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Ab Initio Methods (ab + initio_methods)
Selected AbstractsThe embedded ion method: A new approach to the electrostatic description of crystal lattice effects in chemical shielding calculationsCONCEPTS IN MAGNETIC RESONANCE, Issue 5 2006Dirk Stueber Abstract The nuclear magnetic shielding anisotropy of NMR active nuclei is highly sensitive to the nuclear electronic environment. Hence, measurements of the nuclear magnetic shielding anisotropy represent a powerful tool in the elucidation of molecular structure for a wide variety of materials. Quantum mechanical ab initio nuclear magnetic shielding calculations effectively complement the experimental NMR data by revealing additional structural information. The accuracy and capacity of these calculations has been improved considerably in recent years. However, the inherent problem of the limitation in the size of the systems that may be studied due to the relatively demanding computational requirements largely remains. Accordingly, ab initio shielding calculations have been performed predominantly on isolated molecules, neglecting the molecular environment. This approach is sufficient for neutral nonpolar systems, but leads to serious errors in the shielding calculations on polar and ionic systems. Conducting ab initio shielding calculations on clusters of molecules (i.e., including the nearest neighbor interactions) has improved the accuracy of the calculations in many cases. Other methods of simulating crystal lattice effects in shielding calculations that have been developed include the electrostatic representation of the crystal lattice using point charge arrays, full ab initio methods, ab initio methods under periodic boundary conditions, and hybrid ab initio/molecular dynamics methods. The embedded ion method (EIM) discussed here follows the electrostatic approach. The method mimics the intermolecular and interionic interactions experienced by a subject molecule or cluster in a given crystal in quantum mechanical shielding calculations with a large finite, periodic, and self-consistent array of point charges. The point charge arrays in the EIM are generated using the Ewald summation method and embed the molecule or ion of interest for which the ab initio shielding calculations are performed. The accuracy with which the EIM reproduces experimental nuclear magnetic shift tensor principal values, the sensitivity of the EIM to the parameters defining the point charge arrays, as well as the strengths and limitations of the EIM in comparison with other methods that include crystal lattice effects in chemical shielding calculations, are presented. © 2006 Wiley Periodicals, Inc. Concepts Magn Reson Part A 28A: 347,368, 2006 [source] Density functional and ab initio studies on structures and energies of the ground state of CrCOINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2007Joonghan Kim Abstract CrCO was studied using density functional theory (DFT) and ab initio methods. We obtained the two-dimensional potential energy surface (PES), geometry, and vibrational frequencies for CrCO in a septet state. Two minimum structures were found in the CCSD(T) calculation, including a local minimum that is a weak van der Waals (vdW) complex. All DFT methods yield only one minimum structure. We demonstrate that the bond dissociation energy (0.50 kcal/mol) and vibrational frequency (1981.1 cm,1) of CrCO calculated using CCSD(T) are in better agreement with experimental values (<1.5 kcal/mol and 1977 cm,1) than any of the reported theoretical studies. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] First principles study of 1,2-dichlorobenzene adsorption on metallic carbon nanotubesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2006Solange B. Fagan Abstract A systematic study of the structural and electronic properties of a 1,2-dichlorobenzene (DCB) molecule interacting with metallic single-wall carbon nanotubes is reported. The calculations were performed through ab initio methods using the SIESTA code. The interaction between DCB and nanotube is observed to depend on the diameter and it is larger for metallic nanotubes when compared with semiconducting. The binding energies are small thus suggesting that the interaction is through a physisorption process. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] The crystal structure of perdeuterated methanol hemiammoniate (CD3OD·0.5ND3) determined from neutron powder diffraction data at 4.2 and 180,KJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2010A. D. Fortes The crystal structure of perdeuterated methanol hemiammoniate, CD3OD·0.5ND3, has been solved from neutron powder diffraction data collected at 4.2 and 180,K. The structure is orthorhombic, space group Pn21a (Z = 4), with unit-cell dimensions a = 12.70615,(16), b = 8.84589,(9), c = 4.73876,(4),Å, V = 532.623,(8),Å3 [,calc = 1149.57,(2),kg,m,3] at 4.2,K, and a = 12.90413,(16), b = 8.96975,(8), c = 4.79198,(4),Å, V = 554.656,(7),Å3 [,calc = 1103.90,(1),kg,m,3] at 180,K. The crystal structure was determined by ab initio methods from the powder data; atomic coordinates and isotropic displacement parameters were subsequently refined by the Rietveld method to Rp, 2% at both temperatures. The crystal structure comprises a three-dimensionally hydrogen-bonded network in which the ND3 molecules are tetrahedrally coordinated by the hydroxy moieties of the methanol molecule. This connectivity leads to the formation of zigzag chains of ammonia,hydroxy groups extending along the c axis, formed via N,D···O hydrogen bonds; these chains are cross-linked along the a axis through the hydroxy moiety of the second methanol molecule via N,D···O and O,D···O hydrogen bonds. This `bridging' hydroxy group in turn donates an O,D···N hydrogen bond to ammonia in adjacent chains stacked along the b axis. The methyl deuterons in methanol hemiammoniate, unlike those in methanol monoammoniate, do not participate in hydrogen bonding and reveal evidence of orientational disorder at 180,K. The relative volume change on warming from 4.2 to 180,K, ,V/V, is + 4.14%, which is comparable to, but more nearly isotropic (as determined from the relative change in axial lengths, e.g.,a/a) than, that observed in deuterated methanol monohydrate, and very similar to what is observed in methanol monoammoniate. [source] Trends of the bonding effect on the performance of DFT methods in electric properties calculations: A pattern recognition and metric space approach on some XY2 (X = O, S and Y = H, O, F, S, Cl) moleculesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2010Christos Christodouleas Abstract A test set of 10 molecules (open and ring forms of ozone and sulfur dioxide as well as water and hydrogen sulfide and their respective fluoro- and chloro-substituted analogs) of specific atmospheric interest has been formed as to assess the performance of various density functional theory methods in (hyper)polarizability calculations against well-established ab initio methods. The choice of these molecules was further based on (i) the profound change in the physics between isomeric systems, e.g., open (C2v) and ring (D3h) forms of ozone, (ii) the relation between isomeric forms, e.g., open and ring form of sulfur dioxide (both of C2v symmetry), and (iii) the effect of the substitution, e.g., in fluoro- and chloro-substituted water analogs. The analysis is aided by arguments chosen from the information theory, graph theory, and pattern recognition fields of Mathematics: In brief, a multidimensional space is formed by the methods which are playing the role of vectors with the independent components of the electric properties to act as the coordinates of these vectors, hence the relation between different vectors (e.g., methods) can be quantified by a proximity measure. Results are in agreement with previous studies revealing the acceptable and consistent behavior of the mPW1PW91, B3P86, and PBE0 methods. It is worth noting the remarkable good performance of the double hybrid functionals (namely: B2PLYP and mPW2PLYP) which are for the first time used in calculations of electric response properties. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010 [source] Interesting properties of Thomas,Fermi kinetic and Parr electron,electron-repulsion DFT energy functional generated compact one-electron density approximation for ground-state electronic energy of molecular systemsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2009Sandor Kristyan Abstract The reduction of the electronic Schrodinger equation or its calculating algorithm from 4N -dimensions to a (nonlinear, approximate) density functional of three spatial dimension one-electron density for an N -electron system, which is tractable in the practice, is a long desired goal in electronic structure calculation. If the Thomas-Fermi kinetic energy (,,,5/3dr1) and Parr electron,electron repulsion energy (,,,4/3dr1) main-term functionals are accepted, and they should, the later described, compact one-electron density approximation for calculating ground state electronic energy from the 2nd Hohenberg,Kohn theorem is also noticeable, because it is a certain consequence of the aforementioned two basic functionals. Its two parameters have been fitted to neutral and ionic atoms, which are transferable to molecules when one uses it for estimating ground-state electronic energy. The convergence is proportional to the number of nuclei (M) needing low disc space usage and numerical integration. Its properties are discussed and compared with known ab initio methods, and for energy differences (here atomic ionization potentials) it is comparable or sometimes gives better result than those. It does not reach the chemical accuracy for total electronic energy, but beside its amusing simplicity, it is interesting in theoretical point of view, and can serve as generator function for more accurate one-electron density models. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal: A theoretical investigation of the concerted and stepwise mechanismsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2008Daniel Norberg Abstract The stepwise and concerted pathways for the McLafferty rearrangement of the radical cations of butanal (Bu+) and 3-fluorobutanal (3F-Bu+) are investigated with density functional theory (DFT) and ab initio methods in conjunction with the 6-311+G(d,p) basis set. A concerted transition structure (TS) for Bu+, (H), is located with a Gibbs barrier height of 37.7 kcal/mol as computed with CCSD(T)//BHandHLYP. Three pathways for the stepwise rearrangement of Bu+ have been located, which are all found to involve different complexes. The barrier height for the H, transfer is found to be 2.2 kcal/mol, while the two most favorable TSs for the C,,C, cleavage are located 8.9 and 9.2 kcal/mol higher. The energies of the 3F-Bu+ system have been calculated with the promising hybrid meta-GGA MPWKCIS1K functional of DFT. Interestingly, the fluorine substitution yields a barrier height of only 20.5 kcal/mol for the concerted TS, (3F-H). A smaller computed dipole moment, 12.1 D, for (3F-H) compared with 103.2 D for (H) might explain the stabilization of the substituted TS. The H, transfer, with a barrier height of 4.9 kcal/mol, is found to be rate-determining for the stepwise McLafferty rearrangement of 3F-Bu+, in contrast to the unsubstituted case. By inspection of the spin and charge distributions of the stationary points, it is noted that the bond cleavages in the concerted rearrangements are mainly of heterolytic nature, while those in the stepwise channels are found to be homolytic. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Assessment of theoretical methods for the calculation of methyl cation affinitiesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2008Y. Wei Abstract The methyl cation affinity (MCA; 298 K) of a variety of neutral and anionic bases has been examined computationally with a wide variety of theoretical methods. These include high-level composite procedures such as W1, G3, G3B3, and G2, conventional ab initio methods such as CCSD(T) and MP2, as well as a selection of density functional theory (DFT) methods. Experimental results for a variety of small model systems are well reproduced with practically all these methods, and the performance of DFT based methods are far superior in comparison to their MP2 analogs for these small models. For larger model, systems including motifs frequently encountered in organocatalysts, the performance deteriorates somewhat for DFT methods, while it improves significantly for MP2, rendering the former methods unreliable for common organic bases. Thus, MP2 calculations performed in combination with basis sets such as 6-31+G(2d, p) or larger, appear to offer a practical and reliable approach to compute MCAs of organic bases. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2007Ross C. Walker Abstract The electronic absorption and emission spectra of large molecules reflect the extent and timescale of electron-vibration coupling and therefore the extent and timescale of relaxation/reorganization in response to a perturbation. In this paper, we present a comparison of the calculated absorption and emission spectra of NADH in liver alcohol dehydrogenase (LADH), using quantum mechanical/molecular mechanical methods, in which we vary the QM component. Specifically, we have looked at the influence of basis set (STO-3G, 3-21G*, 6-31G*, CC-pVDZ, and 6-311G**), as well as the influence of applying the DFT TD-B3LYP and ab initio TD-HF and CIS methods to the calculation of absorption/emission spectra and the reorganization energy (Stokes shift). The ab initio TD-HF and CIS methods reproduce the experimentally determined Stokes shift and spectral profiles to a high level of agreement, while the TD-B3LYP method significantly underestimates the Stokes shift, by 45%. We comment on the origin of this problem and suggest that ab initio methods may be naturally more suited to predicting molecular behavior away from equilibrium geometries. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 478,490, 2007 [source] Systematic quantum chemical study of DNA-base tautomersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2004M. Piacenza Abstract The relative energies of the energetically low-lying tautomers of pyridone, cytosine, uracil, thymine, guanine, and iso-cytosine are studied by a variety of different quantum chemical methods. In particular, we employ density functional theory (DFT) using the six functionals HCTH407, PBE, BP86, B-LYP, B3-LYP, and BH-LYP, and the ab initio methods Hartree-Fock (HF), standard second-order Møller-Plesset perturbation theory (MP2), an improved version of it (SCS-MP2), and quadratic configuration interaction including single and double excitations (QCISD) and perturbative triple corrections [QCISD(T)]. A detailed basis set study is performed for the formamide/formamidic acid tautomeric pair. In general, large AO basis sets of at least valence triple-, quality including f-functions (TZV) are employed, which are found to be necessary for an accurate energetic description of the various structures. The performance of the more approximate methods is evaluated with QCISD(T)/TZV(2df,2dp) data taken as reference. In general it is found that DFT is not an appropriate method for the problem. For the tautomers of pyridone and cytosine, most density functionals, including the popular B3-LYP hybrid, predict a wrong energetic order, and only for guanine, the correct sequence of tautomers is obtained with all functionals. Out of the density functionals tested, BH-LYP, which includes a rather large fraction of HF exchange, performs best. A consistent description of the nonaromatic versus aromatic tautomers seems to be a general problem especially for pure, nonhybrid functionals. Tentatively, this could be assigned to the exchange potentials used while the functional itself, including the correlation part, seems to be appropriate. Out of the ab initio methods tested, the new SCS-MP2 approach seems to perform best because it effectively reduces some outliers obtained with standard MP2. It outperforms the much more costly QCISD method and seems to be a very good compromise between computational effort and accuracy. © 2003 Wiley Periodicals, Inc. J Comput Chem 1: 83,98, 2004 [source] A facile synthesis of pyrazolo[3,4- D]pyridazines Via the 1,3-dipolar cycloaddition of 3-arylsydnones.JOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 20064- D]pyridazine-, 5-dihydro-1H -pyrazolo[, 6-dichloro derivatives., 6-diones, Synthesis, computational studies of 1-aryl-, their The synthetic utility of 1,3-dipolar cycloaddition of DMAD to sydnones has been exploited in the preparation of new 1-aryl-4,5-dihydro-1H -pyrazolo[3,4- d]pyridazine-3,6-diones 7a-j and their aromatic 3,6-dichloro analogues 8a-j. The lactam-lactim tautomerism of compound 7a has been studied by the semi emperical (PM3) and ab initio methods. [source] Computational study of stereoelectronic effects in fluorinated alkylamines,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 11 2005Joseph J. Urban Abstract A systematic evaluation of the stereoelectronic effects in a series of fluorinated amine compounds has been carried out. A variety of computational methods have been employed, including molecular mechanics, semi-empirical, density functional and ab initio methods. An analysis of the natural bond orbital populations has been carried out and the effect of solvent was considered via the polarized continuum model (PCM). The results indicate a preference for conformations that result in an anti-periplanar arrangement between the nitrogen lone pair and the CX bond (XF or CF3). There are variations in geometry and natural bond orbital population, with conformation that are consistent with a stereoelectronic effect whereby electron density from the nitrogen lone pair is delocalized into the CX ,* orbital. Similar results are obtained for trifluoromethyl methylamines, although the magnitude of the stereoelectronic effect is attenuated resulting in greater expected conformational diversity for these compounds. The PCM results suggest that these preferences should persist in solution. Comparison among the computational methods used reveals that there is good agreement among the ab initio and density functional methods (at the HF/6-31,+,G(d), MP2/6-31,+,G(d), MP2/6-311,+,G(2d,p) and B3LYP/6-31,+,G(d) levels) and these methods agree well with the available experimental data for ethylmethylamine. Published in 2005 by John Wiley & Sons, Ltd. [source] Determination of the 2,3-pentadienedioic acid enantiomer interconversion energy barrier 1.JOURNAL OF SEPARATION SCIENCE, JSS, Issue 15 2006Classical kinetic approach Abstract A classical kinetic method was used to determine the energy barrier for the interconversion of 2,3-pentadienedioic acid enantiomers. Each individual enantiomer was isolated by collecting the appropriate peaks from the HPLC enantiomeric separation, of racemic 2,3-pentadienedioic acid. The isolated enantiomers were racemized at 22°C using various interconversion times. The ratio of enantiomers in each reaction solution was determined by HPLC at 22°C. The corresponding peak areas of the enantiomers and the interconversion times obtained from the HPLC chromatograms were used to calculate both the interconversion rate constants describing (+) , (,) and (,) , (+) interconversions as well as the energy barriers. It was confirmed that the interconversion of 2,3-pentadienedioic acid enantiomers is a first-order kinetic reaction. Both semiempirical and ab initio methods were used to explore the mechanism of the interconversion of 2,3-pentadienedioic acid enantiomers, and to calculate the interconversion energy barrier. Comparison of the interconversion energy barriers found by the ab initio method (,G# = 110.7 kJ/mol) and by classical kinetics in the mobile phase solution at 22°C (,Gapp = 93.9 ± 0.2 kJ/mol) shows a difference which may be attributed to the different conditions assumed in the theoretical calculation (i. e., a gaseous state) and the actual experimental conditions (i. e., liquid solution) and a possible catalytic effect of the solution composition. [source] Electronic Structure and Bonding of All Crystalline Phases in the Silica,Yttria,Silicon Nitride Phase Equilibrium DiagramJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 11 2004Wai-Yim Ching This paper reviews the structures and properties of 10 binary, ternary, and quaternary crystals within the equilibrium phase diagram of the SiO2,Y2O3,Si3N4 system. They are binary compounds SiO2, Y2O3, Si3N4; ternary compounds Si2N2O, Y2Si2O7, and YSi2O5; and quaternary crystals Y2Si3N4O3 (M-melilite), Y4Si2O7N2, (N-YAM), YSiO2N (wallastonite), and Y10(SiO4)6N2 (N-apatite, N-APT). Although the binary compounds are well-known and extensively studied, the ternary and the quaternary crystals are not. Most of the ternary and the quaternary crystals simply have been referenced as secondary phases in the processing of nitrogen ceramics. Their crystal structures are complex and not precisely determined. In the quaternary crystals, there exists O/N disorder in that the exact atomic positions of the anions cannot be uniquely determined. It is envisioned that a variety of cation,anion bonding configurations exist in these complex crystals. The electronic structure and bonding in these crystals are, therefore, of great interest and are indispensable for a fundamental understanding of structural ceramics. We have used ab initio methods to study the structure and bonding properties of these 10 crystals. For crystals with unknown or incomplete structural information, we use an accurate total energy relaxation scheme to obtain the most likely atomic positions. Based on the theoretically modeled structures, the electronic structure and bonding in these crystals are investigated and related to various local cation,anion bonding configurations. These results are presented in the form of atom-resolved partial density of states, Mulliken effective charges, and bond order values. It is shown that Y,O and Y,N bonding are not negligible and should be a part of the discussion of the overall bonding schemes in these crystals. Spectroscopic properties in the form of complex, frequency-dependent dielectric functions, X-ray absorption near-edge structure (XANES), and the electron energy-loss near-edge structure (ELNES) spectra in these crystals also are calculated and compared. These results are discussed in the context of specific bonding configurations between cations (silicon and yttrium) and anions (oxygen and nitrogen) and their implications on intergranular thin films in polycrystalline Si3N4 containing rare-earth elements. [source] Experimental and theoretical NMR study of selected oxocarboxylic acid oximesMAGNETIC RESONANCE IN CHEMISTRY, Issue 1 2004Kamilla Malek Abstract 1H and 13C NMR spectra of the oxocarboxylic acid oximes 2-hydroxyiminopropanoic acid (1), 2-(4-methylthiazol-2-yl)-2-(hydroxyimino)acetic acid (2) and 2-cyano-2-(hydroxyimino)acetic acid (3) were measured in DMSO- d6, D2O and acetone- d6 solutions. The data indicate the presence of hydrogen bonding in 1 and 2 and a strong electron-withdrawing effect due to the cyano group in 3. The effect of intra- and intermolecular hydrogen bonding on the hydrogen and carbon chemical shifts in these molecules was studied theoretically. Total energy calculations of the stability of various hydrogen-bonded species, in addition to equilibrium parameters and chemical shifts, were calculated using ab initio methods (RHF, MP2) and density functional theory (B3LYP), implemented in the Gaussian 98 software package. The gauge-including atomic orbital (GIAO) method was used to predict magnetic shielding constants. Chemical shift calculations for the most stable species agree fairly well with the observed data, especially for the hydroxyl protons. Substituents adjacent to the ,-carbon show some influence of the oximic and carboxyl groups on the 13C chemical shifts, as expected for groups with different polar and anisotropic character. Copyright © 2003 John Wiley & Sons, Ltd. [source] Oxidation of dimers at the Si(100) surface studied by first-principles simulation of high-resolution EELSPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 8 2010Lucia Caramella Abstract Electron energy loss spectra of the Si(100) and Si(100):O surfaces are investigated using ab initio methods based on density functional theory. Computed spectra for the clean surface are found to be in good agreement with published experimental data, providing further confirmation that reconstructions of higher order than (2,×,1) are present on Si(100). The origins of the main spectral structures are analyzed and their relation to the surface bandstructure is illustrated. Oxygen adsorption on the surface dimers is found to cause strong modifications to the calculated spectra, thereby partially explaining the results of surface differential reflectivity experiments. [source] Isostructural BaSi2, BaGe2 and SrGe2: electronic and optical propertiesPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 7 2007D. B. Migas Abstract We have performed a theoretical study of the electronic band structure, density of states, dielectric function and absorption coefficient of isostructural BaSi2, BaGe2 and SrGe2 compounds by means of different ab initio methods. All materials are found to be indirect band-gap semiconductors displaying almost equal dispersion of bands close to the gap region. The energy gaps of 0.83, 0.57 and 0.44 eV are estimated for BaSi2, BaGe2 and SrGe2, respectively. Analysis of the absorption coefficient of BaSi2 in comparison with data for other semiconducting silicides indicates its prospects for a solar cell application. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] 3-Oxoandrosta-4,6-dien-17,-yl 2-methyl-1H -imidazole-1-carboxylate and 3-oxo-5,-androst-17,-yl 2-methyl-1H -imidazole-1-carboxylate: C,H..., and ,,, intermolecular interactionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2009Manuela Ramos Silva The title compounds, C24H30N2O3, (I), and C24H34N2O3, (II), both contain an androstane backbone and a 2-methylimidazole-1-carboxylate moiety at the 17-position. Compound (I) contains two symmetry-independent molecules (denoted 1 and 2), while compound (II) contains just one molecule in the asymmetric unit. The C,C,O,C torsion angle that reflects the twisting of the 2-methylimidazole-1-carboxylate moiety from the mean steroid plane is 143.1,(2)° for molecule 1 of (I), 73.1,(3)° for molecule 2 of (I) and 86.63,(17)° for (II). The significance of this study lies in its observation of significant differences in both molecular conformation and supramolecular aggregation between the molecules of the title compounds. The solid-state conformations compared with those obtained theoretically from ab initio methods for the isolated molecules show large differences, especially in the orientation of the methylimidazole substituent. [source] Analysis of the conformational profile of trishomocubane amino acid dipeptideBIOPOLYMERS, Issue 5 2006Krishna Bisetty Abstract 4-Amino-(D3)-trishomocubane-4-carboxylic acid is a constrained ,-amino acid residue that exhibits promising conformational characteristics, i.e., helical and ,-turns. As part of the development of conformational guidelines for the design of peptides and protein surrogates, the conformational energy calculations on trishomocubane using molecular mechanics and ab initio methods are presented. The C, carbon of trishomocubane forms part of the cyclic structure, and consequently a peptidic environment was simulated with an acetyl group on its N-terminus and a methylamide group on its C-terminus. Ramachandran maps computed at the molecular mechanics level using the standard AMBER (parm94) force field libraries compared reasonably well with the corresponding maps computed at the Hartree Fock level, using the 6-31G* basis set. Trishomocubane peptide (Ac-Tris-NHMe) is characterized by four low energy conformers corresponding to the C7ax, C7eq, 310, and ,L helical structures. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 339,349, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Copper(II)-Mediated Aromatic ortho -Hydroxylation: A Hybrid DFT and Ab Initio ExplorationCHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2008Peter Comba Prof. Dr. Abstract Mechanistic pathways for the aromatic hydroxylation by [CuII(L1)(TMAO)(O)], (L1=hippuric acid, TMAO=trimethylamine N -oxide), derived from the ON bond homolysis of its [CuII(L1)(TMAO)2] precursor, were explored by using hybrid density functional theory (B3LYP) and highly correlated ab initio methods (QCISD and CCSD). Published experimental studies suggest that the catalytic reaction is triggered by a terminal copper,oxo species, and a detailed study of electronic structures, bonding, and energetics of the corresponding electromers is presented. Two pathways, a stepwise and a concerted reaction, were considered for the hydroxylation process. The results reveal a clear preference for the concerted pathway, in which the terminal oxygen atom directly attacks the carbon atom of the benzene ring, leading to the ortho -selectively hydroxylated product. Solvent effects were probed by using the PCM and CPCM solvation models, and the PCM model was found to perform better in the present case. Excellent agreement between the experimental and computational results was found, in particular also for changes in reactivity with derivatives of L1. [source] Probing the Local Structure of Pure Ionic Liquid Salts with Solid- and Liquid-State NMR,CHEMPHYSCHEM, Issue 1 2010Peter G. Gordon Abstract Room-temperature ionic liquids (RTILs) are gaining increasing interest and are considered part of the green chemistry paradigm due to their negligible vapour pressure and ease of recycling. Evidence of liquid-state order, observed by IR and Raman spectroscopy, diffraction studies, and simulated by ab initio methods, has been reported in the literature. Here, quadrupolar nuclei are used as NMR probes to extract information about the solid and possible residual order in the liquid state of RTILs. To this end, the anisotropic nature and field dependence of quadrupolar and chemical shift interactions are exploited. Relaxation time measurements and a search for residual second-order quadrupolar coupling were employed to investigate the molecular motions present in the liquid state and infer what kind of order is present. The results obtained indicate that on a timescale of ,10,8 sec or longer, RTILs behave as isotropic liquids without residual order. [source] Ab initio Study of the Interactions between CO2 and N-Containing Organic HeterocyclesCHEMPHYSCHEM, Issue 2 2009Konstantinos D. Vogiatzis Abstract In the garden of dispersion: High-accuracy ab initio calculations are performed to determine the nature of the interactions and the most favorable geometries between CO2 and heteroaromatic molecules containing nitrogen (see figure). Dispersion forces play a key role in the stabilization of the dimer, because correlation effects represent about 50,% of the total interaction energy. The interactions between carbon dioxide and organic heterocyclic molecules containing nitrogen are studied by using high-accuracy ab initio methods. Various adsorption positions are examined for pyridine. The preferred configuration is an in-plane configuration. An electron donor,electron acceptor (EDA) mechanism between the carbon of CO2 and the nitrogen of the heterocycle and weak hydrogen bonds stabilize the complex, with important contributions from dispersion and induction forces. Quantitative results of the binding energy of CO2 to pyridine (C5H5N), pyrimidine, pyridazine, and pyrazine (C4H4N2), triazine (C3H3N3), imidazole (C3H4N2), tetrazole (CH2N4), purine (C5H4N4), imidazopyridine (C6H5N3), adenine (C5H5N5), and imidazopyridamine (C6H6N4) for the in-plane configuration are presented. For purine, three different binding sites are examined. An approximate coupled-cluster model including single and double excitations with a perturbative estimation of triple excitations (CCSD(T)) is used for benchmark calculations. The CCSD(T) basis-set limit is approximated from explicitly correlated second-order Møller,Plesset (MP2-F12) calculations in the aug-cc-pVTZ basis in conjunction with contributions from single, double, and triple excitations calculated at the CCSD(T)/6-311++G** level of theory. Extrapolations to the MP2 basis-set limit coincide with the MP2-F12 calculations. The results are interpreted in terms of electrostatic potential maps and electron density redistribution plots. The effectiveness of density functional theory with the empirical dispersion correction of Grimme (DFT-D) is also examined. [source] Does Negative Hyperconjugation Assist Enzymatic Dehydrogenations?CHEMPHYSCHEM, Issue 9 2007Gloria Tabacchi Dr. Enzyme mechanisms: Using ab initio methods and natural bond orbital analysis, negative hyperconjugation is shown to govern L -lactate oxidation chemistry and may help to determine its enzymatic dehydrogenation mechanism. The picture shows the negative hyperconjugation interaction between the lone pair on the oxygen atom and the ,*(C,H,) orbital. [source] Theoretical Determination of the Vibrational Raman Optical Activity Signatures of Helical Polypropylene ChainsCHEMPHYSCHEM, Issue 11 2006Ewa Lamparska Abstract Raman and vibrational Raman optical activity (VROA) spectra of helical conformers of polypropylene chains are simulated using ab initio methods to unravel the relationships between the vibrational signatures and the primary and secondary structures of the chains. For a polypropylene chain containing three units, conformational effects are shown to lead to more acute signatures for VROA than for Raman spectra. In addition to regular polypropylene chains, which can display right and left helicities with the same probability, chirality and therefore helicity are enforced by substituting one chain end with a phenyl group. The simulations predict that the threefold helical structures, which correspond to (TG)N conformations of the backbone, have a specific VROA backward signature in the form of an intense couplet around 1100 cm,1. This couplet is associated with collective wagging and twisting motions, while most of its intensity comes from the anisotropic invariants combining normal coordinate derivatives of the electric dipole,electric dipole polarizability and of the electric dipole,magnetic dipole polarizability. A similar signature has already been found in model helical polyethylene chains, whereas it is very weak in forward VROA. [source] | ||||||||||||||||||||||