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Energy Minimization (energy + minimization)
Selected AbstractsDiagrammatic Separation of Different Crystal Structures of A2BX4 Compounds Without Energy Minimization: A Pseudopotential Orbital Radii ApproachADVANCED FUNCTIONAL MATERIALS, Issue 12 2010Xiuwen Zhang Abstract The A2BX4 family of compounds manifest a wide range of physical properties, including transparent conductivity, ferromagnetism, and superconductivity. A 98% successful diagrammatic separation of the 44 different crystal structures of 688 oxide A2BX4 compounds (96% for 266 oxide-only) is described by plotting the total radius of the A atom RA versus the radius of the B atom RB for many A2BX4 compounds of known structure types and seeking heuristically simple, straight boundaries in the RA versus RB plane that best separate the domains of different structure types. The radii are sums RA,=,Rs(A),+,Rp(A) of the quantum-mechanically calculated "orbital radii" Rs(Rp), rather than empirical radii or phenomenological electronegativity scales. These success rates using first-principles orbital radii uniformly exceed the success rates using classic radii. Such maps afford a quick guess of the crystal structure of a yet unmade A2BX4 compound by placing its atomic orbital radii on such maps and reading off its structure type. [source] A variational r -adaption and shape-optimization method for finite-deformation elasticityINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 1 2004P. Thoutireddy Abstract This paper is concerned with the formulation of a variational r -adaption method for finite-deformation elastostatic problems. The distinguishing characteristic of the method is that the variational principle simultaneously supplies the solution, the optimal mesh and, in problems of shape optimization, the equilibrium shapes of the system. This is accomplished by minimizing the energy functional with respect to the nodal field values as well as with respect to the triangulation of the domain of analysis. Energy minimization with respect to the referential nodal positions has the effect of equilibrating the energetic or configurational forces acting on the nodes. We derive general expressions for the configurational forces for isoparametric elements and non-linear, possibly anisotropic, materials under general loading. We illustrate the versatility and convergence characteristics of the method by way of selected numerical tests and applications, including the problem of a semi-infinite crack in linear and non-linear elastic bodies; and the optimization of the shape of elastic inclusions. Copyright © 2004 John Wiley & Sons, Ltd. [source] Crystal structure of achiral nonapeptide Boc,(Aib,,zPhe)4,Aib,OMe at atomic resolution: Evidence for a 310 -helixBIOPOLYMERS, Issue 3 2003Yoshihito Inai Abstract An x-ray crystallographic analysis was carried out for Boc,(Aib,,ZPhe)4,Aib,OMe (1: Boc = t -butoxycarbonyl; Aib = ,-aminoisobutyric acid; ,ZPhe = Z -,,,-didehydrophenylalanine) to provide the precise conformational parameters of the octapeptide segment ,(Aib,,ZPhe)4,. Peptide 1 adopted a typical 310 -helical conformation characterized by ,,, = ±55.8° (50°,65°), ,,, = ±26.7° (15°,45°), and ,,, = ±179.5° (168°,188°) for the average values of the ,(Aib,,ZPhe)4, segment (the range of the eight values). The 310 -helix contains 3.1 residues per turn, being close to the "perfect 310 -helix" characterized by 3.0 residues per turn. NMR and Fourier transform infrared (FTIR) spectroscopy revealed that the 310 -helical conformation at the atomic resolution is essentially maintained in solution. Energy minimization of peptide 1 by semiempirical molecular orbital calculation converged to a 310 -helical conformation similar to the x-ray crystallographic 310 -helix. The preference for a 310 -helix in the ,(Aib,,ZPhe)4, segment is ascribed to strong inducers of the 310 -helix inherent in Aib and ,ZPhe residues,in particular, the Aib residues tend to stabilize a 310 -helix more effectively. Therefore, the ,(Aib,,ZPhe)4, segment is useful to rationally design an optically inactive 310 -helical backbone, which will be of great importance to provide novel insights into noncovalent and covalent chiral interactions of a helical peptide with a chiral molecule. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 310,322, 2003 [source] Chain Conformations in the Crystalline Field of Syndiotactic Vinyl Polymers Deriving from 1,3-Diene Monomers.MACROMOLECULAR THEORY AND SIMULATIONS, Issue 8 2004Analysis by Molecular Mechanics Abstract Summary: Conformational energy calculations on the chain conformation in the crystalline field have been performed for various syndiotactic vinyl polymers deriving from 1,3-diene monomers. Energy maps as a function of the independent torsion angles have evidenced for all the polymers minima corresponding to highly extended and to helical chains. Energy minimizations as a function of all the internal parameters for the s(2/1)2 and tcm symmetries have allowed the evaluation of the energy differences between chains having the two symmetries and the prediction of the values of the conformational parameters for each polymer. The results have been compared with the experimental data reported in the literature for some of the studied polymers. Conformational energy map of sPBD12. [source] Energy-Based Image DeformationCOMPUTER GRAPHICS FORUM, Issue 5 2009Z. Karni Abstract We present a general approach to shape deformation based on energy minimization, and applications of this approach to the problems of image resizing and 2D shape deformation. Our deformation energy generalizes that found in the prior art, while still admitting an efficient algorithm for its optimization. The key advantage of our energy function is the flexibility with which the set of "legal transformations" may be expressed; these transformations are the ones which are not considered to be distorting. This flexibility allows us to pose the problems of image resizing and 2D shape deformation in a natural way and generate minimally distorted results. It also allows us to strongly reduce undesirable foldovers or self-intersections. Results of both algorithms demonstrate the effectiveness of our approach. [source] Low temperature powder diffraction and DFT solid state computational study of hydrogen bonding in NH4VO3CRYSTAL RESEARCH AND TECHNOLOGY, Issue 9 2009. Smr Abstract The crystal structure of NH4VO3 was refined by the geometry optimization done by total energy minimization in solid state using DFT/plane waves approach. The lattice parameters were derived by the Le Bail technique from the low temperature X-ray (40-293 K) and synchrotron (100-293 K) powder diffraction data. The structure is formed by the infinite chains of irregular VO4 tetrahedra running approximately parallel to the c -axis, which are interlinked by the ammonium ions placed between them. The ammonium ions link to the [VO4], chains through one linear, one bifurcated and two trifurcated N-H,O hydrogen bonds. Considering their stability there are six distinct N-H,O hydrogen bonds: two strong with the N-H,O bond angles close to the straight, two medium with the bond angles of 123° and 148° and two very bent (105° and 107°) and hence weak hydrogen bonds. There is a reasonable agreement between the energies of the stretching ,(NH) modes estimated using the optimised N,O contact distances and those obtained experimentally. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Conformational studies on a unique bis-sulfated glycolipid using NMR spectroscopy and molecular dynamics simulationsFEBS JOURNAL, Issue 23 2000Naoko Iida-Tanaka The time-averaged solution conformation of a unique bis-sulfated glycolipid (HSO3)2 -2,6Man,-2Glc,-1- sn -2,3- O -alkylglycerol, was studied in terms of the torsional angles of two glycosidic linkages, , (H1-C1-O-Cx) and , (C1-O-Cx-Hx), derived from heteronuclear three-bond coupling constants (3JC,H), and inter-residual proton,proton distances from J-HMBC 2D and ROESY experiments, respectively. The dihedral angles of Glc,1Gro in glycolipids were determined for the first time. The C1-C4 diagonal line of the ,-glucose ring makes an angle of ,,120 ° with the glycerol backbone, suggesting that the ,-glucose ring is almost parallel to the membrane surface in contrast with the perpendicular orientation of the ,-isomer. Furthermore, minimum-energy states around the conformation were estimated by Monte Carlo/stochastic dynamics (MCSD) mixed-mode simulations and the energy minimization with assisted model building and energy refinement (AMBER) force field. The Glc,1Gro linkage has a single minimum-energy structure. On the other hand, three conformers were observed for the Man,2Glc linkage. The flexibility of Man,2Glc was further confirmed by the absence of inter-residual hydrogen bonds which were judged from the temperature coefficients of the chemical shifts, d,/dT (,10,3 p.p.m.·°C,1), of hydroxy protons. The conformational flexibility may facilitate interaction of extracellular substances with both sulfate groups. [source] Solution structure of the functional domain of Paracoccus denitrificans cytochrome c552 in the reduced stateFEBS JOURNAL, Issue 13 2000Primo, Pristov In order to determine the solution structure of Paracoccus denitrificans cytochrome c552 by NMR, we cloned and isotopically labeled a 10.5-kDa soluble fragment (100 residues) containing the functional domain of the 18.2-kDa membrane-bound protein. Using uniformly 15N-enriched samples of cytochrome c552 in the reduced state, a variety of two-dimensional and three-dimensional heteronuclear double-resonance NMR experiments was employed to achieve complete 1H and 15N assignments. A total of 1893 distance restraints was derived from homonuclear 2D-NOESY and heteronuclear 3D-NOESY spectra; 1486 meaningful restraints were used in the structure calculations. After restrained energy minimization a family of 20 structures was obtained with rmsd values of 0.56 ± 0.10 Å and 1.09 ± 0.09 Å for the backbone and heavy atoms, respectively. The overall topology is similar to that seen in previously reported models of this class of proteins. The global fold consists of two long helices at the N-terminus and C-terminus and three shorter helices surrounding the heme moiety; the helices are connected by well-defined loops. Comparison with the X-ray structure shows some minor differences in the positions of the Trp57 and Phe65 side-chain rings as well as the heme propionate groups. [source] Thermodynamic study of capillary pressure curves based on free energy minimizationGEOFLUIDS (ELECTRONIC), Issue 3 2001Y. Deng Abstract This paper presents a new method for pore level network simulation of the distribution of two immiscible phases in a permeable medium. The method requires that the Helmholtz free energy of the system , the medium and the two phases contained within the pore space , be a minimum at all saturation states. We describe the method here and show some typical results from a computer algorithm that implements it. The results include (i) an explanation of the ,scanning' behaviour of capillary pressure curves based wholly on the free energy minimization, (ii) predictions of capillary pressure at arbitrary wetting states, including negative capillary pressures, and (iii) illustrations of how the minimized free energy changes along the scanning curves. The method also predicts the known dependency of the capillary pressure on the pore size distribution and interfacial tension. The current work is restricted to two-dimensional networks, but the free energy minimization appears to be generalizable to three dimensions and to more than two fluid phases. Moreover, functions generated through the minimization, specifically contact areas between the medium surface and the phases, appear to have applications predicting other multiphase petrophysical properties. [source] A robust algorithm for configurational-force-driven brittle crack propagation with R-adaptive mesh alignmentINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 2 2007C. Miehe Abstract The paper considers a variational formulation of brittle fracture in elastic solids and proposes a numerical implementation by a finite element method. On the theoretical side, we outline a consistent thermodynamic framework for crack propagation in an elastic solid. It is shown that both the elastic equilibrium response as well as the local crack evolution follow in a natural format by exploitation of a global Clausius,Planck inequality in the sense of Coleman's method. Here, the canonical direction of the crack propagation associated with the classical Griffith criterion is the direction of the material configurational force which maximizes the local dissipation at the crack tip and minimizes the incremental energy release. On the numerical side, we exploit this variational structure in terms of crack-driving configurational forces. First, a standard finite element discretization in space yields a discrete formulation of the global dissipation in terms configurational nodal forces. As a consequence, the constitutive setting of crack propagation in the space-discretized finite element context is naturally related to discrete nodes of a typical finite element mesh. Next, consistent with the node-based setting, the discretization of the evolving crack discontinuity is performed by the doubling of critical nodes and interface segments of the mesh. Critical for the success of this procedure is its embedding into an r-adaptive crack-segment reorientation procedure with configurational-force-based directional indicator. Here, successive crack releases appear in discrete steps associated with the given space discretization. These are performed by a staggered loading,release algorithm of energy minimization at frozen crack state followed by the successive crack releases at frozen deformation. This constitutes a sequence of positive-definite discrete subproblems with successively decreasing overall stiffness, providing an extremely robust algorithmic setting in the postcritical range. We demonstrate the performance of the formulation by means of representative numerical simulations. Copyright © 2007 John Wiley & Sons, Ltd. [source] Crystal structure prediction of organic pigments: quinacridone as an exampleJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2007N. Panina The structures of the ,, , and , polymorphs of quinacridone (Pigment Violet 19) were predicted using Polymorph Predictor software in combination with X-ray powder diffraction patterns of limited quality. After generation and energy minimization of the possible structures, their powder patterns were compared with the experimental ones. On this basis, candidate structures for the polymorphs were chosen from the list of all structures. Rietveld refinement was used to validate the choice of structures. The predicted structure of the , polymorph is in accordance with the experimental structure published previously. Three possible structures for the , polymorph are proposed on the basis of X-ray powder patterns comparison. It is shown that the , structure in the Cambridge Structural Database is likely to be in error, and a new , structure is proposed. The present work demonstrates a method to obtain crystal structures of industrially important pigments when only a low-quality X-ray powder diffraction pattern is available. [source] Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2009Seonah Kim Abstract This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] A new method for the gradient-based optimization of molecular complexesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2009Jan Fuhrmann Abstract We present a novel method for the local optimization of molecular complexes. This new approach is especially suited for usage in molecular docking. In molecular modeling, molecules are often described employing a compact representation to reduce the number of degrees of freedom. This compact representation is realized by fixing bond lengths and angles while permitting changes in translation, orientation, and selected dihedral angles. Gradient-based energy minimization of molecular complexes using this representation suffers from well-known singularities arising during the optimization process. We suggest an approach new in the field of structure optimization that allows to employ gradient-based optimization algorithms for such a compact representation. We propose to use exponential mapping to define the molecular orientation which facilitates calculating the orientational gradient. To avoid singularities of this parametrization, the local minimization algorithm is modified to change efficiently the orientational parameters while preserving the molecular orientation, i.e. we perform well-defined jumps on the objective function. Our approach is applicable to continuous, but not necessarily differentiable objective functions. We evaluated our new method by optimizing several ligands with an increasing number of internal degrees of freedom in the presence of large receptors. In comparison to the method of Solis and Wets in the challenging case of a non-differentiable scoring function, our proposed method leads to substantially improved results in all test cases, i.e. we obtain better scores in fewer steps for all complexes. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensemblesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2008Ivelin Georgiev Abstract One of the main challenges for protein redesign is the efficient evaluation of a combinatorial number of candidate structures. The modeling of protein flexibility, typically by using a rotamer library of commonly-observed low-energy side-chain conformations, further increases the complexity of the redesign problem. A dominant algorithm for protein redesign is dead-end elimination (DEE), which prunes the majority of candidate conformations by eliminating rigid rotamers that provably are not part of the global minimum energy conformation (GMEC). The identified GMEC consists of rigid rotamers (i.e., rotamers that have not been energy-minimized) and is thus referred to as the rigid-GMEC. As a postprocessing step, the conformations that survive DEE may be energy-minimized. When energy minimization is performed after pruning with DEE, the combined protein design process becomes heuristic, and is no longer provably accurate: a conformation that is pruned using rigid-rotamer energies may subsequently minimize to a lower energy than the rigid-GMEC. That is, the rigid-GMEC and the conformation with the lowest energy among all energy-minimized conformations (the minimized-GMEC) are likely to be different. While the traditional DEE algorithm succeeds in not pruning rotamers that are part of the rigid-GMEC, it makes no guarantees regarding the identification of the minimized-GMEC. In this paper we derive a novel, provable, and efficient DEE-like algorithm, called minimized-DEE (MinDEE), that guarantees that rotamers belonging to the minimized-GMEC will not be pruned, while still pruning a combinatorial number of conformations. We show that MinDEE is useful not only in identifying the minimized-GMEC, but also as a filter in an ensemble-based scoring and search algorithm for protein redesign that exploits energy-minimized conformations. We compare our results both to our previous computational predictions of protein designs and to biological activity assays of predicted protein mutants. Our provable and efficient minimized-DEE algorithm is applicable in protein redesign, protein-ligand binding prediction, and computer-aided drug design. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Fully quantum mechanical energy optimization for protein,ligand structureJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2004Yun Xiang Abstract We present a quantum mechanical approach to study protein,ligand binding structure with application to a Adipocyte lipid-binding protein complexed with Propanoic Acid. The present approach employs a recently develop molecular fractionation with a conjugate caps (MFCC) method to compute protein,ligand interaction energy and performs energy optimization using the quasi-Newton method. The MFCC method enables us to compute fully quantum mechanical ab initio protein,ligand interaction energy and its gradients that are used in energy minimization. This quantum optimization approach is applied to study the Adipocyte lipid-binding protein complexed with Propanoic Acid system, a complex system consisting of a 2057-atom protein and a 10-atom ligand. The MFCC calculation is carried out at the Hartree,Fock level with a 3-21G basis set. The quantum optimized structure of this complex is in good agreement with the experimental crystal structure. The quantum energy calculation is implemented in a parallel program that dramatically speeds up the MFCC calculation for the protein,ligand system. Similarly good agreement between MFCC optimized structure and the experimental structure is also obtained for the streptavidin,biotin complex. Due to heavy computational cost, the quantum energy minimization is carried out in a six-dimensional space that corresponds to the rigid-body protein,ligand interaction. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1431,1437, 2004 [source] Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystalsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2001Donald E. Williams Abstract A new intermolecular force field for nitrogen atoms in organic molecules was derived from a training dataset of 76 observed azahydrocarbon crystal structures and 11 observed heats of sublimation. The previously published W99 force field for hydrogen, carbon, and oxygen was thus extended to include nitrogen atoms. Nitrogen atoms were divided into four classes: N(1) for triply bonded nitrogen, N(2) for nitrogen with no bonded hydrogen (except the triple bonded case), N(3) for nitrogen with one bonded hydrogen, and N(4) for nitrogen with two or more bonded hydrogens. H(4) designated hydrogen bonded to nitrogen. Wavefunctions of 6-31g** quality were calculated for each molecule and the molecular electric potential (MEP) was modeled with net atomic and supplementary site charges. Lone pair electron charge sites were included for nitrogen atoms where appropriate, and methylene bisector charges were used for CH2 and CH3 groups when fitting the MEP. XH bond distances were set to standard values for the wave function calculation and then foreshortened by 0.1 Å for the MEP and force field fitting. Using the force field optimized to the training dataset, each azahydrocarbon crystal structure was relaxed by intermolecular energy minimization. Predicted maximum changes in unit cell edge lengths for each crystal were 3% or less. The complete force field for H, C, N, and O atoms was tested by intermolecular energy relaxation of nucleoside and peptide molecular crystals. Even though these molecules were not included in any of the training datasets for the force field, agreement with their observed crystal structures was very good, with predicted unit cell edge shifts usually less than 2%. These tests included crystal structures of representatives of all eight common nucleosides found in DNA and RNA, 15 dipeptides, four tripeptides, two tetrapeptides, and a pentapeptide with two molecules in the asymmetric unit. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1154,1166, 2001 [source] Textured growth and microstructure of pulsed laser deposited Nb/Cr/SmCo5 hybrid structuresPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 8 2010R. Schaarschuch Abstract Hybrid structures based on superconducting Nb and highly coercive ferromagnetic SmCo5 films grown on MgO(100) substrates were fabricated by pulsed laser deposition under UHV conditions. Thin film architectures of SmCo5 on Nb and the reversed system both with and without Cr spacer layer between superconductor and ferromagnet were examined by transmission electron microscopy and X-ray diffraction concerning their microstructure and epitaxial relationship, respectively. For SmCo5 on Nb with thick intermediate Cr spacer the epitaxial relationship MgO(001)[100]//Cr(001)[110]//Nb(001)[110]//Cr(001)[110]//SmCo5(11,,,20)[0001]//Cr(001)[110] was found. With decreasing thickness of the Cr spacer layer the strength of the texture decreases and finally crystallinity of SmCo5 is lost. In the reversed layer system, Nb on Cr on SmCo5, with decreasing thickness of the Cr spacer layer the epitaxial relationships change from SmCo5(11,,,20)[0001]//Nb(001)[110] to local SmCo5(11,,,20) [0001]//Nb(110)[1,,,11] and the Nb texture changes from the (001)[110] component to a ,110, fibre. The orientation relationships observed are discussed with regard to elastic strain energy minimization. [source] On rate independent models for crack propagationPROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2008Dorothee Knees We model the evolution of a single crack as a rate,independent process based on the Griffith criterion. Three approaches are presented, namely a model based on global energy minimization, a model based on a local description involving the energy release rate and a refined local model which is the limit problem of regularized, viscous models. Finally we present an example which sheds light on the different predictions of the models. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Joint And Muscle Forces During ClenchingPROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2006Stefan Rues The masticatory system is highly redundant. Therefore, complete knowledge about the activation patterns of the chewing muscles belonging to a specific resultant bite force can only be gained either by simultaneous force- and EMG-measurement or with the help of optimization strategies. In this study, such EMG and force measurements were carried out with 10 test persons and the results compared to those computed with several objective functions. The results show an increase of the joint forces with an increase of the horizontal component of the resultant bite force. The test persons seem to favor energy minimization as control mechanism. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Deformation Driven Homogenization of Fracturing SolidsPROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2005Ercan Gürses The paper discusses numerical formulations of the homogenization for solids with discrete crack development. We focus on multi,phase microstructures of heterogeneous materials, where fracture occurs in the form of debonding mechanisms as well as matrix cracking. The definition of overall properties critically depends on the developing discontinuities. To this end, we extend continuous formulations [1] to microstructures with discontinuities [2]. The basic underlying structure is a canonical variational formulation in the fully nonlinear range based on incremental energy minimization. We develop algorithms for numerical homogenization of fracturing solids in a deformation,driven context with non,trivial formulations of boundary conditions for (i) linear deformation and (ii) uniform tractions. The overall response of composite materials with fracturing microstructures are investigated. As a key result, we show the significance of the proposed non,trivial formulation of a traction,type boundary condition in the deformation,driven context. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] CIRSE: A solvation energy estimator compatible with flexible protein docking and design applicationsPROTEIN SCIENCE, Issue 7 2006David S. Cerutti Abstract We present the Coordinate Internal Representation of Solvation Energy (CIRSE) for computing the solvation energy of protein configurations in terms of pairwise interactions between their atoms with analytic derivatives. Currently, CIRSE is trained to a Poisson/surface-area benchmark, but CIRSE is not meant to fit this benchmark exclusively. CIRSE predicts the overall solvation energy of protein structures from 331 NMR ensembles with 0.951 ± 0.047 correlation and predicts relative solvation energy changes between members of individual ensembles with an accuracy of 15.8 ± 9.6 kcal/mol. The energy of individual atoms in any of CIRSE's 17 types is predicted with at least 0.98 correlation. We apply the model in energy minimization, rotamer optimization, protein design, and protein docking applications. The CIRSE model shows some propensity to accumulate errors in energy minimization as well as rotamer optimization, but these errors are consistent enough that CIRSE correctly identifies the relative solvation energies of designed sequences as well as putative docked complexes. We analyze the errors accumulated by the CIRSE model during each type of simulation and suggest means of improving the model to be generally useful for all-atom simulations. [source] The interplay between experiment and theory in charge-density analysisACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2004Philip Coppens The comparison of theory and experiment remains a cornerstone of scientific inquiry. Various levels of such comparison applicable to charge-density analysis are discussed, including static and dynamic electron densities, topological properties, d -orbital occupancies and electrostatic moments. The advantages and drawbacks of the pseudoatom multipole are discussed, as are the experimentally constrained wavefunctions introduced by Jayatilaka and co-workers, which combine energy minimization with the requirement to provide a reasonable fit to the X-ray structure factors. The transferability of atomic densities can be exploited through construction of a pseudoatom databank, which may be based on analysis of ab initio molecular electron densities, and can be used to evaluate a host of physical properties. Partitioning of theoretical energies with the Morokuma,Ziegler energy decomposition scheme allows direct comparison with electrostatic interaction energies obtained from electron densities represented by the pseudoatom formalism. Compared with the Buckingham expression for the interaction between non-overlapping densities, the agreement with theory is much improved when a newly developed hybrid EP/MM (exact potential/multipole model) method is employed. [source] Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2010Jacco Van De Streek This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095,Å (0.084,Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25,Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect. [source] K3TaF8 from laboratory X-ray powder dataACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2010ubomír Smr The crystal structure of tripotassium octafluoridotantalate, K3TaF8, determined from laboratory powder diffraction data by the simulated annealing method and refined by total energy minimization in the solid state, is built from discrete potassium cations, fluoride anions and monocapped trigonal,prismatic [TaF7]2, ions. All six atoms in the asymmetric unit are in special positions of the P63mc space group: the Ta and one F atom in the 2b (3m) sites, the K and two F atoms in the 6c (m) sites, and one F atom in the 2a (3m) site. The structure consists of face-sharing K6 octahedra with a fluoride anion at the center of each octahedron, forming chains of composition [FK3]2+ running along [001] with isolated [TaF7]2, trigonal prisms in between. The structure of the title compound is different from the reported structure of Na3TaF8 and represents a new structure type. [source] PRODRG: a tool for high-throughput crystallography of protein,ligand complexesACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2004Alexander W. Schüttelkopf The small-molecule topology generator PRODRG is described, which takes input from existing coordinates or various two-dimensional formats and automatically generates coordinates and molecular topologies suitable for X-ray refinement of protein,ligand complexes. Test results are described for automatic generation of topologies followed by energy minimization for a subset of compounds from the Cambridge Structural Database, which shows that, within the limits of the empirical GROMOS87 force field used, structures with good geometries are generated. X-ray refinement in X-PLOR/CNS, REFMAC and SHELX using PRODRG -generated topologies produces results comparable to refinement with topologies from the standard libraries. However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors. [source] A series of molecular dynamics and homology modeling computer labs for an undergraduate molecular modeling courseBIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 4 2010Donald E. Elmore Abstract As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations, and homology modeling. These labs were created as part of a one-semester course on the molecular modeling of biochemical systems. Students who completed these activities felt that they were an effective component of the course, reporting improved comfort with the conceptual background and practical implementation of the computational methods. Although created as a component of a larger course, these activities could be readily adapted for a variety of other educational contexts. As well, all of these labs utilize software that is freely available in an academic environment and can be run on fairly common computer hardware, making them accessible to teaching environments without extensive computational resources. [source] Pressure Drop in Liquid-liquid Two Phase Horizontal Flow: Experiment and PredictionCHEMICAL ENGINEERING & TECHNOLOGY (CET), Issue 9 2005D. P. Chakrabarti Abstract The present study is aimed at an investigation of the pressure drop characteristics during the simultaneous flow of a kerosene-water mixture through a horizontal pipe of 0.025,m diameter. Measurements of pressure gradient were made for different combinations of phase superficial velocities ranging from 0.03,2,m/s such that the regimes encountered were smooth stratified, wavy stratified, three layer flow, plug flow and oil dispersed in water, and water flow patterns. A model was developed, which considered the energy minimization and pressure equalization of both phases. [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] Minimum sequence requirements for selective RNA-ligand binding: A molecular mechanics algorithm using molecular dynamics and free-energy techniquesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2006Peter C. Anderson Abstract In vitro evolution techniques allow RNA molecules with unique functions to be developed. However, these techniques do not necessarily identify the simplest RNA structures for performing their functions. Determining the simplest RNA that binds to a particular ligand is currently limited to experimental protocols. Here, we introduce a molecular-mechanics based algorithm employing molecular dynamics simulations and free-energy methods to predict the minimum sequence requirements for selective ligand binding to RNA. The algorithm involves iteratively deleting nucleotides from an experimentally determined structure of an RNA-ligand complex, performing energy minimizations and molecular dynamics on each truncated structure, and assessing which truncations do not prohibit RNA binding to the ligand. The algorithm allows prediction of the effects of sequence modifications on RNA structural stability and ligand-binding energy. We have implemented the algorithm in the AMBER suite of programs, but it could be implemented in any molecular mechanics force field parameterized for nucleic acids. Test cases are presented to show the utility and accuracy of the methodology. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [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] | ||||||||||||||||||||||||||||||||||