synthesis, Morphology, and Properties of Poly(3-hexylthiophene)- block -Poly(vinylphenyl oxadiazole) Donor,Acceptor Rod,Coil Block Copolymers and Their Memory Device ApplicationsADVANCED FUNCTIONAL MATERIALS, Issue 18 2010Yi-Kai Fang Abstract Novel donor,acceptor rod,coil diblock copolymers of regioregular poly(3-hexylthiophene) (P3HT)- block -poly(2-phenyl-5-(4-vinylphenyl)-1,3,4-oxadiaz-ole) (POXD) are successfully synthesized by the combination of a modified Grignard metathesis reaction (GRIM) and atom transfer radical polymerization (ATRP). The effects of the block ratios of the P3HT donor and POXD pendant acceptor blocks on the morphology, field effect transistor mobility, and memory device characteristics are explored. The TEM, SAXS, WAXS, and AFM results suggest that the coil block fraction significantly affects the chain packing of the P3HT block and depresses its crystallinity. The optical absorption spectra indicate that the intramolecular charge transfer between the main chain P3HT donor and the side chain POXD acceptor is relatively weak and the level of order of P3HT chains is reduced by the incorporation of the POXD acceptor. The field effect transistor (FET) hole mobility of the system exhibits a similar trend on the optical properties, which are also decreased with the reduced ordered P3HT crystallinity. The low-lying highest occupied molecular orbital (HOMO) energy level (,6.08 eV) of POXD is employed as charge trap for the electrical switching memory devices. P3HT- b -POXD exhibits a non-volatile bistable memory or insulator behavior depending on the P3HT/POXD block ratio and the resulting morphology. The ITO/P3HT44 - b - POXD18/Al memory device shows a non-volatile switching characteristic with negative differential resistance (NDR) effect due to the charge trapped POXD block. These experimental results provide the new strategies for the design of donor-acceptor rod-coil block copolymers for controlling morphology and physical properties as well as advanced memory device applications. [source] Triplet Formation in Fullerene Multi-Adduct Blends for Organic Solar Cells and Its Influence on Device PerformanceADVANCED FUNCTIONAL MATERIALS, Issue 16 2010Clare Dyer-Smith Abstract In organic solar cells, high open circuit voltages may be obtained by choosing materials with a high offset between the donor highest occupied molecular orbital (HOMO) and acceptor lowest unoccupied molecular orbital (LUMO). However, increasing this energy offset can also lead to photophysical processes that compete with charge separation. In this paper the formation of triplet states is addressed in blends of polyfluorene polymers with a series of PCBM multi-adducts. Specifically, it is demonstrated that the formation of such triplets occurs when the offset energy between donor ionization potential and acceptor electron affinity is ,1.6 eV or greater. Spectroscopic measurements support a mechanism of resonance energy transfer for triplet formation, influenced by the energy levels of the materials, but also demonstrate that the competition between processes at the donor,acceptor interface is strongly influenced by morphology. [source] Conjugated Polymer Based on Polycyclic Aromatics for Bulk Heterojunction Organic Solar Cells: A Case Study of Quadrathienonaphthalene Polymers with 2% EfficiencyADVANCED FUNCTIONAL MATERIALS, Issue 4 2010Shengqiang Xiao Abstract Polycyclic aromatics offer great flexibility in tuning the energy levels and bandgaps of resulting conjugated polymers. These features have been exploited in the recent examples of benzo[2,1- b:3,4- b']dithiophene (BDT)-based polymers for bulk heterojunction (BHJ) photovoltaics (ACS Appl. Mater. Interfaces2009, 1, 1613). Taking one step further, a simple oxidative photocyclization is used here to convert the BDT with two pendent thiophene units into an enlarged planar polycyclic aromatic ring,quadrathienonaphthalene (QTN). The reduced steric hindrance and more planar structure promotes the intermolecular interaction of QTN- based polymers, leading to increased hole mobility in related polymers. As-synthesized homopolymer (HMPQTN) and donor,acceptor polymer (PQTN - BT) maintain a low highest occupied molecular orbital (HOMO) energy level, ascribable to the polycyclic aromatic (QTN) moiety, which leads to a good open-circuit voltage in BHJ devices of these polymers blended with PCBM ([6,6]-phenyl-C61 -butyric acid methyl ester; HMPQTN: 0.76,V, PQTN - BT: 0.72,V). The donor,acceptor polymer (PQTN - BT) has a smaller optical bandgap (1.6,eV) than that of HMPQTN (2.0,eV), which explains its current (5.69,mA,cm,2) being slightly higher than that of HMPQTN (5.02,mA,cm,2). Overall efficiencies over 2% are achieved for BHJ devices fabricated from either polymer with PCBM as the acceptor. [source] Electron Trapping in Higher Adduct Fullerene-Based Solar CellsADVANCED FUNCTIONAL MATERIALS, Issue 18 2009Martijn Lenes Abstract Here, the performance of bulk-heterojunction solar cells based on a series of bisadduct analogues of commonly used derivatives of C60 and C70, such PCBMs and their thienyl versions, is investigated. Due to their higher lowest unoccupied molecular orbital an increase in open-circuit voltage and thus performance is expected. It is shown that the occurrence of a multitude of different isomers results in a decrease in the electron transport for some of the materials. Surprisingly, the solar-cell characteristics are very similar for all materials. This apparent discrepancy is explained by a significant amount of shallow trapping occurring in the fullerene phase that does not hamper the solar cell performance due the filling of these shallow traps during illumination. Furthermore, the trisadduct analogue of [60]PCBM has been investigated, which, despite an even further increase in open-circuit voltage, results in a significantly reduced device performance due to a strong deterioration of the electron mobility in the fullerene phase. [source] Effect of Electric Field on Coulomb-Stabilized Excitons in Host/Guest Systems for Deep-Blue ElectrophosphorescenceADVANCED FUNCTIONAL MATERIALS, Issue 15 2009Stephan Haneder Abstract Here, a study of the electric field induced quenching on the phosphorescence intensity of a deep-blue triplet emitter dispersed in different host materials is presented. The hosts are characterized by a higher triplet excitonic level with respect to the emitter, ensuring efficient energy transfer and exciton confinement, whereas they differ in the highest occupied molecular orbital (HOMO) alignment, forming type I and type II host/guest heterostructures. While the type I structure shows negligible electric field induced quenching, a quenching up to 25% for the type II at a field of 2,MV/cm is reported. A similar quenching behaviour is also reported for thin films of the pure emitter, revealing an important luminescence loss mechanism for aggregated emitter molecules. These results are interpreted by considering Coulomb stabilized excitons in the type II heterostructure and in the pure emitter, that become very sensitive to dissociation upon application of the field. These results clarify the role of external electric field quenching on the phosphorescence of triplet emitters and provide useful insights for the design of deep-blue electrophosphorescent devices with a reduced efficiency roll-off. [source] Structure,Property Relationship of Pyridine-Containing Triphenyl Benzene Electron-Transport Materials for Highly Efficient Blue Phosphorescent OLEDsADVANCED FUNCTIONAL MATERIALS, Issue 8 2009Shi-Jian Su Abstract Three triphenyl benzene derivatives of 1,3,5-tri(m -pyrid-2-yl-phenyl)benzene (Tm2PyPB), 1,3,5-tri(m -pyrid-3-yl-phenyl)benzene (Tm3PyPB) and 1,3,5-tri(m -pyrid-4-yl-phenyl)benzene (Tm4PyPB), containing pyridine rings at the periphery, are developed as electron-transport and hole/exciton-blocking materials for iridium(III) bis(4,6-(di-fluorophenyl)pyridinato- N,C2,)picolinate (FIrpic)-based blue phosphorescent organic light-emitting devices. Their highest occupied molecular orbital and lowest unoccupied molecular orbital (LUMO) energy levels decrease as the nitrogen atom of the pyridine ring moves from position 2 to 3 and 4; this is supported by both experimental results and density functional theory calculations, and gives improved electron-injection and hole-blocking properties. They exhibit a high electron mobility of 10,4,10,3,cm2,V,1,s,1 and a high triplet energy level of 2.75,eV. Confinement of FIrpic triplet excitons is strongly dependent on the nitrogen atom position of the pyridine ring. The second exponential decay component in the transient photoluminescence decays of Firpic-doped films also decreases when the position of the nitrogen atom in the pyridine ring changes. Reduced driving voltages are obtained when the nitrogen atom position changes because of improved electron injection as a result of the reduced LUMO level, but a better carrier balance is achieved for the Tm3PyPB-based device. An external quantum efficiency (EQE) over 93% of maximum EQE was achieved for the Tm4PyPB-based device at an illumination-relevant luminance of 1000,cd,m,2, indicating reduced efficiency roll-off due to better confinement of FIrpic triplet excitons by Tm4PyPB in contrast to Tm2PyPB and Tm3PyPB. [source] New Ruthenium Complexes Containing Oligoalkylthiophene-Substituted 1,10-Phenanthroline for Nanocrystalline Dye-Sensitized Solar Cells,ADVANCED FUNCTIONAL MATERIALS, Issue 1 2007C.-Y. Chen Abstract Two new ruthenium complexes [Ru(dcbpy)(L)(NCS)2], where dcbpy is 4,4,-dicarboxylic acid-2,2,-bipyridine and L is 3,8-bis(4-octylthiophen-2-yl)-1,10-phenanthroline (CYC-P1) or 3,8-bis(4-octyl-5-(4-octylthiophen-2-yl)thiophen-2-yl)-1,10-phenanthroline (CYC-P2), are synthesized, characterized by physicochemical and semiempirical computational methods, and used as photosensitizers in nanocrystalline dye-sensitized solar cells. It was found that the difference in light-harvesting ability between CYC-P1 and CYC-P2 is associated mainly with the location of the frontier orbitals, in particular the highest occupied molecular orbital (HOMO). Increasing the conjugation length of the ancillary ligand decreases the energy of the metal-to-ligand charge transfer (MLCT) transition, but at the same time reduces the molar absorption coefficient, owing to the HOMO located partially on the ancillary ligand of the ruthenium complex. The incident photon-to-current conversion efficiency curves of the devices are consistent with the MLCT band of the complexes. Therefore, the overall efficiencies of CYC-P1 and CYC-P2 sensitized cells are 6.01 and 3.42,%, respectively, compared to a cis- di(thiocyanato)-bis(2,2,-bipyridyl)-4,4,-dicarboxylate ruthenium(II)-sensitized device, which is 7.70,% using the same device-fabrication process and measuring parameters. [source] Structure, Characterization, and Metal-Complexation Properties of a New Tetraazamacrocycle Containing Two Phenolic Pendant ArmsHELVETICA CHIMICA ACTA, Issue 10 2004Xiuling Cui The new tetraazamacrocycle 2 (=2,2,-[[7-Methyl-3,7,11,17-tetraazabicyclo[11.3.1]heptadeca-1(17),13,15-triene-3,11-diyl]bis(methylene)]bis(4-bromophenol)) was synthesized and used as a ligand for different metal-ion complexes. The X-ray crystal structures of the complexes of the general formula [M(H- 2)]+NO,MeOH (M=Ni2+, Zn2+), in which only one of the two pendant phenolic OH groups of 2 is deprotonated, were determined. In both complexes, the coordination environment is of the [5+1] type, the four N-atoms of the macrocyclic framework defining a square-planar arrangement around the metal center, with similar NiN and ZnN distances of 1.961(9) to 2.157(9),Å and 2.021(9) to 2.284(8),Å, respectively. In contrast, the MO distances are markedly different, 2.060(6) and 2.449(8),Å in the NiII complex, and 2.027(7) and 2.941(9),Å in the ZnII complex. The UV/VIS spectra of the NiII and CuII complexes with ligand 2, and the EPR spectra of the CuII system, suggest the same type of structure for the complexes in solution as in the solid state. Theoretical studies by means of density functional theory (DFT) confirmed the experimental structures of the NiII and ZnII complexes, and led to a proposal of a similar structure for the corresponding CuII complex. The calculated EPR parameters for the latter and comparison with related data support this interpretation. The singly occupied molecular orbital (SOMO) in these systems is mainly made of a d orbital of Cu, with a strong antibonding (,*) contribution of the axially bound phenolate residue. [source] Photocycloaddition of Some Difluoro(aminoenonato)boron Complexes with ArylalkenesHELVETICA CHIMICA ACTA, Issue 2 2004Kuniaki Itoh The photocycloaddition of some difluoro[(methylamino- ,N)alkenonato- ,O]boron complexes 1 with arylalkenes 2 is discussed. The resulting [2+2] photoaddition gave the cyclobutane and azetidine derivatives (Schemes,1, 3, and 5). Rearrangements of the cyclobutane gave 1,5-diketones derivatives (Schemes,2, 4, and 5). The yields of the photoadducts were governed by the reduction and oxidation potentials. Furthermore, the configurations of the products established high regio- and stereoselectivity, suggesting the presence of a singlet exciplex. The reactivity and the stereochemistry were rationalized by means of FMO (frontier molecular orbital) calculations. [source] Substituted 1,3,2,4-benzodithiadiazines: Novel derivatives, by-products, and intermediates,HETEROATOM CHEMISTRY, Issue 7 2001Alexander Yu. The synthesis of the title compounds 1 by 1:1 condensation of ArNSNSiMe3 2 with SCl2 followed by intramolecular ortho-cyclization of each [ArNSNSCl] intermediate is complicated by further reaction of 1 with SCl2 to give Herz salts 3. With the 2:SCl2 ratio of 2:1, the formation of by-products 3 is reduced and novel compounds 1 are accessible. With ortho-I containing starting material 2j, the parent compound 1s is obtained as the result of an unexpected I, not H, substitution. The rate of the 1 + SCl2 reaction depends upon a substituent's position, and the minor 8-R isomers 1l,p (R = Br, I) are isolated for the first time from mixtures with the major 6-R isomers due to reduced reactivity toward SCl2. The synthesized compounds 1,3 are characterized by multinuclear (including nitrogen) NMR and X-ray crystallography. According to the X-ray diffraction data, 1j (6-Br) and 1k (7-Br) derivatives are planar, whereas 1i (5-Br) and 1l (8-Br) are bent along the S1···N4 line by ,5° and ,4°, respectively, and the 1r (7-OCH3) derivative is planar in contrast to the known 5-OCH3 isomer, which possesses a significantly folded heterocycle. The distortion of the planar geometry of some compounds 1 is interpreted in terms of a pseudo-Jahn-Teller effect as the result of ,-highest occupied molecular orbital (HOMO) ,*-(LUMO) lowest unoccupied molecular orbital + 1 mixing in a planar conformation. The 2p compound is the first structurally defined Ar,N = S = N,SiMe3 azathiene. The compound Ar,N = S = N,S,NH-Ar 6 modeling the aforementioned intermediate has been isolated and structurally characterized. We describe the attempts to synthesize compounds 1 from 2-aminobenzenethiols and (SN)4 and from salts 3 and Me3SiN3, and we discuss the reaction pathways. © 2001 John Wiley & Sons, Inc. Heteroatom Chem 12:563,576, 2001 [source] Solution-Processable Carbazole-Based Conjugated Dendritic Hosts for Power-Efficient Blue-Electrophosphorescent DevicesADVANCED MATERIALS, Issue 48 2009Junqiao Ding A novel class of hosts suitable for solution processing has been developed based on a conjugated dendritic scaffold. By increasing the dendron generation, the highest occupied molecular orbital (HOMO) energy level can be tuned to facilitate hole injection, while the triplet energy remains at a high level, sufficient to host high-energy-triplet emitters. A power-efficient blue-electrophosphorescent device based on H2 (see figure) is presented. [source] Measurements of the kinetics of the OH + ,-pinene and OH + ,-pinene reactions at low pressureINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 5 2002B. Chuong The rate constants for the OH + ,-pinene and OH + ,-pinene reactions have been measured in 5 Torr of He using discharge-flow systems coupled with resonance fluorescence and laser-induced fluorescence detection of the OH radical. At room temperature, the measured effective bimolecular rate constant for the OH + ,-pinene reaction was (6.08 ± 0.24) × 10,11 cm3 molecule,1 s,1. These results are in excellent agreement with previous absolute measurements of this rate constant, but are approximately 13% greater than the value currently recommended for atmospheric modeling. The measured effective bimolecular rate constant for the OH + ,-pinene reaction at room temperature was (7.72 ± 0.44) × 10,11 cm3 molecule,1 s,1, in excellent agreement with previous measurements and current recommendations. Above 300 K, the effective bimolecular rate constants for these reactions display a negative temperature dependence suggesting that OH addition dominates the reaction mechanisms under these conditions. This negative temperature dependence is larger than that observed at higher pressures. The measured rate constants for the OH + ,-pinene and OH + ,-pinene reactions are in good agreement with established reactivity trends relating the rate constant for OH + alkene reactions with the ionization potential of the alkene when ab initio calculated energies for the highest occupied molecular orbital are used as surrogates for the ionization potentials for ,- and ,-pinene. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 300,308, 2002 [source] Theoretical study of NMR chemical shift induced by H/D isotope effectINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2010Kimikazu Sugimori Abstract The isotope effect induced by deuterium substituted species is observed in molecular properties, such as geometry, kinetics, and electronic state, of the molecules through nuclear-electron interaction. Theoretical considerations and experimental alignments have been studied by ab initio molecular orbital, density functional theory, and other empirical strategies. The Born-Oppenheimer approximation with nuclear vibrational wavefunction can treat isotope effect because nuclear mass effect account for the average distance of vibrational motion. In this study, we introduce Morse anharmonic oscillator model to calculate average internuclear distance of diatomic molecules having X-H bonding and X-D bonding. Morse parameters are determined by fitting to potential energy surface of molecular orbital and/or density functional calculations, and then the average distance are obtained as the expectation value of the analytical Morse vibrational wavefunction. Nuclear magnetic resonance shielding constants of the H/D isotopomer are calculated again on the average distance by using GIAO with B3LYP and CCSD calculation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Theory of chemical bonds in metalloenzymes XIII: Singlet and triplet diradical mechanisms of hydroxylations with iron-oxo species and P450 are revisitedINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2009Kizashi Yamaguchi Abstract Electronic structures of the Compound I (CpdI) in P450 are investigated on the basis of spin coupling forms of iron-oxo (Fe(IV)O) cores and radical ligand (,L) groups to generalize previous singlet and triplet diradical (TD) mechanisms for oxygenations of alkanes with Fe( IV)O. Orbital interaction schemes for four lower-lying spin configurations of CpdI with HC bond of substrate are examined to elucidate how magnetic coupling modes correlate with radical reaction pathways for hydroxylation reactions on the basis of the broken symmetry (BS) molecular orbital (MO) model. The configuration correlation diagrams for the four configurations model are depicted on the basis of the isoelectronic analogy among O, O2, and Fe( IV)O, in addition to Coulomb exchange energy on the iron site, which determines its local spin configuration. Important role of ligand spin (,L) of CpdI for regulation of hydroxylation mechanisms is clarified with the aid of the spin coupling forms. Transition states for one quartet and three doublet configurations under the BS MO approximation are examined on the basis of potential curve crossings along reaction pathways. The four transition structures and corresponding radical intermediates for methane and trimethyl methane with CpI are located by the BS hybrid Kohn,Sham density functional theory (DFT) (B3LYP) method to confirm the orbital interaction schemes. Spin density populations obtained by the BS B3LYP calculations are found to be consistent with the theoretical predictions based on the four configurations model. The configuration and state correlation diagrams by BS B3LYP before and after spin projection are also consistent with the BS MO interaction schemes, which provide local SD and TD mechanisms of hydroxylation with CpdI. The present BS MO-theoretical framework is useful for systematic understanding of a lot of recent BS hybrid DFT computational results for hydroxylation reactions with CpdI and configuration correlation diagrams reported by several groups. Implications of the present theoretical and computational results are discussed in relation to several experimental characteristics of hydroxylation reactions with iron-oxo species and P450. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Charge transfer in single- and double-strand DNAs: Theoretical analysis based on molecular orbital methodINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2006Kenichi Dedachi Abstract Electrochemical DNA chips determine the sequence of DNA bases by detecting the change in charge conductivity through single- or double-strand DNA. Experimentally, double-strand DNAs were found to conduct much greater electric current than single-strand DNAs. To gain insight into the underlying mechanism leading to such a disparity in charge conductivity, the hole/electron conductivities in single- and double-strand DNAs were examined theoretically by molecular dynamics and molecular orbital (MO) calculations. The hole/electron transfer integrals between the neighboring DNA bases were estimated from the frontier MO energy levels. The current-voltage characteristics of single- and double-strand DNAs, derived from the transfer integrals and the site energy of each DNA base, are qualitatively in agreement with experiment. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] DFT study of the electronic properties of DNA,DNA and PNA,DNA double strandsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2006Takayuki Natsume Abstract The electronic properties of DNA,DNA and PNA,DNA double strands having 3,6 base pairs (bp) were investigated by density functional theory (DFT) calculations. The binding energies and the highest occupied molecular orbital,lowest unoccupied molecular orbital (HOMO,LUMO) energy gaps for the PNA,DNA hybrids in the vapor phase are found to be greater than those for the DNA,DNA hybrids, regardless of the number of base pairs involved. The study supports the experimental finding that PNA displays high affinity toward a complementary DNA and that PNA,DNA strands are much more thermodynamically stable than their DNA,DNA counterparts. The results suggest much higher sensitivity in DNA sequencing with the arrays of PNA than with those of DNA. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [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] Valence and valence,core interactions in transition-metal diatomic moleculesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Edward A. Boudreaux Abstract In this study, the correlation between open-shell valence and closed-shell valence-core electrons is shown to be significant, with regard to an adequate description of the bonding in transition metal diatomic molecules. The SCMEH-MO (self-consistent modified extended Huckel molecular orbital) method is well suited for partitioning these two influences, in terms of their independent and collective effects on the electrons within the occupied mo-s. Two test cases, Cr2 and Mo2 are presented to demonstrate the nature and magnitude of these valence/valence-core interactions. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Temperature effects on the UV,Vis electronic spectrum of trans-stilbeneINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2001S. P. Kwasniewski Abstract The ultraviolet (UV),Visible absorption spectrum of trans-stilbene (tS) is computed at different temperatures by coupling molecular dynamics (MD) simulations with the classical MM3 force field to ZINDO/S-CIS calculations of vertical excitation energies and transition dipole moments. The selection of a large number of structures along the MD trajectories enables a consistent treatment of temperature effects in the vacuum, whereas the ZINDO/S-CIS calculations permit a reliable treatment of electron correlation and relaxation, taking account of multistate interactions in the final state. Thermal motions are found to alter very differently the width and shape of bands. Structural alterations such as the stretching and the torsion of the vinyl single and double bonds very strongly influence the appearance of the first valence state, pertaining to the highest occupied and lowest unoccupied molecular orbital (HOMO,LUMO) transition. At temperatures less than 400 K, these are found to yield a merely Gaussian and very pronounced thermal broadening of the related band (A), up to nearly 30 nm, together with a minor blue shift of its maximum ,max. In contrast, a red shift by several nanometers occurs due to thermal motions for the remaining three valence bands. As can be expected, the broadening intensifies at higher temperatures, and for the A-band, becomes markedly asymmetric when T exceeds 400 K. The combination of MD(MM3) and ZINDO/S-CIS computations enables also consistent calculations of hot bands, which are forbidden by symmetry at 0 K. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] A hybrid density functional theory study of the low-temperature dimethyl ether combustion pathways.ISRAEL JOURNAL OF CHEMISTRY, Issue 2-3 2002I: Chain-propagation Dimethyl ether (DME) has been proposed to be a promising alternative to conventional diesel fuel because of its favorable compression ignition property (high cetane number) and its soot-free combustion. A radical chain mechanism for hydrocarbon autoignition has been proposed for DME at low temperatures. In this mechanism, the chain initiation step consists of DME undergoing hydrogen abstraction by a highly reactive species (typically ·OH). The CH3O·H2 created in the initiation step then combines with O2; the subsequent CH3OCH2OO· radical is involved in a Lindemann-type mechanism, which can lead to the production of formaldehyde (CH2 = O) and ·OH. This concludes the chain-propagating step: the one ·OH produced then sustains the chain-reaction by creating another CH3O·H2. A relatively stable intermediate (·CH2OCH2OOH), formed via isomerization of CH3OCH2OO· in the chain-propagation step, can combine with a second O2 to produce a radical (·OOCH2OCH2OOH) that can potentially decompose into two ·OH radical (and other products). This path leads to chain-branching and an exponential increase in the rate of DME oxidation. We have used spin-polarized density functional theory with the Becke-3-parameter Lee,Parr,Yang exchange-correlation functional to calculate the structures and energies of key reactants, intermediates, and products involved in (and competing with) the chain-propagating and chain-branching steps of low-temperature DME oxidation. In this article, Part I, we consider only the chain-propagation mechanism and its competing mechanisms for DME combustion. Here, we show that only certain conformers can undergo the isomerization to ·CH2OCH2OOH. A new transition state has been discovered for the disproportionation reaction ·CH2OCH2OOH , 2CH2O + ·OH in the chain-propagating step of DME autoignition that is much lower than previous barriers. The key to making this decomposition pathway facile is initial cleavage of the O,O rather than the C,O bond. This renders all transition states along the chain-propagation potential energy surface below the CH3O·H2 + O2 reactants. In contrast with the more well-studied CH3·H2 (ethyl radical) + O2 system, the H-transfer isomerization of CH3OCH2OO· to ·CH2OCH2OOH in low-temperature DME oxidation has a much lower activation energy. This is most likely due to the larger ring strain of the analogous transition state in ethane oxidation, which is a five-membered ring opposed to a six-membered ring in dimethyl ether oxidation. Thus low-temperature ethane oxidation is much less likely to form the ·ROOH (where R is a generic group) radicals necessary for chain-branching, which leads to autoignition. Three competing reactions are considered: CH3O·H2 , CH2O + ·CH3; ·CH2OCH2OOH , 1,3-dioxetane + ·OH; and ·CH2OCH2OOH , ethylene oxide + HOO·. The reaction barriers of all these competing paths are much higher in energy (7,10 kcal/mol) than the reactants CH3O·H2 + O2 and, therefore, are unlikely low-temperature paths. Interestingly, an analysis of the highest occupied molecular orbital along the CH3O·H2 decomposition path shows that electronically excited (1A2 or 3A2) CH2O can form; this can also be shown for ·CH2OCH2OOH, which forms two formaldehyde molecules. This may explain the luminosity of DME's low-temperature flames. [source] Synthesis and characterization of imine-coupled polyphenols containing carbazole unitsJOURNAL OF APPLIED POLYMER SCIENCE, Issue 3 2009smet Kaya Abstract Imine coupled phenolic monomers containing carbazole unit were synthesized in four steps. The monomers were polymerized via oxidative polycondensation by air as oxidant in an aqueous alkaline medium at 50°C. The structures of compounds were confirmed by ultraviolet,visible (UV,vis), Fourier transform infrared, and 1H- and 13C-NMR techniques. The conductivity measurements of these polymers were made by the four-point probe technique and iodine was used as doping agent. The highest occupied molecular orbital, the lowest unoccupied molecular orbital, and electrochemical and optical band gap values were calculated by the results of the UV,vis and the cyclic voltammetry measurement, respectively. The number-average molecular weight, weight-average molecular weight, and polydispersity index values were determined by the size exclusion chromatography technique. Also, thermal behavior of these polymers was determined by thermogravimetric/differential thermal analysis measurements in a N2 atmosphere between 20 and 1000°C. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009 [source] G-protein coupled receptors: SAR analyses of neurotransmitters and antagonistsJOURNAL OF CLINICAL PHARMACY & THERAPEUTICS, Issue 3 2004C. L. Kuo MS Summary Background:, From the deductive point of view, neurotransmitter receptors can be divided into categories such as cholinergic (muscarinic, nicotinic), adrenergic (, - and , -), dopaminergic, serotoninergic (5-HT1,5-HT5), and histaminergic (H1 and H2). Selective agonists and antagonists of each receptor subtype can have specific useful therapeutic applications. For understanding the molecular mechanisms of action, an inductive method of analysis is useful. Objective:, The aim of the present study is to examine the structure,activity relationships of agents acting on G-protein coupled receptors. Method:, Representative sets of G-PCR agonists and antagonists were identified from the literature and Medline [P.M. Walsh (2003) Physicians' desk reference; M.J. O'Neil (2001) The Merck index]. The molecular weight (MW), calculated logarithm of octanol/water partition coefficient (C log P) and molar refraction (CMR), dipole moment (DM), Elumo (the energy of the lowest unoccupied molecular orbital, a measure of the electron affinity of a molecule and its reactivity as an electrophile), Ehomo (the energy of the highest occupied molecular orbital, related to the ionization potential of a molecule, and its reactivity as a nucleophile), and the total number of hydrogen bonds (Hb) (donors and receptors), were chosen as molecular descriptors for SAR analyses. Results:, The data suggest that not only do neurotransmitters share common structural features but their receptors belong to the same ensemble of G-protein coupled receptor with seven to eight transmembrane domains with their resultant dipoles in an antiparallel configuration. Moreover, the analysis indicates that the receptor exists in a dynamic equilibrium between the closed state and the open state. The energy needed to open the closed state is provided by the hydrolysis of GTP. A composite 3-D parameter frame setting of all the neurotransmitter agonists and antagonists are presented using MW, Hb and , as independent variables. Conclusion:, It appears that all neurotransmitters examined in this study operate by a similar mechanism with the G-protein coupled receptors. [source] Theoretical study of the prion protein based on the fragment molecular orbital methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2009Takeshi Ishikawa Abstract We performed fragment molecular orbital (FMO) calculations to examine the molecular interactions between the prion protein (PrP) and GN8, which is a potential curative agent for prion diseases. This study has the following novel aspects: we introduced the counterpoise method into the FMO scheme to eliminate the basis set superposition error and examined the influence of geometrical fluctuation on the interaction energies, thereby enabling rigorous analysis of the molecular interaction between PrP and GN8. This analysis could provide information on key amino acid residues of PrP as well as key units of GN8 involved in the molecular interaction between the two molecules. The present FMO calculations were performed using an original program developed in our laboratory, called "Parallelized ab initio calculation system based on FMO (PAICS)". © 2009 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Structural, electronic, and optical properties of 9-heterofluorenes: A quantum chemical studyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2007Run-Feng Chen Abstract Density-functional theory studies were applied to investigate the structural, electronic, and optical properties of 9-heterofluorenes achieved by substituting the carbon at 9 position of fluorene with silicon, germanium, nitrogen, phosphor, oxygen, sulfur, selenium, or boron. These heterofluorenes and their oligomers up to pentamers are highly aromatic and electrooptically active. The alkyl and aryl substituents of the heteroatom have limited influence, but the oxidation of the atom has significant influence on their molecular structures and properties. The highest occupied molecular orbital (HOMO)-lowest occupied molecular orbital (LUMO) interaction theory was successfully applied to analyze the energy levels and the frontier wave functions of these heterofluorenes. Most heterofluorenes belong to type B of interaction with low-lying LUMO and have the second kind of wave function. Carbazole and selenafluorene have type C of interaction with high-lying HOMO and the third kind of wave function. Types C and D of heterofluorenes, such as carbazole, oxygafluorene, sulfurafluorene, and selenafluorene also have high triplet state energies. The extrapolated HOMO and LUMO for polyheterofluorenes indicate that polyselenonafluorene has the lowest LUMO; polycarbazole has the highest HOMO; polyselenafluorene has the highest bandgap (Eg); and polyborafluorene has the lowest Eg. Heterofluorenes and their oligomers and polymers are of great experimental interests, especially those having extraordinary properties revealed in this study. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Metal,thiolate bonds in bioinorganic chemistryJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2006Edward I. Solomon Abstract Metal,thiolate active sites play major roles in bioinorganic chemistry. The MSthiolate bonds can be very covalent, and involve different orbital interactions. Spectroscopic features of these active sites (intense, low-energy charge transfer transitions) reflect the high covalency of the MSthiolate bonds. The energy of the metal,thiolate bond is fairly insensitive to its ionic/covalent and ,/, nature as increasing MS covalency reduces the charge distribution, hence the ionic term, and these contributions can compensate. Thus, trends observed in stability constants (i.e., the Irving,Williams series) mostly reflect the dominantly ionic contribution to bonding of the innocent ligand being replaced by the thiolate. Due to high effective nuclear charges of the CuII and FeIII ions, the cupric, and ferric,thiolate bonds are very covalent, with the former having strong , and the latter having more , character. For the blue copper site, the high , covalency couples the metal ion into the protein for rapid directional long range electron transfer. For rubredoxins, because the redox active molecular orbital is , in nature, electron transfer tends to be more localized in the vicinity of the active site. Although the energy of hydrogen bonding of the protein environment to the thiolate ligands tends to be fairly small, H-bonding can significantly affect the covalency of the metal,thiolate bond and contribute to redox tuning by the protein environment. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1415,1428, 2006 [source] Theoretical studies on the role of ,-electron delocalization in determining the conformation of N-benzylideneaniline with three types of LMO basis setsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2006Peng Bao Abstract To understand the role of ,-electron delocalization in determining the conformation of the NBA (Ph,NCH,Ph) molecule, the following three LMO (localized molecular orbital) basis sets are constructed: a LFMO (highly localized fragment molecular orbital), an NBO (natural bond orbital), and a special NBO (NBO-II) basis sets, and their localization degrees are evaluated with our suggesting index DL. Afterward, the vertical resonance energy ,EV is obtained from the Morokuma's energy partition over each of three LMO basis sets. ,EV = ,EH (one electron energy) + ,Etwo (two electron energy), and ,Etwo = ,ECou (Coulomb) + ,Eex (exchange) + ,Eec (or ,,En) (electron correction). ,EH is always stabilizing, and ,ECou is destabilizing for all time. In the case of the LFMO basis set, ,ECou is so great that ,Etwo > |,EH|. Therefore, ,EV is always destabilizing, and is least destabilizing at about the , = 90° geometry. Of the three calculation methods such as HF, DFT, and MPn (n = 2, 3, and 4), the MPn method provides ,EV with the greatest value. In the case of the NBO basis set, on the contrary, ,EV is stabilizing due to ,ECou being less destabilizing, and it is most stabilizing at a planar geometry. The LFMO basis set has the highest localization degree, and it is most appropriate for the energy partition. In the NBA molecule, ,-electron delocalization is destabilization, and it has a tendency to distort the NBA molecular away from its planar geometry as far as possible. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 809,824, 2006 [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] Analyses of the partition coefficient, log P, using ab initio MO parameter and accessible surface area of solute moleculesJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2004Hiroshi Chuman Abstract To analyze the log Psol/w values (sol: n -octanol or chloroform, w: water) in the framework of the molecular orbital (MO) procedure, we selected solute descriptors such as the solvation energy difference between aqueous and organic solvent phases and the "surface" area of solute molecules to which water molecules are accessible. The solvation energy of solute molecules in their minimum free-energy conformation was calculated using the ab initio self-consistent reaction field-MO method with the conductor-like screening model. The experimentally measured log Psol/w value of various solutes except for those of amphiprotics was shown to be analyzable reasonably well by the MO model with additional descriptors for the hydrogen-bonding patterns in the solute,solvent interactions. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:2681,2697, 2004 [source] | ||||||||||||||||||||||||||||||||||