Showing papers on "Dihedral angle published in 2012"

Cholesteryl-based liquid crystal dimers containing a sulfur–sulfur link in the flexible spacer

Abstract: Seven members of the homologous series of the liquid crystal dimers, the bis(ω-(cholesteryloxycarbonyl)alkyl)disulfides, which contain a sulfur−sulfur link in the flexible spacer have been synthesised and their liquid crystal properties characterised. The dimers are referred to using the acronym Chol-n-SS-n-Chol in which n denotes the number of carbon atoms linking the cholesteryl-based groups and the sulfur atoms, and was varied between 3, 5, 6, 8, 10, 11 and 12. All seven homologues exhibit a chiral nematic phase and for the longest three members a smectic A phase was also observed. An odd−even effect is apparent in both the transition temperatures and the values of the entropy change associated with the chiral nematic−isotropic transition, ΔSN*I /R, in which dimers with even values of n show the higher values. This is interpreted in terms of the average molecular shapes in which the C−S−S−C dihedral angle is around 90°. The values of ΔSN*I/R shown by these dimers are very small for liquid crystal dimer...

Accurate Force Field Development for Modeling Conjugated Polymers.

Abstract: The modeling of the conformational properties of conjugated polymers entails a unique challenge for classical force fields. Conjugation imposes strong constraints upon bond rotation. Planar configurations are favored, but the concomitantly shortened bond lengths result in moieties being brought into closer proximity than usual. The ensuing steric repulsions are particularly severe in the presence of side chains, straining angles, and stretching bonds to a degree infrequently found in nonconjugated systems. We herein demonstrate the resulting inaccuracies by comparing the LMP2-calculated inter-ring torsion potentials for a series of substituted stilbenes and bithiophenes to those calculated using standard classical force fields. We then implement adjustments to the OPLS-2005 force field in order to improve its ability to model such systems. Finally, we show the impact of these changes on the dihedral angle distributions, persistence lengths, and conjugation length distributions observed during molecular dy...

Can a C-H···O interaction be a determinant of conformation?

Abstract: Whether nonconventional hydrogen bonds, such as the C-H···O interaction, are a consequence or a determinant of conformation is a long-running and unresolved issue. Here we outline a solid-state and quantum mechanical study designed to investigate whether a C-H···O interaction can override the significant trans-planar conformational preferences of α-fluoroamide substituents. A profound change in dihedral angle from trans-planar((OCCF)) to cis-planar((OCCF)) observed on introducing an acceptor group for a C-H···O hydrogen bond is consistent with this interaction functioning as a determinant of conformation in certain systems. This testifies to the potential influence of the C-H···O hydrogen bond and is consistent with the assignment of this interaction as a contributor to overall conformation in both model and natural systems.

RMC_POT: A computer code for reverse monte carlo modeling the structure of disordered systems containing molecules of arbitrary complexity

Abstract: An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness-of-fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard-Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X-ray structure factor-based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future. © 2012 Wiley Periodicals, Inc.

CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates.

Abstract: Presented is an extension of the CHARMM additive all-atom carbohydrate force field to enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates. Target data for parameter optimization included full two-dimensional energy surfaces defined by the glycosidic dihedral angle pairs in the phosphate/sulfate model compound analogs of hexopyranose monosaccharide phosphates and sulfates, as determined by quantum mechanical (QM) MP2/cc-pVTZ single point energies on MP2/6-31+G(d) optimized structures. In order to achieve balanced, transferable dihedral parameters for the dihedral angles, surfaces for all possible anomeric and conformational states were included during the parametrization process. In addition, to model physiologically relevant systems, both the mono- and dianionic charged states were studied for the phosphates. This resulted in over 7000 MP2/cc-pVTZ//MP2/6-31G+(d)...

Conduction mechanisms in biphenyl dithiol single-molecule junctions

Abstract: Based on density-functional theory calculations, we report a detailed study of the single-molecule charge-transport properties for a series of recently synthesized biphenyl-dithiol molecules. The torsion angle ϕ between the two phenyl rings, and hence the degree of π conjugation, is controlled by alkyl chains and methyl side groups. We consider three different coordination geometries, namely, top-top, bridge-bridge, and hollow-hollow, with the terminal sulfur atoms bound to one, two, and three gold surface atoms, respectively. Our calculations show that different coordination geometries give rise to conductances that vary by one order of magnitude for the same molecule. Irrespective of the coordination geometries, the charge transport calculations predict a cos2ϕ dependence of the conductance, which is confirmed by our experimental measurements. We demonstrate that the calculated transmission through biphenyl dithiols is typically dominated by a single transmission eigenchannel formed from π electrons. For perpendicular orientation of the rings a residual conductance arises from σ-π couplings. But only for a single molecule with a completely broken conjugation we find a nearly perfect degeneracy of the σ-π eigenchannels for the hollow-hollow-type contact in our theory.

Conformational analysis of supramolecular polymerization processes of disc-like molecules

Abstract: N,N′,N′′-Trialkylbenzene-1,3,5-tricarboxamides (BTAs) cooperatively self-assemble into one-dimensional, helical supramolecular polymers in apolar alkane solutions. Previous studies revealed that the position and configuration of the methyl group on the aliphatic side-chain gives rise to an ‘odd–even effect’ both in the shape and the sign of the CD-effect. In this study, we elucidate the molecular origin of this odd–even effect by a combination of TD-DFT calculations and spectroscopic experiments. In addition, we observed a pronounced effect of the molecular structure of the alkane solvent on the shape of the Cotton effects and the thermodynamic parameters describing the cooperative supramolecular polymerization. The results revealed a different ability of solvent molecules governed by the shape of their structure to intercalate into the helical stacks, which influences the conformation of the monomer within the supramolecular polymer. The solvent affects the dihedral angle (θ) between the CO group and the benzene central core of the BTA molecule. These findings help to increase a molecular-level understanding of how the solvent controls the conformation of repeating units in a supramolecular system.

Excited-State Dynamics and Self-Organization of Poly(3-hexylthiophene) (P3HT) in Solution and Thin Films

Abstract: The fluorescence decays of a stereoregular head-to-tail RR-HT poly(3-hexylthiophene), P3HT, in methylcyclohexane (MCH) are described by sums of three or four exponential terms, respectively above and below −10 °C. In the high-temperature region, the polymer lifetime (ca. 500 ps) is accompanied by two shorter decay times (ca. 20 and 120 ps), which are assigned to intrachain energy transfer from high to lower energy excitons on the basis of temperature and wavelength dependence of the fluorescence decays. The absence of conformational (torsional) relaxation is attributed to the small dihedral angle between monomers that is predicted for the stereoregular polymer in the ground state. Below −10 °C, the polymer forms excimer-like aggregates, showing vibrational structured absorption and emission bands similar to those observed in thin films. The vibrational structure is attributed to a deep minimum in the ground-state energy surface of the dimer or aggregate. Below −40 °C, the fluorescence measured at the aggr...

Control and femtosecond time-resolved imaging of torsion in a chiral molecule

Abstract: We study how the combination of long and short laser pulses can be used to induce torsion in an axially chiral biphenyl derivative (3,5-difluoro-3',5'-dibromo-4'-cyanobiphenyl). A long, with respect to the molecular rotational periods, elliptically polarized laser pulse produces 3D alignment of the molecules, and a linearly polarized short pulse initiates torsion about the stereogenic axis. The torsional motion is monitored in real-time by measuring the dihedral angle using femtosecond time-resolved Coulomb explosion imaging. Within the first 4 picoseconds (ps), torsion occurs with a period of 1.25 ps and an amplitude of 3° in excellent agreement with theoretical calculations. At larger times, the quantum states of the molecules describing the torsional motion dephase and an almost isotropic distribution of the dihedral angle is measured. We demonstrate an original application of covariance analysis of two-dimensional ion images to reveal strong correlations between specific ejected ionic fragments from Coulomb explosion. This technique strengthens our interpretation of the experimental data.

2,2′‐Biphospholes: Building Blocks for Tuning the HOMO–LUMO Gap of π‐Systems Using Covalent Bonding and Metal Coordination

Abstract: new angle: The insertion of a 2,2′-biphosphole subunit into π-conjugated systems offers a new way to control the HOMO-LUMO gap. Tuning of the dihedral angle (θ) between the two phosphorous heterocycles, either by metal coordination or covalent bonding through the P substitution can lead to control of the band gap. These new π-conjugated systems can be used as emitting materials in white organic light-emitting devices (WOLEDs).

Atomistic molecular dynamics study of cross-linked phenolic resins

Abstract: In this study, we analyzed cross-linked phenolic resins by using atomistic molecular dynamics simulations. Cross-linked structures consisting of a network of three functional phenols and two functional methylenes with degrees of cross-linking of 0.70, 0.82, and 0.92 were prepared by cross-linking reactions of linear novolac-type phenolic resins in a unit cell under three-dimensional periodic boundary conditions. Uniaxial elongations of the cross-linked structures to a strain of 0.03 were performed at 300 K. At this temperature, all structures were apparently in a glassy state, which was confirmed by the analysis of specific volume as a function of the temperature. The uniaxial elongation did not cause a significant change in the distribution of bonding potential energies (i.e., bond stretching, angle bending, and torsion angle potentials). On the other hand, the change in the potential energies owing to the uniaxial elongation indicated that cross-links suppressed local segmental motions in the cross-linked structure, probably at the region around the linear and terminal phenols, which resulted in an increase in the degree of cross-linking accompanied by a decrease in Poisson's ratio and an increase in Young's modulus.

Relation between photochromic properties and molecular structures in salicylideneaniline crystals

Abstract: The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloro­aniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloro­aniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

Switching orientation of two axial imidazole ligands between parallel and perpendicular in low-spin Fe(III) and Fe(II) nonplanar porphyrinates.

Abstract: We have reported here the synthesis, structure, and properties of low-spin bis-imidazole-coordinated Fe(III) and Fe(II) complexes of 5,10,15,20-tetrakis(pentafluorophenyl)-2,3,7,8,12,13,17,18-octachloroporphyrin, [FeIII(TFPPCl8)(L)2]ClO4 and FeII(TFPPCl8)(L)2 (L = 1-methylimidazole, 4-methylimidazole, imidazole). The X-ray structure of FeII(TFPPCl8)(1-MeIm)2 is reported here, which demonstrated the near-perpendicular axial ligand orientation (dihedral angle between two 1-methylimidazoles is 80.7°) for Fe(II) porphyrins in a highly saddle-distorted macrocyclic environment. Oxidation of FeII(TFPPCl8)(L)2 using thianthrenium perchlorate produces [FeIII(TFPPCl8)(L)2]ClO4, which was also isolated in the solid state and characterized spectroscopically. The complex gives rhombic EPR spectra in both solid and solution phases at 77 K and thus represents a rare example of nearly parallel axial ligand orientations for the unhindered imidazoles in a saddle-distorted porphyrin macrocycle. Geometry optimization using D...

Analytic Physical Optics Solution for Bistatic, 3D Scattering From a Dihedral Corner Reflector

Abstract: We derive an analytic scattering model for 3D bistatic scattering from a dihedral using geometrical optics (GO) and physical optics (PO). We use GO to trace ray reflections, and we evaluate the PO integral(s) for the field scattered by each plate of the dihedral. Multiple cases of reflection geometry are considered to account for effects of the dihedral plate size and antenna aspect angles. The complex-valued (amplitude and phase) scattering response is derived. The resulting parametric scattering model is presented in terms of the vertical and horizontal co-polarization and cross-polarization responses that correspond to the outputs of industry-standard numerical prediction codes. Comparing the derived model to available codes for method of moments (MoM), shooting and bouncing rays (SBR), and parametric models (PM), we demonstrate that the derived solution achieves the same accuracy as SBR, approximates MoM, is more accurate than PM, and does so in fast computation time comparable to a PM.

Folding helical proteins in explicit solvent using dihedral-biased tempering

Abstract: Using a single-trajectory-based tempering method with a high-temperature dihedral bias, we repeatedly folded four helical proteins [α3D (PDB ID: 2A3D, 73 residues), α3W (1LQ7, 67 residues), Fap1-NRα (2KUB, 81 residues) and S-836 (2JUA, 102 residues)] and some of the mutants in explicit solvent within several microseconds. The lowest root-mean-square deviations of backbone atoms from the experimentally determined structures were 1.9, 1.4, 1.0, and 2.1 A, respectively. Cluster analyses of folding trajectories showed the native conformation usually occupied the most populated cluster. The simulation protocol can be applied to large-scale simulations of other helical proteins on commonly accessible computing platforms.

Synthesis of the smallest axially chiral molecule by asymmetric carbon-fluorine bond activation.

Abstract: Surprisingly, thecarbon backbones of 3 and 5adeviate by 4.4(3)8 and 4.6(2)8from the linearity that would be expected based on their sp-hybridized central carbon atoms (Figure 2). Furthermore, thetwo terminal F-C-H planes in5a have a torsion angle of91.9(2)8. The previously reported structures derived frommicrowave spectroscopy do not show the same distortions(Supporting Information, Table S2), because erroneously, therefinement was based on a constrained linear geometry.

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

Abstract: Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the Cα-N bond (Phi) and the Cα-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction of protein structures. In this study, we develop a new approach called TANGLE (Torsion ANGLE predictor) to predict the protein backbone torsion angles from amino acid sequences. TANGLE uses a two-level support vector regression approach to perform real-value torsion angle prediction using a variety of features derived from amino acid sequences, including the evolutionary profiles in the form of position-specific scoring matrices, predicted secondary structure, solvent accessibility and natively disordered region as well as other global sequence features. When evaluated based on a large benchmark dataset of 1,526 non-homologous proteins, the mean absolute errors (MAEs) of the Phi and Psi angle prediction are 27.8° and 44.6°, respectively, which are 1% and 3% respectively lower than that using one of the state-of-the-art prediction tools ANGLOR. Moreover, the prediction of TANGLE is significantly better than a random predictor that was built on the amino acid-specific basis, with the p-value<1.46e-147 and 7.97e-150, respectively by the Wilcoxon signed rank test. As a complementary approach to the current torsion angle prediction algorithms, TANGLE should prove useful in predicting protein structural properties and assisting protein fold recognition by applying the predicted torsion angles as useful restraints. TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/.

Synthesis, crystal structure and magnetism of new salicylamidoxime-based hexanuclear manganese(III) single-molecule magnets

Abstract: Salicylamidoxime was used to synthesize 13 new polynuclear Mn(III) complexes. We present the crystallographic structures, the magnetic susceptibility and the magnetization measurements of eight of them (1-8) with the general formula [Mn(6)O(2)(H(2)N-sao)(6)(L)(2)(solvent)(4-6)] (L = carboxylate, chloride, 2-cyanophenolate; solvent = H(2)O, MeOH, EtOH, py). These complexes consist of two trinuclear {Mn(III)(3)(μ(3)-O)(H(2)N-sao)(3)}(+) cationic units linked together via two oximate and two phenolate oxygen atoms. All behave as single-molecule magnets, with the spin ground state varying from 4 to 12 and anisotropy energy barriers from 24 to 86 K, the latter being as high as the present record barrier in the Mn(6) complexes. DFT calculations were performed to compute the exchange magnetic coupling constants J between the metallic ions and to provide an orbital interpretation of exchange. Our results are in line with previously reported results with the parent salicylaldoxime derivatives. The Mn-N-O-Mn torsion angle appears as the main parameter controlling the J values. The critical angle where the exchange coupling between two Mn(III) switches from antiferromagnetic to ferromagnetic is 27°, less than the one found in related complexes with salicylaldoxime (30°). We propose a structural classification of the {Mn(6)} complexes in four classes depending on the coordination of the axial carboxylate. The work points out the structural flexibility of such systems, their sensitivity to solvent effects and their ability to achieve high anisotropy energy barriers by simple desolvation.

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

Abstract: Structural fluctuations of a protein are essential for a protein to function and fold. By using molecular dynamics (MD) simulations of the model α/β protein VA3 in its native state, the coupling between the main-chain (MC) motions [represented by coarse-grained dihedral angles (CGDAs) γn based on four successive Cα atoms (n - 1, n, n + 1, n + 2) along the amino acid sequence] and its side-chain (SC) motions [represented by CGDAs δn formed by the virtual bond joining two consecutive Cα atoms (n, n + 1) and the bonds joining these Cα atoms to their respective Cβ atoms] was analyzed. The motions of SCs (δn) and MC (γn) over time occur on similar free-energy profiles and were found to be subdiffusive. The fluctuations of the SCs (δn) and those of the MC (γn) are generally poorly correlated on a ps time-scale with a correlation increasing with time to reach a maximum value at about 10 ns. This maximum value is close to the correlation between the δn(t) and γn(t) time-series extracted from the entire duration of the MD runs (400 ns) and varies significantly along the amino acid sequence. High correlations between the SC and MC motions [δ(t) and γ(t) time-series] were found only in flexible regions of the protein for a few residues which contribute the most to the slowest collective modes of the molecule. These results are a possible indication of the role of the flexible regions of proteins for the biological function and folding.

Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine.

Abstract: The potentials of mean force (PMF's) for the deformation of the C(α) ⋯ C(α) virtual bonds in polypeptide chains were determined from the diabatic energy surfaces of N-methylacetamide (modeling regular peptide groups) and N-acetylpyrrolidine (modeling the peptide groups preceding proline), calculated at the Moller-Plesset (MP2) ab initio level of theory with the 6-31G(d,p) basis set The energy surfaces were expressed in the C(α) ⋯ C(α) virtual-bond length (d) and the H-N-C(α) ⋯ C' improper dihedral angle (α) that describes the pyramidicity of the amide nitrogen, or in the C(α)-C'(O)-N-C(α) dihedral angle (ω) and the angle α For each grid point, the potential energy was minimized with respect to all remaining degrees of freedom The PMF's obtained from the (d, α) energy surfaces produced realistic free-energy barriers to the trans-cis transition (10 kcal/mol and 13 kcal/mol for the regular and proline peptide groups, respectively, compared to 126 - 139 kcal/mol and 173 - 196 kcal/mol determined experimentally for glycylglycine and N-acylprolines, respectively), while those obtained from the (ω, α) energy maps produced either low-quality PMF curves when direct Boltzmann summation was implemented to compute the PMF's or too-flat curves with too-low free-energy barriers to the trans-cis transition if harmonic extrapolation was used to estimate the contributions to the partition function An analytical bimodal logarithmic-Gaussian expression was fitted to the PMF's, and the potentials were implemented in the UNRES force field Test Langevin-dynamics simulations were carried out for the Gly-Gly and Gly-Pro dipeptides, which showed a 10(6)-fold increase of the simulated rate of the trans-cis isomerization with respect to that measured experimentally; effectively the same result was obtained with the analytical Kramers theory of reaction rate applied to the UNRES representation of the peptide groups Application of Kramers' theory to compute the rate constants from the all-atom ab initio energy surfaces of the model compounds studied resulted in isomerization rates close to the experimental values, which demonstrates that the increase of the isomerization rate in UNRES simulations results solely from averaging out the secondary degrees of freedom

Torsional Entropy at the Origin of the Reversible Temperature-Induced Phase Transition of Cellulose

Abstract: The temperature-induced phase transition of native cellulose was studied by X-ray diffraction and molecular dynamics (MD) simulation. Upon heating, this transition is characterized by an important expansion of the distance between the planes of glucopyranose rings, which is observed both experimentally and in MD. Computed trajectories suggest that this expansion is caused by a rotation of the exocyclic hydroxymethyl groups. Upon cooling, the phase transition, experimentally known as reversible, was found to be irreversible in the MD simulation when using current GROMOS 53a6 force field parameters. By varying one of these, related to the potential energy of the hydroxymethyl conformers, a reversible phase transition could be observed in silico. From the linear dependence of the transition temperature on the dihedral energy of the different conformers, the entropy change due to the phase transition could be estimated to be about 26 JK–1 mol–1. This value essentially reflects the additive contribution of the...

Structure fluctuations and conformational changes in protein binding.

Abstract: Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the side-chains upon binding. Normal mode analysis and an elastic network model were applied to a set of protein complexes to calculate the residue fluctuations and develop the residue classification. Comparison with a classification based on normalized B-factors suggests that the B-factors may underestimate protein flexibility in solvent. Our classification shows that protein loops and disordered fragments are enriched with highly fluctuating residues and depleted with weakly fluctuating residues. Strategies for engineering thermostable proteins are discussed. To calculate the dihedral angles distribution functions, the configuration space was divided into cells by a cubic grid. The effect of protein association on the distribution functions depends on the amino acid type and a grid step in the dihedral angles space. The changes in the dihedral angles increase from the near-backbone dihedral angle to the most distant one, for most residues. On average, one fifth of the interface residues change the rotamer state upon binding, whereas the rest of the interface residues undergo local readjustments within the same rotamer.

The Oxalate Dianion, C2O42–: Planar or Nonplanar?

Abstract: Theoretical studies have shown that for the isolated oxalate dianion, C2O42–, which contains a long C–C single bond, the conformer with a 90° twist about the C–C bond (D2d symmetry) is more stable than the planar (D2h) conformer that is almost invariably drawn for the dianion. The D2d conformer has been shown to persist in aqueous solutions of simple oxalate salts. However, in oxalato complexes or in solid oxalates, the O–C–C–O dihedral angle for C2O42– is commonly observed to be quite different from the 90° of the D2d conformer. This indicates that bonding or “crystal packing” forces usually outweigh the 2–6 kcal/mol barrier calculated for rotation between the two conformers.