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Electrostatic Potential (electrostatic + potential)
Kinds of Electrostatic Potential Terms modified by Electrostatic Potential Selected AbstractsMOLCAS 7: The Next GenerationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2010Francesco Aquilante Abstract Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010 [source] Observation of Unusual Homoepitaxy in Ultrathin Pentacene Films and Correlation with Surface Electrostatic PotentialADVANCED MATERIALS, Issue 30 2009Vivek Kalihari Pentacene second layer grows with a twist (,76,°) on the first layer, while the third and subsequent layers show commensurism with their respective underlayers. The preferred twisting of the second layer on the first layer gives rise to epitaxial and non-epitaxial domains which also reflect in the surface electrostatic potential measurements. [source] Computational characterization of nucleotide bases: Molecular surface electrostatic potentials and local ionization energies, and local polarization energiesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3-4 2001Jane S. Murray Abstract Electrostatic potentials and local ionization energies have been computed at the HF/6-31G* level on the molecular surfaces of the five nucleotide bases. The potentials are analyzed in terms of their most positive and negative values as well as several statistically defined quantities that reflect their patterns over the entire surface. Considerable charge separation and variability are found for all five molecules. The results are consistent with the base pairing that is known to occur. The observed reactive behavior toward electrophiles can be interpreted in terms of the complementary roles of the surface potential and the local electron lability. Local polarization energies, corresponding to a test charge being placed at specific points above the molecules, are also calculated (HF/6-31+G*), and their relationship to the local ionization energies is examined. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 245,254, 2001 [source] Presheath in Fully Ionized Collisional Plasma in a Magnetic FieldCONTRIBUTIONS TO PLASMA PHYSICS, Issue 7 2005B. Alterkop Abstract The quasineutral presheath layer at the boundary of fully ionized, collisional, and magnetized plasma with an ambipolar flow to an adjacent absorbing wall was analyzed using a two fluid magneto-hydrodynamic model. The plasma is magnetized by a uniform magnetic field B, imposed parallel to the wall. The analysis did not assume that the dependence of the particle density on the electric potential in the presheath is according to the Boltzmann equilibrium, and the dependence of the mean collision time , on the varying plasma density within the presheath was not neglected. Based on the model equations, algebraic expressions were derived for the dependence of the plasma density, electron and ion velocities, and the electrostatic potential on the position within the presheath. The solutions of the model equations depended on two parameters: Hall parameter (, ), and the ratio (, ), where , = ZTe /(ZTe + Ti ), and Te , Ti and Z are the electron and ion temperatures and ionicity, respectively. The characteristic scale of the presheath extension is several times ri /, , where ri is the ion radius at the ion sound velocity. The electric potential could have a non monotonic distribution in the presheath. The ions are accelerated to the Bohm velocity (sound velocity) in the presheath mainly near the presheath-sheath boundary, in a layer of thickness ,ri /, . The electric field accelerates the ions in the whole presheath if their velocity in the wall direction exceeds their thermal velocity. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Engineering thermal stability of l- asparaginase by in vitro directed evolutionFEBS JOURNAL, Issue 6 2009Georgia A. Kotzia l- Asparaginase (EC 3.5.1.1, l- ASNase) catalyses the hydrolysis of l- Asn, producing l- Asp and ammonia. This enzyme is an anti-neoplastic agent; it is used extensively in the chemotherapy of acute lymphoblastic leukaemia. In this study, we describe the use of in vitro directed evolution to create a new enzyme variant with improved thermal stability. A library of enzyme variants was created by a staggered extension process using the genes that code for the l- ASNases from Erwinia chrysanthemi and Erwinia carotovora. The amino acid sequences of the parental l- ASNases show 77% identity, but their half-inactivation temperature (Tm) differs by 10 °C. A thermostable variant of the E. chrysamthemi enzyme was identified that contained a single point mutation (Asp133Val). The Tm of this variant was 55.8 °C, whereas the wild-type enzyme has a Tm of 46.4 °C. At 50 °C, the half-life values for the wild-type and mutant enzymes were 2.7 and 159.7 h, respectively. Analysis of the electrostatic potential of the wild-type enzyme showed that Asp133 is located at a neutral region on the enzyme surface and makes a significant and unfavourable electrostatic contribution to overall stability. Site-saturation mutagenesis at position 133 was used to further analyse the contribution of this position on thermostability. Screening of a library of random Asp133 mutants confirmed that this position is indeed involved in thermostability and showed that the Asp133Leu mutation confers optimal thermostability. [source] Auxiliary functions for molecular integrals with Slater-type orbitals.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2008Abstract The Gauss transform of Slater-type orbitals is used to express several types of molecular integrals involving these functions in terms of simple auxiliary functions. After reviewing this transform and the way it can be combined with the shift operator technique, a master formula for overlap integrals is derived and used to obtain multipolar moments associated to fragments of two-center distributions and overlaps of derivatives of Slater functions. Moreover, it is proved that integrals involving two-center distributions and irregular harmonics placed at arbitrary points (which determine the electrostatic potential, field and field gradient, as well as higher order derivatives of the potential) can be expressed in terms of auxiliary functions of the same type as those appearing in the overlap. The recurrence relations and series expansions of these functions are thoroughly studied, and algorithms for their calculation are presented. The usefulness and efficiency of this procedure are tested by developing two independent codes: one for the derivatives of the overlap integrals with respect to the centers of the functions, and another for derivatives of the potential (electrostatic field, field gradient, and so forth) at arbitrary points. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Electronic structure and physicochemical properties of selected penicillinsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2007Catalina Soriano-Correa Abstract Traditionally, penicillins have been used as antibacterial agents due to their characteristics and widespread applications with few collateral effects, which have motivated several theoretical and experimental studies. Despite the latter, their mechanism of biological action has not been completely elucidated. We present a theoretical study at the Hartree,Fock and density functional theory (DFT) levels of theory of a selected group of penicillins such as the penicillin-G, amoxicillin, ampicillin, dicloxacillin, and carbenicillin molecules, to systematically determine the electron structure of full ,-lactam antibiotics. Our results allow us to analyze the electronic properties of the pharmacophore group, the aminoacyl side-chain, and the influence of the substituents (R and X) attached to the aminoacyl side-chain at 6, (in contrast with previous studies focused at the 3, substituents), and to corroborate the results of previous studies performed at the semiempirical level, solely on the ,-lactam ring of penicillins. Besides, several density descriptors are determined with the purpose of analyzing their link to the antibacterial activity of these penicillin compounds. Our results for the atomic charges (fitted to the electrostatic potential), the bond orders, and several global reactivity descriptors, such as the dipole moments, ionization potential, hardness, and the electrophilicity index, led us to characterize: the active sites, the effect of the electron-attracting substituent properties and their physicochemical features, which altogether, might be important to understand the biological activity of these type of molecules. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Auxiliary functions for molecular integrals with Slater-type orbitals.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2006Abstract Many types of molecular integrals involving Slater functions can be expressed, with the ,-function method in terms of sets of one-dimensional auxiliary integrals whose integrands contain two-range functions. After reviewing the properties of these functions (including recurrence relations, derivatives, integral representations, and series expansions), we carry out a detailed study of the auxiliary integrals aimed to facilitate both the formal and computational applications of the ,-function method. The usefulness of this study in formal applications is illustrated with an example. The high performance in numerical applications is proved by the development of a very efficient program for the calculation of two-center integrals with Slater functions corresponding to electrostatic potential, electric field, and electric field gradient. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Theoretical study of the substituent effect on the intramolecular hydrogen bonds in di(4-hydroxycoumarin) derivativesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2006Tzvetan Mihaylov Abstract Geometry optimization of ortho -, meta -, and para -pyridyl-substituted di(4-hydroxycoumarin) [di(4-HC)] was performed with the density functional theory (DFT) [B3LYP/6-31G(d)] method. Two asymmetrical intramolecular OH,O hydrogen bonds (HBs) stabilized the structures. The calculated single HB energies varied from ,62.56 to ,47.53 kJ mol,1 and pointed to a relative strong hydrogen bond in the systems studied. The 2- and 6-pyridyl substituents produced the largest geometrical changes in di(4-hydroxycoumarin) fragment. The highest total HB energy was found for 2-pyridyl-substituted and the lowest one for 6-pyridyl-substituted di(4-hydroxycoumarin). The HB energy variations were confirmed with rotational barrier method calculations. Both steric and electrostatic factors were found to be responsible for the HB asymmetry in the compounds studied. According to the molecular electrostatic potential (MEP) calculations the most preferred reactive site for electrophilic attack of pyridyl-substituted di(4-hydroxycoumarin)s are the pyridine nitrogen and the carbonyl oxygens, followed by the hydroxyl oxygens. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Thinking inside the box: Novel linear scaling algorithm for Coulomb potential evaluationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2006David C. Thompson Abstract Beginning with the Poisson equation, and expanding the electronic potential in terms of sine functions, the natural orbitals for describing the particle-in-a-box problem, we find that simple analytic forms can be found for the evaluation of the Coulomb energy for both the interacting and non-interacting system of N -electrons in a box. This method is reminiscent of fast-Fourier transform and scales linearly. To improve the usefulness of this result, we generalize the idea by considering a molecular system, embedded in a box, within which we determine the electrostatic potential, in the same manner as that described for our model systems. Within this general formalism, we consider both periodic and aperiodic recipes with specific application to systems described using Gaussian orbitals; although in principle the method is seen to be completely general. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Principal component analysis of the effects of wavefunction modification on the electrostatic potential of indoleINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005Maíra 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] When, in the context of drug design, can a fluorine atom successfully substitute a hydroxyl group?INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2002Marcin Hoffmann Abstract In this article, we deal with the question of whether a fluorine atom can substitute a hydroxyl group in such a way that will lead to a compound showing a desired biologic activity, that is, a potential new drug. It is obvious that a fluorine atom differs from a hydroxyl group, as it cannot donate hydrogen bonds. However, it can accept them. Moreover, both fluorine and oxygen are of similar size and are the most electronegative elements. Therefore, a fluorine atom is thought to be a good substitute for a hydroxyl group. However, it was shown that for conformationally labile aliphatic compounds a replacement of a hydroxyl by a fluorine increases conformational diversity, so the fluorine-containing aliphatic molecules are present in equilibrium at room temperature as a mixture of several different conformers. In contrast, for cyclic compounds the substitution of an OH group by an F atom does not much change shape and electrostatic potential around corresponding conformers. Moreover, these compounds are present in equilibrium at room temperature in aqueous solution as a mixture of the same most favored structures. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Molecular surface electrostatic potentials in relation to noncovalent interactions in biological systemsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2001Peter Politzer Abstract Noncovalent interactions are predominantly electrostatic in nature. It follows that an effective tool for their investigation and elucidation is the electrostatic potential on the molecular surface. We have shown that a variety of condensed phase macroscopic properties can be expressed quantitatively in terms of certain site-specific and global statistical quantities that characterize the overall pattern of the surface potential. We are now extending this approach to interactions in biological systems. Several applications will be discussed, including initial qualitative studies of dioxins, a series of anticonvulsants and some tetracyclines, the nucleotide bases, and a recent quantitative treatment of the anti-HIV activities of three groups of reverse transcriptase inhibitors. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] Modeling and predicting binding affinity of phencyclidine-like compounds using machine learning methodsJOURNAL OF CHEMOMETRICS, Issue 1 2010Ozlem Erdas Abstract Machine learning methods have always been promising in the science and engineering fields, and the use of these methods in chemistry and drug design has advanced especially since the 1990s. In this study, molecular electrostatic potential (MEP) surfaces of phencyclidine-like (PCP-like) compounds are modeled and visualized in order to extract features that are useful in predicting binding affinities. In modeling, the Cartesian coordinates of MEP surface points are mapped onto a spherical self-organizing map (SSOM). The resulting maps are visualized using electrostatic potential (ESP) values. These values also provide features for a prediction system. Support vector machines and partial least-squares method are used for predicting binding affinities of compounds. Copyright © 2009 John Wiley & Sons, Ltd. [source] Theoretical investigation of an energetic fullerene derivativeJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2010Bisheng Tan Abstract A self-consistent estimation method for the thermochemical properties of N -methyl-3-(2,,4,,6,-trinitrobenzene)-fulleropyrrolidine (MTNBFP) is presented. This method is based on enthalpy of formation (,fH) and enthalpy of combustion obtained from BLYP/DNP calculations of the total energies and frequencies for MTNBFP. The enthalpy of formation was calculated by an optimized set of isodesmic reactions given the available experimental ,fH of relative compounds. MTNBFP has a high enthalpy of formation, 2782.2 kJ/mol. Detonation velocity and detonation pressure were also presented in terms of Kamlet and Jacobs equations. Drop hammer impact sensitivity tests and blasting point per 5 s tests indicate MTNBFP may be a potential candidate primary explosive. To understand the test results well, we proposed a series of chemical reaction mechanisms and interpreted the relationship between impact sensitivity and electronic structures from the viewpoint of nitro group charge, electrostatic potential, and vibrational modes. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Stereoelectronic properties of spiroquinazolinones in differential PDE7 inhibitory activityJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2008Pankaj R. Daga Abstract A detailed computational study on a series of spiroquinazolinones showing phosphodiesterase 7 (PDE7) inhibitory activity was performed to understand the binding mode and the role of stereoelectronic properties in binding. Our docking studies reproduced the essential hydrogen bonding and hydrophobic interactions for inhibitors of this class of enzymes. The N1 proton of the quinazolinone scaffold was involved in H-bonding to an amide side chain of the conserved glutamine residue in the active site. The central bicyclic ring of the molecules showed hydrophobic and ,-stacking interactions with hydrophobic and aromatic amino acid residues, respectively, present in the PDE7 active site. The docked conformations were optimized with density functional theory (DFT) and DFT electronic properties were calculated. Comparison of molecular electrostatic potential (MEP) plots of inhibitors with the active site of PDE7 suggested that the electronic distribution in the molecules is as important as steric factors for binding of the molecules to the receptor. The hydrogen bonding ability and nucleophilic nature of N1 appeared to be important for governing the interaction with PDE7. For less active inhibitors (pIC50 < 6.5), the MEP maximum at N1 of the spiroquinazolinone ring was high or low based on the electronic properties of the substituents. All the more active molecules (pIC50 > 6.5) had MEP highest at N3, not N1. Efficient binding of these inhibitors may need some rearrangement of side chains of active-site residues, especially Asn365. This computational modeling study should aid in design of new molecules in this class with improved PDE7 inhibition. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008 [source] Electric field-derived point charges to mimic the electrostatics in molecular crystalsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2006Andrew E. Whitten Abstract Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree,Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1063,1070, 2006 [source] Study of peptide conformation in terms of the ABEEM/MM methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2006Zhong-Zhi Yang Abstract The ABEEM/MM model (atom-bond electronegativity equalization method fused into molecular mechanics) is applied to study of the polypeptide conformations. The Lennard,Jones and torsional parameters were optimized to be consistent with the ABEEM/MM fluctuating charge electrostatic potential. The hydrogen bond was specially treated with an electrostatic fitting function. Molecular dipole moments, dimerization energies, and hydrogen bond lengths of complexes are reasonably achieved by our model, compared to ab initio results. The ABEEM/MM fluctuating charge model reproduces both the peptide conformational energies and structures with satisfactory accuracy with low computer cost. The transferability is tested by applying the parameters of our model to the tetrapeptide of alanine and another four dipeptides. The overall RMS deviations in conformational energies and key dihedral angles for four di- or tetrapeptide, is 0.39 kcal/mol and 7.7°. The current results agree well with those by the accurate ab initio method, and are comparable to those from the best existing force fields. The results make us believe that our fluctuating charge model can obtain more promising results in protein and macromolecular modeling with good accuracy but less computer cost. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 1,10, 2006 [source] A new GROMOS force field for hexopyranose-based carbohydratesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005Roberto D. Lins Abstract A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) 4C1 chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (,- and ,-D-glucose, ,- and ,-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400,1412, 2005 [source] Wave functions derived from experiment.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2003Abstract The constrained Hartree,Fock method using experimental X-ray diffraction data is extended and applied to the case of noncentrosymmetric molecular crystals. A new way to estimate the errors in derived properties as a derivative with respect to added Gaussian noise is also described. Three molecular crystals are examined: ammonia [NH3], urea [CO(NH2)2], and alloxan [(CO)4(NH)2]. The energetic and electrical properties of these molecules in the crystalline state are presented. In all cases, an enhancement of the dipole moment is observed upon application of the experimental constraint. It is found that the phases of the structure factors are robustly determined by the constrained Hartree,Fock model, even in the presence of simulated noise. Plots of the electron density, electrostatic potential, and the electron localization function for the molecules in the crystal are displayed. In general, relative to the Hartree,Fock model, there is a depletion of charge around hydrogen atoms and lone pair regions, and a build-up of charge within the molecular framework near nuclei, directed along the bonds. The electron localization function plots reveal an increase in the pair density between vicinal hydrogen atoms. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 470,483, 2003 [source] Ab initio quality one-electron properties of large molecules: Development and testing of molecular tailoring approachJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2003K. Babu Abstract The development of a linear-scaling method, viz. "molecular tailoring approach" with an emphasis on accurate computation of one-electron properties of large molecules is reported. This method is based on fragmenting the reference macromolecule into a number of small, overlapping molecules of similar size. The density matrix (DM) of the parent molecule is synthesized from the individual fragment DMs, computed separately at the Hartree,Fock (HF) level, and is used for property evaluation. In effect, this method reduces the O(N3) scaling order within HF theory to an n·O(N,3) one, where n is the number of fragments and N,, the average number of basis functions in the fragment molecules. An algorithm and a program in FORTRAN 90 have been developed for an automated fragmentation of large molecular systems. One-electron properties such as the molecular electrostatic potential, molecular electron density along with their topography, as well as the dipole moment are computed using this approach for medium and large test chemical systems of varying nature (tocopherol, a model polypeptide and a silicious zeolite). The results are compared qualitatively and quantitatively with the corresponding actual ones for some cases. This method is also extended to obtain MP2 level DMs and electronic properties of large systems and found to be equally successful. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 484,495, 2003 [source] Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2002Pengyu Ren Abstract A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter- and intramolecular polarization are handled within a single scheme. An analytical formula for removing intramolecular polarization from a set of atomic multipoles for an arbitrary static structure or conformation is given. With the help of the intramolecular polarization, these permanent atomic multipoles can then be applied in modeling alternative conformations of a molecule. Equipped with this simple technique, one can derive transferable electrostatic parameters for peptides and proteins using flexible model compounds such as dipeptides. The proposed procedure is tested for its ability to describe the electrostatic potential around various configurations of the N -methylacetamide dimer. The effect of different intramolecular polarization schemes on the accuracy of a force field model of the electrostatic potential of alanine dipeptide is investigated. A group-based scheme for including direct intramolecular polarization is shown to be most successful in accounting for the conformational dependence of electrostatic potentials. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1497,1506, 2002 [source] Off-axis electron holography of electrostatic potentials in unbiased and reverse biased focused ion beam milled semiconductor devicesJOURNAL OF MICROSCOPY, Issue 3 2004A. C. TWITCHETT Summary Off-axis electron holography in the transmission electron microscope (TEM) is used to measure two-dimensional electrostatic potentials in both unbiased and reverse biased silicon specimens that each contain a single p,n junction. All the specimens are prepared for examination in the TEM using focused ion beam (FIB) milling. The in situ electrical biasing experiments make use of a novel specimen geometry, which is based on a combination of cleaving and FIB milling. The design and construction of an electrical biasing holder are described, and the effects of TEM specimen preparation on the electrostatic potential in the specimen, as well as on fringing fields beyond the specimen surface, are assessed. [source] Prediction of solvent effect on the reaction rate and endo/exo selectivity of a Diels,Alder reaction using molecular surface electrostatic potentialJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 7 2003M. R. Gholami Abstract Molecular surface electrostatic potential was used to predict the solvent effect on the reaction rate, endo/exo selectivity and diastereomeric excess of a Diels,Alder reaction. It is shown that these quantities can be expressed in terms of molecular surface electrostatic potentials of solvents which are obtained computationally by the HF/6,31++G* procedure. Regression analyses and an experimental database are used to obtain analytical representation of rate constant, endo/exo selectivity and diastereomeric excess. The models obtained show that the hydrogen bond donor ability of solvents on the above mentioned properties is substantial, whereas solvophobicity only affects the reaction rate and endo/exo selectivity of the reaction. Copyright © 2003 John Wiley & Sons, Ltd. [source] Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteinsJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2008Claude Lecomte With an increasing number of biological macromolecular crystal structures measured at ultrahigh resolution (1,Å or better), it is necessary to extend to large systems the experimental valence electron density modelling that is applied to small molecules. A database of average multipole populations has been built, describing the electron density of chemical groups in all 20 amino acids found in proteins. It allows calculation of atomic aspherical scattering factors, which are the starting point for refinement of the protein electron density, using the MoPro software. It is shown that the use of non-spherical scattering factors has a major impact on crystallographic statistics and results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. It is also possible to obtain a realistic valence electron density model, which is used in the calculation of the electrostatic potential and energetic properties of proteins. [source] Cover Picture: QSAR Comb.MOLECULAR INFORMATICS, Issue 8 2009The transmembrane protein aquaporin spans biological membranes and forms channels that allow the passage of water molecules. The water channels consist of alpha helices (purple cylinders) and are shown as a Conolly surface,in which the electrostatic potential is represented by colors (blue: negative, red: positive). Peter Agre and Roderick MacKinnon were awarded the 2003 Nobel Prize in chemistry for the discovery of water channels and for structural and mechanistic studies on ion channels, respectively. Cover illustration by courtesy of Prof. Dr. Jürgen Brickmann, Dr. Thorsten Borosch, MOLNET e.V. [source] Cover Picture: QSAR Comb.MOLECULAR INFORMATICS, Issue 1 2009The transmembrane protein aquaporin spans biological membranes and forms channels that allow the passage of water molecules. The water channels consist of alpha helices (purple cylinders) and are shown as a Conolly surface,in which the electrostatic potential is represented by colors (blue: negative, red: positive). Peter Agre and Roderick MacKinnon were awarded the 2003 Nobel Prize in chemistry for the discovery of water channels and for structural and mechanistic studies on ion channels, respectively. Cover illustration by courtesy of Prof. Dr. Jürgen Brickmann, Dr. Thorsten Borosch, MOLNET e.V. [source] Cover Picture: QSAR Comb.MOLECULAR INFORMATICS, Issue 11-12 2008The transmembrane protein aquaporin spans biological membranes and forms channels that allow the passage of water molecules. The water channels consist of alpha helices (purple cylinders) and are shown as a Conolly surface,in which the electrostatic potential is represented by colors (blue: negative, red: positive). Peter Agre and Roderick MacKinnon were awarded the 2003 Nobel Prize in chemistry for the discovery of water channels and for structural and mechanistic studies on ion channels, respectively. Cover illustration by courtesy of Prof. Dr. Jürgen Brickmann, Dr. Thorsten Borosch, MOLNET e.V. [source] Cover Picture: QSAR Comb.MOLECULAR INFORMATICS, Issue 11-12 2007The transmembrane protein aquaporin spans biological membranes and forms channels that allow the passage of water molecules. The water channels consist of alpha helices (purple cylinders) and are shown as a Conolly surface,in which the electrostatic potential is represented by colors (blue: negative, red: positive). Peter Agre and Roderick MacKinnon were awarded the 2003 Nobel Prize in chemistry for the discovery of water channels and for structural and mechanistic studies on ion channels, respectively. Cover illustration by courtesy of Prof. Dr. Jürgen Brickmann, Dr. Thorsten Borosch, MOLNET e.V. [source] Cover Picture: QSAR Comb.MOLECULAR INFORMATICS, Issue 1 2007The transmembrane protein aquaporin spans biological membranes and forms channels that allow the passage of water molecules. The water channels consist of alpha helices (purple cylinders) and are shown as a Conolly surface,in which the electrostatic potential is represented by colors (blue: negative, red: positive). Peter Agre and Roderick MacKinnon were awarded the 2003 Nobel Prize in chemistry for the discovery of water channels and for structural and mechanistic studies on ion channels, respectively. Cover illustration by courtesy of Prof. Dr. Jürgen Brickmann, Dr. Thorsten Borosch, MOLNET e.V. [source] | ||||||||||||||||||||||||||||||||||