Showing papers on "Dihedral angle published in 2002"

Effect of pore geometry on VP/VS: From equilibrium geometry to crack

Abstract: Seismic wave velocities of melt or aqueous fluid containing systems are studied over a wide range of pore shapes, including oblate spheroids, tubes, cracks, and an equilibrium geometry controlled by a dihedral angle. The relative role of liquid compressibility and pore geometry on the V P /V S velocity ratio is clarified. The result clearly indicates that P and S velocity structures determined by seismic tomography can be used to verify whether interfacial energy-controlled melt or fluid geometry (equilibrium geometry) is achieved. Relationships between the diverse models are clearly established by relating each model to the oblate spheroid model in terms of the equivalent aspect ratio. As a function of the aspect ratio, a significant effect of pore geometry on d In V S /d In V P , the ratio of the fractional changes in V S and V P , is shown. Equilibrium geometry of the partially molten rocks, characterized by a dihedral angle of 20°-40°, corresponds to an aspect ratio of 0.1-0.15. The value of d In V S /d In V P expected for the texturally equilibrated partially molten rocks is shown to be 1-1.5, which is much smaller than that expected for cracks and dikes with an aspect ratio of <10 -2 -10 -3 . In the upper mantle low-velocity regions the seismologically obtained value of d In V S /d In V P is within this range beneath the Bolivian Andes (1.1-1.4) but is as high as 2 beneath Iceland (1.7-2.3) and beneath northeastern Japan (2.0). The former region can be regarded as a region where equilibrium geometry is achieved, and the latter regions can be regarded as regions where dikes and veins typical of a system far from the textural equilibrium dominate.

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy.

Abstract: The three-dimensional structure of the chemotactic peptide N-formyl-l-Met-l-Leu-l-Phe-OH was determined by using solid-state NMR (SSNMR). The set of SSNMR data consisted of 16 (13)C-(15)N distances and 18 torsion angle constraints (on 10 angles), recorded from uniformly (13)C,(15)N- and (15)N-labeled samples. The peptide's structure was calculated by means of simulated annealing and a newly developed protocol that ensures that all of conformational space, consistent with the structural constraints, is searched completely. The result is a high-quality structure of a molecule that has thus far not been amenable to single-crystal diffraction studies. The extensions of the SSNMR techniques and computational methods to larger systems appear promising.

Characterization of the folding degree of proteins

Abstract: MOTIVATION The characterization of the folding degree of chains is central to the elucidation of structure--function relationships in proteins. Here we present a new index for characterizing the folding degree of a (protein) chain. This index shows a range of features that are desirable for the study of the relation between structure and function in proteins. RESULTS A novel index characterizing the folding degree of (protein) chains is developed based on the spectral moments of a matrix representing the dihedral angles (phi, omega and epsilon) of the protein main chain. The proposed index is normalized to the chain size, is not correlated to the gyration radius of the backbone chain and is able to distinguish between structures for which the sum of the main-chain dihedral angles is identical. The index is well correlated to the percentages of helix and strand in proteins, shows a linear dependence with temperature changes, and is able to differentiate among protein families. AVAILABILITY On request from the author.

Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study.

Abstract: We have measured the band profile of amide I in the infrared, isotropic, and anisotropic Raman spectra of L-alanyl-D-alanyl-L-alanine, acetyl-L-alanyl-L-alanine, L-vanyl-L-vanyl-L-valine, L-seryl-L-seryl-L-serine, and L-lysyl-L-lysyl-L-lysine at acid, neutral, and alkaline pD. The respective intensity ratios of the two amide I bands depend on the excitonic coupling between the amide I modes of the peptide group. These intensity ratios were obtained from a self-consistent spectral decomposition and then were used to determine the dihedral angles between the two peptide groups by means of a recently developed algorithm (Schweitzer-Stenner, R. Biophys. J. 2002, 83, 523-532). The validity of the obtained structures were checked by measuring and analyzing the vibrational circular dichroism of the two amide I bands. Thus, we found two solutions for all protonation states of trialanine. Assuming a single conformer, one obtains a very extended beta-helix-like structure. Alternatively, the data can be explained by the coexistence of a 3(1)(PII) and a beta-sheet-like structure. Acetyl-L-alanyl-L-alanine exhibits a structure which is very similar to that obtained for trialanine. The tripeptide with the central D-alanine adopts an extended structure with a negative psi and a positive phi angle. Trivaline and triserine adopt single beta(2)-like structures such as that identified in the energy landscape of the alanine dipeptide. Trilysine appears different from the other investigated homopeptides in that it adopts a left-handed helix which at acid pD is in part stabilized by hydrogen bonding between the protonated carboxylate (donor) and the N-terminal peptide carbonyl. Our result provides compelling evidence for the capability of short peptides to adopt stable structures in an aqueous solution, which at least to some extent reflect the intrinsic structural propensity of the respective amino acids in proteins. Furthermore, this paper convincingly demonstrates that the combination of different vibrational spectroscopies provides a powerful tool for the determination of the secondary structure of peptides in solution.

Twist Angles and Rotational Energy Barriers of Biphenyl and Substituted Biphenyls

Abstract: Using B3LYP/6-311+G* and other methods, twist angles and torsional energies were obtained for biphenyl (BP), 2-halogen BPs, 2,2‘-dihalogen BPs, and 3,3‘-dihalogen BPs, the halogens ranging from F to I. The results were compared with available gas phase and X-ray data. 2,2‘-difluoro BP has a rotational double minimum, at 57.9 and 128.9°, whereas the other 2,2‘-dihalogen BPs have a single minimum at dihedral angles ranging from 84.9 to 94.8°. All 3,3‘-dihalogen BPs have a double minimum at about 45 and 135°. Optimized twist angles and energy barriers were also calculated for 2,2‘-dimethyl BP and for perfluoro as well as perchloro BP. Most structures are accounted for by steric effects. For 2,2‘-dihalogen BPs, however, attractive forces also appear to play a role, as evidenced by the dihedral angle of 2,2‘-dichloro BP lying well below 90°.

Protonation and subsequent intramolecular hydrogen bonding as a method to control chain structure and tune luminescence in heteroatomic conjugated polymers.

Abstract: We report the effects of protonation on the structural and spectroscopic properties of 1,4-dimethoxy-2,5-bis(2-pyridyl)benzene (9) and the related AB coploymer poly{2,5-pyridylene-co-1,4-[2,5-bis(2-ethylhexyloxy)]phenylene} (7). X-ray crystallographic analysis of 9, 1,4-dimethoxy-2,5-bis(2-pyridyl)benzene bis(formic acid) complex 10, and 1,4-dimethoxy-2,5-bis(2-pyridinium)benzene bis(tetrafluoroborate salt) (11) establishes that reaction of formic acid with 9 does not form an ionic pyridinium salt in the solid state, rather, the product 10 is a molecular complex with strong hydrogen bonds between each nitrogen atom and the hydroxyl hydrogen in formic acid. In contrast, reaction of 9 with tetrafluoroboric acid leads to the dication salt 11 with significant intramolecular hydrogen bonding (N−H···O−Me) causing planarization of the molecule. The pyridinium and benzene rings in 11 form a dihedral angle of only 3.9° (cf. pyridine−benzene dihedral angles of 35.4° and 31.4° in 9, and 43.8° in 10). Accordingly, th...

Structural dependencies of interresidue scalar coupling h3JNC, and donor 1H chemical shifts in the hydrogen bonding regions of proteins

Abstract: A study is presented of the structural dependencies for scalar J-coupling and the amide donor 1H chemical shifts in the hydrogen bonding regions of proteins. An analysis of the interactions between the donor hydrogen and acceptor oxygen orbitals in an N−H···OC moiety suggests that there are three major structural factors for 15N−13C coupling across hydrogen bonds: (1) the H···O‘ internuclear separation rHO‘, (2) the H···O‘C‘ angle θ2, and (3) indirect contributions involving the oxygen loan pair electrons should lead to a dependence on the H···O‘C‘−N‘ dihedral angle ρ. Density functional theory (DFT) and finite perturbation theory (FPT) were used to obtain the Fermi contact (FC) contributions to interresidue coupling in formamide dimers with systematic variation of these structural parameters. The computed h3JNC‘ exhibit good correlations with cos2 θ2 combined with an exponential dependence on rHO‘. The correlation is further improved by including a dependence on the dihedral angle ρ. For each of the 34 H...

Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution.

Abstract: The conformational behavior of the title compounds has been investigated by Hartree–Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed γ turn (γl), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4–0.5 kcal/mol for helical structures and about 2 kcal/mol for γl structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for γl structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 341–350, 2002

Sampling along reaction coordinates with the Wang-Landau method

Abstract: The multiple range random walk algorithm recently proposed by Wang and Landau [2001, Phys. Rev. Lett., 86, 2050] is adapted to the computation of free energy profiles for molecular systems along reaction coordinates. More generally, we show how to extract partial averages in various statistical ensembles without invoking simulations with constraints, biasing potentials or unknown parameters. The method is illustrated on a model 10-dimensional potential energy surface, for which analytical results are obtained. It is then applied to the potential of mean force associated with the dihedral angle of the butane molecule in the gas phase and in carbon tetrachloride solvent. Finally, isomerization in a small rocksalt cluster, (NaF)4, is investigated in the microcanonical ensemble, and the results are compared to those of parallel tempering Monte Carlo.

11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore.

Abstract: Density functional theory (DFT) calculations based on the self-consistent-charge tight-binding approximation have been performed to study the influence of the protein pocket on the 3-dimensional structure of the 11-cis-retinal Schiff base (SB) chromophore. Starting with an effectively planar chromophore embedded in a protein pocket consisting of the 27 next-nearest amino acids, the relaxed chromophore geometry resulting from energy optimization and molecular dynamics (MD) simulations has yielded novel insights with respect to the following questions: (i) The conformation of the beta-ionone ring. The protein pocket tolerates both conformations, 6-s-cis and 6-s-trans, with a total energy difference of 0.7 kcal/mol in favor of the former. Of the two possible 6-s-cis conformations, the one with a negative twist angle (optimized value: -35 degrees ) is strongly favored, by 3.6 kcal/mol, relative to the one in which the dihedral is positive. (ii) Out-of-plane twist of the chromophore. The environment induces a nonplanar helical deformation of the chromophore, with the distortions concentrated in the central region of the chromophore, from C10 to C13. The dihedral angle between the planes formed by the bonds from C7 to C10 and from C13 to C15 is 42 degrees. (iii) The absolute configuration of the chromophore. The dihedral angle about the C12-C13 bond is +170 degrees from planar s-cis, which imparts a positive helicity on the chromophore, in agreement with earlier considerations based on theoretical and spectroscopic evidence.

Chi(1) rotamer populations and angles of mobile surface side chains are accurately predicted by a torsion angle database potential of mean force.

Abstract: The equilibrium angles and distributions of chi(1) rotamers for mobile surface side chains of the small, 63-residue, B1 domain of protein L have been calculated from the static crystal structure by rigid body/torsion angle simulated annealing using a torsion angle database potential of mean force and compared to those deduced by Monte Carlo analysis of side chain residual dipolar couplings measured in solution. Good agreement between theory and experiment is observed, indicating that for side chains undergoing rotamer averaging that is fast on the chemical shift time scale, the equilibrium angles and distribution of chi(1) rotamers are largely determined by the backbone phi/psi torsion angles.

Three-Dimensional Solution Structure of the Calcium-Signaling Protein Apo-S100A1 As Determined by NMR†,‡

Abstract: S100A1, a member of the S100 protein family, is an EF-hand containing Ca(2+)-binding protein (93 residues per subunit) with noncovalent interactions at its dimer interface. Each subunit of S100A1 has four alpha-helices and a small antiparallel beta-sheet consistent with two helix-loop-helix calcium-binding domains [Baldiserri et al. (1999) J. Biomol. NMR 14, 87-88]. In this study, the three-dimensional structure of reduced apo-S100A1 was determined by NMR spectroscopy using a total of 2220 NOE distance constraints, 258 dihedral angle constraints, and 168 backbone hydrogen bond constraints derived from a series of 2D, 3D, and 4D NMR experiments. The final structure was found to be globular and compact with the four helices in each subunit aligning to form a unicornate-type four-helix bundle. Intermolecular NOE correlations were observed between residues in helices 1 and 4 from one subunit to residues in helices 1' and 4' of the other subunit, respectively, consistent with the antiparallel alignment of the two subunits to form a symmetric X-type four-helix bundle as found for other members of the S100 protein family. Because of the similarity of the S100A1 dimer interface to that found for S100B, it was possible to calculate a model of the S100A1/B heterodimer. This model is consistent with a number of NMR chemical shift changes observed when S100A1 is titrated into a sample of (15)N-labeled S100B. Helix 3 (and 3') of S100A1 was found to have an interhelical angle of -150 degrees with helix 4 (and 4') in the apo state. This crossing angle is quite different (>50 degrees ) from that typically found in other EF-hand containing proteins such as apocalmodulin and apotroponin C but more similar to apo-S100B, which has an interhelical angle of -166 degrees. As with S100B, it is likely that the second EF-hand of apo-S100A1 reorients dramatically upon the addition of Ca(2+), which can explain the Ca(2+) dependence that S100A1 has for binding several of its biological targets.

Structure Analysis of Dipeptides in Water by Exploring and Utilizing the Structural Sensitivity of Amide III by Polarized Visible Raman, FTIR−Spectroscopy and DFT Based Normal Coordinate Analysis

Abstract: A series of dipeptides AX and XA (X = G, K, L, S, and V) were investigated by polarized visible Raman and FTIR-spectroscopy to examine the conformational determinants of the amide III band. A spectral decomposition combined with density functional calculations revealed that the amide III band has a multicomponent structure in that three different modes contribute to amide III vibrations. One of them (amide III2) dominates the Raman spectra particularly of the cationic species. Its normal mode displays an in-phase combination of NH and Cα1H in plane bending vibrations, which makes it sensitive to changes of the dihedral angle ψ. Indeed, our Raman data show that amide III2 varies with ψ but remains practically unaffected by variation of φ in the region between −95° and −75°, which is sampled by the investigated AX peptides. Our data support the Lord hypothesis that amide III depends solely on ψ (Lord, R. Appl. Spectrosc. 1977, 31, 187) but specifies to which of the amide III modes this statement applies. Ou...

Torsion Energy Profiles and Force Fields Derived from Ab Initio Calculations for Simulations of Hydrocarbon-Fluorocarbon Diblocks and Perfluoroalkylbromides

Abstract: Force fields with explicit atoms are proposed for the molecular simulation of two families of substituted perfluorocarbons: hydrocarbon−perfluorocarbon diblocks, or partially fluorinated alkanes, and 1-bromoperfluoroalkanes, or perfluoroalkylbromides. Both types of molecules are of interest for formulations of synthetic in vivo gas carriers, or blood substitutes, and for drug-delivery systems. Some semifluorinated alkanes have amphiphile character between hydrogenated and fluorinated liquid phases. The present molecular models are based on the OPLS all-atom force field, published in 2001 for perfluoroalkanes, completed with potential energy functions for the torsion around chemical bonds near the junction between the hydrocarbon and fluorocarbon blocks and close to the bromine atom, respectively. The dihedral terms have been derived from ab initio calculations on series of molecules of both families containing between two and five carbon atoms. Whenever possible, comparisons were made with experimental b...

Perfluoroterephthalate bridged complexes with M-M quadruple bonds: ((t)BuCO(2))(3)M(2)(mu-O(2)CC(6)F(4)CO(2))M(2)(O(2)C(t)Bu)(3), where M = Mo or W. Studies of solid-state, molecular, and electronic structure and correlations with electronic and Raman spectral data.

Abstract: The compounds [(tBuCO2)3M2(μ-O2CC6F4CO2)M2(O2CtBu)3], M4PFT, where M = Mo or W, are shown by model fitting of the powder X-ray diffraction data to have an infinite “twisted” structure involving M···O intermolecular interactions in the solid state. The dihedral angle between the M2 units of each molecule is 54°. Electronic structure calculations employing density functional theory (Gaussian 98 and ADF2000.01, gradient corrected and time dependent) on the model compounds (HCO2)3M2(μ-O2CC6F4CO2)M2(O2CH)3, where M = Mo or W, reveal that in the gas phase the model compounds adopt planar D2h ground-state structures wherein M2 δ to bridge π* back-bonding is maximized. The calculations predict relatively small HOMO−LUMO gaps of 1.53 eV for M = Mo and 1.22 eV for M = W for this planar structure and that, when the “conjugation” is removed by rotation of the plane of the C6F4 ring to become orthogonal to the M4 plane, this energy gap is nearly doubled to 2.57 eV for M = Mo and 2.18 eV for M = W. The Raman and resona...

Chromophore Distortions in the Bacteriorhodopsin Photocycle: Evolution of the H−C14−C15−H Dihedral Angle Measured by Solid-State NMR†

Abstract: In recent years, structural information about bacteriorhodopsin has grown substantially with the publication of several crystal structures. However, precise measurements of the chromophore conformation in the various photocycle states are still lacking. This information is critical because twists about the chromophore backbone chain can influence the Schiff base nitrogen position, orientation, and proton affinity. Here, we focus on the C14−C15 bond, using solid-state nuclear magnetic resonance spectroscopy to measure the H−C14−C15−H dihedral angle. In the resting state (bR568), we obtain an angle of 164 ± 4°, indicating a 16° distortion from a planar all-trans chromophore. The dihedral angle is found to decrease to 147 ± 10° in the early M intermediate (Mo) and to 150 ± 4° in the late M intermediate (Mn). These results demonstrate changes in the chromophore conformation undetected by recent X-ray diffraction studies.

Crystallographic evidence for oxygen acceptor directionality in oxyanion hydrogen bonds.

Abstract: A survey of 2632 D-H...O-A hydrogen bonds in crystal structures (where D is any atom and A is the central atom of a trigonal planar (A = C, N) or tetrahedral (A = P, S, Cl, As, Se, Cr, Mo) oxyanion, has established the existence of a distinct directionalities at the oxygen atom acceptors. The directionality depends primarily on the geometry of the oxyanion. With the trigonal planar oxyanions NO3-, HCO3-, and CO32-, the average H...O-A angle is 115 +/- 12 degrees and there is a clear preference for the hydrogen to lie within the plane of the anion. With the tetrahedral oxyanions H2PO4-, HPO42-, HSO4-, SO42-, ClO4-, H2AsO4-, HAsO42-, AsO43-, HSeO4-, SeO42-, CrO42-, and MoO42-, the average H...O-A angle is 122 +/- 12 degrees , and there is a weak preference for eclipsed H...O-X-O dihedral angles. The observed directionality closely coincides with minima on electrostatic potential surfaces calculated for the anions.

Effects of Thioamide Substitutions on the Conformation and Stability of α- and 310-Helices

Abstract: Thiopeptides, formed by replacing the amide oxygen atom with a sp2 sulfur atom, are useful in protein engineering and drug design because they confer resistance to enzymatic degradation and are predicted to be more rigid. This report describes our free molecular dynamics simulations with explicit water and free energy calculations on the effects of thio substitutions on the conformation of α-helices, 310-helices, and their relative stability. The most prominent structural effect of thio substitution is the increase in the hydrogen bond distance from 2.1 A for normal peptides to 2.7 A for thiopeptides. To accommodate for the longer CS···H−N hydrogen bond, the (φ, ψ) dihedral angles of the α-helix changed from (−66°, −42°) to (−68°, −38°), and the rise per turn increased from 5.5 to 6.3 A. For 310-helices, the (φ, ψ) dihedral angles (−60°, −20°) and rise per turn (6.0 A) changed to (−66°, −12°) and 6.8 A, respectively. In terms of relative stability, the most prominent change upon thio substitution is the d...

Conformation of ligands bound to the muscarinic acetylcholine receptor.

Abstract: Many biogenic amines evoke a variety of physiological responses by acting on G protein-coupled receptors. We have determined the conformation of two acetylcholine analogs, (S)-methacholine and (2S,4R,5S)-muscarine, bound to the M(2) muscarinic acetylcholine receptor (M(2) mAChR) by NMR spectroscopy. The analysis of the transferred nuclear Overhauser effect indicated that the receptor selectively recognized the conformers of (S)-methacholine and (2S,4R,5S)-muscarine with the gauche O-C2-C1-N dihedral angle at +60 degrees. This is distinct from the predominant conformations of these ligands in solution with O-C2-C1-N dihedral angle (+80 to approximately 85 degrees ) in the absence of the M(2) mAChR, as assessed by analyses of the coupling constants and nuclear Overhauser effect spectroscopy. We have also built a molecular model of the M(2) mAChR-(S)-methacholine complex, based on the X-ray crystallographic structure of rhodopsin. This model indicated that the conformation with the gauche O-C2-C1-N dihedral angle at +55.5 degrees, which is similar to the one determined by NMR measurement, is energetically favored in the binding of (S)-methacholine to the receptor. We suggest that this conformation represents the binding of the agonist to the M(2) mAChR in the absence of G protein.

Conformational analysis of furanose rings with PSEUROT: parametrization for rings possessing the arabino, lyxo, ribo, and xylo stereochemistry and application to arabinofuranosides.

Abstract: The solution conformation of a furanose ring can be assessed through PSEUROT analysis of three-bond 1H−1H coupling constants (3JHH) of the ring hydrogens. For each coupling constant, PSEUROT requires two parameters, A and B, which are used to translate the H−C−C−H dihedral angle predicted from the 3JHH into an endocyclic torsion angle from which the identity of the conformers can be determined. In this paper, we have used density functional theory methods to generate a family of envelope conformers for methyl furanosides 1−8. From these structures, A and B were calculated for each H−C−C−H fragment. In turn, the values of these parameters for the arabinofuranose ring were used in PSEUROT calculations to determine the conformers populated by monosaccharides 1 and 2 as well as the furanose rings in oligosaccharides 9−15. The results of these analyses are consistent with the low-energy conformers identified from previous computational and X-ray crystallographic studies of 1 and 2.

Bis(1,1‐di­methyl­biguanido)copper(II) octahydrate

Abstract: A complex of a deprotonated form of metformin with Cu2+, [Cu(C4H10N5)2]·8H2O, was prepared from alkaline aqueous solution. The coordination geometry around the Cu atom is square planar, with four N atoms from two bidentate ligands. The deprotonation of the ligand causes an increase in the π conjugation of the C—N—C system, reducing the bond angle at the central N atom to nearly 120°. The dihedral angle between the two six-membered chelate rings in the complex is 11.31 (5)°. The Cu atom lies on a twofold rotation axis.

Interfacial energies for quartz and albite in pelitic schist

Abstract: Interfacial energies of quartz/quartz (qz/qz), albite/albite (ab/ab), and quartz/albite (qz/ab) boundaries in low-grade pelitic schist were determined based on measured values of dihedral angles. Three kinds of microstructures were investigated, and the interfacial energies were obtained in two independent ways. (1) Relative values of interfacial energy were calculated from dihedral angles formed at quartz and albite triple junctions. (2) Subgrain boundary energy was calculated using the Read–Shockley theory for a boundary connected to an intergranular pore. Dihedral angles formed at the corners of intergranular pores were measured. From the interfacial tension balance equation, the value of the qz/qz grain boundary energy was then obtained. (3) Dihedral angles formed at intersections of either pericline or albite twin boundaries with either ab/ab or qz/ab boundaries were measured. The twin boundary energy was calculated based on a previously derived equation using Landau potential, twin wall thickness, and critical temperature for a phase transition in albite. With a modified interfacial tension balance equation for a twin boundary fixed to a facet orientation, the interfacial energies of ab/ab and qz/ab boundaries were obtained. Energies obtained by methods of (2) and (3) are in good agreement. The interfacial energies for qz/qz, ab/ab, and qz/ab boundaries obtained in this study are 270±110, 300±150, and 250±120 mJ/m2, respectively.

Synthesis and solid-state structures of dimethyl 2,2'-bithiophenedicarboxylates.

Abstract: The syntheses of dimethyl 2,2‘-bithiophene-4,4‘-dicarboxylate (3), dimethyl 2,2‘-bithiophene-3,4‘-dicarboxylate (4), and dimethyl 2,2‘-bithiophene-3,3‘-dicarboxylate (5) are described. Single-crystal X-ray structural analysis of these compounds shows that the thiophene rings in 3 and 4 are nearly coplanar (dihedral angle close to 0°) and they adopt the anti sulfur conformation in the solid state. Further, the structure of 4 is in agreement with our previous suggestion that there is an electrostatic stabilization of the planar structure due to attraction of the 3-carbonyl oxygen to the sulfur of the distal ring. In 5, however, the thiophene rings are nearly perpendicular (dihedral angle 75°), indicating considerable steric hindrance between the two large ester groups at the 3- and 3‘-positions. Unlike compounds 3 and 4, where the thiophene rings have the sulfur atoms anti, the sulfur atoms in 5 are completely syn. This is the first instance where a bithiophene has been shown to adopt a conformation where t...