Showing papers on "Dihedral angle published in 2000"
TL;DR: A new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment is described.
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 A RMSD error for the mainchain N, C(alpha), C, and O atoms; the average accuracies were 0.59 +/- 0.05, 1.16 +/- 0.10, and 2.61 +/- 0.16 A, 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 A, 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.
1,999 citations
TL;DR: In this article, the FT-IR spectra of I β cellulose were recorded on films made of hydrothermally treated Valonia microcrystals and a critical analysis of the spectra allowed to propose a detailed assignment for most of the bands at wavenumbers higher than 800 cm −1.
467 citations
TL;DR: Transition path sampling has been applied to the molecular dynamics of the alanine dipeptide in vacuum and in aqueous solution, and solvent variables are shown to play a significant role, and this role appears to be more specific than can be captured by friction models.
Abstract: Transition path sampling has been applied to the molecular dynamics of the alanine dipeptide in vacuum and in aqueous solution. The analysis shows that more degrees of freedom than the traditional dihedral angles, φ and ψ, are necessary to describe the reaction coordinates for isomerization of this molecule. In vacuum, an additional dihedral angle is identified as significant. In solution, solvent variables are shown to play a significant role, and this role appears to be more specific than can be captured by friction models. Implications for larger molecules are discussed.
401 citations
TL;DR: The similarity among these proteins has been determined, showing that the most folded proteins are not similar among them, while the less folded ones are similar to each other.
368 citations
TL;DR: In this paper, the central backbone structure of trialanine in aqueous solution is investigated using polarization sensitive two-dimensional (2D) vibrational spectroscopy on the amide I mode.
Abstract: Using polarization sensitive two-dimensional (2D) vibrational spectroscopy on the amide I mode, the central backbone structure of trialanine in aqueous solution is investigated. We exploit the polarization sensitivity of the 2D pump−probe signal to reveal the cross-peak structure hidden under the strong diagonal peaks. The dihedral angles φ and ψ characterizing the peptide backbone structure are derived directly from the cross-peak intensity and anisotropy, demonstrating the potential of 2D spectroscopy as a tool for peptide structure elucidation.
361 citations
TL;DR: Considering the magnetic and structural data obtained for various dinuclear (Cu-Gd) complexes leads to a correlation between the magnitude of the magnetic interaction and the exponential of the dihedral angle between the two halves of the CuO2Gd bridging core.
Abstract: The monometallic precursor L1Cu (L1H2 standing for 1,3-bis((3-methoxysalicylidene)amino)-2,2'-dimethylpropane) reacts with GdC13 x 6H2O to afford a dinuclear complex which crystallizes in the orthorhombic space group Pca2(1) (No. 29) in a cell having the dimensions a = 9.0246(11) A, b = 16.5198(14) A, c = 20.286(2) A, and Z = 4. Analysis of the structural data shows that it may be formulated as [L1CuCl2Gd(H2O)4]Cl x 2H2O. The cationic dinuclear unit possesses a CuO2Gd bridging core which is almost planar. The complex displays a ferromagnetic interaction (10.1 cm(-1) which is the largest yet reported for a structurally characterized dinuclear (Cu-Gd) complex. Lower magnetic interactions are observed for neutral L1CuGdX3 x H2O complexes (X = N3C2, CF3COO). Consideration of the magnetic and structural data obtained for various dinuclear (Cu-Gd) complexes leads to a correlation between the magnitude of the magnetic interaction and the exponential of the dihedral angle between the two halves of the CuO2Gd bridging core.
286 citations
TL;DR: The interactions revealed in crystal structures and EPR spectra provide an important link between the dynamics of the R1 side chain, reflected in the EPR spectrum, and local protein structure.
Abstract: High resolution (1.43-1.8 A) crystal structures and the corresponding electron paramagnetic resonance (EPR) spectra were determined for T4 lysozyme derivatives with a disulfide-linked nitroxide side chain [-CH(2)-S-S-CH(2)-(3-[2,2,5,5-tetramethyl pyrroline-1-oxyl]) identical with R1] substituted at solvent-exposed helix surface sites (Lys65, Arg80, Arg119) or a tertiary contact site (Val75). In each case, electron density is clearly resolved for the disulfide group, revealing distinct rotamers of the side chain, defined by the dihedral angles X(1) and X(2). The electron density associated with the nitroxide ring in the different mutants is inversely correlated with its mobility determined from the EPR spectrum. Residue 80R1 assumes a single g(+)()g(+)() conformation (Chi(1) = 286, X(2) = 294). Residue 119R1 has two EPR spectral components, apparently corresponding to two rotamers, one similar to that for 80R1 and the other in a tg(-)() conformation (Chi(1) = 175, X(2) = 54). The latter state is apparently stabilized by interaction of the disulfide with a Gln at i + 4, a situation also observed at 65R1. R1 residues at helix surface site 65 and tertiary contact site 75 make intra- as well as intermolecular contacts in the crystal and serve to identify the kind of molecular interactions possible for the R1 side chain. A single conformation of the entire 75R1 side chain is stabilized by a variety of interactions with the nitroxide ring, including hydrophobic contacts and two unconventional C-H.O hydrogen bonds, one in which the nitroxide acts as a donor (with tyrosine) and the other in which it acts as an acceptor (with phenylalanine). The interactions revealed in these structures provide an important link between the dynamics of the R1 side chain, reflected in the EPR spectrum, and local protein structure. A library of such interactions will provide a basis for the quantitative interpretation of EPR spectra in terms of protein structure and dynamics.
238 citations
TL;DR: In this paper, the global fold of a two-domain Maltose-binding protein was determined by solution NMR methods, where discrete orientations were calculated for each peptide plane on the basis of the dipolar couplings described above. And the orientation which best matches that in initial NMR structures calculated from NOE and dihedral angle restraints exclusively was used to refine further the structures using a new module written for CNS.
155 citations
TL;DR: Poon et al. as discussed by the authors used model dipeptides to provide the basic elements of secondary structure (flexible backbone dihedral angles) of a dihedral angle model.
Abstract: Chi-Duen Poon and Edward T. SamulskiDepartment of ChemistryUniVersity of North Carolina-Chapel HillVenable and Kenan Laboratories CB 3290Chapel Hill, North Carolina 27599-3290Christoph F. Weise and James C. Weisshaar*Department of Chemistry, UniVersity of Wisconsin-Madison1101 UniVersity AVenue, Madison, Wisconsin 53706-1396ReceiVed NoVember 9, 1999ReVised Manuscript ReceiVed April 24, 2000Model dipeptides provide the basic elements of secondarystructure (flexible backbone dihedral angles
142 citations
TL;DR: In this paper, a refined set of parameters for dihedral angle interactions and third-neighbour interactions involving CH2 and CH3 atoms is proposed by fitting to the heat of vaporization, pressure and trans-gauche ratio for liquids of three n-alkanes, n-butane, N-pentane and n-hexane.
Abstract: The parameters of the GROMOS96 force field governing dihedral angle transitions in aliphatic chains have been reconsidered, since these parameters produce a too large ratio of trans to gauche conformations in such chains. A refined set of parameters for dihedral angle interactions and third-neighbour interactions involving CH2 and CH3 atoms is proposed. They were obtained by fitting to the heat of vaporization, pressure and trans-gauche ratio for liquids of three n-alkanes, n-butane, n-pentane and n-hexane. The new parameter set does reproduce better these quantities and should therefore be more appropriate for use in simulations of polymers and membranes. A comparison of the mentioned properties obtained from simulations with united-atom models and from simulations with an all-atom model shows that the latter does not necessarily yield an improved description of molecular behaviour.
118 citations
TL;DR: In this paper, an extension to the configurational-bias Monte Carlo method is presented which allows for the efficient conformational sampling of the interior segments of chain molecules whose interactions include strong bonded terms (governing bond stretching, bond angle bending and dihedral angle rotation).
Abstract: An extension to the configurational-bias Monte Carlo method is presented which allows for the efficient conformational sampling of the interior segments of chain molecules whose interactions include strong bonded terms (governing bond stretching, bond angle bending, and dihedral angle rotation). The ability to regrow interior segments overcomes the limitations of conventional configurational-bias methods (where the regrowth is always directed to a free chain end) and now allows for the simulation of chain systems with low concentrations of chain ends, that is, higher molecular weights, networks, or cyclic structures. As previously proposed by Dijkstra et al. [J. Chem. Phys. 1994, 101, 3179] for lattice polymers and by Vendruscolo [J. Chem. Phys. 1997, 106, 2970] for freely jointed polymers, an additional biasing (closing) probability is used that guides the bead-by-bead configurational-bias regrowth of interior segments toward its desired fixed target. However, while the previous methods are limited to ch...
TL;DR: The ferromagnetic exchange coupling is discussed using DFT calculations on model compounds that have shown a countercomplementary effect of the hydroxo and acetate bridges.
Abstract: The structural and magnetic data of the trinuclear compound [Cu3(L)2(CH3COO)2(OH)2(dmf)2] (HL = N-(2-methylpyridyl)toluensulfonylamide) are reported. The compound crystallizes in the monoclinic system, space group P2(1)/n (no. 14), with a = 11.6482(6) A, b = 13.5772(6) A, c = 13.5306(7) A, alpha = 90 degrees, beta = 92.859(5) degrees, gamma = 90 degrees, and Z = 2. The three copper atoms form an exact linear arrangement. Neighboring coppers are connected by a hydroxo bridge and a bidentate syn-syn carboxylato group. The coordination spheres of the terminal copper atoms are square pyramidal with a dmf molecule as the apical ligand. The central copper has a regular square planar geometry. The mixed bridging by a hydroxide oxygen atom and a bidentate carboxylato group leads to a noncoplanarity of the adjacent basal coordination planes with a dihedral angle of 51.96(9) degrees. Susceptibility measurements (2-300 K) reveal a strong ferromagnetic coupling, J = 93(6) cm-1, in the mixed-bridged moiety leading to a quartet ground state that is confirmed by the EPR spectra. The ferromagnetic exchange coupling is discussed using DFT calculations on model compounds that have shown a countercomplementary effect of the hydroxo and acetate bridges.
TL;DR: In this paper, a molecular dynamics simulation study of the conformations and chain dimensions of poly(ethylene oxide) (PEO) in aqueous solution was performed, and it was found that the dimensions of solution chains depend only weakly on temperature despite changes in local conformations that significantly influence RIS chain dimensions.
Abstract: We have performed a molecular dynamics (MD) simulation study of the conformations and chain dimensions of poly(ethylene oxide) (PEO) in aqueous solution. Local conformations were found to depend on temperature and composition in agreement with spectroscopy; in particular, an increase in the C-C dihedral gauche (g) population with decreasing temperature and polymer concentration was observed. In concentrated solution chains were compact relative to the melt due to a decrease in the C-C g dihedral angle and an increase in C-C g population. With dilution chains became more extended. A rotational isomeric state (RIS) model was utilized to examine the influence of local conformations on the dimensions of ideal chains. The RIS chains did not extend with dilution, indicating that this effect is not attributable to changes in local conformations. Additionally, the dimensions of solution chains were found to depend only weakly on temperature despite changes in local conformations that significantly influence RIS chain dimensions. These differences between solution and ideal chains can be attributed to excluded volume and other chain extensional effects in solution. Finally, in contrast to previous simulations and interpretation of some experiments, no tendency for extended helical conformations of the PEO chains was observed despite the large O-C-C-O tgt conformer population. Its wide use, prototypical behavior and simple chemical structure make PEO an excellent candidate for experimental and simulation studies aimed at gaining a better understanding of polymer-water interactions. Our previous simulations revealed that the conformations of glyme and diglyme depend strongly upon temperature and solution composition. In order to determine if the same behavior holds for longer PEO chains and to investigate the influence of local conformations on PEO chain dimensions we have performed MD simulations of H—[ CH2–O–CH2— ] 12 H (PEO-530) using quantum chemistry based atomistic potentials
TL;DR: In this paper, the 1:1 water complex was assigned to a structure in which water binds as a proton acceptor to the alcohol group and as a weak proton donor to the π-system of the aromatic ring.
Abstract: The structures of benzyl alcohol, its 1:1 water complex, and its dimer have been investigated by R2PI spectroscopy and IR−UV ion dip spectroscopy, combined with ab initio computation. The sole molecular conformer observed in the jet has a gauche arrangement of the gauche arrangement of the OH group relative to the C1−Cα bond, but the extent of π-type intramolecular H-bonding is small. Analysis of its rotational band contours suggests the incidence of vibronic coupling involving motion of the side chain and also leads to an estimate for the dihedral angle τ1(OCCC) lying in the range 35°−60°, in good agreement with the values (50°−60°) indicated by high-level ab initio calculations. The 1:1 water complex is assigned to a structure in which water binds as a proton acceptor to the alcohol group, and as a weak proton donor to the π-system of the aromatic ring. The arrangement of H-bonds is similar within the dimer: the OH of one molecule acts as both acceptor to the alcohol group and as donor to the π-system ...
TL;DR: In this article, the authors measured the reduction of shear and longitudinal wave velocities caused by grain boundary melt, having nearly equilibrium textures, was measured accurately as functions of both melt fraction and dihedral angle.
Abstract: Borneol-diphenylamine, a binary eutectic system of the organic compounds, provides an appropriate analogue of melting in the Earth's mantle. Eutectic temperature is just above room temperature (43°C), and at this temperature the dihedral angle is about 40°. As the temperature increases, the dihedral angle gradually decreases at a rate of about 1.5° per 1°C, and becomes nearly zero at 70°C. Melt fraction change is small at this temperature range; this system is therefore appropriate in investigating a systematic effect of dihedral angle. Using this system, reduction of the shear and longitudinal wave velocities caused by grain boundary melt, having nearly equilibrium textures, was measured accurately as functions of both melt fraction and dihedral angle. The results demonstrate the significant effect of equilibrium melt geometry on shear wave velocities, while also showing that the effects of melting and dihedral angles are much smaller on the longitudinal waves. The quantitative effects of the melt fraction and dihedral angles on the acoustic wave velocities can be predicted theoretically using the elasticities of granular media derived as functions of grain-boundary contiguity [Takei, 1998]. The present experimental results described in this paper agree well with the theoretical predictions and demonstrate the validity of the theory. Clarifying the analogy and difference between the present organic system and the Earth's materials, the shear and longitudinal wave velocities of the partially molten rocks in the Earth were predicted as functions of melt fraction, dihedral angle, and the compressibility ratio between solid and melt.
TL;DR: In this paper, the effects of incorporating dipolar couplings in the structure determinations of nucleic acids were performed with simulated constraints derived from two DNA duplex target molecules, and the results showed that dipolar coupling significantly improved the local structure while also dramatically improving the...
Abstract: The local structure of nucleic acids can be determined from traditional solution NMR techniques, but it is usually not possible to uniquely define the global conformation of DNA or RNA double helices. This results from the short-range nature of the NOE-distance and torsion angle constraints used in generating the solution structures. However, new alignment techniques make it possible to readily measure residual dipolar couplings, which provide information on the relative orientation of individual bond vectors in the molecule. To determine the effects of incorporating dipolar couplings in the structure determinations of nucleic acids, molecular dynamics calculations were performed with simulated constraints derived from two DNA duplex target molecules. Refinements that included NOE, torsion angle, and dipolar coupling constraints were compared to refinements without dipolar couplings. These results show that dipolar couplings significantly improved the local structure while also dramatically improving the ...
TL;DR: A modification is described that completely eliminates problems by replacing the original potential surfaces by a sum of multidimensional Gaussian functions and structures refined with the new Gaussian implementation now simultaneously enjoy excellent global sampling and excellent local choices of torsion angles.
TL;DR: The anisotropy of structural distortion of the monoclinic polymorph of acetaminophen induced by hydrostatic pressure up to 4.0 GPa was studied by single-crystal X-ray diffraction in a Merrill-Bassett diamond anvil cell by analysing the relative shifts of the centroids of the hydrogen-bonded cycles and of the centres of the benzene rings with pressure.
Abstract: The anisotropy of structural distortion of the monoclinic polymorph of acetaminophen induced by hydrostatic pressure up to 4.0 GPa was studied by single-crystal X-ray diffraction in a Merrill–Bassett diamond anvil cell (DAC). The space group (P21/n) and the general structural pattern remained unchanged with pressure. Despite the overall decrease in the molar volume with pressure, the structure expanded in particular crystallographic directions. One of the linear cell parameters (c) passed through a minimum as the pressure increased. The intramolecular bond lengths changed only slightly with pressure, but the changes in the dihedral and torsion angles were very large. The compressibility of the intermolecular hydrogen bonds NH⋯O and OH⋯O was measured. NH⋯O bonds were shown to be slightly more compressible than OH⋯O bonds. The anisotropy of structural distortion was analysed in detail in relation to the pressure-induced changes in the molecular conformations, to the compression of the hydrogen-bond network, and to the changes in the orientation of molecules with respect to each other in the pleated sheets in the structure. Dirichlet domains were calculated in order to analyse the relative shifts of the centroids of the hydrogen-bonded cycles and of the centroids of the benzene rings with pressure.
TL;DR: Vicinal scalar J-coupling constants in polypeptides are analyzed using density functional theory (DFT) in combination with molecular dynamics computer simulations and assumptions that underlie the widely used Karplus relationships can be independently tested.
Abstract: Vicinal scalar J-coupling constants in polypeptides are analyzed using density functional theory (DFT) in combination with molecular dynamics (MD) computer simulations. The couplings studied are the six 3J-coupling constants that involve the φ backbone torsion angle, 3J(HN−Hα), 3J(HN−Cβ), 3J(HN−C‘), 3J(C‘−Hα), 3J(C‘−Cβ), and 3J(C‘−C‘), and two 3J-coupling constants, 3J(Hα−N) and 3J(N−N), that involve the ψ backbone torsion angle. The dependence of these couplings on their main torsion angle as well as other degrees of freedom are investigated by computations performed on two different versions of the alanine dipeptide, Ala-Ala-NH2 and Ace-Ala-NMe, with sets of coordinates obtained by different structure optimization schemes and from snapshots extracted from a MD trajectory of ubiquitin. In this way, assumptions that underlie the widely used Karplus relationships can be independently tested. Static Karplus curves, which are fitted to the computed couplings as a function of the φ-torsion angle, are generall...
TL;DR: In this article, the absorption and CD spectra of a series of Frechet and backfolding dendrimers derived from enantiopure (S)-2,2′-dihydroxy-1,1′-binaphthalene have been recorded in the range 200-350 nm.
TL;DR: In the presence of a covalent bridge that restricts the rotation around the C(1)-C(1') bond a reliable estimate of the conformational helicity could be obtained and is complementary to CD spectroscopy that presents the same exciton patterns irrespective of the actual theta value.
Abstract: The twisting ability of a series of 1,1‘-binaphthalene compounds used as dopants in nematic solvents has been related to the dihedral angle θ between the two naphthalene moieties. While in the case of the more flexible compounds the sign and value of the helical twisting power is affected by several structural features that prevent a simple assignment of the conformation, in the presence of a covalent bridge that restricts the rotation around the C(1)−C(1‘) bond a reliable estimate of the conformational helicity could be obtained. This technique is complementary to CD spectroscopy that, for the investigated molecules, presents the same exciton patterns irrespective of the actual θ value.
TL;DR: In this paper, the authors calculated the bare V of the highest occupied molecular orbitals (HOMO) of BEDT-TTF (bis(ethylenedithio)tetrathiafulvalene) is calculated for various molecular geometries.
Abstract: Intermolecular Coulomb repulsion, V, of the highest occupied molecular orbitals (HOMO) of BEDT-TTF (bis(ethylenedithio)tetrathiafulvalene) is calculated for various molecular geometries. The bare V is a quantity that is easily estimated under the point charge approximation. As far as the screened V in actual crystals is proportional to the calculated bare V, the usual θ-phase prefers the horizontal or diagonal stripe, whereas the vertical stripe becomes comparatively stable in the limit of the small dihedral angle (in the metallic limit). The phase diagrams of the θ-phase are discussed under the combination of the static charge distribution (the atomic limit) and the Stoner model (the extended Stoner model). The model contains two order parameters: the spin polarization, Sz, and the charge order, n-1/2. This model explains why the insulating state of the Rb salt below 190 K is a paramagnetic charge-ordered state, while the Cs salt has a different insulating phase below 20 K. The lattice dimerization of th...
TL;DR: In this paper, an ab initio geometry optimization was carried out on 10 selected conformations of maltose and two 2-methoxytetrahydropyran conformations using the density functional denoted B3LYP combined with two basis sets.
Abstract: Ab initio geometry optimization was carried out on 10 selected conformations of maltose and two 2-methoxytetrahydropyran conformations using the density functional denoted B3LYP combined with two basis sets. The 6-31G and 6-311CCG basis sets make up the B3LYP/6-31G and B3LYP/6-311CCG procedures. Internal coordinates were fully relaxed, and structures were gradient optimized at both levels of theory. Ten conformations were studied at the B3LYP/6-31G level, and five of these were continued with full gradient optimization at the B3LYP/6-311CCG level of theory. The details of the ab initio optimized geometries are presented here, with particular attention given to the positions of the atoms around the anomeric center and the effect of the particular anomer and hydrogen bonding pattern on the maltose ring structures and relative conformational energies. The size and complexity of the hydrogen-bonding network prevented a rigorous search of conformational space by ab initio calculations. However, using empirical force fields, low-energy conformers of maltose were found that were subsequently gradient optimized at the two ab initio levels of theory. Three classes of conformations were studied, as defined by the clockwise or counterclockwise direction of the hydroxyl groups, or a flipped conformer in which the -dihedral is rotated by180 .D ifferent combinations of! side-chain rotations gave energy differences of more than 6 kcal/mol above the lowest energy structure found. The lowest energy structures bear remarkably close resemblance to the neutron and X-ray diffraction crystal structures. c 2000 John Wiley & Sons, Inc. JC omput Chem 21: 1204-1219, 2000
TL;DR: The most important consequence of this structural alteration is the dramatic increase in configurational stability of homochiral F8BINOL.
TL;DR: The stablebeta-turn conformations in the free energy landscape were consistent with the empirically preferred beta-turn types for each amino acid sequence and correlated well with the empirical values estimated from the solvent accessible surface area of each molecular conformation during the trajectories.
TL;DR: In this paper, double-quantum NMR was applied to two 13 C2-labeled carbohydrate samples, (1,2-13 C2)-glucose and methyl-R-D-(1,3- 13 C 2)-Glucose, in both solution and solid phases.
Abstract: Double-quantum heteronuclear local field NMR was applied to two 13 C2-labeled carbohydrate samples, (1,2- 13 C2)-glucose and methyl-R-D-(1,3- 13 C2)-glucose. The geometry of the H- 13 C- 13 C-H moeity was estimated using the evolution of double-quantum coherences under correlated heteronuclear dipolar interactions. For (1,2- 13 C2)-glucose, double-quantum techniques were used both in solution and solid phases. The measured H-C1-C2-H torsion angles in crystalline glucose were 170° ( 5° for the ‚-anomer and 40° ( 15° for the R-anomer, in good agreement with reported crystal structures. In the solution phase we give a full analysis of an experiment in which the cross-correlation effects are isolated by the use of a heteronuclear multiple-quantum filter. We consider the influence of anisotropic rotational diffusion, chemical shift anisotropy, and proton - proton spin diffusion on the torsion angle estimate. We show that it is possible to determine the torsion angle and the rotational correlation time independently. The measured H-C1-C2-H torsion angles in solution differ slightly from the solid-state results: 159 ° ( 10° for the ‚-anomer and 57° ( 7° for the R-anomer. For methyl-R-D-(1,3- 13 C2)-glucose, the solid phase double-quantum heteronuclear local field experiment was applied for the first time to a HCCH moiety in which the carbons are not directly bonded. These techniques may be applied to other structural problems such as the determination of glycosidic linkage conformations and the conformation of sugar rings in nucleotides.
TL;DR: In this paper, it was shown that right-handed twisting is an intrinsic property of a peptide main chain because of the difference in rotational potentials around N(sp2)−Cα(sp3) and C(sp 2−C α(sp 3) bonds, which results in decreasing absolute values of dihedral angles but not ψ.
Abstract: Right-handed twisting is a fundamental structural feature of β-pleated sheets in globular proteins which is critical for their geometry and function. The origin of this twisting is poorly understood and has represented a challenge for theoretical chemistry for almost 30 years. Density functional theory using the B3LYP exchange-correlation functional and the split-valence 6-31G** basis set has been utilized to investigate the structure and conformational transitions of single and double-stranded antiparallel β-sheet models to determine the driving force for the right-handed twisting. Right-handed twisting is found to be an intrinsic property of a peptide main chain because of the difference in rotational potentials around N(sp2)−Cα(sp3) and C(sp2)−Cα(sp3) bonds. The difference arises from a tendency of the single Cα(sp3)−C(sp2) bonds to eclipse the lone pair of atoms N(sp2), which results in decreasing absolute values of dihedral angles φ but not ψ. This tendency is suppressed by hydrogen bonding between a...
TL;DR: In this article, Ab initio optical rotations have been obtained for allene, 1,3-dichloroallene, H 2 O 2, and H 2 S 2 as a function of dihedral angles, both at SCF and post-SCF levels.
TL;DR: The influence of the cations on bond length, valence, and torsion angle of S4( 2-) and S5(2-) anions was examined in a series of solid alkali tetra- and pentasulfides by relating their Raman spectra to their known X-ray structures through a force-field analysis.
Abstract: The influence of the cations on bond length, valence, and torsion angle of S4(2-) and S5(2-) anions was examined in a series of solid alkali tetra- and pentasulfides by relating their Raman spectra to their known X-ray structures through a force-field analysis. The IR and Raman spectra of BaS4.H2O and the Raman spectra of (NH4)2S4.nNH3, gamma-Na2S4, and delta-Na2S5 are presented. The similarity of spectra of gamma-Na2S4 with those of BaS4.H2O suggests similar structures of the S4(2-) anions in these two compounds with a torsion angle smaller than 90 degrees. The variations of SS bond length, SSS valence angle, and dihedral angle of Sn2- anions are related to the polarization of the lone pair and electronic charge of the anion by the electric field of the cations. A correlation between the torsion angle and the SSS valence angle is shown as that previously reported between the length of the bond around which the torsion takes place and the dihedral angle value. These geometry changes are explained by the hyperconjugation concept and the electron long-pair repulsion.
TL;DR: Intercalation of the azaamino acid residue into the i+2 position in synthetic peptides is expected to provide a stable beta-turn formation, and this could be utilized in the design of new peptidomimetics adopting a beta- turn scaffold.
Abstract: The structural perturbation induced by C(alpha)-->N(alpha) exchange in azaamino acid-containing peptides was predicted by ab initio calculation of the 6-31G* and 3-21G* levels. The global energy-minimum conformations for model compounds, For-azaXaa-NH2 (Xaa=Gly, Ala, Leu) appeared to be the beta-turn motif with a dihedral angle of phi= +/- 90 degrees, psi=0 degrees. This suggests that incorporation of the azaXaa residue into the i+2 position of designed peptides could stabilize the beta-turn structure. The model azaLeu-containing peptide, Boc-Phe-azaLeu-Ala-OMe, which is predicted to adopt a beta-turn conformation was designed and synthesized in order to experimentally elucidate the role of the azaamino acid residue. Its structural preference in organic solvents was investigated using 1H NMR, molecular modelling and IR spectroscopy. The temperature coefficients of amide protons, the characteristic NOE patterns, the restrained molecular dynamics simulation and IR spectroscopy defined the dihedral angles [ (phi i+1, psi i+1) (phi i+2, psi i+2)] of the Phe-azaLeu fragment in the model peptide, Boc-Phe-azaLeu-Ala-OMe, as [(-59 degrees, 127 degrees) (107 degrees, -4 degrees)]. This solution conformation supports a betaII-turn structural preference in azaLeu-containing peptides as predicted by the quantum chemical calculation. Therefore, intercalation of the azaamino acid residue into the i+2 position in synthetic peptides is expected to provide a stable beta-turn formation, and this could be utilized in the design of new peptidomimetics adopting a beta-turn scaffold.