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Energy Conformation (energy + conformation)
Kinds of Energy Conformation Selected AbstractsMacrocyclic Receptor Showing Improved PbII/ZnII and PbII/CaII SelectivitiesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 17 2010Raquel Ferreirós-Martínez Abstract Herein we report on the macrocyclic receptor N,N,-bis[(6-carboxy-2-pyridyl)methyl]-1,10-diaza-15-crown-5 (H2bp15c5) and its coordination properties towards ZnII, CdII, PbII, and CaII. The stability constants of these complexes determined by pH-potentiometric titration at 25 °C in 0.1 M KNO3 vary in the following order: PbII > CdII >> ZnII > CaII. As a result, bp15c5 presents very important PbII/ZnII and PbII/CaII selectivities. These results are in contrast to those reported for the related receptor derived from 1,7-diaza-12-crown-4, which provides very similar complex stabilities for ZnII and PbII. The X-ray crystal structure of [Cd(Hbp15c5)]+ shows heptadentate binding of the ligand to the metal ion, with two oxygen atoms of the macrocyclic unit remaining uncoordinated. The 1H NMR spectra of the complexes formed with PbII, ZnII, and CaII (D2O) show very broad peaks in the region 2,5 ppm, indicating an important degree of flexibility of the crownmoiety in these complexes. On the contrary, the 1H and 13C NMR spectra recorded for the CdII complex are well resolved and could be fully assigned. A detailed conformational investigation using theoretical calculations performed at the DFT (B3LYP) level predict a minimum energy conformation for [Cd(bp15c5)] that is very similar to that observed in the solid state. Analogous calculations performed on the [M(bp15c5)] (M = Zn or Pb) systems predict hexadentate binding of the ligand to these metal ions. In the case of the PbII complex our calculations indicate that the 6s lone pair is stereochemically active, which results in a hemidirected coordination geometry around the metal ion. The minimum energy conformations calculated for the ZnII, CdII, and PbII complexes are compatible with the experimental NMR spectra obtained in D2O solution. [source] Planarity of acetamides, thioacetamides, and selenoacetamides: Crystal structure of N,N -dimethylselenoacetamideHETEROATOM CHEMISTRY, Issue 4 2002Shuqiang Niu The planarity of acetamides 1a,3a, thioacetamides 4a,6a, and selenoacetamides 7a,9a, R1R2NC(=E)CH3 where E = O, S, Se, and R1, R2 = H or CH3, was investigated using theoretical calculations at the density functional theory (DFT) level. The calculations showed that the methyl substitution on nitrogen and the change from the amide moiety (NCO) to NCS or NCSe group increased the double bond character of the NC bond. In other words, the planarity of these compounds (1a,9a) increases in the order NH2 < NHCH3 < N(CH3)2 and O < S < Se. The calculations of bending energy suggest that the planar geometry represents the lowest energy conformation for all compounds investigated in this work. N,N-Dimethyl-selenoacetamide (9a), (CH3)2NC(Se) CH3, has the largest bending energy of 10.37 kcal/mol, which suggests that it possesses the greatest planarity among the compounds 1a,9a. However, the solid phase molecular structure of 9a was found to be slightly nonplanar by X-ray crystallography. The slight nonplanarity observed experimentally is very likely the consequence of intermolecular interactions arising within the crystal packing. © 2002 Wiley Periodicals, Inc. Heteroatom Chem 13:380,386, 2002; Published online in Wiley Interscience (www.interscience.wiley.com). DOI 10.1002/hc.10056 [source] Rotamer optimization for protein design through MAP estimation and problem-size reductionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2009Eun-Jong Hong Abstract The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP-hard optimization problem. Dead-end elimination (DEE) methods combined with systematic A* search (DEE/A*) has proven useful, but may not be strong enough as we attempt to solve protein design problems where a large number of similar rotamers is eligible and the network of interactions between residues is dense. In this work, we present an exact solution method, named BroMAP (branch-and-bound rotamer optimization using MAP estimation), for such protein design problems. The design goal of BroMAP is to be able to expand smaller search trees than conventional branch-and-bound methods while performing only a moderate amount of computation in each node, thereby reducing the total running time. To achieve that, BroMAP attempts reduction of the problem size within each node through DEE and elimination by lower bounds from approximate maximum-a-posteriori (MAP) estimation. The lower bounds are also exploited in branching and subproblem selection for fast discovery of strong upper bounds. Our computational results show that BroMAP tends to be faster than DEE/A* for large protein design cases. BroMAP also solved cases that were not solved by DEE/A* within the maximum allowed time, and did not incur significant disadvantage for cases where DEE/A* performed well. Therefore, BroMAP is particularly applicable to large protein design problems where DEE/A* struggles and can also substitute for DEE/A* in general GMEC search. © 2009 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] Modeling of loops in protein structuresPROTEIN SCIENCE, Issue 9 2000András Fiser Abstract Comparative protein structure prediction is limited mostly by the errors in alignment and loop modeling. We describe here a new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures. The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy function. The energy is a sum of many spatial restraints that include the bond length, bond angle, and improper dihedral angle terms from the CHARMM-22 force field, statistical preferences for the main-chain and side-chain dihedral angles, and statistical preferences for nonbonded atomic contacts that depend on the two atom types, their distance through space, and separation in sequence. The energy function is optimized with the method of conjugate gradients combined with molecular dynamics and simulated annealing. Typically, the predicted loop conformation corresponds to the lowest energy conformation among 500 independent optimizations. Predictions were made for 40 loops of known structure at each length from 1 to 14 residues. The accuracy of loop predictions is evaluated as a function of thoroughness of conformational sampling, loop length, and structural properties of native loops. When accuracy is measured by local superposition of the model on the native loop, 100, 90, and 30% of 4,, 8,, and 12,residue loop predictions, respectively, had <2 Å RMSD error for the mainchain N, Ca, C, and O atoms; the average accuracies were 0.59 6 0.05, 1.16 6 0.10, and 2.61 6 0.16 Å, respectively. To simulate real comparative modeling problems, the method was also evaluated by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment. When the RMSD distortion of the main-chain stem atoms is 2.5 Å, the average loop prediction error increased by 180, 25, and 3% for 4,, 8,, and 12,residue loops, respectively. The accuracy of the lowest energy prediction for a given loop can be estimated from the structural variability among a number of low energy predictions. The relative value of the present method is gauged by (1) comparing it with one of the most successful previously described methods, and (2) describing its accuracy in recent blind predictions of protein structure. Finally, it is shown that the average accuracy of prediction is limited primarily by the accuracy of the energy function rather than by the extent of conformational sampling. [source] S,S -1,2-Dicyclohexylethane-1,2-diol and its racemic compound: a striking exception to Wallach's ruleACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2006Brian O. Patrick The structures of enantiopure S,S -1,2-dicyclohexylethane-1,2-diol and its racemic compound (rac - S,S -1,2-dicyclohexylethane-1,2-diol) have been determined at 295 and 173,K. The crystals of the enantiopure material are more than 4% denser than the crystals of the racemic compound, but the melting points indicate that the crystals of the less dense racemic compound are considerably more stable than those of the racemic conglomerate. This apparent exception to the correlation of crystal density and melting point is explained. The enantiopure crystals have four molecules in the asymmetric unit (Z, = 4). Two of the molecules have the conformation observed for the one independent molecule of the racemic compound and two have a higher energy conformation; the overall P21 structure is a perturbed version of a P212121 structure with Z, = 2. The enantiopure and racemic crystals have the same hydrogen-bonding motif, but the motif in the former appears to be significantly strained. A reason why crystals of enantiopure material might be systematically less dense than crystals of its racemic compound and to be more likely to have Z, > 1 is suggested. [source] The lack of C2 molecular symmetry in (1R,2R,3S,6S)-3,6-dibenzyloxycyclohex-4-ene-1,2-diolACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2001Robert W. Clark The results of a single-crystal X-ray experiment and density functional theory calculations performed for the title compound, C20H22O4, demonstrate that the lowest energy conformation of this molecule does not contain C2 molecular symmetry. [source] Chiral molecules with polyhedral T, O, or I symmetry: Theoretical solution to a difficult problem in stereochemistryCHIRALITY, Issue 8 2008Sri Kamesh Narasimhan Abstract Ever since point groups of symmetry have been used to describe molecules after Van't Hoff and Le Bel proposed tetrahedral structures for carbon atoms in 1874, it remains difficult to design chiral molecules with polyhedral symmetry T, O, or I. Past theoretical and experimental studies have mainly accomplished molecular structures that have the conformations for satisfying the T symmetry. In this work, we present a general theoretical approach to construct rigid molecular structures that have permanently the symmetry of T, O, and I. This approach involves desymmetrizaton of the vertices or the edges of Platonic solid-shaped molecules with dissymmetric moieties. Using density functional theory (DFT) and assisted model building and energy refinement (AMBER) computational methods, the structure, the rigidity, and the symmetry of the molecule are confirmed by assessing the lowest energy conformation of the molecule, which is initially presented in a planar graph. This method successfully builds molecular structures that have the symmetry of T, O, and I. Interestingly, desymmetrization of the edges has a more stringent requirement of rigidity than desymmetrization of the vertices for affording the T, O, or I symmetry. Chirality, 2008. © 2008 Wiley-Liss, Inc. [source] Study of the conformational profile of the norbornane analogues of phenylalanineJOURNAL OF PEPTIDE SCIENCE, Issue 6 2002Arnau Cordomí Abstract The conformational profile of the eight stereoisomeric 2-amino-3-phenylnorbornane-2-carboxylic acids (2-amino-3-phenylbicyclo[2.2.1]heptane-2-carboxylic acids) has been assessed by computational methods. These molecules constitute a series of four enantiomeric pairs that can be considered as rigid analogues of either L - or D -phenylalanine. The conformational space of their N -acetyl methylamide derivatives has been explored within the molecular mechanics framework, using the parm94 set of parameters of the AMBER force field. Local minimum energy conformations have been further investigated at the ab initio level by means of the Hartree-Fock and second order Moller-Plesset perturbation energy calculations using a 6,31G(d) basis set. The results of the present work suggest that the bulky norbornane structure induces two kinds of conformational constraints on the residues. On one hand, those of a steric nature directly imposed by the bicycle on the peptide backbone and, on the other hand, those that limit the orientations attainable by the phenyl ring which, in turn, reduces further the flexibility of the peptide backbone. A comparative analysis of the conformational profile of the phenylnorbornane amino acids with that of the norbornane amino acids devoid of the ,-phenyl substituent suggests that the norbornane system hampers the residue to adopt extended conformations in favour of C7-like structures. However, the bicycle itself does not impart a clear preference for any of the two possible C7 minima. It is the aromatic side chain, which is forced to adopt an almost eclipsed orientation, that breaks this symmetry introducing a marked preference for a single region of the (,, ,) conformational space in each of the phenylalanine norbornane analogues investigated. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] Synthesis and Preferred All- syn Conformation of C3 -Symmetrical N -(Hetero)arylmethyl TriindolesCHEMISTRY - A EUROPEAN JOURNAL, Issue 28 2008Abstract A new series of C3 -symmetrical N -(hetero)arylmethyl triindoles has been synthesized in a straightforward procedure. The structure and conformation in the solid state have been determined for three derivatives (3, 4, and 6) by X-ray crystallographic analysis. In all three cases, the molecules adopt a tripodal conformation with all of the flexible arms directed towards the same side, thereby delimiting an inner cavity. Compound 6 crystallizes and forms C3 -symmetric dimeric cagelike complexes. Guest molecules of chloroform and water are confined within the resulting cavities with stabilization by different intermolecular interactions; this highlights the potential of these compounds in the construction of supramolecular systems. A computational analysis has been performed to predict the most stable conformers. As a general trend, a preference for a conformation with all branches directed to the same side has been predicted. Comparison between theoretical and experimental results indicates that the computational level selected for the present study, B3LYP/6-31G*, is able to reproduce both the minimum energy conformations and the rotation barriers about the NCH2 bond. [source] | |||||||||||||||||||