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Equilibrium Geometry (equilibrium + geometry)
Selected AbstractsTopological Analysis of Electron Densities: Is the Presence of an Atomic Interaction Line in an Equilibrium Geometry a Sufficient Condition for the Existence of a Chemical Bond?CHEMISTRY - A EUROPEAN JOURNAL, Issue 18 2004Arne Haaland Prof. Abstract The structure, energetics, and electron density in the inclusion complex of He in adamantane, C10H16, have been studied by density functional theory calculations at the B3LYP6-311++G(2p,2d) level. Topological analysis of the electron density shows that the He atom is connected to the four tertiary tC atoms in the cage by atomic interaction lines with (3,,1) critical points. The calculated dissociation energy of the complex He@adamantane(g)=adamantane(g) + He(g) of ,E=,645 kJ,mol,1 nevertheless shows that the He,tC interactions are antibonding. [source] Molecular structure, conformational analysis and charge distribution of pralidoxime: Ab initio and DFT studiesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2002Alexandre T. Castro Abstract A detailed structural study of pralidoxime (2-PAM), the main antidote against organophosphate intoxication, was performed using Hartree-Fock, Möller,Plesset (MP2), and density functional theory (Becke, Lee, Yang, and Paar [B3LYP]) methods. Rotational barriers, equilibrium geometries, and charge distributions were calculated, showing important differences between the two forms available in physiological conditions, namely with the oxime group protonated or unprotonated. For the protonated form, conjugation between the side chain and the pyridinium ring, although present, has little importance, resulting in a flexible structure. On the other hand, the unprotonated form has a more rigid structure and a smaller charge density on the oxime oxygen. Contrary to the common belief, those results strongly suggest that it may be the protonated form of 2-PAM, instead of the unprotonated form, that is responsible for the antidote activity of this compound. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Computational analyses of singlet,singlet and singlet,triplet transitions in mononuclear gold-capped carbon-rich conjugated complexesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2005Zexing Cao Abstract Density functional theory and CASSCF calculations have been used to determine equilibrium geometries and vibrational frequencies of metal-capped one-dimensional ,-conjugated complexes (H3P)Au(CC)n(Ph) (n = 1,6), (H3P)Au(CCC6H4)(CCPh), and H3PAu(CCC6H4)CCAuPH3 in their ground states and selected low-lying ,,* excited states. Vertical excitation energies for spin-allowed singlet,singlet and spin-forbidden singlet,triplet transitions determined by the time-dependent density functional theory show good agreement with available experimental observations. Calculations indicate that the lowest energy 3(,,*) excited state is unlikely populated by the direct electronic excitation, while the low-lying singlet and triplet states, slightly higher in energy than the lowest triplet state, are easily accessible by the excitation light used in experiments. A series of radiationless transitions among related excited states yield the lowest 3(,,*) state, which has enough long lifetimes to exhibit its photochemical reactivities. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1214,1221, 2005 [source] Transition-Metal Complexes [(PMe3)2Cl2M(E)] and [(PMe3)2(CO)2M(E)] with Naked Group,14 Atoms (E=C,Sn) as Ligands; Part 2: Complexation with W(CO)5CHEMISTRY - A EUROPEAN JOURNAL, Issue 35 2009Pattiyil Parameswaran Dr. Abstract Density functional calculations at the BP86/TZ2P level were carried out to understand the ligand properties of the 16-valence-electron(VE) Group,14 complexes [(PMe3)2Cl2M(E)] (1ME) and the 18-VE Group,14 complexes [(PMe3)2(CO)2M(E)] (2ME; M=Fe, Ru, Os; E=C, Si, Ge, Sn) in complexation with W(CO)5. Calculations were also carried out for the complexes (CO)5W,EO. The complexes [(PMe3)2Cl2M(E)] and [(PMe3)2(CO)2M(E)] bind strongly to W(CO)5 yielding the adducts 1ME,W(CO)5 and 2ME,W(CO)5, which have C2v equilibrium geometries. The bond strengths of the heavier Group,14 ligands 1ME (E=Si,Sn) are uniformly larger, by about 6,7,kcal,mol,1, than those of the respective EO ligand in (CO)5W-EO, while the carbon complexes 1MC,W(CO)5 have comparable bond dissociation energies (BDE) to CO. The heavier 18-VE ligands 2ME (E=Si,Sn) are about 23,25,kcal,mol,1 more strongly bonded than the associated EO ligand, while the BDE of 2MC is about 17,21,kcal,mol,1 larger than that of CO. Analysis of the bonding with an energy-decomposition scheme reveals that 1ME is isolobal with EO and that the nature of the bonding in 1ME,W(CO)5 is very similar to that in (CO)5W,EO. The ligands 1ME are slightly weaker , acceptors than EO while the ,-acceptor strength of 2ME is even lower. [source] Geometric H/D Isotope Effects and Cooperativity of the Hydrogen Bonds in PorphyceneCHEMPHYSCHEM, Issue 2 2007Mohamed F. Shibl Dr. Abstract We investigate the primary, secondary, and vicinal hydrogen/deuterium (H/D) isotope effects on the geometry of the two intramolecular hydrogen bonds in porphycene. Multidimensional potential energy surfaces describing the anharmonic motion in the vicinity of the trans isomer are calculated for the different symmetric (HH/DD) and asymmetric (HD) isotopomers. From the solution of the nuclear Schrödinger equation the ground-state wavefunction is obtained, which is further used to determine the quantum corrections to the classical equilibrium geometries of the hydrogen bonds and thus the geometric isotope effects. In particular, it is found that the hydrogen bonds are cooperative, that is, both expand simultaneously even in the case of an asymmetric isotopic substitution. The theoretical predictions compare favorably with NMR chemical-shift data. [source] High-level ab initio calculations on HGeCl and the equilibrium geometry of the Ã1A, state derived from Franck-Condon analysis of the single-vibronic-level emission spectra of HGeCl and DGeClJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2010Daniel K. W. Mok Abstract CCSD(T) and/or CASSCF/MRCI calculations have been carried out on the X,1A, and Ã1A, states of HGeCl. The fully relativistic effective core potential, ECP10MDF, and associated standard valence basis sets of up to the aug-cc-pV5Z quality were employed for Ge. Contributions from core correlation and extrapolation to the complete basis set limit were included in determining the computed equilibrium geometrical parameters and relative electronic energy of these two states of HGeCl. Based on the currently, most systematic CCSD(T) calculations performed in this study, the best theoretical geometrical parameters of the X,1A, state are re(HGe) = 1.580 ± 0.001 Å, ,e = 93.88 ± 0.01° and re(GeCl) = 2.170 ± 0.001 Å. In addition, Franck-Condon factors including allowance for anharmonicity and Duschinsky rotation between these two states of HGeCl and DGeCl were calculated employing CCSD(T) and CASSCF/MRCI potential energy functions, and were used to simulate Ã1A, , X,1A, SVL emission spectra of HGeCl and DGeCl. The iterative Franck-Condon analysis (IFCA) procedure was carried out to determine the equilibrium geometrical parameters of the Ã1A, state of HGeCl by matching the simulated, and available experimental SVL emission spectra of HGeCl and DGeCl of Tackett et al., J Chem Phys 2006, 124, 124320, using the available, estimated experimental equilibrium (r) structure for the X,1A, state, while varying the equilibrium geometrical parameters of the Ã1A, state systematically. Employing the derived IFCA geometry of re(HGe) = 1.590 Å, re(GeCl) = 2.155 Å and ,e(HGeCl) = 112.7° for the Ã1A, state of HGeCl in the spectral simulation, the simulated absorption and SVL emission spectra of HGeCl and DGeCl agree very well with the available experimental LIF and SVL emission spectra, respectively. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Development of the force field parameters for phosphoimidazole and phosphohistidineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2004Yuri A. Kosinsky Abstract Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule,a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1313,1321, 2004 [source] B3LYP calculations on bishomoaromaticity in substituted semibullvalenes*JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2001David A. Hrovat Abstract B3LYP/6-31G* calculations on the degenerate rearrangements of substituted semibullvalenes spuriously predict the relative enthalpies of the bishomoaromatic TSs to be lower than the experimental values. However, the calculations do make the useful and experimentally testable prediction that the two cyano and two phenyl substituents in 2,6-dicyano-4,8-diphenylsemibullvalene (9d) are more likely than four cyano substituents in 2,4,6,8-tetracyanosemibullvalene (9f) or the four phenyl substituents in 2,4,6,8-tetraphenylsemibullvalene (9g) to produce a semibullvalene that has a bishomoaromatic equilibrium geometry in the gas phase. The major reason for the surprising finding that 9d is more likely to be bishomoaromatic than 9g is shown to be steric interactions between the phenyl groups at C-2 and C-8 and at C-4 and C-6 in bishomoaromatic structure 10g. These interactions inhibit the conjugative stabilization of 10g; but they are absent in bishomoaromatic structure 10d, where cyano groups replace the phenyl groups at C-2 and C-6 in 10g. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1565,1573, 2001 [source] Density functional study on the structural conformations and intramolecular charge transfer from the vibrational spectra of the anticancer drug combretastatin-A2JOURNAL OF RAMAN SPECTROSCOPY, Issue 4 2009L. Padmaja Abstract Combretastatin-A2 (CA2), a potential anticancer drug in advanced preclinical development, is extracted from the medicinal plant Combretum caffrum. The NIR-FT Raman and FT-IR spectral studies of the molecule were carried out and ab initio calculations performed at the B3LYP/6-31G(d) level to derive the equilibrium geometry as well as the vibrational wavenumbers and intensities of the spectral bands. The vibrational analysis showed that the molecule has a similar geometry as that of cis-stilbene, and has undergone steric repulsion resulting in twisting of the phenyl ring with respect to the ethylenic plane. Vibrational analysis was used to investigate the lowering of the stretching modes, and enhancement of infrared band intensities of the C,H stretching modes of Me2 may be attributed to the electronic effects caused by back-donation and induction from the oxygen atom. Analysis of phenyl ring modes shows that the CA2 stretching mode 8 and the aromatic C,H in-plane bending mode are equally active as strong bands in both IR and Raman spectra, which can be interpreted as the evidence of intramolecular charge transfer (ICT) between the OH and OCH3groups via conjugated ring path and is responsible for bioactivity of the molecule. Copyright © 2008 John Wiley & Sons, Ltd. [source] Vibrational spectral studies and the non-linear optical properties of a novel NLO material L -prolinium tartrateJOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2006L. Padmaja Abstract Vibrational spectral analysis of the novel non-linear optical (NLO) material, L -prolinium tartrate (LPT) was carried out using NIR-FT-Raman and FT-IR spectroscopy. The density functional theoretical (DFT) computations have been performed at B3LYP/6,31G (d) level to derive equilibrium geometry, vibrational wavenumbers, intensities and first hyperpolarizability. The reasonable NLO efficiency, predicted for the first time in this novel compound, has been confirmed by Kurtz,Perry powder second-harmonic generation (SHG) experiments. The charge-transfer interaction between the pyrrolidine ring and the carbonyl group of the tartrate anion through the intramolecular ionic hydrogen bonds is confirmed by the simultaneous activation of ring modes in IR and Raman spectra. The splitting of the ring-breathing mode, pseudo-rotational ring puckering modes and the NH2 modes of the pyrrolidine ring lead to the conclusion that the pyrrolidine ring adopts a conformation intermediate between the envelope (bent) form and the half-chair (twisted) form, resulting in the lowering of symmetry from C2 to Cs. The lowering of the methylenic stretching wavenumbers and the enhancement of the stretching intensities suggest the existence of the electronic effects of back-donation in LPT. The positional disorder of the pyrrolidine ring, the presence of blue-shifting H-bonds as well as other non-bonded interactions in LPT, low frequency H-bond vibrations and the role of intramolecular charge transfer and the hydrogen bonds in making the molecule NLO active have been analysed on the basis of the vibrational spectral features. Copyright © 2006 John Wiley & Sons, Ltd. [source] Intramolecular charge delocalization and nonlinear optical properties of Methyl 3-(4-methoxy phenyl) prop-2-enoate from vibrational spectraLASER PHYSICS LETTERS, Issue 7 2005D. Sajan Abstract The density functional computations of MMP are performed at B3LYP/6-31G (d,p) level to derive equilibrium geometry, vibrational wavenumbers and intensities, and first hyperpolarizability. Large NLO efficiency predicted for the first time in this new class of compounds has been confirmed by powder efficiency experiments. DFT calculation reveals that endocyclic angle at the junction of the propenoate group and the phenyl ring is decreased from 120° by 2.5°, whereas two neighbouring angles around the ring are increased by 2.1° and 1.2° respectively, associated with intramolecular charge transfer interaction. The vibrational spectra confirm the charge transfer interaction between ,COOCH3 group and phenyl ring through the ethylenic bridge with simultaneous infrared and Raman activation of C7=C18 stretching and ring modes 8 and 19. The large intensity differences observed between 8a and 8b modes in both IR and Raman spectrum due to the algebraic difference of the electronic effects of the substitutents have been discussed. The charge transfer interaction between ,COOCH3 group and phenyl ring through the ethylenic bridge resulting in , -electron cloud movement from donor to acceptor can make the molecule highly polarized and must be responsible for the NLO activity of MMP. (© 2005 by Astro, Ltd. Published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA) [source] Ab initio investigation of the LiNbO3 (0001) surfacePHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 2 2010Simone Sanna Abstract The polar surfaces of ferroelectric LiNbO3 have been investigated by an ab initio thermodynamical approach. Basing on density functional theory total energy calculations, we discuss the relative stability of a series of candidate surface structures with varying stoichiometry and surface reconstruction in dependence on the chemical environment. We determine the equilibrium geometry for the positively and negatively polarised surfaces and then discuss the influence of different stabilising mechanisms on the preferred terminations. Positive and negative surfaces are found to have different structure, stoichiometry and ionisation energy. The positive surface is found to contain more oxygen than the negative surface at similar conditions. Different stabilisation mechanisms like stoichiometry modification and reconstruction contribute to stabilise the polar surfaces (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] 6,-Azido-7,-hydroxy-17-oxo-5,-androstan-3,-yl acetateACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2004J. I. F. Paixão In the title compound, C21H31N3O4, a potential inhibitor of aromatase, all rings are fused trans. Rings A, B and C have chair conformations which are slightly flattened. Ring D has a 14,-envelope conformation. The steroid nucleus has a small twist, as shown by the C19,C10,C13,C18 torsion angle of 6.6,(2)°. Ab initio calculations of the equilibrium geometry of the molecule reproduce this small twist, which appears to be due to the steric effect of the 6,-azide substituent rather than to packing effects. [source] The Breakdown of the Minimum Polarizability Principle in Vibrational Motions as an Indicator of the Most Aromatic CenterCHEMISTRY - A EUROPEAN JOURNAL, Issue 20 2005Miquel Torrent-Sucarrat Dr. Abstract The vibrational motions that disobey the minimum polarizability principle (MPP) in ,-conjugated molecules are distortions of the equilibrium geometry that produce a reduction in the polarizability due to the localization of , electrons. For aromatic species, this electronic localization is responsible for the subsequent reduction in the aromaticity of the system. In the present work, we diagonalize the Hessian matrix of the polarizability with respect to the vibrational nontotally symmetric normal coordinates, to calculate the nontotally symmetric distortions that produce the maximum breakdown of the MPP in a series of twenty polycyclic aromatic hydrocarbons. It is shown that the nuclear displacements that break the MPP have larger components in those rings that possess the highest local aromaticity. Thus, these vibrational motions can be used as an indicator of local aromaticity. [source] | |||||||||||||