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State Geometries (state + geometry)
Selected AbstractsAbsorption, resonance, and near-resonance Raman studies of the tetracyanoquinodimethane neutral and its monoanion in terms of density functional theory and complete active space self-consistent field methodsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2006Marcin Makowski Abstract The electronic structure of the 11B1u and 12B3u excited electronic states of the tetracyanoquinodimethane (TCNQ) neutral and its charged derivative are studied within the framework of complete active space self-consistent field (CASSCF) and Becke's three-parameter hybrid method with Lee,Yang,Parr correlation functional (B3LYP) methods applied to the level aug-cc-p-VDZ basis set. Both CASSCF/aug-cc-p-VDZ and B3LYP/aug-cc-p-VDZ treatments provide the ground-state and the excited state geometries; these are then used to assess the Franck,Condon (FC) parameters in the 11B1u state of the neutral TCNQ and in the 12B3u state of the TCNQ monoanion. The quality of numerical results is then tested on the base of available experimental near-resonance and resonance Raman data. The studies are performed in terms of the vibronic model, which takes both FC and mode-mixing (Dushinsky) effects into account. This somewhat simplified vibronic model leads to very good agreement between the theory and the Raman experiments concerning both neutral TCNQ and its monoanion. In particular, the calculated excitation profiles of the ,2 = 2215 cm,1, ,4 = 1389 cm,1, ,5 = 1195 cm,1, and ,9 = 336 cm,1 fundamentals are shown to be in excellent agreement with those for the TCNQ monoanion. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] TDDFT investigation on nucleic acid bases: Comparison with experiments and standard approachJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2004M.K. Shukla Abstract A comprehensive theoretical study of electronic transitions of canonical nucleic acid bases, namely guanine, adenine, cytosine, uracil, and thymine, was performed. Ground state geometries were optimized at the MP2/6-311G(d,p) level. The nature of respective potential energy surfaces was determined using the harmonic vibrational frequency analysis. The MP2 optimized geometries were used to compute electronic vertical singlet transition energies at the time-dependent density functional theory (TDDFT) level using the B3LYP functional. The 6-311++G(d,p), 6-311(2+,2+)G(d,p), 6-311(3+,3+)G(df,pd), and 6-311(5+,5+)G(df,pd) basis sets were used for the transition energy calculations. Computed transition energies were found in good agreement with the corresponding experimental data. However, in higher transitions, the Rydberg contaminations were also obtained. The existence of ,,* type Rydberg transition was found near the lowest singlet ,,* state of all bases, which may be responsible for the ultrafast deactivation process in nucleic acid bases. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 768,778, 2004 [source] Applicability of MNDO techniques AM1 and PM3 to ring-structured polymersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2002L. Y. A. Dávila Abstract Semiempirical Hartree-Fock techniques are widely used to study properties of long ring-structured chains, although these types of systems were not included in the original parametrization ensembles. These techniques are very useful for an ample class of studies, and their predictive power should be tested. We present here a study of the applicability of some techniques from the NDDO family (MNDO, AM1, and PM3) to the calculation of the ground state geometries of a specific set of molecules with the ring-structure characteristic. For this we have chosen to compare results against ab initio Restricted Hartree-Fock 6-31G(d,p) calculations, extended to Mřller-Plesset 2 perturbation theory for special cases. The systems investigated comprise the orthobenzoquinone (O2C6H4) molecule and dimers (O2C6H4)2, as well as trimers of polyaniline, which present characteristics that extend to several systems of interest in the field of conducting polymers, such as ring structure and heterosubstitution. We focus on the torsion between rings, because this angle is known to affect strongly the electronic and optical properties of conjugated polymers. We find that AM1 is always in qualitative agreement with the ab initio results, and is thus indicated for further studies of longer, more complicated chains. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1135,1142, 2002 [source] Theoretical design study on multifunctional triphenyl amino-based derivatives for OLEDsJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 11 2009Lu-Yi Zou Abstract The use of triphenyl amino-based derivatives in organic light-emitting diodes (OLEDs) can significantly improve their efficiency and stability and especially their electroluminescence characteristics , most of the new hole-transport materials have this feature. In this study, a series of triphenyl amino-based compounds were computed, including two newly designed molecules. They can function as charge transport materials and emitters with high efficiency and stability. To reveal the relationship between the properties and structures of these bifunctional and multifunctional electroluminescent materials, the ground and excited state geometries were optimized at the B3LYP/6-31G(d), HF/6-31G(d), TD-B3LYP/6-31G(d), and CIS/6-31G(d) levels, respectively. The ionization potentials (IPs) and electron affinities (EAs) were computed. The lowest excitation energies, the maximum absorption, and emission wavelengths of these compounds were calculated by employing the time-dependent density functional theory (TD-DFT) method. Also, the mobilities of holes and electrons were studied computationally based on the Marcus electron transfer theory. The CH2Cl2 solvent effect on the absorption spectra of N,N,-di-1-naphthyl- N,N,-diphenylbenzidine (NPB) was considered by polarizable continuum model (PCM). The results obtained for these compounds are in good agreement with the experimental values. These data show that the proposed compounds 1 and 2 (N,B-di-1-naphthyl-N,B-diphenylbenzidine and Mes2N[p-4,4,-biphenyl-NPh(1-naphthyl)]), are multifunctional and bifunctional materials similar to Mes2B[p -4,4,-biphenyl-NPh(1-naphthyl)] (BNPB) and NPB, respectively. Copyright © 2009 John Wiley & Sons, Ltd. [source] Surface-enhanced Raman scattering and density functional theory studies of bis(4-aminophenyl)sulfone,JOURNAL OF RAMAN SPECTROSCOPY, Issue 2 2010Guillermo Diaz-Fleming Abstract Raman and surface-enhanced Raman scattering (SERS) spectra of dapsone by using colloidal silver nanoparticles have been recorded. Density functional theory was used for the optimization of ground state geometries and simulation of the vibrational spectrum of this molecule. The SERS spectrum with a large silver cluster as a model metallic surface was simulated for the first time. Taking into account the experimental and calculated Raman as well as the SERS normal modes and the corresponding assignments, along with the modeling of the free dapsone and the one in the presence of the colloidal silver nanoparticles, the importance of the sulfone group on the SERS effect in dapsone was inferred. Copyright © 2009 John Wiley & Sons, Ltd. [source] Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzymeJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2004Nuno M. F. S. A. Cerqueira Abstract This article focuses on the first step of the catalytic mechanism for the reduction of ribonucleotides catalyzed by the enzyme Ribonucleotide Reductase (RNR). This corresponds to the activation of the substrate. In this work a large model of the active site region involving 130 atoms was used instead of the minimal gas phase models used in previous works. The ONIOM method was employed to deal with such a large system. The results gave additional information, which previous small models could not provide, allowing a much clearer evaluation of the role of the enzyme in this step. Enzyme,substrate interaction energies, specific transition state stabilization, and substrate steric strain energies were obtained. It was concluded that the transition state is stabilized in 4.0 kcal/mol by specific enzyme,substrate interactions. However, this stabilization is cancelled by the cost in conformational energy for the enzyme to adopt the transition state geometry; the overall result is that the enzyme machinery does not lead to a rate enhancement in this step. It was also found that the substrate binds to the active site with almost no steric strain, emphasizing the complementarity and specificity of the RNR active site for nucleotide binding. The main role of the enzyme at the very beginning of the catalytic cycle was concluded to be to impose stereospecifity upon substrate activation and to protect the enzyme radical from the solvent, rather than to be an reaction rate enhancement. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 2031,2037, 2004 [source] Computational Study of the Phosphoryl Transfer Catalyzed by a Cyclin-Dependent KinaseCHEMISTRY - A EUROPEAN JOURNAL, Issue 30 2007Marco De, Vivo Dr. Abstract A cyclin-dependent kinase, Cdk2, catalyzes the transfer of the ,-phosphate from ATP to a threonine or serine residue of its polypeptide substrates. Here, we investigate aspects of the reaction mechanism of Cdk2 by gas-phase density functional calculations, classical molecular dynamics, and Car,Parrinello QM/MM simulations. We focus on the role of the conserved Asp127 and on the nature of the phosphoryl transfer reaction mechanism catalyzed by Cdk2. Our findings suggest that Asp127 is active in its deprotonated form by assisting the formation of the near-attack orientation of the substrate serine or threonine. Therefore, the residue does not act as a general base during the catalysis. The mechanism for the phosphoryl transfer is a single SN2-like concerted step, which shows a phosphorane-like transition state geometry. Although the resulting reaction mechanism is in agreement with a previous density functional study of the same catalytic reaction mechanism (Cavalli et,al., Chem. Comm.2003, 1308,1309), the reaction barrier is considerably lower when QM/MM calculations are performed, as in this study (,42,kcal,mol,1 QM vs. ,24,kcal,mol,1 QM/MM); this indicates that important roles for the catalysis are played by the protein environment and solvent waters. Because of the high amino acid sequence conservation among the whole family of cyclin-dependent kinases (CDKs), these results could be general for the CDK family. [source] | ||||||||||