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Energy Minima (energy + minimum)
Kinds of Energy Minima Selected AbstractsSolvent and structural effects on the kinetics of the reactions of 2-substituted cyclohex-1-enylcarboxylic and 2-substituted benzoic acids with diazodiphenylmethaneINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 12 2007J. B. Nikoli The rate constants for the reaction of 2-methyl-cyclohex-1-enylcarboxylic, 2-phenylcyclohex-1-enylcarboxylic, and 2-methylbenzoic and 2-phenylbenzoic acids with diazodiphenyl-methane were determined in 14 various solvents at 30°C. To explain the kinetic results through solvent effects, the second-order rate constants of the examined acids were correlated using the Kamlet,Taft solvatochromic equation. The correlations of the kinetic data were carried out by means of multiple linear regression analysis, and the solvent effects on the reaction rates were analyzed in terms of initial and transition state contributions. The quantitative relationship between the molecular structure and the chemical reactivity has been discussed, as well as the effect of geometry on the reactivity of the examined molecules. The geometric data of all the examined compounds corresponding to the energy minima in solvent, simulated as dielectric continuum, obtained using semiempirical MNDO-PM3 energy calculations. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 664,671, 2007 [source] DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphatesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010Valeri I. Poltev Abstract We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the "classical" B conformation (BI-form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence-dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII-like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548,2559, 2010 [source] New valley ridge inflection point associated to the bifurcation of a valley on potential energy surfacesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 14 2007R. Palmeiro Abstract There are currently two definitions of valley ridge inflection point on an adiabatic potential energy surface (PES), one introduced by Basilevsky and the other by Valtazanos and Ruedenberg. Here, we investigate the validity of both definitions on bidimensional surfaces without symmetry constraints, with neither producing completely satisfactory results. Hence, we propose new conditions which must obey a valley bifurcation point (VBP) locally and demonstrate that such conditions are necessary when a valley splits into two, finishing at two energy minima. Finally, we localize such VBPs on the bidimensional surfaces and check the certainty of our previous deductions. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Performance of SuSi: A method for generating atomistic models of amorphous polymers based on a random search of energy minimaJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2004David Curcó Abstract The performance of a recently developed method to generate representative atomistic models of amorphous polymers has been investigated. This method, which is denoted SuSi, can be defined as a random generator of energy minima. The effects produced by different parameters used to define the size of the system and the characteristics of the generation algorithm have been examined. Calculations have been performed on poly(L,D -lactic) acid (, = 1.25 g/cm3) and nylon 6 (, = 1.084 g/cm3), which are important commercial polymers. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 790,798, 2004 [source] Isomers of C20: An energy profile IIJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2003Kyle A. Beran Abstract Semi-empirical calculations, at the PM3 level provided within the Winmopac v2.0 software package, are used to geometrically optimize and determine the absolute energies (heats of formation) of a variety of C20 isomers that are predicted to exist in and around the bowl and cage isomers. Using the optimized Cartesian coordinates for the bowl and the cage isomers, a saddle-point calculation was performed. The output file generated, containing energy, distance, and geometry information, is then organized into a graphical format. The resulting graph, which plots the energy of the 20-atom system as a function of the distance from the geometric midpoint, is a two-dimensional energy profile. This profile illustrates an estimation of the contours on the potential energy surface, showing energy minima and maxima that are encountered as the bowl evolves into the cage structure, or vice-versa. To expand the surface into three dimensions, geometry optimizations were performed on the sets of Cartesian coordinates that correspond to energy minima in the bowl-cage profile. Based on these optimizations, eight additional isomers of C20 have been identified and are predicted to be energetically stable. These additional isomers were subsequently subjected to saddle-point calculations in order to identify those isomers that lie adjacent to one another on the three-dimensional surface. Two isomers that are adjacent to each other will exhibit an energy profile that progresses smoothly from the potential well of each isomer up to the saddle point separating them. Consequently, these adjacent pairs of isomers establish a step-wise transformation between the bowl and the cage. This process, which extends out over the three-dimensional surface, is predicted to require less energy than that of the direct, two-dimensional transformation predicted in the bowl-cage profile. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1287,1290, 2003 [source] Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibilityJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2002Visvaldas Kairys Abstract The ligand,protein docking algorithm based on the Mining Minima method has been substantially enhanced. First, the basic algorithm is accelerated by: (1) adaptively determining the extent of each energy well to help avoid previously discovered energy minima; (2) biasing the search away from ligand positions at the surface of the receptor to prevent the ligand from staying at the surface when large sampling regions are used; (3) quickly testing multiple different ligand positions and orientations for each ligand conformation; and (4) tuning the source code to increase computational efficiency. These changes markedly shorten the time needed to discover an accurate result, especially when large sampling regions are used. The algorithm now also allows user-selected receptor sidechains to be treated as mobile during the docking procedure. The energies associated with the mobile side chains are computed as if they belonged to the ligand, except that atoms at the boundary between side chains and the rigid backbone are treated specially. This new capability is tested for several well-known ligand/protein systems, and preliminary application to an enzyme whose substrate is unknown,the recently solved hypothetical protein YecO (HI0319) from Haemophilus influenzae,indicates that side-chains relaxations allow candidate substrates of various sizes to be accommodated. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1656,1670, 2002 [source] Structural characterization of isomeric 2,3,5-substituted tetrahydropyrrolo[3,4- d]isoxazole-4,6-diones prepared by cycloaddition of N -methyl- C -arylnitrones to N -phenyl- or N -methylmaleimideJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 5 2004Kalevi Pihlaja 1,3-Dipolar cycloaddition reactions of N -methyl- C -arylnitrones with N -phenyl- or N -methylmaleimide were studied. The reaction of p -dimethylamino-, 4-benzyloxy-3-methoxy-, p -nitro- and p -chloro-substituted phenylnitrones with N -phenylmaleimide gave cis and trans cycloadducts but that of the corresponding phenylnitrones with N -methylmaleimides only the cis adducts in the case of p -dimethylamino and 4-benzyloxy-3-methoxy substitution. All cis adducts attain a biased conformation whereas the trans forms are shown (by 1H NMR at 233 K and 13C NMR at 208 K) to be mixtures of two invertomers, namely o -(N-lone pair antiperiplanar to 3H; minor) and i -conformations (3H-C-C-3aH dihedral angle close to 90°; major). PM3 and DFT calculations at the B3LYP/6,31G(d) level of theory prove qualitatively that these two conformers of the trans adduct are of comparable stability and represent energy minima. [source] Unfolding the fold of cyclic cysteine-rich peptidesPROTEIN SCIENCE, Issue 3 2008Amarda Shehu Abstract We propose a method to extensively characterize the native state ensemble of cyclic cysteine-rich peptides. The method uses minimal information, namely, amino acid sequence and cyclization, as a topological feature that characterizes the native state. The method does not assume a specific disulfide bond pairing for cysteines and allows the possibility of unpaired cysteines. A detailed view of the conformational space relevant for the native state is obtained through a hierarchic multi-resolution exploration. A crucial feature of the exploration is a geometric approach that efficiently generates a large number of distinct cyclic conformations independently of one another. A spatial and energetic analysis of the generated conformations associates a free-energy landscape to the explored conformational space. Application to three long cyclic peptides of different folds shows that the conformational ensembles and cysteine arrangements associated with free energy minima are fully consistent with available experimental data. The results provide a detailed analysis of the native state features of cyclic peptides that can be further tested in experiment. [source] Identification of possible kinetically significant anion-binding sites in human serum transferrin using molecular modeling strategiesBIOPOLYMERS, Issue 2 2004Elizabeth Ambrose Amin Abstract Certain anions have been shown experimentally to influence the rate of iron release from human serum transferrin (HST), implying the existence of one or more allosteric kinetically significant anion- binding (KISAB) sites on or near the surface of the protein. A rank-ordered selection of potential HST KISAB sites has been obtained using a novel three-stage molecular modeling strategy. The crystal structure of HST (1A8E.pdb) was first subjected to a heuristic analysis, in which positively charged and hydrogen-bonding residues on or near the surface of the protein were identified. In this stage, a preliminary electrostatic potential map was also calculated, yielding six preliminary sites. Next, energy-grid calculations were conducted in order to identify anion,protein interaction energy minima, which resulted in the inclusion of three additional sites. Finally, three anions already shown experimentally to demonstrate varied effects on HST iron-release kinetics were placed at each potential site; molecular dynamics and molecular mechanics calculations were performed in order to elucidate the hydrogen-bonding environment around each anion of the protein as well as to calculate anion,protein-binding energies. © 2003 Wiley Periodicals, Inc. Biopolymers 73: 205,215, 2004 [source] Structures and Vibrational Spectra of the Sulfur-Rich Oxides SnO (n = 4,9): The Importance of ,*,,* InteractionsCHEMISTRY - A EUROPEAN JOURNAL, Issue 2 2007Wah Wong Prof. Abstract The structures of a large number of isomers of the sulfur oxides SnO with n = 4,9 have been calculated at the G3X(MP2) level of theory. In most cases, homocyclic molecules with exocyclic oxygen atoms in an axial position are the global minimum structures. Perfect agreement is obtained with experimentally determined structures of S7O and S8O. The most stable S4O isomer as well as some less stable isomers of S5O and S6O are characterized by a strong ,*,,* interaction between SO and SS groups, which results in relatively long SS bonds with internuclear distances of 244,262,pm. Heterocyclic isomers are less stable than the global minimum structures, and this energy difference approximately increases with the ring size: 17 (S4O), 40 (S5O), 32 (S6O), 28 (S7O), 45 (S8O), and 54,kJ,mol,1 (S9O). Owing to a favorable ,*,,* interaction, preference for an axial (or endo) conformation is calculated for the global energy minima of S7O, S8O, and S9O. Vapor-phase decomposition of SnO molecules to SO2 and S8 is strongly exothermic, whereas the formation of S2O and S8 is exothermic if n<7, but slightly endothermic for S7O, S8O, and S9O. The calculated vibrational spectra of the most stable isomers of S6O, S7O, and S8O are in excellent agreement with the observed data. [source] Molecular Recognition and Crystal Energy Landscapes: An X-ray and Computational Study of Caffeine and Other MethylxanthinesCHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2005Lucia Carlucci Dr. Abstract We introduce a new approach to crystal-packing analysis, based on the study of mutual recognition modes of entire molecules or of molecular moieties, rather than a search for selected atom,atom contacts, and on the study of crystal energy landscapes over many computer-generated polymorphs, rather than a quest for the one most stable crystal structure. The computational tools for this task are a polymorph generator and the PIXEL density sums method for the calculation of intermolecular energies. From this perspective, the molecular recognition, crystal packing, and solid-state phase behavior of caffeine and several methylxanthines (purine-2,6-diones) have been analyzed. Many possible crystal structures for anhydrous caffeine have been generated by computer simulation, and the most stable among them is a thermodynamic, ordered equivalent of the disordered phase, revealed by powder X-ray crystallography. Molecular recognition energies between two caffeine molecules or between caffeine and water have been calculated, and the results reveal the largely predominant mode to be the stacking of parallel caffeine molecules, an intermediately favorable caffeine,water interaction, and many other equivalent energy minima for lateral interactions of much less stabilization power. This last indetermination helps to explain why caffeine does not crystallize easily into an ordered anhydrous structure. In contrast, the mono- and dimethylxanthines (theophylline, theobromine, and the 1,7-isomer, for which we present a single-crystal X-ray study and a lattice energy landscape) do crystallize in anhydrous form thanks to the formation of lateral hydrogen bonds. [source] Motif Reconstruction in Clusters and Layers: Benchmarks for the Kawska,Zahn Approach to Model Crystal FormationCHEMPHYSCHEM, Issue 4 2010Theodor Milek Abstract A recently developed atomistic simulation scheme for investigating ion aggregation from solution is transferred to the morphogenesis of metal clusters grown from the vapor and layers deposited on a substrate surface. Both systems are chosen as benchmark models for intense motif reorganization during aggregate/layer growth. The applied simulation method does not necessarily involve global energy minimization after each growth event, but instead describes crystal growth as a series of structurally related configurations which may also include local energy minima. Apart from the particularly favorable high-symmetry configurations known from experiments and global energy minimization, we also demonstrate the investigation of transient structures. In the spirit of Ostwald's step rule, a continuous evolution of the aggregate/layer structure during crystal growth is observed. [source] Searching the global minimum of a peptide/bilayer potential energy surface by fast heating and cooling cycles of simulated annealingINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2008C. A. Fuzo Abstract The total time reached by molecular dynamics simulation in the study of the interactions between hydrated bilayers and peptides is still very short. A scheme of fast heating and cooling cycles of simulated annealing (FHCCSA) is proposed to improve the efficiency of the search for the global minimum of the peptide/bilayer potential energy surface. In FHCCSA, the high temperatures facilitate the transitions between stable configurations; i.e., heating and cooling cycles make easier the escape of the system outside the local energy minimum. The FHCCSA efficiency is confirmed by comparing its results with conventional NpT simulations. The new scheme saves more than 90% of the total cpu time compared with ordinary NpT simulations. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Using 1,3-butadiene and 1,3,5-hexatriene to model the cis-trans isomerization of retinal, the chromophore in the visual pigment rhodopsinINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2002Fredrik Blomgren Abstract The short polyenes 1,3-butadiene and 1,3,5-hexatriene are used to model the cis-trans isomerization of the protonated Schiff base of retinal (PSBR) in rhodopsin (Rh). We employed the complete active space self-consistent field (CASSCF) method for calculation of the potential energy surfaces (PESs) in C2 symmetry. In the calculations, the central bond was twisted from 0 to 180° in the first singly excited singlet state (Sse), i.e., the state dominated by a configuration with one electron excited from HOMO to LUMO. It was found that the PES of 1,3-butadiene has a maximum whereas the PES of 1,3,5-hexatriene has a minimum for a twist angle of 90°. This is explained by a shift in border of single and double bonds in the Sse state. The first step in the cis-trans isomerization of PSBR, which is the formation of the C6C7 (see Scheme 1 for numbering) twisted PSBR in the first excited singlet state (S1), inside the protein binding pocket of the visual pigment Rh is modeled using crystal coordinates and the calculations performed on 1,3-butadiene and 1,3,5-hexatriene. More specifically, a plausible approximate structure is calculated in a geometric way for the C6C7 90° twisted PSBR, which fits into the protein binding pocket in the best possible way. It has been shown earlier that PSBR has an energy minimum for this angle in S1. The CASSCF method was used to investigate the wave function of the calculated structure of PSBR. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphinJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2004S. Banu Ozkan Abstract The energy function of a protein consists of a tremendous number of minima. Locating the global energy minimum (GEM) structure, which corresponds approximately to the native structure, is a severe problem in global optimization. Recently we have proposed a conformational search technique based on the Monte Carlo minimization (MCM) method of Li and Scheraga, where trial dihedral angles are not selected at random within the range [,180°,180°] (as with MCM) but with biased probabilities depending on the increased structure-energy correlations as the GEM is approached during the search. This method, called the Monte Carlo minimization with an adaptive bias (MCMAB), was applied initially to the pentapeptide Leu-enkephalin. Here we study its properties further by applying it to the larger peptide with bulky side chains, deltorphin (H-Tyr-D-Met-Phe-His-Leu-Met-Asp-NH2). We find that on average the number of energy minimizations required by MCMAB to locate the GEM for the first time is smaller by a factor of approximately three than the number required by MCM,in accord with results obtained for Leu-enkephalin. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 565,572, 2004 [source] Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solutionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2002Caterina Benzi The conformational behavior of the title compounds has been investigated by Hartree,Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed , turn (,l), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4,0.5 kcal/mol for helical structures and about 2 kcal/mol for ,l structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for ,l structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 341,350, 2002 [source] Ab initio crystal structure predictions for flexible hydrogen-bonded molecules.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2001Part III. Abstract In crystal structure predictions possible structures are usually ranked according to static energy. Here, this criterion has been replaced by the free energy at any temperature. The effects of harmonic lattice vibrations were found by standard lattice-dynamical calculations, including a rough estimate of the effects of thermal expansion. The procedure was tested on glycol and glycerol, for which accurate static energies had been obtained previously (Part II of this series). It was found that entropy and zero-point energy give the largest contribution to free energy differences between hypothetical crystal structures, adding up to about 3 kJ/mol for the structures with lowest energy. The temperature-dependent contribution to the energy and the effects of thermal expansion showed less variation among the structures. The overall accuracy in relative energies was estimated to be a few kJ/mol. The experimental crystal structure for glycol corresponded to the global free energy minimum, whereas for glycerol it ranked second at 1 kJ/mol. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 816,826, 2001 [source] Effect of Sr adsorption on stability of and epitaxial SrTiO3 growth on Si(001) surfacePHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 9 2006Y. Liang Abstract The geometric and electronic structures of the Sr adsorbed Si(001) surface were investigated using photoemission spectroscopy, electron diffraction, scanning tunneling microscopy, and Rutherford backscattering spectrometry. Results showed that the Sr adsorbed Si(001) exhibited several reconstructions depending upon the Sr coverage. Photoemission results revealed that at one half mono-layer of Sr coverage the dimer-derived surface states disappeared and the stability of Si increased accordingly against oxidation at elevated temperatures. Using this Sr covered surface as a template, epitaxial SrTiO3 films were grown on the vicinal Si(001) substrates using molecular beam epitaxy. The growth process is explained in terms of kinetically limited reaction facilitated by a local energy minimum induced by the Sr adsorption at Si(001) surface. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Structure of the 21,30 fragment of amyloid ,-proteinPROTEIN SCIENCE, Issue 6 2006Andrij Baumketner Abstract Folding and self-assembly of the 42-residue amyloid ,-protein (A,) are linked to Alzheimer's disease (AD). The 21,30 region of A,, A,(21,30), is resistant to proteolysis and is believed to nucleate the folding of full-length A,. The conformational space accessible to the A,(21,30) peptide is investigated by using replica exchange molecular dynamics simulations in explicit solvent. Conformations belonging to the global free energy minimum (the "native" state) from simulation are in good agreement with reported NMR structures. These conformations possess a bend motif spanning the central residues V24,K28. This bend is stabilized by a network of hydrogen bonds involving the side chain of residue D23 and the amide hydrogens of adjacent residues G25, S26, N27, and K28, as well as by a salt bridge formed between side chains of K28 and E22. The non-native states of this peptide are compact and retain a native-like bend topology. The persistence of structure in the denatured state may account for the resistance of this peptide to protease degradation and aggregation, even at elevated temperatures. [source] Infrared Spectra of Protonated Uracil, Thymine and CytosineCHEMPHYSCHEM, Issue 15 2007Jean-Yves Salpin Dr. Abstract The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d,Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm,1 in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap. [source] | ||||||||||