Computational Chemistry (computational + chemistry)

Distribution by Scientific Domains

Selected Abstracts

Foreword by the Guest Editors: Computational Chemistry of Quantum Mechanical Processes

Eran Rabani
No abstract is available for this article. [source]

ChemInform Abstract: Computational Chemistry of Modified [MFe3S4] and [M2Fe2S4] Clusters: Assessment of Trends in Electronic Structure and Properties

CHEMINFORM, Issue 10 2009
Kasper P. Jensen
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]

Rationalizing the Solution Properties of Zwitterions by Means of Computational Chemistry

This short review describes our computational studies of carnitine, acetylcarnitines, and betaines over the past two decades. Interspersed among the three computational studies , a molecular mechanics study of the conformer population of carnitine and acetylcarnitine, an AM1 study of the energetics of hydrolysis of acetylcarnitine, and an HF 6-31G* study of the solvation energies and structures of a homologous series of betaines , are brief overviews of our research in designing and testing new therapeutic agents for non-insulin dependent diabetes and for protection against sexually transmitted diseases. The three studies also show how computational chemistry has evolved during this time to enable an evaluation of the structure and energetics of zwitterions in aqueous solution. [source]

Molecular modelling of the androgen receptor axis: rational basis for androgen receptor intervention in androgen-independent prostate cancer

Androgen depletion in combination with antiandrogenic agents is initially highly effective for treating prostate cancer, and is the recommended treatment for more advanced or higher-grade tumours. However, many tumours eventually become insensitive to androgens, even though the androgen receptor (AR) continues to be expressed. Computational chemistry combined with structural analysis of nuclear receptors and determination of binding affinities of natural and designed coregulators (coactivators and corepressors) provides the theoretical framework for the rational design of novel therapeutic agents directed at the AR. Adding alternative groups to various sites throughout the receptor can alter the conformation of the molecule and its functional binding with coactivators or corepressors. Possible molecules can be identified thoroughly and systematically using intelligent high-throughput screening and FASTrack chemistry (three-dimensional crystallography). Applying these techniques should eventually result in therapeutic agents for androgen-independent prostate cancer that can block binding of AR coactivators while simultaneously increasing binding of AR corepressors. [source]

Boron,Nitrogen Adducts of 1,3,5-Triaza-7-phosphaadamantane (PTA): Synthesis, Reactivity, and Molecular Structure

Brian J. Frost
Abstract Addition of BH3 to 1,3,5-triaza-7-phosphaadamantane (PTA) leads to the formation of the first coordination complex of PTA in which a nitrogen and not the phosphorus of PTA is involved in the bonding. Multinuclear NMR spectroscopy, X-ray crystallography, and computational chemistry are utilized in the characterization of the products. Crystal structures of PTA,BH3 (1) and O=PTA,BH3 (2) adducts are described. In addition a coordination polymer, [CpRu(PTA)2Cl(Ph3B3O3)]n (3), resulting from Lewis acid,base adduct formation between the PTA ligands of CpRu(PTA)2Cl and the product of the cyclocondensation of phenylboronic acid is described. The polymeric compound 3 was also characterized by X-ray crystallography. ( Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

Molecular determinants of ligand specificity in family 11 carbohydrate binding modules , an NMR, X-ray crystallography and computational chemistry approach

FEBS JOURNAL, Issue 10 2008
Aldino Viegas
The direct conversion of plant cell wall polysaccharides into soluble sugars is one of the most important reactions on earth, and is performed by certain microorganisms such as Clostridium thermocellum (Ct). These organisms produce extracellular multi-subunit complexes (i.e. cellulosomes) comprising a consortium of enzymes, which contain noncatalytic carbohydrate-binding modules (CBM) that increase the activity of the catalytic module. In the present study, we describe a combined approach by X-ray crystallography, NMR and computational chemistry that aimed to gain further insight into the binding mode of different carbohydrates (cellobiose, cellotetraose and cellohexaose) to the binding pocket of the family 11 CBM. The crystal structure of C. thermocellum CBM11 has been resolved to 1.98 in the apo form. Since the structure with a bound substrate could not be obtained, computational studies with cellobiose, cellotetraose and cellohexaose were carried out to determine the molecular recognition of glucose polymers by CtCBM11. These studies revealed a specificity area at the CtCBM11 binding cleft, which is lined with several aspartate residues. In addition, a cluster of aromatic residues was found to be important for guiding and packing of the polysaccharide. The binding cleft of CtCBM11 interacts more strongly with the central glucose units of cellotetraose and cellohexaose, mainly through interactions with the sugar units at positions 2 and 6. This model of binding is supported by saturation transfer difference NMR experiments and linebroadening NMR studies. [source]

Thermochemistry for enthalpies and reaction paths of nitrous acid isomers

Rubik Asatryan
Recent studies show that nitrous acid, HONO, a significant precursor of the hydroxyl radical in the atmosphere, is formed during the photolysis of nitrogen dioxide in soils. The term nitrous acid is largely used interchangeably in the atmospheric literature, and the analytical methods employed do not often distinguish between the HONO structure (nitrous acid) and HNO2 (nitryl hydride or isonitrous acid). The objective of this study is to determine the thermochemistry of the HNO2 isomer, which has not been determined experimentally, and to evaluate its thermal and atmospheric stability relative to HONO. The thermochemistry of these isomers is also needed for reference and internal consistency in the calculation of larger nitrite and nitryl systems. We review, evaluate, and compare the thermochemical properties of several small nitric oxide and hydrogen nitrogen oxide molecules. The enthalpies of HONO and HNO2 are calculated using computational chemistry with the following methods of analysis for the atomization, isomerization, and work reactions using closed- and open-shell reference molecules. Three high-level composite methods G3, CBS-QB3, and CBS-APNO are used for the computation of enthalpy. The enthalpy of formation, ,Hof(298 K), for HONO is determined as ,18.90 0.05 kcal mol,1 (,79.08 0.2 kJ mol,1) and as ,10.90 0.05 kcal mol,1 (,45.61 0.2 kJ mol,1) for nitryl hydride (HNO2), which is significantly higher than values used in recent NOx combustion mechanisms. H-NO2 is the weakest bond in isonitrous acid; but HNO2 will isomerize to HONO with a similar barrier to the HONO bond energy; thus, it also serves as a source of OH in atmospheric chemistry. Kinetics of the isomerization is determined; a potential energy diagram of H/N/O2 system is presented, and an analysis of the triplet surface is initiated. 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 378,398, 2007 [source]

MaSK: A visualization tool for teaching and research in computational chemistry

Yevgeniy Podolyan
Abstract The number of researchers using computational chemistry tools is growing every year. There are multiple programs used for calculation of various molecular and electronic properties such as optimized geometry, energy, vibrational spectra, and so forth. Another set of programs is used for the visualization of these properties. However, such programs are either too complex for a beginner or too simple for an intermediate user for everyday use. Molecular Modeling and Simulation Kit (MaSK) is designed to fill this gap by presenting an easy-to-use intuitive interface to quantum chemical programs such as GAMESS and Gaussian with an array of advanced tools. The program can be used as a postprocessor to visualize calculated properties or as a preprocessor to prepare the input files for quantum chemical programs. In addition, some properties such as the surfaces of molecular orbitals, electron and spin densities, and molecular electrostatic potentials are actually calculated by MaSK. If MaSK is combined with PC GAMESS, the preparation of the input, running of the calculations, and the display of the results can all be done without leaving the program's interface. 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source]

QSAR model for alignment-free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP-lattice networks

Santiago Vilar
Abstract Network theory allows relationships to be established between numerical parameters that describe the molecular structure of genes and proteins and their biological properties. These models can be considered as quantitative structure,activity relationships (QSAR) for biopolymers. The work described here concerns the first QSAR model for 122 proteins that are associated with human breast cancer (HBC), as identified experimentally by Sjblom et al. (Science 2006, 314, 268) from over 10,000 human proteins. In this study, the 122 proteins related to HBC (HBCp) and a control group of 200 proteins that are not related to HBC (non-HBCp) were forced to fold in an HP lattice network. From these networks a series of electrostatic potential parameters (,k) was calculated to describe each protein numerically. The use of ,k as an entry point to linear discriminant analysis led to a QSAR model to discriminate between HBCp and non-HBCp, and this model could help to predict the involvement of a certain gene and/or protein in HBC. In addition, validation procedures were carried out on the model and these included an external prediction series and evaluation of an additional series of 1000 non-HBCp. In all cases good levels of classification were obtained with values above 80%. This study represents the first example of a QSAR model for the computational chemistry inspired search of potential HBC protein biomarkers. 2008 Wiley Periodicals, Inc. J Comput Chem 2008 [source]

On the performance of some aromaticity indices: A critical assessment using a test set

Ferran Feixas
Abstract Aromaticity is a central chemical concept widely used in modern chemistry for the interpretation of molecular structure, stability, reactivity, and magnetic properties of many compounds. As such, its reliable prediction is an important task of computational chemistry. In recent years, many methods to quantify aromaticity based on different physicochemical properties of molecules have been proposed. However, the nonobservable nature of aromaticity makes difficult to assess the performance of the numerous existing indices. In the present work, we introduce a series of fifteen aromaticity tests that can be used to analyze the advantages and drawbacks of a group of aromaticity descriptors. On the basis of the results obtained for a set of ten indicators of aromaticity, we conclude that indices based on the study of electron delocalization in aromatic species are the most accurate among those examined in this work. 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source]

The Amber biomolecular simulation programs

David A. Case
Abstract We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1668,1688, 2005 [source]

Neural network-based prediction of transmembrane ,-strand segments in outer membrane proteins

M. Michael Gromiha
Abstract Prediction of transmembrane ,-strands in outer membrane proteins (OMP) is one of the important problems in computational chemistry and biology. In this work, we propose a method based on neural networks for identifying the membrane-spanning ,-strands. We introduce the concept of "residue probability" for assigning residues in transmembrane ,-strand segments. The performance of our method is evaluated with single-residue accuracy, correlation, specificity, and sensitivity. Our predicted segments show a good agreement with experimental observations with an accuracy level of 73% solely from amino acid sequence information. Further, the predictive power of N- and C-terminal residues in each segments, number of segments in each protein, and the influence of cutoff probability for identifying membrane-spanning ,-strands will be discussed. We have developed a Web server for predicting the transmembrane ,-strands from the amino acid sequence, and the prediction results are available at 2004 Wiley Periodicals, Inc. J Comput Chem 25: 762,767, 2004 [source]

Structure elucidation, conformational analysis and thermal effects on membrane bilayers of an antimicrobial myricetin ether derivative

C. Demetzos
The membrane perturbing 3,7,4,,5,-tetramethyl ether of myricetin 1 was isolated from Cistus monspelien-sis L. Its structure was elucidated and its conformational properties were explored using a combination of 2D NMR spectroscopy and computational chemistry. The obtained results showed that compound 1 adopts four enantiomeric pairs of low energy conformers characterized: (a) by an aromatic ring B twisted through rotation about C2-C1, bond from the rigid isoflavone ring; (b) a 4,-O-CH3 bond oriented out of the plane with equal probability upwards or downwards the phenyl ring B, while all the other O-CH3 bonds are oriented in the plane of the aryl ring. Two of these enantiomeric pairs are lowest in energy. These possible bioactive con-formers are possibly stabilized by van Der Waals interactions. The 3,,5-diacetyl derivative 2 of compound 1 was synthesized and its structure elucidation was achieved based on the chemical shift assignment of the parent compound 1. The Differential Scanning Calorimetry (DSC) results revealed that the degree of the thermal effects exerted by the flavonoids at dipalmitoylphosphatidyl choline (DPPC) bilayers followed the order 1 > 2 > myricetin. Their antimicrobial activity against Gram positive bacteria followed the same order. [source]

Establishment of a quantitative structure,activity relationship model for evaluating and predicting the protective potentials of phenolic antioxidants on lipid peroxidation

Zhiyong Cheng
Abstract Antioxidant activities of phenolic compounds have been extensively explored, but the determinant factors underlying their mechanisms of action remain to be elucidated. In the present work, a series of phenolic compounds (hydroxylated connamic, benzoic acid, and polyphenol) were studied for their protection against lipid peroxidation (LPO) in two model experiments, pre-emulsified linoleic acid system and phosphate buffered linolenic acid system. The mechanisms of action as well as activity determinants were investigated by computational chemistry and multiple-linear regression analysis. Upon elucidating the LPO inhibition properties and the relationship between their structural natures and antioxidant activities (SAR), a fairly satisfactory multidescriptor quantitative SAR model was derived, which extended our understanding of LPO inhibition mechanisms and should be valuable in assessing or predicting the anti-LPO activity of phenolic antioxidants. 2003 Wiley-Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 92:475,484, 2003 [source]

Experimental and theoretical vibrational spectroscopic study on symmetric and asymmetric halo-bridged complexes of palladium(II) and platinum(II)

E. Kessenich
The symmetric chloro-bridged complexes [(Et3P)2PtCl(-Cl)]2, [(Et3P)2Pt(-Cl)]22+ and [(C3H5)Pd(-Cl)]2 and the asymmetric complexes [(C3H5)Pd(-Cl)2Pt(PEt3)2]+ and [(C3H5)Pd(-Cl)2Pt(PEt3)Cl] were studied by means of vibrational spectroscopy (infrared, Raman) and computational chemistry. Assignments of all normal modes associated with skeletal stretching are suggested and their displacement vectors are discussed. Copyright 2001 John Wiley & Sons, Ltd. [source]

Computational chemistry study of the environmentally important acid-catalyzed hydrolysis of atrazine and related 2-chloro- s -triazines

Phillip Sawunyama
Abstract Many chlorine-containing pesticides, for example 2-chloro- s -triazines, are of great concern both environmentally and toxicologically. As a result, ascertaining or predicting the fate and transport of these compounds in soils and water is of current interest. Transformation pathways for 2-chloro- s -triazines in the environment include dealkylation, dechlorination (hydrolysis), and ring cleavage. This study explored the feasibility of using computational chemistry, specifically the hybrid density functional theory method, B3LYP, to predict hydrolysis trends of atrazine (2-chloro- N4 -ethyl- N6 -isopropyl-1,3,5-triazine-2,4-diamine) and related 2-chloro- s -triazines to the corresponding 2-hydroxy- s -triazines. Gas-phase energetics are described on the basis of calculations performed at the B3LYP/6-311++G(d,p)//B3LYP/6-31G* level of theory. Calculated free energies of hydrolysis (,hG298) are nearly the same for simazine (2-chloro- N4,N6 -diethyl-1,3,5-triazine-2,4-diamine), atrazine, and propazine (2-chloro- N4,N6 -di-isopropyl-1,3,5-triazine-2,4-diamine), suggesting that hydrolysis is not significantly affected by the side-chain amine-nitrogen alkyl substituents. High-energy barriers also suggest that the reactions are not likely to be observed in the gas phase. Aqueous solvation effects were examined by means of self-consistent reaction field methods (SCRF). Molecular structures were optimized at the B3LYP/6-31G* level using the Onsager model, and solvation energies were calculated at the B3LYP/6-311++G(d,p) level using the isodensity surface polarizable continuum model (IPCM). Although the extent of solvent stabilization was greater for cationic species than neutral ones, the full extent of solvation is underestimated, especially for the transition state structures. As a consequence, the calculated hydrolysis barrier for protonated atrazine is exaggerated compared with the experimentally determined one. Overall, the hydrolysis reactions follow a concerted nucleophilic aromatic substitution (SNAr) pathway. Published in 2002 for SCI by John Wiley & Sons, Ltd [source]

Cover Picture: phys. stat. sol. (RRL) 1/2007

Article first published online: 6 NOV 200
In the Rapid Research Letter on p. R37 Musubu Ichikawa et al. report very high electron mobility above 10,3 cm2/Vs in the electron transporting material bipyridyl substituted oxadiazole (Bpy-OXD). These favourable electrical properties make the amorphous molecular semiconductor promising for potential applications in organic light-emitting diodes (OLEDs), flatpanel displays and lighting. The authors also give reasons , by means of computational chemistry , why this planar material forms stable amorphous solid films. ( 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Polarizable atomic multipole X-ray refinement: application to peptide crystals

Michael J. Schnieders
Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA,IAS model lowered Rfree by 20,40% relative to the original spherically symmetric scattering model. [source]

Rationalizing the Solution Properties of Zwitterions by Means of Computational Chemistry

This short review describes our computational studies of carnitine, acetylcarnitines, and betaines over the past two decades. Interspersed among the three computational studies , a molecular mechanics study of the conformer population of carnitine and acetylcarnitine, an AM1 study of the energetics of hydrolysis of acetylcarnitine, and an HF 6-31G* study of the solvation energies and structures of a homologous series of betaines , are brief overviews of our research in designing and testing new therapeutic agents for non-insulin dependent diabetes and for protection against sexually transmitted diseases. The three studies also show how computational chemistry has evolved during this time to enable an evaluation of the structure and energetics of zwitterions in aqueous solution. [source]