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Showing papers on "Dihedral angle published in 2007"


Journal ArticleDOI
TL;DR: It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide.
Abstract: It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {phi(n)} to the metric coordinate space {x(n)=cos phi(n),y(n)=sin phi(n)} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300 ns molecular dynamics simulation, a critical comparison of the various methods is given.

302 citations


Journal ArticleDOI
TL;DR: A complete, isostructural series of complexes with La-Lu (except Pm) with the ligand TREN-1,2-HOIQO has been synthesized and structurally characterized by means of single-crystal X-ray analysis, providing a significant advance for the prediction and rationalization of the geometric features of the corresponding lanthanide complexes.
Abstract: A complete, isostructural series of complexes with La−Lu (except Pm) with the ligand TREN-1,2-HOIQO has been synthesized and structurally characterized by means of single-crystal X-ray analysis. All complexes are 1D-polymeric species in the solid state, with the lanthanide being in an eight-coordinate, distorted trigonal-dodecahedral environment with a donor set of eight unique oxygen atoms. This series constitutes the first complete set of isostructural complexes from La−Lu (without Pm) with a ligand of denticity greater than two. The geometric arrangement of the chelating moieties slightly deviates across the lanthanide series, as analyzed by a shape parameter metric based on the comparison of the dihedral angles along all edges of the coordination polyhedron. The apparent lanthanide contraction in the individual Ln−O bond lengths deviates considerably from the expected quadratic decrease that was found previously in a number of complexes with ligands of low denticity. The sum of all bond lengths around...

231 citations


Journal ArticleDOI
TL;DR: The temporal spectral evolution relevant to the structural change clearly exhibited an isoemissive point around 675 nm, which manifests that there exists a shallow potential minimum at the perpendicular geometry on the S1 surface, and the S2 state stays undistorted for a finite period as long as 660 fs before the structural distortion.
Abstract: In copper(I) complex [Cu(dmphen)2]+ (dmphen = 2,9-dimethyl-1,10-phenanthroline), a “flattening” structural change is induced with 1MLCT excitation, which is a prototype of the structural change accompanied with Cu(I)/Cu(II) conversion in copper complexes. Femtosecond and picosecond emission dynamics of this complex were investigated in solution at room temperature with optically allowed S2 ← S0 photoexcitation. Time-resolved emission was measured in the whole visible region, and the lifetimes, intrinsic emission spectra, and radiative lifetimes of the transients were obtained by quantitative analysis. It was concluded that the initially populated S2 state is relaxed with a time constant of 45 fs to generate the S1 state retaining the perpendicular structure, and the D2d → D2 structural change (the change of the dihedral angle between the two ligand planes) occurs in the S1 state with a time constant of 660 fs. The intersystem crossing from the S1 state to the T1 state takes place after this structural dis...

199 citations


Journal ArticleDOI
TL;DR: The theoretical results suggest that the HOMO-LUMO gap, ionization potential, and charge distribution of oligomers are strongly dependent on twisting, whereas, similar to the case of polythiophene, twisting of neutral oligothiophenes costs very little energy.
Abstract: Interring twisting (change in the dihedral angle between conjugated rings) of polythiophene was studied theoretically using periodic boundary conditions (PBC) at the B3LYP/6-31G(d) level. We find that the band gap of polymers is strongly dependent on the interring twist angle; yet twisting requires very little energy. A twist of 30 degrees increases the band gap by 0.75 eV in polythiophene, while requiring only 0.41 kcal mol(-1) per monomer unit. Such a small energetic value is of the order of crystal packing or van der Waals forces. These results are compared with calculations performed on model oligomers. Sexithiophene, its radical cations, and its dication are optimized at 0-180 degrees end-to-end twist angles (which correspond to 0-36 degrees interring dihedral angles) using the B3LYP/6-31G(d) method. The theoretical results suggest that the HOMO-LUMO gap, ionization potential, and charge distribution of oligomers are strongly dependent on twisting, whereas, similar to the case of polythiophene, twisting of neutral oligothiophenes costs very little energy. In the case of the radical cation, the lowest energy transition is shifted to a longer wavelength region on twisting, while the second-lowest energy transition is shifted to a shorter wavelength region. This implies that twisted, doped conducting polymers (modeled here by an oligomer radical cation), in contrast to planar, doped polymers, should be transparent within a certain optical window (in the far-visible region, at approximately 1.5 eV). This observation is explained on the basis of changes in the shape and overlap of the frontier molecular orbitals.

163 citations


Journal ArticleDOI
TL;DR: The evidence for the stabilizing nature of the H-H bonding in planar biphenyl is succinctly reviewed in this paper, where it is shown that the barrier to rotation via the planar transition state is the net resultant of a stabilisation of the four ortho-hydrogen atoms (by 8 kcal/mol each), a stabilization of the two para-carbon atoms (By 3 kc/m each), and by the dominant destabilisation of two carbon atoms joining the two rings (the two junction carbon atoms) (by 22kc/mol
Abstract: The evidence for the stabilizing nature of the H–H bonding in planar biphenyl is succinctly reviewed. The stabilizing nature of the H–H bonding is revealed through a comparison of the atomic energy of every atom in planar biphenyl with the same atom in the twisted equilibrium structure. It is shown that the barrier to rotation via the planar transition state is the net resultant of a stabilisation of the four ortho-hydrogen atoms (by 8 kcal/mol each), a stabilisation of the two para-carbon atoms (by 3 kcal/mol each) and by the dominant destabilisation of the two carbon atoms joining the two rings—the two junction carbon atoms—(by 22 kcal/mol each). The energetic stabilisation of the four ortho-hydrogen atoms is further shown to be in large proportion due to the formation of the hydrogen–hydrogen interatomic surface. Furthermore, neither the “bond order” between the two junction carbon atoms nor the total electron delocalisation between the two rings exhibit a significant change in going from the planar to the twisted equilibrium geometry. These findings are in contrast with the classical view of a balance between “steric non-bonded repulsion” and better electron delocalisation as a function of the twist dihedral angle. Similar conclusions have been recently reached by Pacios and Gomez through a study of the electrostatic potential at the position of the hydrogen nuclei.

128 citations


Journal ArticleDOI
TL;DR: Anion conformation of a low-viscosity room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(fluorosulfonyl) imide (EMI+FSI-) has been studied by Raman spectra and theoretical DFT calculations, showing a conformational equilibrium between C1 and C2 analogues.
Abstract: Anion conformation of a low-viscosity room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(fluorosulfonyl) imide (EMI+FSI-) has been studied by Raman spectra and theoretical DFT calculations. Three strong Raman bands were found at 293, 328, and 360 cm(-1), which are ascribed to the FSI- ion. These Raman bands show significant temperature dependence, implying that two FSI- conformers coexist in equilibrium. This is supported by theoretical calculations that the FSI- ion is present as either C2 (trans) or C1 (cis) conformer; the former gives the global minimum, and the latter has a higher SCF energy of about 4 kJ mol(-1). Full geometry optimizations followed by normal frequency analyses show that the observed bands at 293, 328, and 360 cm(-1) are ascribed to the C2 conformer. The corresponding vibrations at 305, 320, and 353 cm(-1) were extracted according to deconvolution of the observed Raman bands in the range280-400 cm(-1 )and are ascribed to the C1 conformer. The enthalpy DeltaH degrees of conformational change from C2 to C1 was experimentally evaluated to be ca. 4.5 kJ mol(-1), which is in good agreement with the predicted value by theoretical calculations. The bis(trifluoromethanesulfonyl) imide anion (TFSI-) shows a conformational equilibrium between C1 and C2 analogues (DeltaH degrees = 3.5 kJ mol(-1)). However, the profile of the potential energy surface of the conformational change for FSI- (the F-S-N-S dihedral angle) is significantly different from that for TFSI- (the C-S-N-S dihedral angle).

123 citations


Journal ArticleDOI
TL;DR: The range of utility of a novel simulation method that accurately predicts the infrared amide I spectral contour from the three-dimensional structure of a protein or peptide is extended and paves the way for a variety of applications.
Abstract: X-ray crystallography of collagen model peptides has provided high-resolution structures of the basic triple-helical conformation and its water-mediated hydration network. Vibrational spectroscopy provides a useful bridge for transferring the structural information from X-ray diffraction to collagen in its native environment. The vibrational mode most useful for this purpose is the amide I mode (mostly peptide bond C=O stretch) near 1650 cm-1. The current study refines and extends the range of utility of a novel simulation method that accurately predicts the infrared (IR) amide I spectral contour from the three-dimensional structure of a protein or peptide. The approach is demonstrated through accurate simulation of the experimental amide I contour in solution for both a standard triple helix, (Pro-Pro-Gly)10, and a second peptide with a Gly --> Ala substitution in the middle of the chain that models the effect of a mutation in the native collagen sequence. Monitoring the major amide I peak as a function of temperature gives sharp thermal transitions for both peptides, similar to those obtained by circular dichroism spectroscopy, and the Fourier transform infrared (FTIR) spectra of the unfolded states were compared with polyproline II. The simulation studies were extended to model early stages of thermal denaturation of (Pro-Pro-Gly)10. Dihedral angle changes suggested by molecular dynamics simulations were made in a stepwise fashion to generate peptide unwinding from each end, which emulates the effect of increasing temperature. Simulated bands from these new structures were then compared to the experimental bands obtained as temperature was increased. The similarity between the simulated and experimental IR spectra lends credence to the simulation method and paves the way for a variety of applications.

98 citations


Journal ArticleDOI
TL;DR: The results suggest that further improvement is likely to be achieved by concentrating on the improvement of the scoring function, in addition to or instead of increasing the variety of sampled conformations, when predicting long and flexible side‐chains.
Abstract: We describe an automated method for the modeling of point mutations in protein structures. The protein is represented by all non-hydrogen atoms. The scoring function consists of several types of physical potential energy terms and homology-derived restraints. The optimization method implements a combination of conjugate gradient minimization and molecular dynamics with simulated annealing. The testing set consists of 717 pairs of known protein structures differing by a single mutation. Twelve variations of the scoring function were tested in three different environments of the mutated residue. The best-performing protocol optimizes all the atoms of the mutated residue, with respect to a scoring function that includes molecular mechanics energy terms for bond distances, angles, dihedral angles, peptide bond planarity, and non-bonded atomic contacts represented by Lennard-Jones potential, dihedral angle restraints derived from the aligned homologous structure, and a statistical potential for non-bonded atomic interactions extracted from a large set of known protein structures. The current method compares favorably with other tested approaches, especially when predicting long and flexible side-chains. In addition to the thoroughness of the conformational search, sampled degrees of freedom, and the scoring function type, the accuracy of the method was also evaluated as a function of the flexibility of the mutated side-chain, the relative volume change of the mutated residue, and its residue type. The results suggest that further improvement is likely to be achieved by concentrating on the improvement of the scoring function, in addition to or instead of increasing the variety of sampled conformations.

83 citations


Journal ArticleDOI
TL;DR: In this paper, a combined quantum/classical force field has been used to investigate the properties of hydrogen peroxide in aqueous solution, and it has been shown that H 2 O 2 is a better proton donor than H O 2 O but a weaker proton acceptor.

69 citations


Journal ArticleDOI
TL;DR: Spectroscopic and electrochemical behaviors of the tetrathiafulvalene acetylene derivatives demonstrate that the TTF unit interacts with the electron-accepting group through the triple bond, thus leading to the intramolecular charge transfer.
Abstract: A series of tetrathiafulvalene acetylene derivatives, [TTF−C⋮C−A] [A = C6H4N(CH3)2-4 (1), C6H4OCH3-4 (2), C6H5 (3), C6H4F-4 (4), C6H4NO2-4 (5), C5H4N-2 (6), C5H4N-3 (7), and C5H4N-4 (8)], have been designed and synthesized to provide insight into the nature of the donor−acceptor interaction via a π-conjugated triple bond. The X-ray crystal structure of [TTF−(C⋮C)−C6H4OCH3-4] (2) reveals that the phenyl ring linked by acetylene is almost coplanar to the plane of TTF with a dihedral angle of 3.6°. The strong intermolecular C−H···O hydrogen bonding was found to direct the molecular helical assemblies with a screw pitch of 5.148 A when viewed along the a-axis. Spectroscopic and electrochemical behaviors of the tetrathiafulvalene acetylene derivatives demonstrate that the TTF unit interacts with the electron-accepting group through the triple bond, thus leading to the intramolecular charge transfer. The pyridine-substituted TTF compounds 6−8 show remarkable sensing and coordinating properties toward Pb2+. Comp...

64 citations


Journal ArticleDOI
TL;DR: Good agreement between calculated and experimentally measured coupling constants revealed that the DFT method was able to accurately predict J-couplings in aqueous solutions.

Journal ArticleDOI
TL;DR: In this article, a correlation between the dihedral angle of the bridging biaryl moiety and the enantioselectivity of bisphosphite ligands was found.

Journal ArticleDOI
TL;DR: Detailed examination of the atomic displacements and dihedral angle changes of the retinal chromophore involved in the interconversion among these isomers suggests the mechanism of isomerization efficiency.

Journal ArticleDOI
TL;DR: Calix[4]thiacrowns with hetero-L(1) and a homodonor set (L(2)) were synthesized and characterized by X-ray analysis and found a considerable decrease of dihedral angles of two opposite aromatic rings upon complexation.

Journal ArticleDOI
TL;DR: In this article, broken symmetry DFT calculations (B3LYP) corroborate the correctness of the electronic structure descriptions of the above neutral 1,4-diaza-1,3-butadienes.
Abstract: The reaction of 2 equivalents of 2-methyl-1,4-bis(2,6-dimethylphenyl)-1,4-diaza-1,3-butadiene, (1LOx)0, or 2-methyl-1,4-bis(2,6-diisopropylphenyl)-1,4-diaza-1,3-butadiene, (2LOx)0, in diethyl ether or n-hexane with 1 equivalent of Ni(cdt) where (cdt)0 is the ligand cyclododecatriene affords dark red, diamagnetic precipitates of [NiII(1L˙)2] (1) and of [NiII(2L˙)2] (3). The ligands (1L˙)1− and (2L˙)1− are the one-electron reduced, monoanionic π radicals of the above neutral 1,4-diaza-1,3-butadienes. 1 and 3 have been structurally characterized by X-ray crystallography; both possess a distorted tetrahedral geometry where the dihedral angle θ between the two metallacycles Ni–N–C–C–N is 47.9° and 53°, respectively, (θ = 0° for square planar and 90° for a regular tetrahedral geometry). The reaction of 1 and 3 with 1 equivalent of ferrocenium hexafluorophosphate gives the paramagnetic (St = 1/2) complexes 2 and 4, respectively: [NiI(1LOx)2](PF6) (2), [NiI(2LOx)2](PF6) (4). Their EPR spectra indicate the presence of a central Ni(I) ion (d9; SNi = 1/2). Thus, the one-electron oxidation of 1 and 3 by [Fc]PF6 induces an intramolecular one-electron reduction of the central Ni ion and a concomitant one-electron oxidation of the second π radical (L˙)1− → (LOx)0 + e. Broken symmetry DFT calculations (B3LYP) corroborate the correctness of the electronic structure descriptions of 1–4. The reaction of (1LOx)0 with NiI2 (1 : 1) in tetrahydrofuran yields tetrahedral [NiII(1LOx)I2] (5) with an St = 1 ground state.

Journal ArticleDOI
TL;DR: It is demonstrated that the same procedure leads to a structure with the unfavorable ca.
Abstract: To further study the preference of the antiperiplanar (ap) conformation in α-fluoro-amide groups, two β-peptides, 1 and 2, containing a (2-F)-β3hAla and a (2-F)-β2hPhe residue, have been synthesized. Their NMR-solution structures in CD3OH were determined and compared with those of non-F-substituted analogs, 3 and 4a. While we have found in a previous investigation (Helv. Chim. Acta2005, 88, 266) that a stereospecifically introduced F-substituent in the central position of a β-heptapeptide is capable of ‘breaking’ the 314-helical structure by enforcing the FCCO ap-conformation, we could now demonstrate that the same procedure leads to a structure with the unfavorable ca. 90° FCCO dihedral angle, enforced by the 314-helical folding in a β-tridecapeptide (cf.1; Fig. 4). This is interpreted as a consequence of cooperative folding in the longer β-peptide. A F-substituent placed in the turn section of a β-peptidic hairpin turn was shown to be in an ap-arrangement with respect to the neighboring CO bond (cf.2; Fig. 7). Analysis of the non-F-substituted β-tetrapeptides (with helix-preventing configurations of the two central β2/β3-amino acid residues) provides unusually tight hairpin structural clusters (cf.3 and 4a; Figs. 8 and 9). The skeleton of the β-tetrapeptide H-(R)β3hVal-(R)β2hVal-(R)β3hAla-(S)β3hPhe-OH (4a) is proposed as a novel, very simple backbone structure for mimicking α-peptidic hairpin turns.

Journal ArticleDOI
TL;DR: The title compounds, (E)-2-[(2-bromophenyl)iminomethyl]-4-methoxyphenol, C(14)H(12)BrNO(2), (I), (E-2)[(3-bROMophenyl]iminometrichyl], and (III), adopt the phenol-imine tautomeric form and there are strong intramolecular O-H...N hydrogen bonds.
Abstract: The title compounds, (E)-2-[(2-bromophenyl)iminomethyl]-4-methoxyphenol, C(14)H(12)BrNO(2), (I), (E)-2-[(3-bromophenyl)iminomethyl]-4-methoxyphenol, C(14)H(12)BrNO(2), (II), and (E)-2-[(4-bromophenyl)iminomethyl]-4-methoxyphenol, C(14)H(12)BrNO(2), (III), adopt the phenol-imine tautomeric form. In all three structures, there are strong intramolecular O-H...N hydrogen bonds. Compound (I) has strong intermolecular hydrogen bonds, while compound (III) has weak intermolecular hydrogen bonds. In addition to these intermolecular interactions, C-H...pi interactions in (I) and (III), and pi-pi interactions in (I), play roles in the crystal packing. The dihedral angles between the aromatic rings are 15.34 (12), 6.1 (3) and 39.2 (14) degrees for (I), (II) and (III), respectively.

Journal ArticleDOI
TL;DR: An important aspect of planetary core formation concerns whether interconnectivity of liquid metal can occur in crystalline silicates, which at low melt fractions requires that the dihedral angle between the two phases is

Journal ArticleDOI
TL;DR: Density functional theory calculations are used to determine the angular dependence of scalar couplings (Karplus equation) for N-acetylated amino sugars and an equation derived that can estimate bond libration from experimental measurements.
Abstract: N-Acetylated amino sugars are essential components of living organisms, but their dynamic conformational properties are poorly understood due to a lack of suitable experimental methodologies. Nuclear magnetic resonance (NMR) is ideally suited to these conformational studies, but accurate equations relating the conformation of key substituents (e.g., the acetamido group) to NMR observables are unavailable. To address this, density functional theory (DFT) methods have been used to calculate vicinal coupling constants in N-acetylated amino sugars and derive empirical Karplus equations for 3J(HNH2) of N-acetyl-D-glucosamine (GlcNAc) and N-acetyl-D-galactosamine (GalNAc). The fitted Karplus parameters were found to be similar to those previously derived for peptide amide groups, but are consistently larger in magnitude. Local intramolecular interactions had a small effect on the calculated J-couplings and comparison with experimental data suggested that DFT slightly overestimated them. An implicit solvation model consistently lowered the magnitude of the calculated values, improving the agreement with the experimental data. However, an explicit solvent model, while having a small effect, worsened the agreement with experimental data. The largest contributor to experimentally-determined 3J(HNH2)-couplings is proposed to be librations of the amide group, which are well approximated by a Gaussian distribution about a mean dihedral angle. Exemplifying the usefulness of our derived Karplus equations, the libration of the amide group could be estimated in amino sugars from experimental data. The dynamical spread of the acetamido group in free α-GlcNAc, β-GlcNAc and α-GalNAc was estimated to be 32°, 42° and 20°, with corresponding mean dihedral angles of 160°, 180° and 146°, respectively.

Journal ArticleDOI
TL;DR: It is concluded that apart from the geometric distortions caused by the protein pocket it is not necessary to postulate other specific interactions between the protein and the chromophore to effect the selective and ultrafast photoreaction in rhodopsin.
Abstract: Ab initio excited-state molecular dynamics calculations have been performed to study the effect of methyl substitution and chromophore distortion on the photoreaction of different four-double-bond retinal model chromophores. Randomly distributed starting geometries were generated by zero-point energy sampling; after Franck−Condon excitation the reaction was followed on the S1 surface. For determining the photoproduct and its configuration, a simplified approachtorsion angle followingis discussed and applied. We find that chromophore distortion significantly affects the outcome of the photoreaction: with dihedral angles taken from the rhodopsin-embedded 11-cis-retinal chromophore, the reaction rate of the model chromophore is increased by a factor of 3 compared to that of the relaxed chromophore. Also, the reaction proceeds in a completely stereoselective manner involving only the cis double bond and with a minimum quantum yield of 72%. Bond torsion is more effective than methyl substitution for fast and ...

Journal ArticleDOI
TL;DR: In this article, the Ni(II) and copper (II) complexes bearing 2′-(4′,6′-di-tert-butylhydroxy-phenyl)-1,4,5-triphenyl imidazole ligand have been synthesized and characterized.

Journal ArticleDOI
TL;DR: The three-dimensional structure of a unique polymorph of the anticancer drug paclitaxel (Taxol) is established using solid state NMR (SSNMR) tensor and heteronuclear correlation data and is thus the first conformational characterization with Z' > 1 established solely by SSNMR.
Abstract: The three-dimensional structure of a unique polymorph of the anticancer drug paclitaxel (Taxol®) is established using solid state NMR (SSNMR) tensor (13C & 15N) and heteronuclear correlation (1H–13C) data. The polymorph has two molecules per asymmetric unit (Z′ = 2) and is thus the first conformational characterization with Z′ > 1 established solely by SSNMR. Experimental data are correlated with structure through a series of computational models that extensively sample all conformations. For each computational model, corresponding tensor values are computed to supply comparisons with experimental information which, in turn, establishes paclitaxel’s structure. Heteronuclear correlation data at thirteen key positions provide shift assignments to the asymmetric unit for each comparison. The two distinct molecules of the asymmetric unit possess nearly identical baccatin III moieties with matching conformations of the C10 acetyl moiety and, specifically, the torsion angle formed by C30–O–C10–C9. Additionally, both are found to exhibit an extended conformation of the phenylisoserine sidechain at C13 with notable differences in the dihedral angles centered around the rotation axes of O–C13, C2′–C1′ and C3′–C2′.

Journal ArticleDOI
TL;DR: In this article, a systematic study by quantum mechanical methods of structural and energetic properties for a series of substitutions by alkyl groups of the hydrogens in hydrogen peroxide is presented.
Abstract: We present here a systematic study by quantum mechanical methods of structural and energetic properties for a series of substitutions by alkyl groups of the hydrogens in hydrogen peroxide. The emphasis is on the torsion around the peroxidic bond, which leads to the chirality changing stereomutation. The dihedral angle dependence of the geometrical features and of the dipole moment is discussed with reference to previous experimental and theoretical information, and with respect to the preceding paper on hydrogen peroxide (Maciel et al., Chem Phys Lett, 2006, 432, 383). This information is of interest for chiral separation experiments as well as in view of a possible dynamical mechanism for chirality exchange by molecular collisions. The cis and trans barriers appear to vary remarkably upon substitution by alkyl groups (methyl, ethyl, n- and iso-propyl, sec- and tert-butyl hydroperoxides), the most important property being their geometrical dimensions. As the latter increase, tendency for the equilibrium configuration towards the trans structure increases, so that the trans barrier becomes negligible for dimethyl and diethyl peroxides and for n- and iso-butyl hydroperoxides, giving essentially achiral molecules. For the chiral ones (HOOH, CH3OOH, and C2H5OOH) torsional level energies and eigenfunctions are calculated and their distribution as a function of temperature determined. Their use is exemplified by a calculation of the dipole moment of hydrogen peroxide at room temperature, reconciling previous disagreement between theory and experiment. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Journal ArticleDOI
TL;DR: In this article, the MP2/cc-pVTZ basis set was used to predict the inversion barrier (247 vs. 232 cm−1) and dihedral angle (26°) of cyclopentene.

Journal ArticleDOI
TL;DR: The observations suggest that: (i) the conformational flexibility of the disulfide linkage is dependent on the amino acid residues that flank the cysteinedisulfide bond, and (ii) in both constructs, the presence of a lipid matrix locks the disolfide bond into a preferred conformation.

Journal ArticleDOI
TL;DR: The molecular geometry and vibrational frequencies of 4,4'-bipyridine (BPE) in the ground state were calculated using density functional theory (DFT) methods (B3LYP) with 6-31++G(d,p) basis set in good agreement with observed results.

Journal ArticleDOI
TL;DR: It is shown that the bimetallic copper dimer selectively cleaves the nucleic acids without affecting the proteins, suggesting a possible application of the copper complex in the removal of nucleic acid contaminants from protein extracts through a simple photolytic pathway.
Abstract: The synthesis and characterization of the first examples of core-modified corrole dimers linked through the meso positions are described. The dimers are obtained by a simple AgI- or FeIII-catalyzed coupling reaction in near-quantitative yields. The corroles obtained are metalated with metal ions, such as CuII and NiII. The electronic-absorption spectral studies reveal weak electronic interaction between the two subunits and the exciton coupling observed for the free-base corrole dimer (1717 cm−1) is lower than that for the corresponding protonated derivative (4081 cm−1). The solution-state structure derived from 1H and two-dimensional NMR spectral studies reveals a noncoplanar arrangement of two corrole units. Geometry optimization at the B3LYP-631G level also confirms the noncoplanar arrangement of corroles with a dihedral angle of 64.8° between two corrole planes. The electron paramagnetic resonance (EPR) and magnetic characterization studies on the paramagnetic copper-metalated dimer indicate that both copper ions behave as independent spins without any noticeable interaction. Results of fluorescence studies reveal a bathochromic shift of about 60 nm upon dimerization. The first hyperpolarizability (β) measured by using the hyper Rayleigh scattering (HRS) method reveals doubling of the β values on progressing from monomer to dimer, attributed to enhanced π conjugation. The use of copper dimers in the photocleavage of DNA is also explored. It is shown that the bimetallic copper dimer selectively cleaves the nucleic acids without affecting the proteins, suggesting a possible application of the copper complex in the removal of nucleic acid contaminants from protein extracts through a simple photolytic pathway.

Journal ArticleDOI
TL;DR: In this paper, the Cabibbo angle theta_C might arise from a dihedral flavor symmetry which is broken to different (directions of) subgroups in the up and down quark sector.
Abstract: In [1] it has been shown that the Cabibbo angle theta_C might arise from a dihedral flavor symmetry which is broken to different (directions of) subgroups in the up and the down quark sector. This leads to a prediction of theta_C in terms of group theoretical quantities only, i.e. the index n of the dihedral group D_n, the index j of the fermion representation 2_j and the preserved subgroups indicated by m_u and m_d. Here we construct a low energy model which incorporates this idea. The gauge group is the one of the Standard Model and D_7 x Z_2 ^(aux) serves as flavor symmetry. The additional Z_2 ^(aux) is necessary in order to maintain two sets of Higgs fields, one which couples only to up quarks and another one coupling only to down quarks. We assume that D_7 is broken spontaneously at the electroweak scale by vacuum expectation values of SU(2)_L doublet Higgs fields. The quark masses and mixing parameters can be accommodated well. Furthermore, the potential of the Higgs fields is studied numerically in order to show that the required configuration of the vacuum expectation values can be achieved. We also comment on more minimalist models which explain the Cabibbo angle in terms of group theoretical quantities, while theta_{13}^q and theta_{23}^q vanish at leading order. Finally, we perform a detailed numerical study of the lepton mixing matrix V_{MNS} in which one of its elements is entirely determined by the group theory of a dihedral symmetry. Thereby, we show that nearly tri-bi-maximal mixing can also be produced by a dihedral flavor group with preserved subgroups.

Journal ArticleDOI
TL;DR: In this article, an asymmetric version of the Karplus equation was used to model the side-chain torsions of the protein flavodoxin, and a sine term was added to the k-means to allow independent modelling of both curve minima typically located near dihedral-angle values of +90 degrees and -90 degrees.
Abstract: The standard Karplus equation for calculating 3J coupling constants from any given dihedral angle requires three empirical coefficients be determined that relate to the magnitudes of three modes of the angle dependency of 3J. Considering cosine modes only (bimodal, unimodal and baseline component), Karplus curves are generally symmetric with respect to the sign of the angle argument. Typically, their primary and secondary maxima differ in amplitude, whereas the two minima are of equal depth. However, chiral molecular topologies, such as those surrounding the main-chain and side-chain torsions in amino-acid residues, preclude, as regards substituent positioning, exact mirror-image conformations from being formed--for any given torsion-angle value. It is therefore unlikely that 3J couplings assume identical values for the corresponding positive and negative dihedral angles. This suggests that a better empirical fit of the torsion-angle dependency of 3J could be obtained when removing the constraint of symmetrically identical coupling constants. A sine term added to the Karplus equation allows independent modelling of both curve minima typically located near dihedral-angle values of +90 degrees and -90 degrees. Revisiting an extensive 3J coupling dataset previously recorded to determine the side-chain torsions chi1 in the protein flavodoxin, the asymmetric Karplus model accomplishes a more accurate fit to the experimental data. Asymmetries revealed in the angle dependencies exceed the experimental precision in determining 3J. Accounting for these effects helps improve molecular models.

Journal ArticleDOI
TL;DR: In this article, the conformational preferences of azaphenylalanine-containing peptide were investigated using a model compound, Ac-azaPhe-NHMe with ab initio method at the HF/3-21G and HF/6-31G levels.