Showing papers on "Dihedral angle published in 2009"

Statistical and energetic analysis of side-chain conformations in oligopeptides.

Abstract: The distributions of side-chain conformations in 258 crystal structures of oligopeptides have been analyzed. The sample contains 321 residues having side chains that extend beyond the C beta atom. Statistically observed preferences of side-chain dihedral angles are summarized and correlated with stereochemical and energetic constraints. The distributions are compared with observed distributions in proteins of known X-ray structures and with computed minimum-energy conformations of amino acid derivatives. The distributions are similar in all three sets of data, and they appear to be governed primarily by intraresidue interactions. In side chains with no beta-branching, the most important interactions that determine chi 1 are those between the C gamma H2 group and atoms of the neighboring peptide groups. As a result, the g- conformation (chi 1 congruent to -60 degrees) occurs most frequently for rotation around the C alpha-C beta bond in oligopeptides, followed by the t conformation (chi 1 congruent to 180 degrees), while the g+ conformation (chi 1 congruent to 60 degrees) is least favored. In residues with beta-branching, steric repulsions between the C gamma H2 or C gamma H3 groups and backbone atoms govern the distribution of chi 1. The extended (t) conformation is highly favored for rotation around the C beta-C gamma and C gamma-C delta bonds in unbranched side chains, because the t conformer has a lower energy than the g+ and g- conformers in hydrocarbon chains. This study of the observed side-chain conformations has led to a refinement of one of the energy parameters used in empirical conformational energy computations.

Insight into Mg(BH4)2 with synchrotron X-ray diffraction: Structure revision, crystal chemistry, and anomalous thermal expansion

Abstract: Pure Mg(BH4)2 has been characterized by single-crystal and powder synchrotron X-ray diffraction and by vibrational spectroscopies. The earlier reported P61 structure of the α-phase is revised in the space group P6122. Location of the H-atoms from powder data in the published P61 models posed the main problem for the identification of the correct symmetry: wrongly determined orientations of some BH4 groups hampered a successful detection of the true P6122 symmetry. Four nearly ideally tetrahedral BH 4 groups form a dodecahedral MgH8 coordination around each Mg atom, which can be described as a slightly distorted snub disphenoid, where two nearly planar BH2-Mg-H2B fragments are situated at ~90° dihedral angle. The H ⋯ H distances between two BH4 groups within the BH2-Mg-H2B fragments are among the shortest (2.18-2.28 A) in the structurally characterized metal borohydrides. α-Mg(BH4)2 contains an unoccupied void, accounting for 6.4% of space in the structure. It is large enough (37 A3) to accommodate a small molecule, such as H2O. The high-temperature β-phase is less dense by ~3% but contains no unoccupied voids. The α-phase transforms into the β-phase above 490 K; the latter is quenched (metastable) on cooling. The anomalous cell expansion of the β-phase down to 100 K may be related to the evolution of the free energy profile far from the phase transition temperature. © 2009 American Chemical Society.

CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates, and Inositol

Abstract: Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates, and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute−water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde, and glycerol. C−C−C−C, C−C−C−O, C−C−O−H, and O−C−C−O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential-energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed co...

Chemically controlled conductivity: torsion-angle dependence in a single-molecule biphenyldithiol junction.

Abstract: Stepwise regulation of the molecular conductance was observed in a series of eight biphenyldithiols with fixed torsion angles between the phenyl rings. These compounds were synthesized and their single-molecule conductance was investigated in an STM junction. A cos2 dependence was found between the interplane torsion angle and the single-molecule conductivity (see plot).

Studies on the conformation of amino acids. VI. Conformation of the proline ring as observed in crystal structures of amino acids and peptides.

Abstract: The paper deals with an analysis of the available crystal structure data related to proline compounds so as to obtain information about bond lengths, bond angles, and the conformation of the pyrrolidine ring. The interesting results are: 1. The atoms Cβ, Cα, N, and Cs are nearly coplanar, with the torsion angle 0 about the Cα - N bond varying from about -15° to -15°. The Cγ atom is displaced from this plane, either up or down, so that the ring exists in one of the two puckered conformations, designated A and B. Conformation A is characterized by negative and may be termed Cγ-exo when referred to the displacement of the carbonyl carbon C. Conformation B has positive x l and is Cγ-endo; Cγ-exo is slightly preferred over C-endo, although both conformations occur simultaneously in some crystal structures with partial probabilities. In the other structures, the non-occurring position for C y is found to be disallowed by intermolecular contacts. The proline conformations observed correspond to the 'envelope' type of conformation of the cyclopentane ring. In peptides, the three bonds at N are nearly coplanar, and the torsion about N- Cα bond is nearly - 60°. 2. The observed ranges of (x 1 , x 2 , x 3 , x 4 ) are (0 to –30°, 15 to 50°, –15 to - -30°, 5 to 25°) for conformation A and (20 to 35 0 , -30 to - 40 0 , 20 to 35°, 5 to -20°) for conformation B; for θ and φ the ranges are -15° to -15°, -45 to -75°. The bond lengths and bond angles are not influenced by the conformation of the ring, unlike ribose.

Experimental and density functional studies on 4-(4-cyanobenzylideneamino)antipyrine

Abstract: 4-(4-cyanobenzylideneamino)antipyrine (CBAP) has been synthesized and characterized by elemental analysis, FT-IR, UV-VIS and X-ray single crystal diffraction techniques. Crystallographic study reveals that the compound adopts trans configuration about the Schiff base imine double bond. The substituted p-cyanophenyl ring indirectly linked to the pyrazoline ring by the C=N double bond is almost coplanar with the pyrazole ring, whereas the phenyl ring directly attached to the pyrazoline ring forms an effective dihedral angle. Density functional calculations have been carried out to optimize and to characterize the title compound by using B3LYP method at 6-31G(d) basis set. The calculated results show that the optimized geometry can well reproduce the crystal structural parameters and the theoretical vibrational frequencies show good agreement with experimental values. On the basis of theoretical vibrational analyses, the thermodynamic properties (standard heat capacities, standard entropies, and standard ent...

Preferred conformation of the benzyloxycarbonyl-amino group in peptides.

Abstract: Structural parameters, derived from X-ray crystallographic data, have been compiled for 35 derivatives of amino acids, peptides, and related compounds, which contain the N-terminal benzyloxycarbonyl (Z) group. The geometry of the urethane moiety of this end group is closely similar to that of the tert-butoxycarbonyl (Boc) group, except for a relaxation of some bond angles because the Z group is sterically less crowded than the Boc group. For the same reason, the Z group has greater conformational flexibility. As a result, packing forces in the crystal may cause greater deformations of bond angles, resulting in larger variations of observed bond lengths and bond angles than in Boc-peptide crystals. The aromatic rings of the Z end groups tend to stack in crystals. Conformational energy calculations indicate that most conformations of Z-amino acid-N'-methylamides and of corresponding Boc derivatives have similar dihedral angles and relative energies, i.e. the nature of the N-terminal end group has little effect on the conformational preferences of the residue next to it. In particular, the computed fraction of molecules with a cis urethane (C-N) bond is similar for the two derivatives: 0.51 and 0.42 in Boc-Pro-NHCH3 and Z-Pro-NHCH3, respectively, and 0.02 in the two Ala derivatives. There exist several computed conformations of Z-Ala-NHCH3 and Z-Pro-NHCH3 in which the phenyl ring and the C-terminal methylamide group are close to each other. Because of favorable nonbonded interactions, such conformations are of low energy.

The normal modes of a protein: Native bovine pancreatic trypsin inhibitor

Abstract: A completely general treatment of normal mode analysis is developed that can be used with any potential energy function and any set of generalized coordinates. The method is applied to the calculation of the normal modes of the small protein bovine pancreatic trypsin inhibitor that has been the subject of many previous theoretical studies. The potential energy function used comprises a torsion angle potential, a van der Waals potential between nonbonded pairs of atoms, and a hydrogen bond potential. Therefore, the generalized coordinates used are the 208 Φ, ϕ, and χ torsion angles about single bonds. This eliminates the difficulties inherent in using internal or Cartesian coordinates for a large molecule. Many dynamic properties of the protein may now be calculated in the normal mode description. In particular, the rms magnitudes and pair correlations of the fluctuations in positions and velocities of the α-carbon atoms and various classes of torsion angles, such as backbone, side chain, β-sheet, and α-helix, are calculated and analyzed to identify the most correlated modes. In addition, the ir intensities are calculated.

Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics.

Abstract: Improving the accuracy of molecular mechanics force field parameters for atomistic simulations of proteins and nucleic acids has been an ongoing effort. The availability of computer power and improved methodologies for conformational sampling has allowed the assessment of these parameters by comparing the free energies calculated from molecular dynamic (MD) simulations and those measured from thermodynamic experiments. Here, we focus on testing and optimizing the AMBER force field parameters for the omega dihedral, which represents rotation around the peptide bond of proteins. Due to the very slow isomerization rate of the peptide bond, it is not possible to sample the phase space with standard MD simulations. We therefore employed an accelerated MD method in explicit water in which the original Hamiltonian is modified to speed up conformational sampling and the correct canonical distribution is recaptured. Using well-studied model systems for the peptide and peptidyl prolyl bonds, we discovered that the AMBER omega dihedral parameters underestimated experimentally measured activation free energy barriers for cis/trans conversion as well as failed to reproduce the free energy difference between the two isomers. We reoptimized the original AMBER omega dihedral parameters and further validated their transferability on several experimentally studied dipeptides. The revised set of parameters successfully reproduced the cis/trans equilibria and free energy barriers within experimental and simulation errors. We also investigated the structures of the transition state and cis/trans isomers of prolyl peptide bonds in terms of pyramidality, a measure of the puckering of the prolyl ring. We observed, as expected from quantum mechanical studies, significant bidirectional, out-of-plane motions of prolyl nitrogen in the transition state.

Massively parallel computation of absolute binding free energy with well-equilibrated states.

Abstract: A force field formulator for organic molecules (FF-FOM) was developed to assign bond, angle, and dihedral parameters to arbitrary organic molecules in a unified manner including proteins and nucleic acids. With the unified force field parametrization we performed massively parallel computations of absolute binding free energies for pharmaceutical target proteins and ligands. Compared with the previous calculation with the ff99 force field in the Amber simulation package (Amber99) and the ligand charges produced by the Austin Model 1 bond charge correction (AM1-BCC), the unified parametrization gave better absolute binding energies for the FK506 binding protein (FKBP) and ligand system. Our method is based on extensive work measurement between thermodynamic states to calculate the free energy difference and it is also the same as the traditional free energy perturbation. There are important requirements for accurate calculations. The first is a well-equilibrated bound structure including the conformational change of the protein induced by the binding of the ligand. The second requirement is the convergence of the work distribution with a sufficient number of trajectories and dense spacing of the coupling constant between the ligand and the rest of the system. Finally, the most important requirement is the force field parametrization.

Conformation of the glycotripeptide repeating unit of antifreeze glycoprotein of polar fish as determined from the fully assigned proton n.m.r. spectrum.

Abstract: With its simple glycotripeptide repeating structure the antifreeze glycoprotein of polar fish may be an especially simple conformational mode for mucin glycoproteins with similar but more complex structures. The fully assigned proton n.m.r. spectrum confirms the anomeric configurations of the hexapyranosidic sugars of the side chains and the coupling constants of the alpha GalNAc and the beta Gal residues show both to be in the expected 4C1 chair conformation. The assignment of a single resonance for each proton of the (Ala-Thr-Ala)n repeat unit coupled with the observation of long range nuclear Overhauser effects (n.O.e.) implies a three-fold repeating conformation. The resonances of the two alanines are distinct and can be assigned to their correct positions in the peptide sequence by n.O.e. observed at the amide proton resonances on saturation of the alpha proton signals. The amide proton coupling constants of all three peptide residues are similar and imply a limited range of peptide backbone torsion angles, phi CN. The large n.O.e. which has been observed between the amide proton and the alpha proton of the residue preceding it in the sequence implies large positive values for the peptide dihedral angle, psi CC. Limits are placed on possible values of side chain dihedral angles by the observation of the coupling constant between the alpha and beta protons of the threonyl residue. The observation of n.O.e. between the anomeric proton of GalNAc and the threonyl side chain protons gives information on the conformation of the alpha glycosidic linkage between the disaccharide and the peptide. n.O.e. observed between the protons of the beta glycosidic linkage indicates the conformation of the disaccharide and the large amide proton coupling constant of the GalNAc residue shows a trans proton relationship. The spectroscopically derived data have been combined with conformational energy calculations to give a conformational model for antifreeze glycoprotein in which the hydrophobic surfaces of the disaccharide side chains are wrapped closely against a three-fold left handed helical peptide backbone. The hydrophilic sides of the disaccharides are aligned so that they may bind to the ice crystal face, which is perpendicular to the fast growth axis inhibiting normal crystal growth.

Photophysics and dihedral freedom of the chromophore in yellow, blue, and green fluorescent protein.

Abstract: Green fluorescent protein (GFP) and GFP-like fluorescent proteins owe their photophysical properties to an autocatalytically formed intrinsic chromophore. According to quantum mechanical calculations, the excited state of chromophore model systems has significant dihedral freedom, which may lead to fluorescence quenching intersystem crossing. Molecular dynamics simulations with freely rotating chromophoric dihedrals were performed on green, yellow, and blue fluorescent proteins in order to model the dihedral freedom available to the chromophore in the excited state. Most current theories suggest that a restriction in the rotational freedom of the fluorescent protein chromophore will lead to an increase in fluorescence brightness and/or quantum yield. According to our calculations, the dihedral freedom of the systems studied (BFP > A5 > YFP > GFP) increases in the inverse order to the quantum yield. In all simulations, the chromophore undergoes a negatively correlated hula twist (also known as a bottom hula twist mechanism).

Experimental evidence for the participation of 5d Gd(III) orbitals in the magnetic interaction in Ni-Gd complexes.

Abstract: The syntheses, structural determinations, and magnetic studies of two trinuclear Ni-Gd-Ni complexes are described. The structural studies demonstrate that the two complexes present a linear arrangement of the Ni and Gd ions, with Ni ions in slightly distorted square-pyramidal or octahedral environments in complexes 1 and 2, respectively. The Ni and Gd ions are linked by two or three phenoxo bridges, so that complexes 1 and 2 present edge-sharing or face-sharing bridging cores. Ferromagnetic interactions operate in these complexes. While a unique J parameter is able to fit the magnetic data of complex 2, two very different J constants are needed for 1. This result is at first sight surprising, for the structural data of the two Ni-O(2)-Gd cores in complex 1 are quite similar (similar Ni-O and Gd-O bond lengths, similar angles, and dihedral angles), the only difference coming from the angle between the planes defined by the Gd ion and the two bridging phenoxo oxygen atoms of each Ni-O(2)-Gd half core. This latter magnetic behavior can be considered as a signature for the participation of 5d Gd(III) orbitals in the exchange interaction mechanism and can explain why edge-sharing complexes have larger J parameters than face-sharing complexes.

Structure and dynamics of copper‐free SOD: The protein before binding copper

Abstract: The solution structure of the copper-free state of a monomeric form of superoxide dismutase (153 amino acids) was determined through (13)C and (15)N labeling. The protein contained two mutations at the native subunit-subunit interface (F50E and G51E) to obtain a soluble monomeric species and a mutation in the active site channel (E133Q). About 93% of carbon atoms, 95% of nitrogen atoms, and 96% of the protons were assigned. A total of 2467 meaningful NOEs and 170 dihedral angles provided a family of 35 conformers with RMSD values of 0.76 +/- 0.09 A for the backbone and 1.22 +/- 0.13 A for all heavy atoms. The secondary structure elements, connected by loops, produce the typical superoxide dismutase Greek key fold, formed by an eight-stranded beta-barrel. The comparison with the copper-bound monomeric and dimeric structures shows that the metal ligands have a conformation very close to that of the copper-bound forms. This feature indicates that the copper-binding site is preorganized and well ordered also in the absence of the copper ion. The active-site channel shows a sizable increase in width, achieving a suitable conformation to receive the copper ion. The histidines ring NH resonances that bind the copper ion and the region around the active-site channel experience, as found from (15)N relaxation studies, conformational exchange processes. The increased width of the channel and the higher mobility of the histidine rings of the copper site in the copper-free form with respect to the holoprotein is discussed in terms of the process of copper insertion.

Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases.

Abstract: We have developed and tested molecular mechanics parameters for [FeS] clusters found in known [FeFe] hydrogenases. Bond stretching, angle bending, dihedral and improper torsion parameters for models of the oxidized and reduced catalytic H-cluster, [4Fe4S](+,2+)Cys4, [4Fe4S](+,2+)Cys3His, and [2Fe2S](+,2+)Cys4, were calculated solely from Kohn-Sham density functional theory and Natural Population Analysis. Circumsphere analysis of the cubane clusters in the energy-minimized structure of the full Clostridium pasteurianum hydrogenase I showed the resulting metallocluster structures to be similar to known cubane structures. All clusters were additionally stable in molecular dynamics simulations over the course of 1.0 ns in the fully oxidized and fully reduced enzyme models. Normal modes calculated by quasiharmonic analysis from the dynamics data show unexpected couplings among internal coordinate motions, which may reflect the effects of the protein structure on metallocluster dynamics.

Short-range coherence of internal protein dynamics revealed by high-precision in silico study.

Abstract: Correlated internal dynamics of proteins, which is believed to be important for their function, is analyzed at unprecedented precision using explicit-solvent submicrosecond molecular dynamics simulations of ubiquitin and calbindin D9k Without exception, all of the mobile dihedral angle pairs in ubiquitin with sizable dynamics correlations (R2 ≥ 01) are at short-range distance In rare cases, they involve sequentially remote dihedral angles that form sparse clusters, suggesting a structural-dynamic propagation mechanism via soft torsional couplings that act over short distances with a rapid loss of coherence over longer distances

Prediction of backbone dihedral angles and protein secondary structure using support vector machines

Abstract: The prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional structure. We predict independently both the secondary structure and the backbone dihedral angles and combine the results in a loop to enhance each prediction reciprocally. Support vector machines, a state-of-the-art supervised classification technique, achieve secondary structure predictive accuracy of 80% on a non-redundant set of 513 proteins, significantly higher than other methods on the same dataset. The dihedral angle space is divided into a number of regions using two unsupervised clustering techniques in order to predict the region in which a new residue belongs. The performance of our method is comparable to, and in some cases more accurate than, other multi-class dihedral prediction methods. We have created an accurate predictor of backbone dihedral angles and secondary structure. Our method, called DISSPred, is available online at http://comp.chem.nottingham.ac.uk/disspred/ .

Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis.

Abstract: To systematically construct a low-dimensional free-energy landscape of RNA systems from a classical molecular dynamics simulation, various versions of the principal component analysis (PCA) are com...

High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters

Abstract: We present new molecular mechanical dihedral parameters for the Ramachandran angles ϕ and ψ of a protein backbone based on high-level ab initio molecular orbital calculations for hydrogen-blocked or methyl-blocked glycine and alanine dipeptides. Fully relaxed 15° (ϕ, ψ) contour maps were calculated at the MP2/6-31G(d) level of theory. Finding out the lowest energy path for ϕ (or ψ) to change from -180° to 180° in the contour map, we performed a DF-LCCSD(T0)/Aug-cc-pVTZ//DF-LMP2/Aug-cc-pVTZ level calculation to get the torsional energy profiles of ϕ (or ψ). Molecular mechanical torsion profiles with AMBER force field variants significantly differed from the ab initio profiles, so we derived new molecular mechanical dihedral parameters of a protein backbone to fit the ab initio profiles.

In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides.

Abstract: Configurational entropies from temperature-dependent free energy calculations of proteins and peptides are compared with entropies determined as the sum of the Shannon entropies of a kernel density estimate of the dihedral angle probability distributions. We find that the entropy changes can be separated into independent contributions from hard and soft degrees of freedom. Furthermore, because the effects of motional correlations between dihedral angles on entropy differences are small, the functional role of configurational entropy changes can be interpreted in a spatially resolved manner.

Molecular dynamics simulation on glass transition temperature of isomeric polyimide

Abstract: It is an abnormal phenomenon that glass transition temperature (Tg) of isomeric polyimide (PI) is higher than its corresponding symmetrical PI. To illustrate this phenomenon at the molecular scale, we applied molecular dynamics method to predict the Tg of PI, which were prepared based on 4,4'-oxydianiline (ODA) and 3,3',4,4'-biphenyltetracar- boxylic dianhydride (3,3',4,4'-BPDA), and its isomeric system (2,2',3,3'-BPDA-ODA). Simulation result is consistent with experimental value. Non-bond energy plays an important role in glass transition process, for it has an abrupt change near Tg. The higher free volume fraction of isomeric PI can provide the polymer with more space to obtain segmental motion. However, from the torsion angle distribution calculations, it is shown that the torsion angle of its biphenyl group is constrained. Furthermore, from mean square displacement and vector autocorrelation functions calculations, this group is observed to rotate against other groups in the glassy state, and increases the chain rigidity to a great extent. So the isomeric PI needs much more relaxation time for the segment motion. Therefore, the higher Tg of isomeric PI is mainly attributed to the chain rigidity for the time scale, not the free volume for the space scale.

Identification of secondary structures in globular proteins--a new algorithm.

Abstract: A new algorithm has been developed for identifying helices, extended structures, and bends from the positions of the alpha-carbon atoms using the virtual bond approach. The parameters used are two virtual bond angles (delta 1 and delta 2), the virtual dihedral angle (theta), and the distance (D) between the terminal alpha-carbon atoms of the tripeptide. The criteria for classification have been worked out by model building as well as from proteins whose complete secondary structures are known. These criteria are as follows: (i) magnitude of theta less than or equal to 60 degrees and (delta 1 + delta 2) less than or equal to 230 degrees for a bend, (ii) for a helix, successive thetas should not differ by more than 30 degrees, and (iii) for an extended structure, the cumulative deviation of the above parameters should not vary by more than 20% from the ideal extended chain. The method developed has been applied successfully to three proteins wherein the coordinates of alpha-carbon atoms alone are known and a complete mapping of the secondary structures has now been obtained. One interesting observation is that the percentage of residues not taking part in helices, extended structures, and bends is very small--of the order of 4%.

Ramachandran revisited. DFT energy surfaces of diastereomeric trialanine peptides in the gas phase and aqueous solution.

Abstract: We report DFT calculations at the B3LYP/D95(d,p) level on the gas phase, aqueous solvation and solvated energies as functions of the central ψ and ϕ dihedral angles (in steps of 5° each) of acetyl-LAla-LAla-LAla-NH2 (3AL) and its diastereomer, acetyl-LAla-DAla-LAla-NH2 (3AD). In addition to structures without internal H-bonds (C5 interactions are neglected), many (95) structures containing internal H-bonds were completely optimized. The only minima for non-H-bonding structures in the gas phase correspond to extended β-strands for both diastereomers. Some (but not all) structures with internal H-bonds are more stable than those without them. The energy landscapes for the solvated species show multiple minima for the non-H-bonding species and a single minimum for the H-bonding species (310-helix), suggesting that the equilibrium conformational mixture in water be composed of the extended β-strand, polyproline II, 310-helix, and α-helix-like (with no H-bonds) conformations which are all within about 1 kcal/m...

Strong Conductance Variation in Conformationally Constrained Oligosilane Tunnel Junctions

Abstract: The effects of molecular conformation on conductance in oligosilane-bridged metal-molecule-metal junctions are studied theoretically using density functional theory combined with a nonequilibrium Green’s function approach. Varying the internal SiSiSiSi dihedral angles in hexasilane diamine chains changes the conductance by up to 3 orders of magnitude. This conformational dependence is due to the effects of σ-delocalization on the positions of the highest occupied molecular orbital (HOMO) energies. The conductance values for the different conformations are related to electron transfer rates in donor-bridge-acceptor systems, and the effect of shifting the injection energy is examined. The transport properties are found to be extremely sensitive to the alignment between the HOMO energies and Fermi level of the gold electrodes. I. Introduction Development of molecular electronic devices requires careful tailoring of the electronic transport properties to achieve the desired functionalities. 1,2 One approach for engineering specific transport properties that has been studied theoretically 3-6 and realized experimentally 7,8 controls the effect of molecular conformation on conductance. Recent experiments 7 have shown that extending π-conjugation to varying degrees in a biphenyl system by altering the twist angle between the two phenyl rings affects the electronic transport, with a conformational dependence predicted by π-orbital overlap arguments. 3,4,9 The conformational dependence of the electronic properties of π-conjugated molecules has an analogue in the electronic properties of σ-conjugated molecules. Methylated and catenated oligosilanes have been the subject of research studying the effects of σ-delocalization on optical properties such as UV and IR absorption. 10-20 These studies indicate that σ-delocalization is extended by anti turns (SiSiSiSi dihedral angles of 180°) but not by cisoid turns (small dihedral angles) in the backbone of silane chains. Given the phenomenon of conformation-dependent transport in π-conjugated structures, it is worth examining whether σ-conjugated structures exhibit a similar effect. In this work, we examine theoretically how the conformational dependence of the electronic properties of oligosilane chains can be used to control electronic transport in single molecule junctions. Charge transport properties are calculated for a series of amine-terminated hexasilane chains between gold electrodes with varying internal dihedral angles ranging from 0° to 180° (Figure 1). Zero-bias conductances for the chains are computed by using a combination of density functional theory (DFT) and nonequilibrium Green’s function (NEGF) techniques. 21 The results indicate a strong dependence of the conductance on the silane backbone conformation and are understood by using an analysis of the offsets between the highest occupied molecular orbital (HOMO) energies and the Fermi level for the different conformations. Comparisons with results

Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol.

Abstract: Forward flux sampling (FFS) simulations were used to study the kinetics of alanine dipeptide both in vacuum and in explicit solvent. The recently proposed FFS least-squares estimation approach and an algorithm that optimizes the position of the interfaces were implemented to determine a reaction coordinate that adequately describes the transition dynamics. A new method is also introduced to try to ensure that the ensemble of "starting points" (for the trial trajectories) is properly sampled. The rate constant estimates for the C7(eq)-->C5 transition of alanine dipeptide in vacuum were used to demonstrate the consistency between Monte Carlo and molecular dynamics (MD) simulations. FFS-MD simulations were then performed for the study of the beta(2)/alpha(R)-->C5/C7(eq) transition in explicit solvent. The kinetic results for both systems in vacuum and explicit solvent are in general agreement with previous experimental and computational studies for this peptide. In vacuum, an additional dihedral angle besides the one typically used as order parameter is identified as a significant variable in the reaction coordinate model. In solution, several dihedral angles and variables that describe the solvent action on the molecule's dynamics are found to play a significant role in the description of the system's dynamics.

Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy

Abstract: We show that quantitative internuclear N15–C13 distances can be obtained in sufficient quantity to determine a complete, high-resolution structure of a moderately sized protein by magic-angle spinning solid-state NMR spectroscopy. The three-dimensional ZF-TEDOR pulse sequence is employed in combination with sparse labeling of C13 sites in the β1 domain of the immunoglobulin binding protein G (GB1), as obtained by bacterial expression with 1,3-C13 or 2-C13-glycerol as the C13 source. Quantitative dipolar trajectories are extracted from two-dimensional N15–C13 planes, in which ∼750 cross peaks are resolved. The experimental data are fit to exact theoretical trajectories for spin clusters (consisting of one C13 and several N15 each), yielding quantitative precision as good as 0.1 A for ∼350 sites, better than 0.3 A for another 150, and ∼1.0 A for 150 distances in the range of 5–8 A. Along with isotropic chemical shift-based (TALOS) dihedral angle restraints, the distance restraints are incorporated into simu...