Showing papers on "Dihedral angle published in 2005"
TL;DR: The structure determination strategies for solid samples described herein are likely to be generally applicable to many proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy.
Abstract: High-resolution solid-state NMR spectroscopy has become a promising method for the determination of three-dimensional protein structures for systems which are difficult to crystallize or exhibit low solubility. Here we describe the structure determination of microcrystalline ubiquitin using 2D 13C−13C correlation spectroscopy under magic angle spinning conditions. High-resolution 13C spectra have been acquired from hydrated microcrystals of site-directed 13C-enriched ubiquitin. Interresidue carbon−carbon distance constraints defining the global protein structure have been evaluated from ‘dipolar-assisted rotational resonance' experiments recorded at various mixing times. Additional constraints on the backbone torsion angles have been derived from chemical shift analysis. Using both distance and dihedral angle constraints, the structure of microcrystalline ubiquitin has been refined to a root-mean-square deviation of about 1 A. The structure determination strategies for solid samples described herein are l...
210 citations
TL;DR: All the experimental results and simulations are consistent with a PP(II)-like conformation for the alanine dipeptide in aqueous solution, in which two amide-I' modes are highly localized and whose frequency distributions are uncorrelated.
Abstract: The linear-infrared and two-dimensional infrared (2D IR) spectra in the amide-I‘ region of the alanine dipeptide and its 13C isotopomers in aqueous solution (D2O) are reported. The two amide-I‘ IR transitions have been assigned unambiguously by using 13C isotopic substitution of the carbonyl group; the amide unit at the acetyl end shows a lower transition frequency in the unlabeled species. The ratio of their transition dipole strengths remains almost unchanged upon 13C substitution, indicating the absence of intensity transfer between two vibrators. The 2D IR cross peaks directly associated with intramode coupling in this case show a small off-diagonal anharmonicity (0.2 ± 0.2 cm-1), leading to a small coupling constant (1.5 ± 0.5 cm-1). The coupling and the 2D IR spectra in two different polarizations (〈zzzz〉 and 〈zxxz〉) are as expected for a polyproline-II (PPII)-like conformation for dialanine, with the backbone dihedral angles (φ, ψ) determined to be in the range of (−70° ± 25°, +120° ± 25°). Ab init...
183 citations
TL;DR: The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximizing at a much larger dihedral angles.
Abstract: Natural bond orbital deletion calculations show that whereas the gauche preference arises from vicinal hyperconjugative interaction between anti C-H bonds and C-F* antibonds, the cis C-H/C-F* interactions are substantial (approximately 25% of the anti interaction). The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can then be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximize at a much larger dihedral angle. This explanation does not invoke repulsive forces to rationalize the 72 degrees equilibrium conformer angle. The relative minimum energy for the trans conformer is the consequence of a balance between decreasing hyperconjugative stabilization and decreasing steric destabilization as the FCCF torsional angle approaches 180 degrees . The torsional coordinate is predicted to be strongly contaminated by CCF bending, with the result that approximately half of the trans --> gauche stabilization energy stems from mode coupling.
143 citations
TL;DR: Overall, these porphyrin rings serve as a well-defined wheel-shaped light harvesting antenna model in light of very efficient excitation energy hopping along the ring.
Abstract: Directly meso−meso linked porphyrin rings CZ4, CZ6, and CZ8 that respectively comprise four, six, and eight porphyrins have been synthesized in a stepwise manner from a 5,10-diaryl zinc(II) porphyrin building block. Symmetric cyclic structures have been indicated by their very simple 1H NMR spectra that exhibit only a single set of porphyrin and their absorption spectra that display a characteristic broad nonsplit Soret band around 460 nm. Energy minimized structures calculated at the B3LYP/6-31G* level indicate that a dihedral angle between neighboring porphyrins decreases in order of CZ6 > CZ8 > CZ4, which is consistent with the 1H NMR data. Photophysical properties of these molecules have been examined by the steady-state absorption, fluorescence, fluorescence lifetime, fluorescence anisotropy decay, and transient absorption measurements. Both the pump-power dependence on the femtosecond transient absorption and the transient absorption anisotropy decay profiles are directly related with the excitation...
134 citations
TL;DR: In this paper, it was shown that the melt-filled pore structure in the final stages of solidification of cumulates must lie somewhere between the two end-members of impingement (in which pore topology is controlled entirely by the juxtaposition of growth faces of adjacent grains) and textural equilibrium, and the exact position between these two endmembers is controlled by the minimization of internal energies.
Abstract: The melt-filled pore structure in the final stages of solidification of cumulates must lie somewhere between the two end-members of impingement (in which pore topology is controlled entirely by the juxtaposition of growth faces of adjacent grains) and textural equilibrium (in which pore topology is controlled by the minimization of internal energies). The exact position between these two end-members is controlled by the relative rates of crystal growth and textural equilibration. For samples in which growth has stopped, or is very slow, textural equilibrium will prevail. A close examination of dihedral angles in natural examples demonstrates that these two end-member textures can be distinguished. The impingement end-member results in a population of apparent solid–melt dihedral angles with a median of ∼60° and a standard deviation of ∼25–30°, whereas the texturally equilibrated end-member population has a median of ∼28° and a standard deviation of ∼14°. For the specific case of cumulates in the Rum Layered Intrusion, residual porosity in troctolitic cumulates was close to the impingement end-member, whereas that in peridotites was close to melt-bearing textural equilibrium. Suites of glass-bearing samples from small, or frequently disturbed, magma systems show modification of initial impingement textures. These modifications may be a consequence of textural equilibration or of diffusion-limited growth during quenching. Distinction can be made between these two processes by a consideration of grain shape. The geometry of interstitial phases in suites of fully solidified cumulates from the Rum Layered Intrusion shows variable approach to sub-solidus textural equilibrium from an initial state inherited by pseudmorphing of the last melt. Textural equilibration at pore corners occurs as a continuous process, with a gradual movement of the entire dihedral angle population towards the equilibrium final state. If the initial, pseudomorphed state is one of disequilibrium (i.e. a melt-present impingement texture) this change is accompanied by a reduction in the spread of the population. If it is one of equilibrium, the change is accompanied by an initial increase in the spread of the population, followed by a decrease. These observations demonstrate that previously published models of dihedral angle change involving the instantaneous establishment of the equilibrium angle in the immediate vicinity of the pore corner are incorrect.
101 citations
TL;DR: The crystal structure of L-serine has been determined at room temperature at pressures between 0.3 and 4.8 GPa and it is shown that the same topology appears in both crystal forms, which explains why it occurs from one single-crystal form to another.
Abstract: The crystal structure of l-serine has been determined at room temperature at pressures between 0.3 and 4.8 GPa. The structure of this phase (hereafter termed l-serine-I), which consists of the molecules in their zwitterionic tautomer, is orthorhombic, space group P212121. The least compressible cell dimension (c), corresponds to chains of head-to-tail NH⋯carboxylate hydrogen bonds. The most compressible direction is along b, and the pressure-induced distortion in this direction takes the form of closing up voids in the middle of R-type hydrogen-bonded ring motifs. This occurs by a change in the geometry of hydrogen-bonded chains connecting the hydroxyl groups of the —CH2OH side chains. These hydrogen bonds are the longest conventional hydrogen bonds in the system at ambient pressure, having an O⋯O separation of 2.918 (4) A and an O⋯O⋯O angle of 148.5 (2)°; at 4.8 GPa these parameters are 2.781 (11) and 158.5 (7)°. Elsewhere in the structure one NH⋯O interaction reaches an N⋯O separation of 2.691 (13) A at 4.8 GPa. This is amongst the shortest of this type of interaction to have been observed in an amino acid crystal structure. Above 4.8 GPa the structure undergoes a single-crystal-to-single-crystal phase transition to a hitherto uncharacterized polymorph, which we designate l-serine-II. The OH⋯OH hydrogen-bonded chains of l-serine-I are replaced in l-serine-II by shorter OH⋯carboxyl interactions, which have an O⋯O separation of 2.62 (2) A. This phase transition occurs via a change from a gauche to an anti conformation of the OH group, and a change in the NCαCO torsion angle from −178.1 (2)° at 4.8 GPa to −156.3 (10)° at 5.4 GPa. Thus, the same topology appears in both crystal forms, which explains why it occurs from one single-crystal form to another. The transition to l-serine-II is also characterized by the closing-up of voids which occur in the centres of other R-type motifs elsewhere in the structure. There is a marked increase in CH⋯O hydrogen bonding in both phases relative to l-serine-I at ambient pressure.
100 citations
TL;DR: In this paper, an iterative set of cascade-correlation neural networks is used to predict both secondary structure and ψ dihedral angles, with predicted values enhancing the subsequent iteration.
Abstract: We present DESTRUCT, a new method of protein secondary structure prediction, which achieves a three-state accuracy (Q3) of 79.4% in a cross-validated trial on a nonredundant set of 513 proteins. An iterative set of cascade–correlation neural networks is used to predict both secondary structure and ψ dihedral angles, with predicted values enhancing the subsequent iteration. Predictive accuracies of 80.7% and 81.7% are achieved on the CASP4 and CASP5 targets, respectively. Our approach is significantly more accurate than other contemporary methods, due to feedback and a novel combination of structural representations. Proteins 2005. © 2005 Wiley-Liss, Inc.
95 citations
TL;DR: In this article, two Schiff base compartmental ligands derived from the condensation of 3-ethoxysalicylaldehyde with 1,2-diaminocyclohexane and orthophenylenediamine, respectively, were used to isolate two diphenoxo-bridged discrete dinuclear Cu I I Gd I I I complexes.
Abstract: Two Schiff base compartmental ligands, H 2 L 1 and H 2 L 2 , derived from the condensation of 3-ethoxysalicylaldehyde with 1,2-diaminocyclohexane and orthophenylenediamine, respectively, have been utilized to isolate two diphenoxo-bridged discrete dinuclear Cu I I Gd I I I complexes, [Cu I I (H 2 O)-L 1 Gd I I I (NO 3 ) 3 ] (3) and [Cu I I L 2 Gd I I I (NO 3 ) 3 ] (4). This is the first report on the 3d-4f compounds derived from compartmental Schiff base ligands with cyclic diamines. The compounds 3 and 4 crystallize in the triclinic Pi and orthorhombic Pna2(1) space groups, respectively, with the following unit cell parameters - 3: a = 8.8713(2) A, b = 12.8399(3) A, c = 14.0067(3) A, a = 80.6649(5)°, β = 77.4059(5)°, γ = 76.8879(5)°, and Z = 2; 4: a = 9.2210(1) A, b = 16.5407(2) A, c = 19.9248(4) A, and Z = 4. Structural analysis reveals that both are discrete dinuclear complexes. In 3, one water molecule is coordinated to the copper(II) ion to result in a square-pyramidal coordination geometry, while the geometry of the coppe(II) center in 4 is square planar. In both complexes, the gadolinium(III) center has an O 1 0 coordination environment. In contrast to expectation, although the N 2 O 2 cavity affords a better planar environment for the copper(II) center in 4, the bridging moiety in complex 3 is more planar than that in 4 or in most of the previously reported examples (the dihedral angle between two CuO 2 Gd planes: 2.1° for 3 and 7.1° for 4). Variable-temperature and variable-field magnetic measurements reveal that the metal centers in both the complexes are ferromagnetically coupled (J values: 6.3 cm - 1 for 3 and 5.4 cm - 1 for 4; H = -2JS C u .S G d ). Interestingly, complex 3 exhibits strongest ferromagnetic interaction among the related compounds.
93 citations
TL;DR: In this article, the parameters which affect the strength and sign of the magnetic superexchange interaction via non-bonding contacts between bromide ions are described and a system for describing the topology of the interaction between tetrahedra is proposed.
87 citations
TL;DR: In this article, a series of bithiophenes based on bis(3,4-alkylenedisulfanylthiophene) and hybrid systems associating 3, 4-ethylenedis-ulfanylthsiophene (EDST) with thiophene or EDOT moieties have been synthesized and characterized by X-ray diffraction and theoretical geometric optimization.
Abstract: A series of bithiophenes based on bis(3,4-alkylenedisulfanylthiophene) and hybrid systems associating 3,4-ethylenedisulfanylthiophene (EDST) with thiophene or 3,4-ethylenedioxythiophene (EDOT) moieties have been synthesized. The molecular structures of these systems are characterized by X-ray diffraction and theoretical geometric optimization. Although bis(alkylenesulfanylthiophenes) present a large dihedral angle between the thiophene cycles, for the hybrid systems the steric hindrance to coplanarity is counterbalanced by the development of intramolecular S···S and S···O interactions. Dramatic structural change from twisted to planar conformation of bis(3,4-ethylenedisulfanylthiophene) is observed when the dimer is associated with TCNQ. The electronic properties of the dimers, analyzed by UV−vis spectroscopy, cyclic voltammetry, and theoretical calculations, are discussed in relation with the molecular structure of the bithiophenes. Finally, the analysis of the electrogenerated polymers confirm the key r...
83 citations
TL;DR: The experimental data are found to be in excellent accord with an oriented dipole model, rather than with the averaged dipoles model conventionally assumed for FRET.
Abstract: The efficiency of fluorescence resonance energy transfer (FRET) between two chromophores positioned at opposite ends of DNA base pair domains has been investigated. The base pair domain serves as a helical scaffold which defines both the distance between chromophores and the dihedral angle between their electronic transition dipole moments, each incremental base pair increasing the distance and stepping the dihedral angle. Fluorescence quantum yields and lifetimes have been determined for both the donor and acceptor chromophores. The experimental data are found to be in excellent accord with an oriented dipole model, rather than with the averaged dipole model conventionally assumed for FRET.
TL;DR: The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved, and reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.
Abstract: We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A “projection” approach (Katritch et al. J Comput Chem 2003, 24, 254–265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone ϕ/ψ and side chain χ1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1565–1578, 2005
TL;DR: This work presents the first normal mode calculation with full dihedral flexibility of several virus capsids, including poliovirus, rhinovirus, and cowpea chlorotic mottle virus, made possible by applying group theoretical methods.
TL;DR: In this paper, the effects of varying sulphur and oxygen contents on the dihedral angle between liquid iron-alloy and crystalline silicates up to 20 GPa were examined.
TL;DR: Systematic discrepancies between MMFF94 and MP2 results were improved by modification of several torsional parameters, and fully optimized geometries are in good agreement with crystal structure data, and PESs are consistent with the experimental dihedral angle distribution.
Abstract: Potential energy surfaces (PES) for rotation about the N-C(sp(3)) or N-C(aryl) bond and energies of stationary points on PES for rotation about the C(sp(2))-N bond are reported for methylurea, ethylurea, isopropylurea, tert-butylurea, and phenylurea, using the B3LYP/DZVP2 and MP2/aug-cc-pVDZ methods The analysis of alkylureas reveals cis and (less stable) trans isomers that adopt anti geometries, whereas syn geometries do not correspond to stationary points In contrast, the analysis of phenylurea reveals that the lowest energy form at the MP2 level is a trans isomer in a syn geometry The fully optimized geometries are in good agreement with crystal structure data, and PESs are consistent with the experimental dihedral angle distribution Rotation about the C(sp(2))-N bond in alkylureas and phenylurea is slightly more hindered (86-94 kcal/mol) than the analogous motion in the unsubstituted molecule (82 kcal/mol) At the MP2 level of theory, the maximum barriers to rotation for the methyl, ethyl, isopropyl, tert-butyl, and phenyl groups are predicted to be 09, 62, 60, 46, and 24 kcal/mol, respectively The results are used to benchmark the performance of the MMFF94 force field Systematic discrepancies between MMFF94 and MP2 results were improved by modification of several torsional parameters
TL;DR: The OPLS-AA force field (DMEFF) as discussed by the authors is a force field that reproduces the conformational behavior of DME in the liquid phase extremely well.
Abstract: The relative conformational energies in the 1,2-dimethoxyethane (DME) molecule have been extensively studied using B3LYP and MP2 ab initio methods, employing a range of commonly used basis sets. These conformational energies have been used to fit new O–C–C–O and C–O–C–C torsional interaction parameters for the OPLS-AA force field. The resulting force field (DMEFF) shows some improvement in conformational populations, calculated from molecular dynamics simulation of bulk DME, compared to two other commonly used force fields. Extensive reverse-engineering of the OPLS-AA energy function has also allowed the development of additional sets of torsion parameters for these two dihedral types, resulting in a force field that reproduces the conformational behaviour of DME in the liquid phase extremely well.
TL;DR: In this paper, the effects of volume fraction on liquid phase sintering of W-Cu are evaluated and a refined expression for the dependence of contiguity on volume fraction that includes the effect of the dihedral angle is developed.
Abstract: Tungsten and copper exhibit negligible solubility for each other, so densification during liquid phase sintering of W-Cu is limited to rearrangement of the W particles and solid-state sintering of the W skeleton. Experiments are conducted to evaluate the effects of Cu volume fraction on liquid phase sintering of W-Cu. Sintered microstructures are quantitatively analyzed and are used to define critical microstructural parameters that prevent distortion and rearrangement densification. Slumping is prevented first by capillary forces, then by formation of a rigid W skeleton at critical values of contiguity and connectivity, which depend on the dihedral angle. A refined expression for the dependence of contiguity on volume fraction that includes the effect of the dihedral angle is developed. An analysis of gravitational, capillary, and bonding forces acting on W particles in liquid Cu explains the ability to achieve high sintered densities through rearrangement despite a lack of distortion with up to 80 vol pct liquid. Capillary forces are sufficient to break weak solid-solid bonds that form during heating, enabling rearrangement to occur even without dissolution of these bonds. At higher solid volume fractions, sufficient particle contacts form to prevent rearrangement by these capillary forces, thus limiting sintered densities.
TL;DR: Two-dimensional J-resolved 1H NMR spectroscopy was used to measure the vicinal spin-spin coupling constants 3JH alpha H beta for numerous, previously individually assigned amino acid residues in the basic pancreatic trypsin inhibitor at various temperatures between 30 and 85 degrees JC.
Abstract: Two-dimensional J-resolved 1H NMR spectroscopy was used to measure the vicinal spin-spin coupling constants 3JHαHβ for numerous, previously individually assigned amino acid residues in the basic pancreatic trypsin inhibitor at various temperatures between 30 and 85° C. An analysis of this data is proposed which enables one to compare the spatial arrangements of individual amino acid side chains in solution and in single crystals of the protein, and which also provides information on the mobility of the side chains in the solution conformation. As a rule, the amino acid side chains in the interior of the protein were found to be locked into unique spatial orientations, with the mobility restricted to rapid rotational fluctuations about this unique value for the dihedral angle Z1. In most, but not all, instances the data for the interior amino acids indicate identical average conformations for the amino acid side chains in single crystals and in solution. For residues on the protein surface structural rearrangements between crystal and solution appear to be common, and the mobility in the solution conformation may include rapid averaging between two or several distinct, preferentially populated values of χ1, analogous to the gauche-trans-gauche isomerization in isolated amino acids.
TL;DR: In this paper, a new OPLSS-AA-SEI force field was obtained by optimizing the Lennard-Jones parameters and charges taking part in 1-4 interactions.
Abstract: Molecular dynamics simulations were used to study pure liquid ethylene glycol (EG) and EG-water binary mixtures as a function of the molar fraction. Calculations were performed in the isothermal and isobaric (NpT) ensemble. New improvement in the OPLSS-AA-SEI force field was obtained optimizing the Lennard-Jones parameters and charges taking part in 1–4 interactions. With the new force field density and heat of vaporization of pure liquid ethylene glycol were obtained in good agreement with experimental data. The value of the O-C-C-O dihedral was also monitored in the course of force field optimization process. The new optimized force field was named OPLSA-AA-SE-M. Concerning the pure liquid simulation, features observed on the radial distribution functions (RDF) show characteristics of intermolecular and intramolecular hydrogen bonding. The RDF integrations show that each EG molecule in the pure liquid has an average coordination number of five molecules in its first coordination shell. Therefore, the average oxygen-hydrogen contact number due to hydrogen bonding is seven: two of them arising from intramolecular and five from interactions with neighboring molecules. Dihedral angle distributions were calculated, showing the predominance of EG molecules with the O-C-C-O dihedral corresponding to gauche conformations. In the study of water-ethylene glycol binary mixtures, the average structural parameters observed for EG molecules are very similar to the ones found in the pure liquid simulation. RDF analyses also present characteristic features of hydrogen bonding. Particularly, no significant changes were observed on the dihedral angle distributions. The structures of EG-EG and EG-water dimers calculated with OPLS-AA-SEI-M force field and DFT at B3LYP 6-311 g (3df,3pd) level are in very good agreement.
TL;DR: The specific rotations derived from the study of 2-chlorobutane are similar to those previously obtained for 3-chloro-1-butene, indicating that the double bond does not have a large effect on the optical rotations, but it did lead to a large difference between calculated and observed specific rotation.
Abstract: The specific rotations of 2-substituted butanes (X = F, Cl, CN, and HCC) were calculated at the B3LYP/ aug-cc-pVDZ level as a function of the C-C-C-C torsion angle. The results for the four compounds are remarkably similar, despite large differences in the electronic transition energies. The temperature dependence of the specific rotations for 2-methylbutyronitrile and for 2-chlorobutane was studied to give experimental information about the effect of the torsion angle on the specific rotation. The results were in good accord with B3LYP/aug-cc-pVDZ calculations. The specific rotations derived from the study of 2-chlorobutane are similar to those previously obtained for 3-chloro-1-butene, indicating that the double bond does not have a large effect on the optical rotations, but it did lead to a large difference between calculated and observed specific rotations.
TL;DR: The conductance of a single 4,4 bipyridine (44BPD) molecule connected to two gold electrodes is calculated using a density functional theory based Green function method and the magnitude of the transmission coefficient at the Fermi level is determined to be T = 1.01 × 10(-2), which is in excellent agreement with the experimental value.
Abstract: The conductance of a single 4,4 bipyridine (44BPD) molecule connected to two gold electrodes is calculated using a density functional theory based Green function method. The atomic geometry of such a molecular junction is constructed from the optimized structure of a gold trimer–44BPD–gold trimer complex. Resonant conduction is the main feature of its transport properties. The magnitude of the transmission coefficient at the Fermi level is determined to be T = 1.01 × 10−2, which is in excellent agreement with the experimental value. The dependence of the transmission on the Au–N bond length and the torsion angle is also discussed.
TL;DR: In this article, the authors extended the normal mode method with the aid of harmonic penalty functions to allow for multiple restraints of geometry parameters, such as bond lengths, bond and dihedral angles, and for simultaneous optimization of more molecules.
Abstract: Optimization in the normal mode coordinates has been established as a useful tool for modeling of vibrational spectra ( J. Chem. Phys . 2002 , 117 , 4126). In this work the algorithm is extended with the aid of harmonic penalty functions to allow for multiple restraints of geometry parameters, such as bond lengths, bond and dihedral angles, and for simultaneous optimization of more molecules. Additionally, geometry optimization when atomic nuclei are maintained on the constant electrostatic potential surface was implemented and its applications for solvent models are discussed. Model systems include small molecules, water cluster, antiparallel β-sheet peptide containing intermolecular hydrogen bonds, periodic α-helix and a parallel β-sheet segments. The normal mode method provided better numerical stability than the conventional redundant internal coordinates, especially for weakly hydrogen-bonded systems, while the speed of the optimization was found similar as for the Cartesian coordinates.
TL;DR: The magnitude of electronic coupling between the terminal chromophores shows a precise dependence on the dihedral angle around a bridging biphenyl group.
Abstract: The magnitude of electronic coupling between the terminal chromophores shows a precise dependence on the dihedral angle around a bridging biphenyl group.
TL;DR: Ramachandran surfaces for the alanine di- and tripeptides in gas phase and solution are mapped out using the recently introduced adiabatic free-energy dynamics (AFED) approach and it is shown that complete surfaces can be mapped out with an order of magnitude of greater efficiency with the AFED approach than they can using the popular umbrella sampling method.
Abstract: Ramachandran surfaces for the alanine di- and tripeptides in gas phase and solution are mapped out using the recently introduced adiabatic free-energy dynamics (AFED) approach introduced by Rosso et al. (J. Chem. Phys. 2002, 116, 4389) as applied to the CHARMM22 force field. It is shown that complete surfaces can be mapped out with an order of magnitude of greater efficiency with the AFED approach than they can using the popular umbrella sampling method. In the alanine dipeptide, it is found, in agreement with numerous other studies using the CHARMM22 force field, that the lowest free-energy structure is the extended beta conformation, (phi, psi) = (-81, 81), while in solution, the extended beta, (phi, psi) = (-81, 153) and right-handed alpha-helical, (phi, psi) = (-81, 63) conformations are nearly isoenergetic. In solution, a secondary minimum at (phi, psi) = (63, -81), corresponding to a C(7)ax conformation, occurs approximately 2.3 kcal/mol above the global free-energy minimum. The alanine tripeptide, a system that has received considerably less attention in the literature, is found to exhibit a similar structure to the alanine dipeptide with the extended beta conformation being the free-energy minimum in the gas phase and the beta and right-handed alpha-helical conformations being isoenergetic in solution. These studies indicate that the AFED method can be a powerful tool for studying multidimensional free-energy surfaces in complex systems.
TL;DR: In this article, the authors identify the stereochemical conditions that favor significant deformations of peptide bond planarity and demonstrate that the values of the ω dihedral angle are strictly correlated with the value of the adjacent ψ angle.
TL;DR: In this article, it was shown that the grain-boundary energy and surface energy function are entirely adequate to determine if a groove-root is faceted or rough, thereby obviating the need for any ad hoc specification of the dihedral angle as a boundary condition.
TL;DR: Ab initio calculations using restricted Hartree-Fock, second-order Møller-Plesset perturbation theory (MP2), density-functional theory (DFT), and coupled-cluster methods have been done to obtain the torsional potential-energy profile of the aza-aromatic molecule 4,4'-bipyridine.
Abstract: Ab initio calculations using restricted Hartree-Fock, second-order Moller-Plesset perturbation theory (MP2), density-functional theory (DFT), and coupled-cluster methods have been done to obtain the torsional potential-energy profile of the aza-aromatic molecule 4,4'-bipyridine. The torsional potential is evaluated adiabatically by fixing the normalized sum of the dihedral angles through the C-C inter-ring bond at several values along the torsional path and relaxing the remaining degrees of freedom. Previous discrepancies between MP2 and DFT internal rotation barrier heights are removed, and seen to be mostly due to the underestimation of the dispersion energy in the coplanar conformer by MP2 when using relatively small basis sets. The calculations indicate that the barrier height between the twisted global minimum and the 0 degrees conformer is around 1.5-1.8 kcal mol-1 while that corresponding to the 90 degrees one is about 2.0-2.2 kcal mol-1. This same relative energy ordering of the coplanar and perpendicular conformers was experimentally derived from nuclear magnetic resonance (NMR) measurements of 1H dipolar couplings on 4,4'-bipyridine solutions in a nematic liquid crystal, although the barrier heights are much lower than those estimated from NMR experiments in the gas phase. The DFT infrared spectrum and zero-point vibrational energy corrections to the torsional energy profile have also been calculated, the latter having a small influence on the torsional potential-energy profiles.
TL;DR: A series of unconventional twisted pi-electron system molecules has been synthesized via Suzuki cross-coupling of two sterically hindered arenes with large ring-ring dihedral twist angle and a highly charge-separated zwitterionic ground state.
TL;DR: The structure of single crystal of FC (O)SSC(O)CF3 was determinate by X-ray diffraction analysis at low temperature using a miniature zone melting procedure, and the geometrical parameters agree with those obtained for the molecule in the gas phase.
Abstract: Fluoroformyl trifluoroacetyl disulfide, FC(O)SSC(O)CF3, is prepared by quantitative reaction between FC(O)SCl and CF3C(O)SH. The conformational properties and geometric structure of the gaseous molecule have been studied by vibrational spectroscopy (IR(gas), Raman(liquid), IR(matrix)), gas electron diffraction (GED), and quantum chemical calculations (B3LYP and MP2 methods). The disulfide bond length derived from the GED analysis amounts 2.023(3) A, and the dihedral angle around this bond, φ(CS−SC), is 77.7(21)°, being the smallest dihedral angle measured for noncyclic disulfides in the gas phase. The compound exhibits a conformational equilibrium at room temperature having the most stable form C1 symmetry with a synperiplanar (sp-sp) orientation of both carbonyl groups with respect to the disulfide bond. A second form was observed in IR spectra of the Ar matrix isolated compound at cryogenic temperatures, corresponding to a conformer that possess the carbonyl bond of the FC(O) moiety in antiperiplanar po...