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Interaction Energies (interaction + energy)
Kinds of Interaction Energies Selected AbstractsProgress in the Understanding of Drug,Receptor Interactions, Part,2: Experimental and Theoretical Electrostatic Moments and Interaction Energies of an Angiotensin II Receptor Antagonist (C30H30N6O3S)CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2007Raffaella Soave Dr. Abstract A combined experimental and theoretical charge density study of an angiotensin II receptor antagonist (1) is presented focusing on electrostatic properties such as atomic charges, molecular electric moments up to the fourth rank and energies of the intermolecular interactions, to gain an insight into the physical nature of the drug,receptor interaction. Electrostatic properties were derived from both the experimental electron density (multipole refinement of X-ray data collected at T=17,K) and the ab initio wavefunction (single molecule and fully periodic calculations at the DFT level). The relevance of S,,,O and S,,,N intramolecular interactions on the activity of 1 is highlighted by using both the crystal and gas-phase geometries and their electrostatic nature is documented by means of QTAIM atomic charges. The derived electrostatic properties are consistent with a nearly spherical electron density distribution, characterised by an intermingling of electropositive and -negative zones rather than by a unique electrophilic region opposed to a nucleophilic area. This makes the first molecular moment scarcely significant and ill-determined, whereas the second moment is large, significant and highly reliable. A comparison between experimental and theoretical components of the third electric moment shows a few discrepancies, whereas the agreement for the fourth electric moment is excellent. The most favourable intermolecular bond is show to be an NH,,,N hydrogen bond with an energy of about 50,kJ,mol,1. Key pharmacophoric features responsible for attractive electrostatic interactions include CH,,,X hydrogen bonds. It is shown that methyl and methylene groups, known to be essential for the biological activity of the drug, provide a significant energetic contribution to the total binding energy. Dispersive interactions are important at the thiophene and at both the phenyl fragments. The experimental estimates of the electrostatic contribution to the intermolecular interaction energies of six molecular pairs, obtained by a new model proposed by Spackman, predict the correct relative electrostatic energies with no exceptions. [source] Interaction Energies for the Purine Inhibitor Roscovitine with Cyclin-Dependent Kinase 2: Correlated Ab Initio Quantum-Chemical, DFT and Empirical CalculationsCHEMISTRY - A EUROPEAN JOURNAL, Issue 16 2006Petr Dobe Abstract The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein,inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution. [source] N2O in small para -hydrogen clusters: Structures and energeticsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2009Hua Zhu Abstract We present the minimum-energy structures and energetics of clusters of the linear N2O molecule with small numbers of para -hydrogen molecules with pairwise additive potentials. Interaction energies of (p- H2),N2O and (p- H2),(p- H2) complexes were calculated by averaging the corresponding full-dimensional potentials over the H2 angular coordinates. The averaged (p- H2),N2O potential has three minima corresponding to the T-shaped and the linear (p- H2),ONN and (p- H2),NNO structures. Optimization of the minimum-energy structures was performed using a Genetic Algorithm. It was found that p- H2 molecules fill three solvation rings around the N2O axis, each of them containing up to five p- H2 molecules, followed by accumulation of two p- H2 molecules at the oxygen and nitrogen ends. The first solvation shell is completed at N = 17. The calculated chemical potential oscillates with cluster size up to the completed first solvation shell. These results are consistent with the available experimental measurements. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Theoretical study of hydrogen-bonded complexes of benzene with hydrides of astrochemical interestINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2008M. Nait Achour Abstract Post Hartree,Fock and DFT calculations have been performed for studying the possibility for a benzene support to be linked to various hydrides through a quasi Bz···HA bond. Interaction energy of compounds, including CH bonds (CH4, CH3F, CH2O, CHN, CHNO), NH bonds (NH3, NH2F, NHC, NHCO, NH3O), and OH bonds (OH2, OHF, NCOH), were evaluated, taking basis set superposition error (BSSE) and zero point vibrational energy (ZPVE) corrections into account. Numerical convergence of results with respect to the ingredients included at different steps of theory (basis set, DFT functionals, correlation treatments, geometry optimization) was tested mainly on the example of the water adduct and, for comparison, the Bz···H3O+ system containing a cation instead of a neutral molecule. A rather large range of adsorption energies is obtained, from about 1 kcal/mol for methane to more than 6 kcal/mol for cyanic acid, according to the acidic character of the adsorbed species in each family of Bz···HA bonds. Some consequences for astrophysical problems involving PAHs in the interstellar medium are pointed out. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Bioisosterism, enantioselectivity, and molecular modeling of new effective N6 - and/or N(9)-substituted 2-phenyl adenines and 8-aza analogs: Different binding modes to A1 adenosine receptorsDRUG DEVELOPMENT RESEARCH, Issue 2 2001A. Maria Bianucci Abstract Bioisosterism of the adenine and 8-azaadenine nuclei was demonstrated by comparison of A1 adenosine receptor binding affinity of 2-phenyl N6 -substituted adenines and the corresponding 8-azaadenines. Some of these new compounds are very potent A1 adenosine receptor antagonists. This work also describes the synthesis and A1 adenosine receptor binding of the enantiomers of some 2-phenyladenines substituted with a 1-phenylethyl chiral group in N6 and N(9) positions. Biological results, showing the same stereoselectivity for all the couples of enantiomers, may supply proof for the hypothesis of a possible double arrangement of 2-phenylsubstituted adenines inside A1 adenosine receptors. Theoretical studies, based on an improved A1 adenosine receptor model and consisting of evaluation and comparison of interaction energies in complexes involving some selected chiral ligands, support the above hypothesis. Drug Dev. Res. 54:52,65, 2001. © 2001 Wiley-Liss, Inc. [source] Multireference coupled-cluster methods for ground and low-lying excited states.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2010A benchmark illustration on CH + potentials Abstract Multireference (MR), general-model-space (GMS), state-universal (SU) coupled-cluster (CC) method that considers singly (S) and doubly (D) excited cluster amplitudes relative to the reference configurations spanning the model space (GMS SU CCSD), as well as its externally corrected (ec) version (N,M)-CCSD that uses N -reference MR CISD as an external source of higher-than-pair cluster amplitudes in a M -reference GMS CCSD, are used to investigate low-lying states of the CH+ ion. Relying on a simple ab initio model that enables a comparison with the exact full configuration interaction energies, the performance of the GMS-based methods is assessed in the whole relevant range of internuclear separations. It is shown that the ec (N,M)-CCSD version provides best results for both the singlet and the triplet states considered. For triplets, the use of high-spin (MS = 1) references is to be preferred. The GMS-based MR SU CC results for the ten low-lying states of CH+ clearly indicate the usefulness and reliability of these approaches. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Davydov's solitons in zigzag carbon nanotubesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2010Larissa Brizhik Abstract Nonlinear mechanism of charge transport in low-dimensional nanosystems is considered, based on the account of the electron,phonon interaction that arises from the deformation dependencies of the on-site and the hopping interaction energies at intermediatevalues of the corresponding coupling constants. In particular, carbon-type hexagonal zigzag nanotubes are studied. It is shown that in the adiabatic approximation the electron,phonon coupling results in the self-trapping of carriers and formation of polaron (soliton) states. We show that the ground state of an electron in a nanotube is a low-dimensional polaron whose symmetry depends on the strength of the coupling. Namely, at relatively weak coupling, the polaron possesses quasi-one-dimensional properties and has an azimuthal symmetry. When the coupling constant exceeds some critical value, the azimuthal symmetry breaks down and two-dimensional polaron on the nanotube surface is formed. There are also polarons formed by the electrons in the conducting band (or by holes in the valence band) in semiconducting zigzag carbon nanotubes. Such polarons are described by the system of coupled nonlinear Schroedinger equations which admits single-band polarons, and entangled (hybridized) polarons. These two types of polarons possess different energies and symmetry properties. Single-band solutions are one-dimensional polarons: they are azimuthally symmetric and localized along the nanotube axis. The entangled polarons are also self-trapped along the nanotube axis, but possess an inner structure and are modulated around the nanotube. The entangled polarons break the azimuthal symmetry and their energy is lower than the energy of single-band polarons. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Convergence radii of the polarization expansion of intermolecular potentialsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2009William H. Adams Abstract A new method is presented to evaluate convergence radii of the polarization expansion of interaction energies for pairs of atoms or molecules. The method is based on an analysis of the variation of the perturbed state vector as a function of the coupling constant , and does not require a calculation of perturbation corrections to high order. The convergence radii at infinite interatomic/intermolecular distances R, as well as a remarkably accurate representation of the R dependence of the convergence radii are obtained from simple calculations involving only monomer wave functions. For the interaction of the lithium and hydrogen atoms, the obtained convergence radii agree well with those obtained previously from the large-order calculations of Patkowski et al. (Patkowski et al., J Chem Phys, 2002, 117, 5124), but are expected to be considerably more accurate. Rigorous upper bounds and reasonable approximations to the convergence radii at R = , are obtained for the pairs of lithium, beryllium, boron, neon, and sodium atoms, as well as for the dimer consisting of two LiH molecules. For all the systems studied, the convergence radii are significantly smaller than the unity and rapidly decrease with the increase of the nuclear charge. It is hoped that the results of this investigation will help to analyze and eventually to compute the convergence radii of the symmetry-adapted perturbation theories which utilize the same partitioning of the Hamiltonian as the polarization expansion. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Chiral discrimination in hydrogen-bonded complexes of 2-methylol oxirane with hydrogen peroxideINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2009Guiqiu Zhang Abstract A systematic quantum chemical study reveals the effects of chirality on the intermolecular interactions between two chiral molecules bound by hydrogen bonds. The methods used are second-order Møller,Plesset perturbation theory (MP2) with the 6-311++g(d,p) basis set. Complexes via the OH···O hydrogen bond formed between the chiral 2-methylol oxirane (S) and chiral HOOH (P and M) molecules have been investigated, which lead to four diastereomeric complexes. The nomenclature of the complexes used in this article is enantiomeric configuration sign corresponding to English letters. Such as: sm, sp. The relative positions of the methylol group and the hydrogen peroxide are designated as syn (same side) and anti (opposite side). The largest chirodiastaltic energy was ,Echir = ,1.329 kcal mol,1 [9% of the counterpoise correct average binding energy De(corr)] between the sm-syn and sp-anti in favor of sm-syn. The largest diastereofacial energy was ,1.428 kcal mol,1 between sm-syn and sm-anti in favor of sm-syn. To take into account solvents effect, the polarizable continuum model (PCM) method has been used to evaluate the chirodiastaltic energies, and diastereofacial energies of the 2-methylol oxirane···HOOH complexes. The chiral 2,3-dimethylol oxirane (S, S) is C2 symmetry which offers two identical faces. Hence, the chirodiastaltic energy is identical to the diastereomeric energy, and is ,Echir = 0.563 kcal mol,1 or 5.3% of the De(corr) in favor of s,s-p. The optimized structures, interaction energies, and chirodiastaltic energies for various isomers were estimated. The harmonic frequencies, IR intensities, rotational constants, and dipole moments were also reported. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Theoretical study of interactions between cysteine and perfluoropropanoic acid in gas and aqueous phaseINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2009Tiffani M. Holmes Abstract The interaction of perfluoropropanoic acid (PFPA) with the amino acid cysteine was investigated using density functional theory. Previous studies suggest that the peroxisome proliferator chemical, perfluorooctanoic acid, is circulated throughout the body by way of sulfur-containing amino acids. We present conformational analysis of the interactions of PFPA, a small model of perfluorooctanoic acid, with the sulfur-containing amino acid which occur by the process of hydrogen bonding, in which the hydrogen of the sulfhydryl group interacts with the carboxyl oxygen, and the amino nitrogen forms a hydrogen bond with the hydrogen of the OH group of the fluorinated alkyl. We also show in our structures a recently characterized weak nonbonded interaction between divalent sulfur and a main chain carboxyl oxygen in proteins. B3LYP calculated free energies and interaction energies predict low-energy, high-interaction conformations for complex systems of perfluorinated fatty acid interactions with cysteine. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Complete basis set extrapolations of dispersion, exchange, and coupled-clusters contributions to the interaction energy: a helium dimer study,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 12 2008gorzata Jeziorska Abstract Effectiveness of various extrapolation schemes in predicting complete basis set (CBS) values of interaction energies has been investigated for the helium dimer as a function of interatomic separation R. The investigations were performed separately for the leading dispersion and exchange contributions to the interaction energy and for the interaction energy computed using the coupled cluster method with single and double excitations (CCSD). For all these contributions, practically exact reference values were obtained from Gaussian-type geminal calculations. Sequences of orbital basis sets augmented with diffuse and bond functions or augmented with two sets of diffuse functions have been employed, with the cardinal numbers up to X = 7. The functional form EX = ECBS + A(X , k),, was applied for the extrapolations, where EX is the contribution to the interaction energy computed with a basis set of cardinal number X. The main conclusion of this work is that CBS extrapolations of an appropriate functional form generally improve the accuracy of the interaction energies at a very small additional computational cost (of the order of 10%) and should be recommended in calculations of interatomic and intermolecular potentials. The effectiveness of the extrapolations significantly depends, however, on the interatomic separation R and on the composition of the basis set. Basis sets with midbond functions, well known to provide at a given size much more accurate nonextrapolated results than bases lacking such functions, have been found to perform best also in extrapolations. The X,1 extrapolations of dispersion energies computed with midbond function turned out to be very efficient (except at large R), reducing the errors by an order of magnitude for small X and a factor of two for large X (where the errors of nonextrapolated results are already very small). If midbond functions are not used, the X,3 formula is most appropriate for the dispersion energies. For the exchange component of the interaction energy, the best results are obtained,in both types of basis sets,with the X,4 extrapolation, which leads (in both cases) to almost an order of magnitude reduction of the error. The X,3 and (X , 1),3 extrapolations work also well, but give smaller improvements. The correlation component of the CCSD interaction energy extrapolates best with , between 2 and 3 for bases with midbond functions and between 3 and 4 for bases without such functions. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Theoretical study in [C2H4,Tl]+ and [C2H2,Tl]+ complexesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2007Fernando Mendizabal Abstract We studied the attraction between [C2Hn] and Tl(I) in the hypothetical [C2Hn,Tl]+ complexes (n = 2,4) using ab initio methodology. We found that the changes around the equilibrium distance C,Tl and in the interaction energies are sensitive to the electron correlation potential. We evaluated these effects using several levels of theory, including Hartree,Fock (HF), second-order Møller,Plesset (MP2), MP4, coupled cluster singles and doubles CCSD(T), and local density approximation augmented by nonlocal corrections for exchange and correlation due to Becke and Perdew (LDA/BP). The obtained interaction energies differences at the equilibrium distance Re (C,Tl) range from 33 and 46 kJ/mol at the different levels used. These results indicate that the interaction between olefinic systems and Tl(I) are a real minimum on the potential energy surfaces (PES). We can predict that these new complexes are viable for synthesizing. At long distances, the behavior of the [C2Hn],Tl+ interaction may be related mainly to charge-induced dipole and dispersion terms, both involving the individual properties of the olefinic ,-system and thallium ion. However, the charge-induced dipole term (R,4) is found as the principal contribution in the stability at long and short distances. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Theoretical study of adsorption of methyl tert -butyl ether on broken clay minerals surfacesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005A. Michalkova Abstract The interactions between methyl tert -butyl ether (MTBE) and differently defected tetrahedral and octahedral fragments of clay minerals containing Si4+, Al3+, and Mg2+ central cations have been studied at the B3LYP and MP2 levels of theory in conjunction with the 6-31G(d) basis set. MTBE interacts with defect clay structures due to the formation of multiple CH,O and OH,O hydrogen bonds. Interactions of MTBE with systems containing different types of defected mineral fragments were found to vary. Systems containing the same type of defected mineral fragment with different central cation interact almost the same way with MTBE. The formation of hydrogen bonds leads to changes in the geometrical parameters and to the polarization of MTBE. The values of the interaction energies depend on the charge of the mineral fragment. They amount to 5 kcal/mol,35 kcal/mol. MTBE interacts more preferably with octahedral fragments than with tetrahedral fragments that contain an Al3+ central cation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Quantum chemical studies on molecular structural conformations and hydrated forms of salicylamide and O-hydroxybenzoyl cyanideINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2005K. Anandan Abstract Ab initio and density functional theory (DFT) methods have been employed to study the molecular structural conformations and hydrated forms of both salicylamide (SAM) and O-hydroxybenzoyl cyanide (OHBC). Molecular geometries and energetics have been obtained in the gaseous phase by employing the Møller,Plesset type 2 MP2/6-311G(2d,2p) and B3LYP/6-311G(2d,2p) levels of theory. The presence of an electron-releasing group (SAM) leads to an increase in the energy of the molecular system, while the presence of an electron-withdrawing group (OHBC) drastically decreases the energy. Chemical reactivity parameters (, and ,) have been calculated using the energy values of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) obtained at the Hartree,Fock (HF)/6-311G(2d,2p) level of theory for all the conformers and the principle of maximum hardness (MHP) has been tested. The condensed Fukui functions have been calculated using the atomic charges obtained through the natural bond orbital (NBO) analysis scheme for all the optimized structures at the B3LYP/6-311G(2d,2p) level of theory, and the most reactive sites of the molecules have been identified. Nuclear magnetic resonance (NMR) studies have been carried out at the B3LYP/6-311G(2d,2p) level of theory for all the conformers in the gaseous phase on the basis of the method of Cheeseman and coworkers. The calculated chemical shift values have been used to discuss the delocalization activity of the electron clouds. The dimeric structures of the most stable conformers of both SAM and OHBC in the gaseous phase have been optimized at the B3LYP/6-311G(2d,2p) level of theory, and the interaction energies have been calculated. The most stable conformers of both compounds bear an intramolecular hydrogen bond, which gives rise to the formation of a pseudo-aromatic ring. These conformers have been allowed to interact with the water molecule. Special emphasis has been given to analysis of the intermolecular hydrogen bonds of the hydrated conformers. Self-consistent reaction field (SCRF) theory has been employed to optimize all the conformers in the aqueous phase (, = 78.39) at the B3LYP/6-311G(2d,2p) level of theory, and the solvent effect has been studied. Vibrational frequency analysis has been performed for all the optimized structures at MP2/6-311G(2d,2p) level of theory, and the stationary points corresponding to local minima without imaginary frequencies have been obtained for all the molecular structures. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Density functional study of HO(H2O)n (n = 1,3) clustersINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005Xiu-Li Dong Abstract The hydrogen bonding complexes HO(H2O)n (n = 1,3) were completely investigated in the present study using DFT and MP2 methods at varied basis set levels from 6-31++G(d,p) to 6-311++G(2d,2p). For n = 1 two, for n = 2 two, and for n = 3 five reasonable geometries are considered. The optimized geometric parameters and interaction energies for various complexes at different levels are estimated. The infrared spectrum frequencies and IR intensities of the most stable structures are reported. Finally, thermochemistry studies are also carried out. The results indicate that the formation and the number of hydrogen bonding have played an important role in the structures and relative stabilities of different complexes. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Coarse-grained model of nucleic acid basesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Maciej Maciejczyk Abstract Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. In this work, we propose a physics-based coarse-grained model of nucleic-acid bases in which each base is represented by several (3,5) interaction centers. van der Waals interactions are modeled by Lennard-Jones spheres with a 12,6 potential energy function. The charge distribution is modeled by a set of electric dipole moments located at the centers of the Lennard-Jones spheres. The method for computing the Lennard-Jones parameters, electric dipole moments (their magnitude and orientation) and positions of the interaction centers is described. Several models with different numbers of interaction centers were tested. The model with three-center cytosine, four-center guanine, four-center thymine, and five-center adenine satisfactorily reproduces the canonical Watson,Crick hydrogen bonding and stacking interaction energies of the all-atom AMBER model. The computation time with the coarse-grained model is reduced seven times compared with that of the all-atom model. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Theoretical study of the prion protein based on the fragment molecular orbital methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2009Takeshi Ishikawa Abstract We performed fragment molecular orbital (FMO) calculations to examine the molecular interactions between the prion protein (PrP) and GN8, which is a potential curative agent for prion diseases. This study has the following novel aspects: we introduced the counterpoise method into the FMO scheme to eliminate the basis set superposition error and examined the influence of geometrical fluctuation on the interaction energies, thereby enabling rigorous analysis of the molecular interaction between PrP and GN8. This analysis could provide information on key amino acid residues of PrP as well as key units of GN8 involved in the molecular interaction between the two molecules. The present FMO calculations were performed using an original program developed in our laboratory, called "Parallelized ab initio calculation system based on FMO (PAICS)". © 2009 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolasesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2009Nikolaj Otte Abstract CHARMM force-field parameters are reported for the tetrahedral intermediate of serine hydrolases. The fitting follows the standard protocol proposed for CHARMM22. The reference data include ab initio (RHF/6-31G*) interaction energies of complexes between water and the model compound 1,1-dimethoxyethoxide, torsional profiles of related model compounds from correlated ab initio (MP2/6-311+G*//B3LYP/6-31+G*) calculations, as well as molecular geometries and vibrational frequencies from density functional theory (B3LYP/6-31+G*). The optimized parameters reproduce the target data well. Their utility is demonstrated by a QM/MM study of the tetrahedral intermediate in Bacillus subtilis lipase A, and by classical molecular modeling of enantioselectivity in Pseudomonas aeruginosa lipase and its mutants. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Reply to "Comment on Aromatic-Backbone Interactions in Model ,-Helical Peptides"JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2008József Csontos Abstract In response to Van Mourik's comments on our paper (J Comput Chem 2007, 28, 1208.) we present an extended version of our rotation method. We also prove that intramolecular interaction energies as well the basis set superposition errors calculated with our rotation method are comparable with those obtained by the counterpoise method of Boys and Bernardi (Mol Phys 1970, 19, 533). In intramolecular interaction energy calculations, if the interacting groups are in proximity, our rotation method is recommended to avoid artificial interactions, which can be induced by fragmentation. © 2007 Wiley Periodicals, Inc.J Comput Chem, 2008 [source] Atom,atom partitioning of total (super)molecular energy: The hidden terms of classical force fieldsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2007M. Rafat Abstract Classical force fields describe the interaction between atoms that are bonded or nonbonded via simple potential energy expressions. Their parameters are often determined by fitting to ab initio energies and electrostatic potentials. A direct quantum chemical guide to constructing a force field would be the atom,atom partitioning of the energy of molecules and van der Waals complexes relevant to the force field. The authors used the theory of quantum chemical topology to partition the energy of five systems [H2, CO, H2O, (H2O)2, and (HF)2] in terms of kinetic, Coulomb, and exchange intra-atomic and interatomic contributions. The authors monitored the variation of these contributions with changing bond length or angle. Current force fields focus only on interatomic interaction energies and assume that these purely potential energy terms are the only ones that govern structure and dynamics in atomistic simulations. Here the authors highlight the importance of self-energy terms (kinetic and intra-atomic Coulomb and exchange). © 2006 Wiley Periodicals, Inc. J Comput Chem 2007 [source] Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2006Christopher S. Page Abstract An application of the Molecular mechanics Poisson,Boltzmann surface area (MM-PBSA) protocol to the prediction of protein kinase inhibitor selectivity is presented. Six different inhibitors are placed in equivalent orientations in each of six different receptors. Fully solvated molecular dynamics is then run for 1 ns on each of the 36 complexes, and the resulting trajectories scored, using the implicit solvent model. The results show some correlation with experimentally-determined specificities; anomalies may be attributed to a variety of causes, including difficulties in quantifying induced fit penalties and variabilities in normal modes calculations. Decomposing interaction energies on a per-residue basis yields more useful insights into the natures of the binding modes and suggests that the real value of such calculations lies in understanding interactions rather than outright prediction. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] A force-field description of short-range repulsions for high density alkane molecular dynamics simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2004Joseph M. Hayes Abstract The use of Buckingham (exp-6) van der Waals potentials in molecular dynamics (MD) simulations can quite successfully reproduce experimental thermodynamic data at low densities. However, they are less successful in producing a description of the repulsive regions of the potential energy surface (PES) that is in accord with the results of high-level ab initio computations. We show that Morse potentials can be parameterized to give excellent fits to both the attractive and repulsive regions of the PES. The best set of alkane van der Waals Morse function parameters reported to date for the description of nonbond repulsive interactions is presented, as determined by comparison with both ab initio and experimental results. C,C, H,H and C,H atom-pair potentials employing parameter sets based on the use of the geometric mean in the fitting procedure are found to be portable from methane to n- butane. Fitting to a combination of methane dimer interaction energies and forces from ab initio calculations yields parameter sets whose performance is superior to those determined from the interaction energies alone. Used in MD simulations, our newly developed parameter sets predict thermodynamic functions that show better agreement with experiment than those based on parameter sets in common use. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1953,1966, 2004 [source] Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzymeJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2004Nuno M. F. S. A. Cerqueira Abstract This article focuses on the first step of the catalytic mechanism for the reduction of ribonucleotides catalyzed by the enzyme Ribonucleotide Reductase (RNR). This corresponds to the activation of the substrate. In this work a large model of the active site region involving 130 atoms was used instead of the minimal gas phase models used in previous works. The ONIOM method was employed to deal with such a large system. The results gave additional information, which previous small models could not provide, allowing a much clearer evaluation of the role of the enzyme in this step. Enzyme,substrate interaction energies, specific transition state stabilization, and substrate steric strain energies were obtained. It was concluded that the transition state is stabilized in 4.0 kcal/mol by specific enzyme,substrate interactions. However, this stabilization is cancelled by the cost in conformational energy for the enzyme to adopt the transition state geometry; the overall result is that the enzyme machinery does not lead to a rate enhancement in this step. It was also found that the substrate binds to the active site with almost no steric strain, emphasizing the complementarity and specificity of the RNR active site for nucleotide binding. The main role of the enzyme at the very beginning of the catalytic cycle was concluded to be to impose stereospecifity upon substrate activation and to protect the enzyme radical from the solvent, rather than to be an reaction rate enhancement. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 2031,2037, 2004 [source] Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2004Application to the ATP-binding site of a binuclear bacterial enzyme. Abstract We have explored the conformation-dependent interaction energy of the triphosphate moiety, a key constituent of ATP and GTP, with a closed-shell divalent cation, Zn2+, used as a probe. This was done using the SIBFA polarizable molecular mechanics procedure. We have resorted to a previously developed approach in which triphosphate is built out from its elementary constitutive fragments, and the intramolecular, interfragment, interaction energies are computed simultaneously with their intermolecular interactions with the divalent cation. This approach has enabled reproduction of the values of the intermolecular interaction energies from ab initio quantum-chemistry with relative errors <3%. It was extended to the complex of a nonhydrolyzable analog of ATP with the active site of a bacterial enzyme having two Mg2+ cations as cofactors. We obtained following energy-minimization a very close overlap of the ATP analog over its position from X-ray crystallography. For models of the ATP analog,enzyme complex encompassing up to 169 atoms, the values of the SIBFA interaction energies were found to match their DFT counterparts with relative errors of <2%. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 160,168, 2004 [source] Converging free energy estimates: MM-PB(GB)SA studies on the protein,protein complex Ras,RafJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2004Holger Gohlke Abstract Estimating protein,protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the complex H-Ras/C-Raf1 using the MM-PB(GB)SA approach, testing the internal consistency and model dependence of the results. Averaging gas-phase energies (MM), solvation free energies as determined by Generalized Born models (GB/SA), and entropic contributions calculated by normal mode analysis for snapshots obtained from 10 ns explicit-solvent molecular dynamics in general results in an overestimation of the binding affinity when a solvent-accessible surface area-dependent model is used to estimate the nonpolar solvation contribution. Applying the sum of a cavity solvation free energy and explicitly modeled solute,solvent van der Waals interaction energies instead provides less negative estimates for the nonpolar solvation contribution. When the polar contribution to the solvation free energy is determined by solving the Poisson,Boltzmann equation (PB) instead, the calculated binding affinity strongly depends on the atomic radii set chosen. For three GB models investigated, different absolute deviations from PB energies were found for the unbound proteins and the complex. As an alternative to normal-mode calculations, quasiharmonic analyses have been performed to estimate entropic contributions due to changes of solute flexibility upon binding. However, such entropy estimates do not converge after 10 ns of simulation time, indicating that sampling issues may limit the applicability of this approach. Finally, binding free energies estimated from snapshots of the unbound proteins extracted from the complex trajectory result in an underestimate of binding affinity. This points to the need to exercise caution in applying the computationally cheaper "one-trajectory-alternative" to systems where there may be significant changes in flexibility and structure due to binding. The best estimate for the binding free energy of Ras,Raf obtained in this study of ,8.3 kcal mol,1 is in good agreement with the experimental result of ,9.6 kcal mol,1, however, further probing the transferability of the applied protocol that led to this result is necessary. © 2003 Wiley Periodicals, Inc. J Comput Chem 2: 238,250, 2003 [source] An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimerJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2003Jinshan Li Abstract Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of CH,ON H-bond ranges from ,9.0 to ,12.4 kJ mol,1 at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated ,EC is within 2.5 kJ mol,1 of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom,atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 Å. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 345,352, 2003 [source] A new thermodynamic model for clino- and orthoamphiboles in the system Na2O,CaO,FeO,MgO,Al2O3,SiO2,H2O,OJOURNAL OF METAMORPHIC GEOLOGY, Issue 6 2007J. F. A. DIENER Abstract A recent thermodynamic model for the Na,Ca clinoamphiboles in the system Na2O,CaO,FeO,MgO,Al2O3,SiO2,H2O,O (NCFMASHO), is improved, and extended to include cummingtonite,grunerite and the orthoamphiboles, anthophyllite and gedrite. The clinoamphibole model in NCMASH is adopted, but the extension into the FeO- and Fe2O3 -bearing systems is revised to provide thermodynamic consistency and better agreement with natural assemblage data. The new model involves order,disorder of Fe,Mg between the M2, M13 and M4 sites in the amphibole structure, calibrated using the experimental data on site distributions in cummingtonite,grunerite. In the independent set of end-members used to represent the thermodynamics, grunerite (rather than ferroactinolite) is used for FeO, with two ordered Fe,Mg end-members, and magnesioriebeckite (rather than ferritschermakite) is used for Fe2O3. Natural assemblage data for coexisting clinoamphiboles are used to constrain the interaction energies between the various amphibole end-members. For orthamphibole, the assumption is made that the site distributions and the non-ideal formulation is the same as for clinoamphibole. The data set end-members anthophyllite, ferroanthophyllite and gedrite, are used; for the others, they are based on the clinoamphibole end-members, with the necessary adjustments to their enthalpies constrained by natural assemblage data for coexisting clino- and orthoamphiboles. The efficacy of the models is illustrated with P,T grids and various pseudosections, with a particular emphasis on the prediction of mineral assemblages in ferric-bearing systems. [source] Critical behavior in quenched random structures: Mean-field lattice-gas approachAICHE JOURNAL, Issue 2 2001S. De A new mean-field equation-of-state model is proposed for predicting the critical behavior of fluids confined in porous, random structures. The approach is based on a lattice-gas formalism and incorporates effects of both fluid confinement and energetically heterogeneous interactions between fluid molecules and pore surfaces. The model was used to predict a variety of thermodynamic properties in these systems, including the dependence of the confined fluid's critical properties on the porosity and relative strength of fluid,fluid and fluid,pore interaction energies. The study of suface-energy heterogeneities show that they significantly affect the critical temperature of the confined fluid, at a given porosity, compared to the uniform energy case. Comparison of the model performance with both grand canonical Monte Carlo simulation results and a set of adsorption data in a silica gel suggest that the approach taken here provides a useful analytic method for calculating physical properties in complex systems of this kind. [source] An examination of binding motifs associated with inter-particle interactions between facetted nano-crystals of acetylsalicylic acid and ascorbic acid through the application of molecular grid-based search methods,JOURNAL OF PHARMACEUTICAL SCIENCES, Issue 12 2009R.B. Hammond Abstract Grid-based intermolecular search methods using atom,atom force fields are used to assess the structural nature of potential crystal,crystal interfacial binding associated with the examination of representative pharmaceutical formulation components, viz acetylsalicylic acid (aspirin) and ascorbic acid (vitamin C). Molecular models of nano-sized molecular clusters for these two compounds, shaped in accordance with an attachment energy model of the respective particle morphologies, are constructed and used together with a grid-based search method to model the likely inter-particle interactions. The most-stable, mutual alignments of the respective nano-clusters based on their interaction energies are identified in the expectation that these are indicative of the most likely inter-particle binding configurations. The stable inter-particle binding configurations identified reveal that the number of interfacial hydrogen bonds formed between the binding particles is, potentially, an important factor in terms of the stability of inter-particle cohesion. All preferred inter-particle alignments are found to involve either the (1,0,0) or the (1,1,0) face of aspirin crystals interacting with a number of the growth forms of ascorbic acid. Four main types of interfacial hydrogen bonds are found to be associated with inter-particle binding and involve acceptor,donor interactions between hydroxyl, carbonyl, ester and lactone acceptor groups and hydroxyl donor groups. This hydrogen bonding network is found to be consistent with the surface chemistry of the interacting habit faces with, in general, the number of hydrogen bonds increasing for the more stable alignments. The likely usefulness of this approach for predicting solid-state formulation properties is reviewed. © 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:4589,4602, 2009 [source] Advanced models for erosion corrosion and its mitigation,MATERIALS AND CORROSION/WERKSTOFFE UND KORROSION, Issue 2 2008G. Schmitt Erosion corrosion, i.e., flow-induced localized corrosion (FILC) is initiated when flow dynamic forces surpass the fracture energy of protective layers or scales on metals. With a new model the maximum interaction energies between flowing media and solid walls can be quantified in terms of "freak" energy densities created during singular events (freak events) of perpendicular impacts by near-wall microturbulence elements. The freak energy densities are in the megaPascal range and match well in the order of magnitude with fracture energies of protective layers and can be estimated from Wavelet diagnostics of electrochemical current noise measured at microelectrodes under mass transport controlled conditions. This solves the problem that wall shear stresses, generally used to quantify critical flow intensities for FILC initiation, range several orders of magnitude (Pa range) below the fracture energies of protective layers. The new advanced model allows for the first time to quantify the maximum fluid dynamic forces exerted on solid walls under different turbulent and disturbed flow conditions (one-phase liquid flow on jet impinged surfaces and on coupons in rotated cages, surfaces impacted by slug flow and gas-pulsed impinging jets). Drag reducing additives were shown to reduce freak energy densities to values significantly below fracture energies of protective layers and hence inhibit initiation of FILC. The onset of FILC can be monitored online with the newly developed CoulCount method, an easy-to-use, non-invasive diagnostic tool which evaluates electrochemical current noise between jet impinged electrode pairs made from the metals to be tested. [source] | ||||||||||||||||||||||||||||||||||||||||