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Molecular Electrostatic Potential (molecular + electrostatic_potential)
Selected AbstractsTheoretical 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] 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] 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] 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] Representation of molecular electrostatic potentials of biopolymer by self-organizing feature map,CHINESE JOURNAL OF CHEMISTRY, Issue 12 2001Xue-Bin Qiao Abstract The Kohonen self-organizing map was introduced to map the protein molecular surface features. The protein or polypeptide properties, such as shape and molecular electrostatic potential, can be visualized by self-organizing map, which was trained by the 3D surface coordinates. Such maps allow the visual comparison of molecular properties between proteins having common topological or chemical features. [source] MaSK: A visualization tool for teaching and research in computational chemistryINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2009Yevgeniy 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] Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2003Pablo A. Molina Two divide-and-conquer (DAQ) approaches for building multipole-based molecular electrostatic potentials of proteins are presented and evaluated for use in QM/MM calculations. One approach is a further development of the neutralization method of Bellido and Rullmann (J Comput Chem 1989, 10, 479,487) while the other is based on removing part of the electron density before performing the multipole expansion. Both methods create systems with integer charges without using charge renormalization. To determine their performance in terms of location of cuts and distance to QM region, the new DAQ approaches are tested in calculations of the proton affinity of N, of Lys55 in the inhibitor turkey ovomucoid third domain. Finally, the two methods are used to build a variety of MM regions, applied to calculations of the pKa of Lys55, and compared to other computational methodologies in which force field charges are employed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1971,1979, 2003 [source] Reassociation of fragments using multicentered multipolar expansions: peptide junction treatments to investigate electrostatic properties of proteinsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2001L. E. Dardenne Abstract We report an analysis of three schemes for fragment reassociation using multicentered multipolar expansions derived from ab initio quantum wave functions at the Hartree,Fock/6-31G* LCAO level, two of them involving single-bond partitioning in the peptide bond region, and the third one using a partially overlapping procedure based on a methodology proposed by Vigné-Maeder21 (OME,overlap of multipolar expansions,reassociation method). The effects of different peptide junction treatments in the derivation of molecular electrostatic potentials and molecular electric fields of three peptide sequences are discussed. The results show that the OME reassociation method gives a better and a more homogeneous description of both the potential and the electric field than the other two treatments. We conclude that the OME method is the most indicated for studies involving electrostatic properties of proteins. Our results also indicate that the use of multicentered multipolar expansions coupled to the OME treatment is the best choice in protein studies including solvent effects using, for example, a continuum boundary method to solve the linearized Poisson,Boltzmann equation. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 689,701, 2001 [source] Representation of molecular electrostatic potentials of biopolymer by self-organizing feature map,CHINESE JOURNAL OF CHEMISTRY, Issue 12 2001Xue-Bin Qiao Abstract The Kohonen self-organizing map was introduced to map the protein molecular surface features. The protein or polypeptide properties, such as shape and molecular electrostatic potential, can be visualized by self-organizing map, which was trained by the 3D surface coordinates. Such maps allow the visual comparison of molecular properties between proteins having common topological or chemical features. [source] | ||||||||||