EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11 2003
Hans-Jörg Himmel
Abstract Herein, the dimerisation of subvalent, binary, main-group element hydrides with the potential for multiple bonding is studied using both hybrid DFT (B3LYP) and ab initio [MP2 and CCSD(T)] methods. The [2+2] cycloaddition is an important and characteristic reaction of derivatives of ethylene. A comparison of dimerisation reactions for several compounds with the potential for multiple bonding should, therefore, shed light on the properties of these species. Our study includes the hydrides E2H2 (E = B, Al, Ga, N P or As), E2H4 (E = C, Si or Ge) and ENH4 (E = B, Al or Ga) and their dimers. Several isomeric forms of the monomers and dimers have to be considered. The trends within a group and a period are established and the factors responsible for them are discussed. It turns out that, generally, the enthalpies for dimerisation increase for heavier homologues, reflecting that the most important factor is the reduced strength of the E,E bonds in the monomers prior to dimerisation and, to some degree, also the reduced ring strain in the cyclic dimers. The exceptions are the dimerisations of B2H2 and Al2H2, both of which lead to the tetrahedral E4H4 species (E = B or Al). Dimerisation of Al2H2 is associated with a smaller enthalpy than that for the dimerisation of B2H2. Comparisons and analyses are made complicated because of the changes in the structures of the isomeric global minima between homologues. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source]

Cycloadditions and Methylene Transfer in Reactions of Substituted Thiocarbonyl S -Methylides with Thiobenzophenone: A Computational Study

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 8 2005
Reiner Sustmann
Abstract Regiochemistry and methylene transfer reactions in cycloadditions of aliphatic thiocarbonyl S -methylides and thiobenzophenone are analyzed by ab initio [(U)HF/3-21G*] and DFT calculations [(U)B3LYP/6-31G*//(U)HF/3-21G* and (U)B3LYP/6-31G*]. The formation of regioisomeric 1,3-dithiolanes is explained by the competition of concerted (2,4-substituted 1,3-dithiolane) and stepwise cycloaddition via C,C -biradicals (4,5-substituted 1,3-dithiolane). Aliphatic thiocarbonyl S -methylides with sterically demanding substituents undergo substantial methylene transfer in the reaction with thiobenzophenone. This process involves dissociation of the C,C -biradical intermediate with liberation of thiobenzophenone S -methylide which, in turn, combines with a second molecule of thiobenzophenone. Calculated activation parameters for the different processes are in agreement with the experimental observations. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source]

A Theoretical ab initio Study of the Capacity of Several Binding Units for the Molecular Recognition of Anions

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 1 2005
Carolina Garau
Abstract Noncovalent bonding between anions and the ,-cloud of electron-deficient aromatic rings has recently attracted considerable attention. Complexes of bromide with different electron-deficient aromatic rings and with other binding units based on hydrogen bonding (urea, thiourea and squaramide) have been studied and compared using high level B3LYP/6-31++G** ab initio and Molecular Interaction Potential with polarization (MIPp) calculations. Our findings reveal that electron-deficient aromatic rings are excellent candidates for constructing anion receptors and that the interaction strength can be modulated by the nature of the ring. Supporting experimental evidence has been obtained from X-ray structures retrieved from the Cambridge Structural Database. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source]

A Mechanistic Rationale for the Mode Selectivity in the Intramolecular Cyclization of Ethylene-Tethered Iminoketenimines: [2+2] versus [4+2] Stepwise Cycloadditions

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 12 2004
Mateo Alajarín
Abstract A stepwise mechanism, via a zwitterionic intermediate, has been established by ab initio and DFT calculations for the intramolecular cyclization of N -(3-azabut-3-enyl)ketenimine into its corresponding [2+2] cycloadduct. The control of the mode selectivity ([2+2] versus [4+2] cycloaddition) in the intramolecular cyclization of C -vinyl- N -(iminoethylene)ketenimines, which favors the [4+2] cycloadducts, also has been rationalized by comparing the energies calculated for both reaction pathways; the results have been confirmed by a quantitative kinetic analysis. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source]

Retrospective selection bias (or the benefit of hindsight)

GEOPHYSICAL JOURNAL INTERNATIONAL, Issue 2 2001
Francesco Mulargia
SUMMARY The complexity of geophysical systems makes modelling them a formidable task, and in many cases research studies are still in the phenomenological stage. In earthquake physics, long timescales and the lack of any natural laboratory restrict research to retrospective analysis of data. Such ,fishing expedition' approaches lead to optimal selection of data, albeit not always consciously. This introduces significant biases, which are capable of falsely representing simple statistical fluctuations as significant anomalies requiring fundamental explanations. This paper identifies three different strategies for discriminating real issues from artefacts generated retrospectively. The first attempts to identify ab initio each optimal choice and account for it. Unfortunately, a satisfactory solution can only be achieved in particular cases. The second strategy acknowledges this difficulty as well as the unavoidable existence of bias, and classifies all ,anomalous' observations as artefacts unless their retrospective probability of occurrence is exceedingly low (for instance, beyond six standard deviations). However, such a strategy is also likely to reject some scientifically important anomalies. The third strategy relies on two separate steps with learning and validation performed on effectively independent sets of data. This approach appears to be preferable in the case of small samples, such as are frequently encountered in geophysics, but the requirement for forward validation implies long waiting times before credible conclusions can be reached. A practical application to pattern recognition, which is the prototype of retrospective ,fishing expeditions', is presented, illustrating that valid conclusions are hard to find. [source]

A Computational Study of the Sub-monolayer Growth of Pentacene

ADVANCED FUNCTIONAL MATERIALS, Issue 13 2006
D. Choudhary
Abstract A computational study of organic thin-film growth using a combination of ab,initio based energy calculations and kinetic Monte Carlo (KMC) simulations is provided. A lattice-based KMC model is used in which binding energies determine the relative rates of diffusion of the molecules. This KMC approach is used to present "landscapes" or "maps" that illustrate the possible structural outcomes of growing a thin film of small organic molecules, represented as a two-site dimer, on a substrate in which the strength of organic,substrate interactions is allowed to vary. KMC provides a mesoscopic-scale view of sub-monolayer deposition of organic thin films on model substrates, mapped out as a function of the flux of depositing molecules and the temperature of the substrate. The morphology of the crystalline thin films is shown to be a strong function of the molecule,molecule and molecule,substrate interactions. A rich variety of maps is shown to occur in which the small organic molecules either stand up or lie down in a variety of different patterns depending on the nature of the binding to the surface. In this way, it is possible to suggest how to tailor the substrate or the small organic molecule in order to create a desired growth habit. In order to demonstrate how this set of allowable maps is reduced in the case where the set of energy barriers between substrate and organic molecule are reliably known, we have used Gaussian,98 calculations to establish binding energies for the weak van der Waals interactions between a),pairs of pentacene molecules as a function of orientation and b),pentacene and two substrates, silicon surfaces passivated with cyclopentene molecules and a crystalline model of silicon dioxide. The critical nucleation size and the mode of diffusion of this idealized two-site dimer model for pentacene molecules are found to be in good agreement with experimental data. [source]

Reactivity and Selectivity of Captodative Olefins as Dienes in Hetero -Diels,Alder Reactions

HELVETICA CHIMICA ACTA, Issue 10 2008
Rubén Sanabria
Abstract The reactivity and selectivity of the the captodative olefins 1-acylvinyl benzoates 1a,1f and 3a as heterodienes in hetero -Diels,Alder reactions in the presence of electron-rich dienophiles is described. Heterodienes 1 undergo regioselective cycloaddition with the alkyl vinyl etherdienophiles 6a,b and 9 to give the corresponding dihydro-2H -pyrans 7, 8, and 10 under thermal conditions. The reactivity of these cycloadditions depends, to a large extent, on the electronic demand of the substituent in the aroyloxy group of the heterodiene. Frontier-molecular-orbital (FMO; ab initio) and density-functional-theory (DFT) calculations of the ground and transition states account for the reactivity and regioselectivity observed in these processes. [source]

Structure Investigation of Bridgehead Aziridine: Synthesis, Theoretical, and Crystallographic Study of 2,4,6-Triphenyl-1,3-diazabicyclo[3.1.0]hex-3-ene

HELVETICA CHIMICA ACTA, Issue 2 2006
Giuseppe Bruno
Abstract A one-pot three-component procedure to efficiently create the 1,3-diazabicyclo[3.1.0]hex-3-ene system is reported. The molecular structure of 2,4,6-triphenyl-1,3-diazabicyclo[3.1.0]hex-3-ene (3) was studied by X-ray diffraction and compared to ab initio and density-functional-theory (DFT) calculations restricted to the core moiety. Geometry optimizations for structural isomers and tautomeric forms of this aziridine fragment, taken as simplified models, were carried out at high calculation levels. Moreover, the same methods were utilized to evaluate the proton affinity of two crucial aziridine tautomers. [source]

Hetero-,-systems from 2 + 2 cycloreversion, part 2.1Ab initio thermochemical study of heterocyclobutanes 2 + 2 cycloreversion to form heteroethenes H2C=X (X=NH, O, SiH2, PH, S),

HETEROATOM CHEMISTRY, Issue 7 2007
Leonid E. Gusel'nikov
Ab initio and DFT thermochemical study of diradical mechanism of 2 + 2 cycloreversion of parent heterocyclobutanes and 1,3-diheterocyclobutanes, cyclo -(CH2CH2CH2X), and cyclo -(CH2XCH2X), where X = NH, O, SiH2, PH, S, was undertaken by calculating closed-shell singlet molecules at three levels of theory: MP4/6-311G(d)//MP2/6-31G(d)+ZPE, MP4/6-311G(d,p)//MP2/6-31G (d,p)+ZPE, and B3LYP/6-311+G(d,p)+ZPE. The enthalpies of 2 + 2 cycloreversion decrease on going from group 14 to group 16 elements, being substantially higher for the second row elements. Normally endothermic 2 + 2 cycloreversion is predicted to be exothermic for 1,3-diazetidine and 1,3-dioxtane. Strain energies of the four-membered rings were calculated via the appropriate homodesmic reactions. The enthalpies of ring opening via the every possible one-bond homolysis that results in the formation of the corresponding 1,4-diradical were found by subtracting the strain energies from the central bond dissociation energies of the heterobutanes CH3CH2,CH2XH, CH3CH2,XCH3, and HXCH2,XCH3. The latter energies were determined via the enthalpies of the appropriate dehydrocondensation reactions, using C,H and X,H bond energies in CH3XH calculated at G2 level of theory. Except 1,3-disiletane, in which ring-opening enthalpy attains 69.7 kcal/mol, the enthalpies of the most economical ring openings do not exceed 60.7 kcal/mol. The 1,4-diradical decomposition enthalpies found as differences between 2 + 2 cycloreversion and ring-opening enthalpies were negative, the least exothermicity was calculated for , CH2SiH2CH2CH2. The only exception was 1,3-disiletane, which being diradical, CH2SiH2CH2SiH2, decomposed endothermically. Since decomposition of the diradical containing two silicon atoms required extra energy, raising the enthalpy of the overall reaction to 78.9 kcal/mol, 1,3-disiletane was predicted to be highly resisting to 2 + 2 cycloreversion. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:704,720, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20377 [source]

Sandwich compounds with central hypercoordinate carbon, nitrogen, and oxygen: A quantum-chemical study

HETEROATOM CHEMISTRY, Issue 6 2006
Ruslan M. Minyaev
Ab initio (MP2(fu)/6-311+G**) and DFT (B3LYP/6-311+G**) calculations predict stable structures of sandwich compounds with the central carbon, nitrogen, and oxygen atoms surrounding lithium counterions between three-membered (BH)3 rings. The lithium counterions play a crucial role in the stabilization of these systems. The topological Bader analysis performed for these sandwich systems demonstrates that the central atom is linked to the ligands by nine-bond paths and, consequently, should be regarded as a nine-coordinated atom. Such a coordination number of carbon is the highest for all known main group organoelement compounds. © 2006 Wiley Periodicals, Inc. Heteroatom Chem 17:464,474, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20268 [source]

Experimental and theoretical studies on some new pyrrol-2,3-diones formation

HETEROATOM CHEMISTRY, Issue 1 2004
Ismail Yildirim
4-Benzoyl-5-phenyl-2,3-furandione (1) reacts with asymmetric disubstituted urea derivatives like 1,1-dimethylurea (2a) and 1,1-diethylurea (2b) by the elimination of a H2O molecule to give the 4-benzoyl-1-(N,N -dialkylcarbamyl)-5-phenyl-2,3-pyrroldiones 3a and 3b. The structures of 3a,b were determined by the 13C NMR, 1H NMR, IR spectroscopic data and elemental analyses. The electronic structures of the reactants, their transition states, intermediate states, and final products of the reactions were investigated on the basis of AM1 and ab initio (DFT) methods. © 2003 Wiley Periodicals, Inc. Heteroatom Chem 15:9,14, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.10204 [source]

Revealing the Design Principles of High-Performance Biological Composites Using Ab initio and Multiscale Simulations: The Example of Lobster Cuticle

ADVANCED MATERIALS, Issue 4 2010
Svetoslav Nikolov
Natural materials are hierarchically structured nanocomposites. A bottom-up multiscale approach to model the mechanical response of the chitin-based mineralized cuticle material of Homarus americanus is presented, by combining quantum-mechanical ab initio calculations with hierarchical homogenization. The simulations show how the mechanical properties are transferred from the atomic scale through a sequence of specifically designed microstructures to realize optimal stiffness. [source]

Toward Site-Specific Stamping of Graphene

ADVANCED MATERIALS, Issue 12 2009
Dongsheng Li
A physical hypothesis based on theory and ab initio modeling for the stamping of graphene and few-layers graphene (FLG) on silica is presented, and the feasibility of site-specific stamping of FLG patterns is demonstrated experimentally (figure shows ten-layer FLG pattern stamped on silica). The site-specific nature of the patterned stamps could enable high-throughput fabrication of future graphene-based integrated devices. [source]

Measurements of the kinetics of the OH + ,-pinene and OH + ,-pinene reactions at low pressure

INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 5 2002
B. 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]

Kinetics and mechanism for the H-for-X exchange process in the H + C6H5X reactions: A computational study

INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 11 2001
I. V. Tokmakov
The addition of H atoms to benzene and toluene and subsequent transformations were investigated using high level ab initio and density functional theory methods. Molecular structures and vibrational frequencies calculated at the B3LYP/6-311++G(d,p) level of theory were used in combination with adjusted G2M energetic parameters for RRKM rate constant calculations. Standard heats of formation for cyclohexadienyl and cyclohexadienyl, 6-methyl radicals calculated through isodesmic reactions amounted to 49.5 ± 2 and 42.9 ± 3 kcal/mol, respectively. Rate constants for various elementary reactions involved in the H-for-X exchange (X = D, CH3) were calculated and closely correlated with the available experimental kinetic data. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 633,653, 2001 [source]

Embryonic reversions and lineage infidelities in tumour cells: genome-based models and role of genetic instability

INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY, Issue 2 2005
Leon P. Bignold
Summary Reversions to ,embryonic precursor'-type cells and infidelities of tumour cell lineage (including metaplasias) have been recognized as aspects of various tumour types since the 19th century. Since then, evidence of these phenomena has been obtained from numerous clinical, biochemical, immunological and molecular biological studies. In particular, microarray studies have suggested that ,aberrant' expressions of relevant genes are common. An unexplained aspect of the results of these studies is that, in many tumour types, the embryonic reversion or lineage infidelity only occurs in a proportion of cases. As a parallel development during the molecular biological investigation of tumours over the last several decades, genetic instability has been found much more marked, at least in some preparations of tumour cells, than that identified by means of previous karyotypic investigations of tumours. This study reviews examples of embryonic reversion and lineage infidelity phenomena, which have derived from the various lines of investigation of cancer over the last 150 or so years. Four categories of circumstances of the occurrence of embryonic reversions or lineage infidelities have been identified , (i) as part of the defining phenotype of the tumour, and hence being presumably integral to the tumour type, (ii) present ab initio in only some cases of the tumour type, and presumably being regularly associated with, but incidental to, the essential features of the tumour type, (iii) occurring later in the course of the disease and thus being possibly a manifestation of in vivo genetic instability and ,tumour progression' and (iv) arising probably by genetic instability, during the processes, especially cell culture, associated with ex vivo investigations. Genomic models are described which might account for the origin of these phenomena in each of these circumstances. [source]

QR-SCMEH-MO calculations on inner-transition metal diatomic molecules having 12 valence electrons-Nd2 and U2

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2010
Edward A. Boudreaux
The QR-SCMEH-MO computational method has been developed and tested on a numerous variety of inorganic systems over some 45-plus years, with surprisingly good success. More recently this method has been applied to the transition metal molecules, Cr2, Mo2, W2, and Sg2 with 12 valence d/s electrons. The results were at least as good as those obtained from the most accurate ab initio and DFT methods currently available. An extension of the method has been made to the diatomic 12 valence electrons, f/s orbital systems, Nd2 and U2, which is the topic of this presentation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source]

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2010
Mahmoud Moradi
Abstract Depending on their environment, polyproline peptides form chiral helices that may be either left- (PPII) or right-handed (PPI). Here, we have characterized both the structure and free energy landscapes of Ace-(Pro)n -Nme (n an integer less than 13) peptides, in vacuo and in implicit water environments. Both ab initio and classical molecular dynamics methods were used. In terms of the latter, we used a recently developed Adaptively Biased Molecular Dynamics (ABMD) method in conjunction with three different force fields (ff99, ff99SB, ff03) and two different Generalized Born models for the implicit solvent environment. Specifically, the ABMD method provides for an accurate description of the free energy landscapes in terms of a set of collective variables, which were carefully chosen as to reflect the "slow modes" of the polyproline peptides. These are primarily based on the cis - trans isomerization associated with the prolyl bonds. In agreement with recent experimental results, the peptides form not only the pure PPII or PPI structures but also a large number of stable conformers having more or less similar free energies, whose distributions we have characterized. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source]

The role of the Frontier orbitals in acid,base chemistry of organic amines probed by ab initio and chemometric techniques

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 11 2010
Felipe A. La Porta
Abstract The Frontier effective-for-reaction molecular orbital (FERMO) concept emerges as a powerful and innovative implement to investigate the role of molecular orbitals (MOs) applied in the description of breakage and formation of chemical bonds. In this work, theoretical calculations were carried out for conjugated acids of 18 amines and their acid,base behavior was analyzed using MO energies. We observed that highest occupied MO (HOMO) energies are inadequate to describe the acid,base behavior of these compounds. By using the FERMO concept, the reactions that are driven by HOMO, and those that are not, can be better explained, independent of the calculation method used, as independent of the calculation method used, both HF and Kohn,Sham methodologies lead to the same FERMO. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source]

Electronic spectrum of 2-pyridone+: Ab initio and time-dependent density functional calculations

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2010
D. Hammoutène
Abstract In a comparative study, the doublet and quartet electronic states of the 2-pyridone+ cation are calculated using the PBE0/6-311+G(d,p) technique and the CASSCF and MRCI(+Q) methods in connection with the cc-pVDZ and cc-pVTZ Dunning's basis sets. Our data show that TD-DFT describes quite well the vertical excitation energies of these electronic states, whereas, multiconfiguration methods should be used for the investigation of the fragmentation and the dynamics of this molecular species. This is related to the change of the nature of the wavefunction of these electronic states along the corresponding reactive coordinates not accounted for by TD-DFT methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source]

Structural and interaction analysis of helical heparin oligosaccharides with the fragment molecular orbital method

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2009
Toshihiko Sawada
Abstract The fragment molecular orbital method (FMO) was applied to the geometry optimization of several heparin oligosaccharides at the RHF/6-31(+)G(d) level combined with the polarizable continuum model (PCM). For comparison, GLYCAM force field optimization in explicit solvent was also conducted. Good accuracy of FMO was demonstrated in comparison to ab initio at the MP2/PCM level. The interaction analysis was conducted using the pair interaction energy decomposition analysis (PIEDA), and the role of hydrogen bonding and solvent was elucidated in the helix formation of heparin in solution. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source]

Ab initio and DFT calculations of benzaldoxime elimination kinetics in the gas phase

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2008
Jose R. Mora
Abstract The mechanism for the gas-phase molecular elimination kinetics of benzaldoxime was examined at MP2/6-31G, MP2/6-31G(d,p), B3LYP/6-31G, B3LYP/6-31G(d,p), MPW1PW91/6-31G, and MPW1PW91/6-31G(d,p) levels of theory. The products of elimination of this oxime are benzonitrile and water. Calculated thermodynamic and kinetic parameters estimated from B3LYP/6-31G was found to be in better agreement with the experimental values. Transition state structure is best described as a four-membered cyclic structure with good approximation to planarity. NBO charges analysis revealed a little greater polarization of the benzylic C,H,+ rather than N,OH,,. Bond indexes and synchronicity parameters are in agreement with a concerted semi-polar type of mechanism with benzylic CH bond breaking as determining step of the reaction. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source]

Erratum for ",-Aminoacrolein: An Ab initio, AIM and NBO Study"

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2008
Isaac Jimenez-Fabian
No abstract is available for this article. [source]

Theoretical investigations on analytical potential energy function and spectroscopic parameters for the state b3,u of dimer 7Li2

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2007
De-Heng Shi
Abstract The SAC-CI (symmetry-adapted-cluster configuration-interaction) method presented in Gaussian 03 program package is applied to investigate the adiabatic potential energy curves (PECs) of 7Li2(b3,u). These calculations are performed at numbers of basis sets, such as 6-311++G(3df,3pd), 6-311++G(2df,2pd), 6-311++G(df,pd), D95V++, D95(3df,3pd), D95(d,p), cc-PVTZ, 6-311++G and 6-311++G(d,p). All the ab initio calculated points are fitted to the analytic Murrell-Sorbie functions and then used to compute the spectroscopic parameters. The analytic potential energy function (APEF) for this b3,u state is reported. By comparison, the spectroscopic parameters reproduced by the APEF attained at 6-311++G(2df,2pd) are found to be very close to the latest experimental findings. With the APEF obtained at the SAC-CI/6-311++G(2df,2pd) level of theory, a total of 62 vibrational states is found when J = 0. The complete vibrational levels, classical turning points, inertial rotation and centrifugal distortion constants for these vibrational states are also reported. The reasonable dissociation limit for this state is deduced using the calculated results at present. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]

Quantum chemical studies on molecular structural conformations and hydrated forms of salicylamide and O-hydroxybenzoyl cyanide

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2005
K. 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]

Principal component analysis of the effects of wavefunction modification on the electrostatic potential of indole

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005
Maíra A. Carvalho
Abstract The molecular electrostatic potential (MEP) of the indole molecule was calculated in a three-dimensional grid in which the molecule was centered at the origin. To evaluate the dependence of MEP on the type of calculation, semiempirical, ab initio, and density functional theory methods with different basis sets were employed. The data matrix generated by these calculations was analyzed by principal component analysis (PCA). The appearance of outliers and the effect of wavefunction modifications such as the introduction of electron correlations and diffuse functions were highlighted by the use of PCA. The spatial localization of such effects around the molecule was possible from the loadings values associated with the graphical analysis of the grid points. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source]

Benzonitriles: Survey of their importance and scaling of their vibrational frequencies

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2003
M. Alcolea Palafox
Abstract This work provides a short survey of the studies carried out on benzonitrile and its derivatives, with special attention on a spectroscopic point of view. The importance and main applications of these molecules are also briefly indicated. For an accurate assignment of their vibrational spectra, the scaling procedures for the wave numbers are described. For this purpose, the performance of semiempirical, ab initio, and density functional methods, with different basis sets, is determined. A "resume" of the main scaling factors to be used in the calculated wave numbers is shown. The results obtained for several benzene derivatives, and in particular for four benzonitriles, are analyzed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 189,204, 2003 [source]

Molecular structure, conformational analysis and charge distribution of pralidoxime: Ab initio and DFT studies

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2002
Alexandre 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]

Low-resolution structure of immunoglobulins IgG1, IgM and rheumatoid factor IgM-RF from solution X-ray scattering data

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2003
Vladimir V. Volkov
Low-resolution structures of immunoglobulins IgG, IgM and rheumatoid factor IgM-RF in solution were analyzed using synchrotron radiation small-angle X-ray scattering and the macromolecular shapes were restored ab initio from the scattering data. The shape of IgG agrees well with the distorted Y-type crystallographic model but has a swollen appearance reflecting flexibility of the molecule in solution. The structures of pentameric IgM and IgM-RF were reconstructed assuming a five-fold symmetry. The IgM displays a flat star-like shape with observable F(ab)2 regions. The overall shape of the IgM-RF is similar to that of the IgM but with distinctly asymmetric F(ab)2 regions. This result agrees with the earlier observed functional dissimilarity of the Fab fragments in the rheumatoid factor and points to their structural dissimilarity. [source]

Interactions of the "piano-stool" [ruthenium(II) (,6 -arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2009
k Futera
Abstract Piano stool ruthenium complexes of the composition [Ru(II)(,6 -arene)(en)Cl]+/2+ (en = ethylenediamine) represent an emerging class of cisplatin-analogue anticancer drug candidates. In this study, we use computational quantum chemistry to characterize the structure, stability and reactivity of these compounds. All these structures were optimized at DFT(B3LYP)/6-31G(d) level and their single point properties were determined by the MP2/6-31++G(2df,2pd) method. Thermodynamic parameters and rate constants were determined for the aquation process, as a replacement of the initial chloro ligand by water and subsequent exchange reaction of aqua ligand by nucleobases. The computations were carried out at several levels of DFT and ab initio theories (B3LYP, MP2 and CCSD) utilizing a range of bases sets (from 6-31G(d) to aug-cc-pVQZ). Excellent agreement with experimental results for aquation process was obtained at the CCSD level and reasonable match was achieved also with the B3LYP/6-31++G(2df,2pd) method. This level was used also for nucleobase-water exchange reaction where a smaller rate constant for guanine exchange was found in comparison with adenine. Although adenine follows a simple replacement mechanism, guanine complex passes by a two-step mechanism. At first, Ru-O6(G) adduct is formed, which is transformed through a chelate TS2 to the Ru-N7(G) final complex. In case of guanine, the exchange reaction is more favorable thermodynamically (releasing in total by about 8 kcal/mol) but according to our results, the rate constant for guanine substitution is slightly smaller than the analogous constant in adenine case when reaction course from local minimum is considered. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source]