Showing papers on "Dihedral angle published in 2013"

Unexpected chirality of nanoparticle dimers and ultrasensitive chiroplasmonic bioanalysis.

Abstract: Chiral assemblies of nanoparticles (NPs) are typically constructed with helical or tetrahedral geometries. Simple pairs of NPs are not expected to display chirality due to basic symmetry considerations made under the assumption of their spherical geometry. In this study we demonstrate that assemblies consisting of two metallic NPs do possess chirality and strongly rotate polarization of light. Their chiroplasmonic properties are attributed to the prolate geometry of individual colloidal particles. When bridged by biomolecules, the NP pairs acquire scissor-like geometry, with the long axes of NPs forming an angle of ∼9°. This small dihedral angle results in chirality of the NP pair, while the consistency of its sign due to the specific conformation of the bridging biomacromolecules breaks the enantiomeric equivalence of the NP pairs. Strong polarization rotation in these nanoassemblies makes possible their utilization in biological analysis. Heterodimers of gold and silver NPs were made using antibody–anti...

Chiral plasmonics of self-assembled nanorod dimers.

Abstract: Chiral nanoscale photonic systems typically follow either tetrahedral or helical geometries that require four or more different constituent nanoparticles. Smaller number of particles and different chiral geometries taking advantage of the self-organization capabilities of nanomaterials will advance understanding of chiral plasmonic effects, facilitate development of their theory, and stimulate practical applications of chiroplasmonics. Here we show that gold nanorods self-assemble into side-by-side orientated pairs and "ladders" in which chiral properties originate from the small dihedral angle between them. Spontaneous twisting of one nanorod versus the other one breaks the centrosymmetric nature of the parallel assemblies. Two possible enantiomeric conformations with positive and negative dihedral angles were obtained with different assembly triggers. The chiral nature of the angled nanorod pairs was confirmed by 4π full space simulations and the first example of single-particle CD spectroscopy. Self-assembled nanorod pairs and "ladders" enable the development of chiral metamaterials, (bio)sensors, and new catalytic processes.

Photodynamic Chiral Molecular Switches with Thermal Stability: From Reflection Wavelength Tuning to Handedness Inversion of Self‐Organized Helical Superstructures

Abstract: A good turn: Three compounds that bear two axially chiral bridged binaphthyl units were developed as photodynamic chiral dopants for nematic liquid crystals. For compounds with suitable bridge lengths, a change in the dihedral angle induced a switch of the binaphthyl units from the cisoid to the transoid form upon UV irradiation, which led to an inversion of the handedness of the helices.

Intimate Interactions with Carbonyl Groups: Dipole–Dipole or n→π*?

Abstract: Amide carbonyl groups in proteins can engage in C═O···C═O and C–X···C═O interactions, where X is a halogen. The putative involvement of four poles suggests that these interactions are primarily dipolar. Our survey of crystal structures with a C–X···C═O contact that is short (i.e., within the sum of the X and C van der Waals radii) revealed no preferred C–X···C═O dihedral angle. Moreover, we found that structures with a short X–···C═O contact display the signatures of an n→π* interaction. We conclude that intimate interactions with carbonyl groups do not require a dipole.

Determining In Situ Protein Conformation and Orientation from the Amide-I Sum-Frequency Generation Spectrum: Theory and Experiment

Abstract: Vibrational sum-frequency generation (VSFG) spectra of the amide-I band of proteins can give detailed insight into biomolecular processes near membranes. However, interpreting these spectra in terms of the conformation and orientation of a protein can be difficult, especially in the case of complex proteins. Here we present a formalism to calculate the amide-I infrared (IR), Raman, and VSFG spectra based on the protein conformation and orientation distribution. Based on the protein conformation, we set up the amide-I exciton Hamiltonian for the backbone amide modes that generate the linear and nonlinear spectroscopic responses. In this Hamiltonian, we distinguish between nearest-neighbor and non-nearest-neighbor vibrational couplings. To determine nearest-neighbor couplings we use an ab initio 6-31G+(d) B3LYP-calculated map of the coupling as a function of the dihedral angles. The other couplings are estimated using the transition-dipole coupling model. The local-mode frequencies of hydrogen-bonded peptid...

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations

Abstract: Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules. To improve the stability and accuracy of coarse-grained molecular dynamics simulations, we propose two approaches. The first makes use of improved forms for the angle potentials: the restricted bending (ReB) potential prevents torsion angles from visiting unstable or unphysical configurations and the combined bending-torsion (CBT) potential smoothly flattens the interactions when such configurations are sampled. In the second approach, dummy-assisted dihedral (DAD), the torsion potential is applied differently: instead of acting directly on the beads, it acts on virtual beads, bound to the real ones. For simple geometrical reasons, the unstable region is excluded from the accessible conformational space. The benefits of the new approaches are demonstrated in simulations of polyethylene glycol (PEG), polystyrene (PS), and polypeptide molecules described by the MARTINI coarse-grained force field. The new potentials are implemented in an in-house version of the Gromacs package, publicly available.

Synthesis and Crystal Structure of a 3D Supramolecular Copper(II) Complex With 1-(3-{[(E)-3-bromo-5-chloro-2-hydroxybenzylidene]amino}phenyl) ethanone Oxime

Abstract: A new Cu(II) complex, [Cu(L)2], has been synthesized via the complexation of copper(II) acetate monohydrate with a new oxime-type ligand (HL = 1-(3-{[(E)-3-bromo-5-chloro-2-hydroxybenzylidene]amino}phenyl)ethanone oxime). X-ray crystallographic analysis reveals that the complex is a mononuclear complex. The Cu(II) atom is four-coordinated by the phenolate O atoms and imine N atoms from two oxime-type ligands, in a square-planar geometry in which the dihedral angle of two coordination plane (Cu1N1O1 and Cu1N#1O#1) is 0°. The crystal packing of the Cu(II) complex shows that a notable feature of this structure resides in the formation of a novel 3D supramolecular networks through intermolecular O–H···N, C–H···O, and C–H···π interactions. Supplemental materials are available for this article. Go to the publisher's online edition of Synthesis and Reactivity in Inorganic, Metal-Organic, and Nano-Metal Chemistry to view the supplemental file.

Gold(I) Complexes of Tetrathiaheterohelicene Phosphanes

Abstract: New tetrathia[7]helicene-based (7-TH-based) gold(I) complexes 6 and 7 have been readily prepared by reaction of the respective phosphine ligands 2 and 3 with Au(tht)Cl in a 1:1 and 1:2 molar ratio, respectively. These complexes have been fully characterized by analytical and spectroscopic techniques as well as quantum chemical calculations. The molecular structure of dinuclear complex 7 has been determined by single-crystal X-ray diffraction, showing a gold-gold interaction of 3.1825(3) A and a significant contraction of the 7-TH total dihedral angle. Au(I) complex 7 displays luminescence emission at room and low temperature in diluted solution and in the solid state. Quantum chemical calculations show that the luminescence emission at room temperature is primarily due to slightly perturbed fluorescence emission from purely ππ* excited states of the conjugated helicene scaffold. At 77 K phosphorescence emission is displayed as well. Preliminary studies on the use of 6 and 7 as catalysts in typical Au(I)-catalyzed cycloisomerizations have demonstrated the reactivity of these systems in the intramolecular allene hydroarylations and the hydroxycarboxylation of allene-carboxylates.

High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Abstract: Coarse-grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full-atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log-likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full-atom models using Rosetta which has implications for multiscale protein modeling using coarse-grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/.

Effects of boron doping on the structural and optoelectronic properties of 9,10-diarylanthracenes

Abstract: Key structural and optoelectronic properties of 9,10-dihydro-9,10-diboraanthracene (DBA) derivatives carrying mesityl (2a), 2-methylnaphthyl- (2b) and 9-phenyl-2,7-di-tert-butylanthryl (2c) substituents at the boron atoms have systematically been compared with the properties of their all-carbon congeners 4a–c. The experimental investigations have been augmented by quantum-chemical calculations. Steric repulsion leads to large dihedral angles between the aryl substituents and the DBA (2a–c) or anthrylene (4a–c) cores; as a result, the B–C bonds of 2a–c are kinetically shielded from hydrolysis and oxidative degradation. Lithium metal reduces the mesityl derivative 2a to the inverse sandwich complexes [Li(OR2)n]2[2a] (X-ray crystallography; OR2 = THF, n = 2; Et2O, n = 1). In line with the nodal structures of the LUMO of 2a/HOMO of [Li(THF)2]2[2a], the C–C bond lengths of the anionic fragment [2a]2− show characteristic differences to those of 2a and come close to the C–C bond lengths of the isoelectronic species 4a. X-ray crystallography on anti-2b × 2 C6H6 and anti-4b × 2 C6H6 reveals an essentially identical packing of the main molecules. The benzene solvate molecules, however, interact in a very different manner with anti-2b or anti-4b, which can be traced down to subtle disparities between the electron density distributions of the two compounds. 2a–c undergo a photoinduced aryl-to-DBA charge transfer; the back electron transfer results in blue (2a), green (2b) and red (2c) emission, albeit with low quantum yields. 4a–c are characterised by a local π–π* photoexcitation of the central 9,10-anthrylene fragments and corresponding blue emission. Each of the compounds 2a–c gives rise to two reversible DBA-centred one-electron transitions in the cyclic voltammogram.

Topology switching in [32]heptaphyrins controlled by solvent, protonation, and meso substituents.

Abstract: The switching of topology between "figure-eight", Mobius, and untwisted conformations in [32]heptaphyrins(1.1.1.1.1.1.1) has been investigated by using density functional theory calculations. Such a change is achieved by variation of one internal dihedral angle and, if properly controlled, can provide access to molecular switches with unique optical and magnetic properties. In this work, we have explored different conformational control methods, such as solvent, protonation and meso substituents. Despite its antiaromatic character, most of the [32]heptaphyrins (R=H, CH(3), CF(3), Ph, C(6)F(5)) adopt a figure-eight conformation in the neutral state, owing to their more-effective hydrogen-bonding interactions. The aromatic Mobius topology is only preferred with dichlorophenyl groups, which minimize the steric hindrance that arises from the bulky chlorine atoms. The conformational equilibrium is sensitive to the solvent, so polar solvents, such as DMSO, further stabilize the Mobius conformation. Protonation induces a conformational change into the Mobius topology, irrespective of the meso-aryl groups. In the triprotonated species, the conformational switch is blocked and a non-twisted conformer becomes much more stable than the figure-eight conformation. We have shown that the relative energies of the protonated [32]heptaphyrins are dominated by aromaticity. Importantly, this topology switching induces a dramatic change in the magnetic properties and reactivity of the macrocycles, as revealed by several energetic, magnetic, structural, and reactivity indices of aromaticity.

Nonequilibrium dynamics of helix reorganization observed by transient 2D IR spectroscopy

Abstract: The relaxation of helical structures very close to equilibrium is observed via transient 2D IR spectroscopy. An initial distribution of synthetically distorted helices having an unnatural bridge linking the 10th and 12th residues of an alanine-rich α-helix is released to evolve into the equilibrium distribution of α-helix conformations. The bridge constrains the structure to be slightly displaced from the full α-helix equilibrium near these residues, yet the peptide is not unfolded completely. The release is accomplished by a subpicosecond pulse of UV irradiation. The resulting 2D IR signals are used to obtain snapshots of the ∼100-ps helical conformational reorganization of the distorted dihedral angle and distance between amide units at chemical bond length-scale resolution. The decay rates of the angle between the dipoles, dihedral angles, and distance autocorrelations obtained from molecular dynamics simulations support the experiments, providing evidence that the final helix collapse conforms to linear response theory.

Effect of Heme–Heme Interactions and Modulation of Metal Spins by Counter Anions in a Series of Diiron(III)‐μ‐hydroxo Bisporphyrins: Unusual Stabilization of Two Different Spins in a Single Molecular Framework

Abstract: A new family of five ethene-bridged diiron(III)-μ-hydroxo bisporphyrins with the same core structure but different counter anions, represented by the general formula [Fe2 (bisporphyrin)]OH·X (X=counter anion), is reported herein. In these complexes, two different spin states of Fe are stabilized in a single molecular framework. Protonation of the oxo-bridged dimer 1 by strong Bronsted acids such as HI, HBF4, HPF6, HSbF6 , and HClO4 produces the μ-hydroxo complexes with I5(-)(2), BF4(-)(3), PF6(-)(4), SbF6(-)(5), and ClO4(-)(6) as counter anions, respectively. The X-ray structures of 2 and 6 have been determined, which provide a rare opportunity to investigate structural changes upon protonation. Spectroscopic characterization has revealed that the two iron(III) centers in 2 are nonequivalent with nearly high and admixed-intermediate spins in both the solid state and solution. Moreover, the two different Fe(III) centers of 3-5 are best described as having admixed-high and admixed-intermediate spins with variable contributions of S=5/2 and 3/2 for each state in the solid, but two different admixed-intermediate spins in solution. In contrast, the two Fe(III) centers in 6 are equivalent and are assigned as having high and intermediate spin states in the solid and solution, respectively. The X-ray structures reveal that the Fe-O bond length increases on going from the μ-oxo to the μ-hydroxo complexes, and the Fe-O(H)-Fe unit becomes more bent, with the dihedral angle decreasing from 150.9(2)° in 1 to 142.3(3)° and 143.85(2)° in 2 and 6, respectively. Variable-temperature magnetic data have been subjected to a least-squares fitting using the expressions derived from the spin Hamiltonians H=-2JS1·S2 -μ·B+D[S(2)(z) - 1/3S(S + 1)] (for 2, 3, 4, and 5) and H=-2JS1·S2 (for 6). The results show that strong antiferromagnetic coupling between the two Fe(III) centers in 1 is attenuated to nearly zero (-2.4 cm(-1)) in 2, whereas the values are -46, -32.6, -33.5, and -34 cm(-1) for 3, 4, 5, and 6, respectively.

Two double helical modes of bidipyrrin–ZnII complexes

Abstract: This paper reports the formation and properties of covalently strapped double helices of bidipyrrin–ZnII complexes, where four dipyrrin chromophores interact with one another by strong exciton coupling. Thorough experimental examination, UV/vis, CD and 1H NMR spectra, and theoretical studies suggest the existence of two modes of the double helix depending on the dihedral angles between two of the dipyrrin units at the pyrrole α–α bond. In fact, the changes of the modes were observed according to the lengths of straps as well as the temperatures.

Preparation, characterization, and reactivity of dinitrogen molybdenum complexes with bis(diphenylphosphino)amine derivative ligands that form a unique 4-membered P-N-P chelate ring.

Abstract: Five dinitrogen-molybdenum complexes bearing bis(diphenylphosphino)amine derivative ligands (L(R)) that form a unique 4-membered P-N-P chelate ring, trans-[Mo(N(2))(2)(L(R))(2)] (2(R): R = Ph, Xy, p-MeOPh, 3,5-iPr(2)Ph, iPr), were prepared for the purpose of binding a dinitrogen molecule. The corresponding two dichloride-molybdenum complexes, trans-[MoCl(2)(L(R))(2)] (1(R): R = Ph, Xy), were also prepared as comparisons. FT-IR spectra of 2(R) were measured and compared the ν(N≡N) values. Moreover, X-ray crystal structure determination of 1(R) (R = Ph, Xy) and 2(R) (R = Xy, 3,5-iPr(2)Ph) is performed. These experimental results indicated that the coordinated dinitrogen molecule gets easily influenced by the N-substitutent of diphosphinoamine ligand. In addition, to investigate the effect of the properties of the diphosphinoamine ligand for the dinitrogen molybdenum complexes, we performed DFT calculations that focused on the difference of N-substituent, the dihedral angle between P-N-P plane and N-substituent aryl group, and the P-N-P bite angle. This calculation revealed that the competition between the back-donation from metal to dinitrogen and that from metal to ligand was affected by P-N-P bite angle and the dihedral angle of N-substituent of ligand. In order to examine the reactivity with respect to conversion of dinitrogen to ammonia, protonation and trimethylsilylation reactions of the coordinated dinitrogens were carried out for 2(R).

Formation of a 1,4-Diamino-2,3-disila-1,3-butadiene Derivative

Abstract: A 1,4-diamino-2,3-disila-1,3-butadiene derivative of composition (Me2-cAAC)2(Si2Cl2) (Me2-cAAC = :C(CMe2)2(CH2)N-2,6-iPr2C6H3) was synthesized by reduction of the Me2-cAAC:SiCl4 adduct with KC8. This compound is stable at 0 °C for 3 months in an inert atmosphere. Theoretical studies reveal that the silicon atoms exhibit pyramidal coordination, where the Cl–Si–Si–Cl dihedral angle is twisted by 43.3° (calcd 45.9°). The two silicon–carbon bonds are intermediates between single and double Si–C bonds due to twisting of the C–Si–Si–C dihedral angle (163.6°).

P4 Activation at Ni0: Selective Formation of an NHC‐Stabilized, Dinuclear Nickel Complex [Ni2(iPr2Im)4(μ,η2:2‐P2)]

Abstract: The reaction of [Ni2(iPr2Im)4(cod)] (1) with white phosphorus led to dinuclear [{Ni(iPr2Im)2}2(μ,η2:2-P2)] (2) in excellent yield. This reaction represents the first example of a conversion of white phosphorus into a complex of the type [{L2Ni}2(μ,η2:2-P2)] and the first example of the formation of a complex of the type [{L2M}2(μ,η2:2-P2)] for a group-10 metal stabilized by two simple, nonchelating, two-electron donor ligands by the reaction of a suitable precursor with P4. The X-ray structure of 2 revealed a bent Ni2P2 core with an Ni–P–P–Ni dihedral angle in the solid state of 102.95°. According to DFT calculations on the symmetrized model systems planar-D2h- and bent-C2v-[{Ni(iPr2Im)2}2(μ,η2:2-P2)], this deviation of the Ni2P2 core from planarity is caused by a second-order Jahn–Teller distortion. Calculations on the related platinum compound [{Pt(iPr2Im)2}2(μ,η2:2-P2)] confirmed this type of bent structure for the higher congener with an even higher barrier to planarization than that calculated for the nickel complex. Energy decomposition analysis and fragment molecular orbital analysis further illustrate the bonding mechanisms in these complexes.

A Hirshfeld Surface Analysis and Crystal Structure of 2’-[1-(2-Fluoro-Phenyl)-1H-tetrazol-5-Yl]-4-Methoxy-Biphenyl-2-Carbaldehyde

Abstract: The title compound, C21H15FN4O2 is synthesized and characterized by 1H NMR, LC-MS and finally confirmed by single crystal X-ray diffraction method. This molecule crystallizes in the monoclinic crystal system and space group P21/c, with crystal parameters a = 9.4386(5) A, b = 20.8082(1) A, c = 9.4338(6) A, β = 99.566(2)0, Z = 4 and V = 1826.98(19) A3. The mean planes of fluro-phenyl moiety makes a dihedral angle of 21.51 (7)0 with biphenyl moiety. The molecules are connected by hydrogen bonds of the type C---H...O and C---H...F. In addition, crystal structure is stabilized with π … π (exhibits intramolecular interaction) and C---O... π interactions. The intercontacts in the crystal structure are analyzed using Hirshfeld surfaces computational method.

Simulation of Fracture Nucleation in Cross-Linked Polymer Networks

Abstract: A novel atomistic simulation method is developed whereby polymer systems can undergo strain-rate-controlled deformation while bond scission is enabled. The aim is to provide insight into the nanoscale origins of fracture. Various highly cross-linked epoxy systems including various resin chain lengths and levels of nonreactive dilution were examined. Consistent with the results of physical experiments, cured resin strength increased and ductility decreased with increasing cross-link density. An analysis of dihedral angle activity shows the locations in the molecular network that are most absorptive of mechanical energy. Bond scission occurred principally at cross-link sites as well as between phenyl rings in the bisphenol moiety. Scissions typically occurred well after yield and were accompanied by steady increases in void size and dihedral angle motion between bisphenol moieties and at cross-link sites. The methods developed here could be more broadly applied to explore and compare the atomistic nature of deformation for various polymers such that mechanical and fracture properties could be tuned in a rational way. This method and its results could become part of a solution system that spans multiple length and time scales and that could more completely represent such mechanical events as fracture.

Unusual Conformation of a Dinuclear Paddle Wheel Copper(II) Complex. Synthesis, Structural Characterization and EPR Studies

Abstract: An unusual and unique conformation of a paddle wheel type binuclear copper(II) complex containing acetate and acetamido ligands, {Cu2(μ2-O2CCH3)4}(OCNH2CH3) (1), was obtained by solvothermal synthesis. The structural characterization of this compound shows that the apical (acetamido) ligands are disposed at a 62° dihedral angle, generating a special conformation as a consequence of the synthetic method used. This conformation has not been reported in other paddle wheel copper(II) tetraacetate compounds. Electron paramagnetic resonance (EPR) spectra of powder samples of (1) were obtained at 9.5 and 33.8 GHz, while single crystal spectra were obtained at 33.8 GHz with a B0 applied in three orthogonal planes. The fit of the single crystal experimental data allowed gave g∥ = 2.345 ± 0.003, and g⊥ = 2.057 ± 0.005. The angular variation of the EPR line allows evaluation of the fine structure of (1), giving D = −0.337 ± 0.002 cm–1 and E = −0.005 ± 0.001 cm–1. The line width angular dependence, used together with...

A ladder polysilane as a template for folding palladium nanosheets

Abstract: Although discrete nano-sized compounds consisting of a monolayer sheet of multiple atoms have attracted much attention, monolayer transition metal nanosheets are difficult to access. Here we report a template synthesis of the folding metal nanosheet (2) consisting of 11 palladium atoms by treatment of a ladder polysilane, decaisopropylbicyclo[2.2.0]hexasilane (1), with Pd(CN(t)Bu)2. Crystallographic analysis reveals that the compound is composed of two monolayer Pd7 sheets sharing three palladium atoms at the junction. Each Pd atom is stabilized by Pd-Si σ-bonds, Pd-Pd bonds and coordination of isocyanides. Ligand exchange of 2 from CN(t)Bu to CN(2,4,6-Me3-C6H2) is accompanied by structural rearrangement, leading to the formation of another folding Pd11 nanosheet (3) consisting of two edge-sharing Pd7 sheets. The shapes of the Pd7 sheets as well as the dihedral angle between the two Pd7 sheets are dependent on the substituent of the isocyanide ligand.

Cyclic constraints on conformational flexibility in γ-peptides: conformation specific IR and UV spectroscopy.

Abstract: Single-conformation spectroscopy has been used to study two cyclically constrained and capped γ-peptides: Ac-γACHC-NHBn (hereafter γACHC, Figure 1a), and Ac-γACHC-γACHC-NHBn (γγACHC, Figure 1b), under jet-cooled conditions in the gas phase. The γ-peptide backbone in both molecules contains a cyclohexane ring incorporated across each Cβ-Cγ bond and an ethyl group at each Cα. This substitution pattern was designed to stabilize a (g+, g+) torsion angle sequence across the Cα-Cβ-Cγ segment of each γ-amino acid residue. Resonant two-photon ionization (R2PI), infrared-ultraviolet hole-burning (IR-UV HB), and resonant ion-dip infrared (RIDIR) spectroscopy have been used to probe the single-conformation spectroscopy of these molecules. In both γACHC and γγACHC, all population is funneled into a single conformation. With RIDIR spectra in the NH stretch (3200-3500 cm(-1)) and amide I/II regions (1400-1800 cm(-1)), in conjunction with theoretical predictions, assignments have been made for the conformations observed in the molecular beam. γACHC forms a single nearest-neighbor C9 hydrogen-bonded ring whereas γγACHC takes up a next-nearest-neighbor C14 hydrogen-bonded structure. The gas-phase C14 conformation represents the beginning of a 2.614-helix, suggesting that the constraints imposed on the γ-peptide backbone by the ACHC and ethyl groups already impose this preference in the gas-phase di-γ-peptide, in which only a single C14 H-bond is possible, constituting one full turn of the helix. A similar conformational preference was previously documented in crystal structures and NMR analysis of longer γ-peptide oligomers containing the γACHC subunit [Guo, L., et al. Angew. Chem. Int. Ed. 2011, 50, 5843-5846]. In the gas phase, the γACHC-H2O complex was also observed and spectroscopically interrogated in the molecular beam. Here, the monosolvated γACHC retains the C9 hydrogen bond observed in the bare molecule, with the water acting as a bridge between the C-terminal carbonyl and the π-cloud of the UV chromophore. This is in contrast to the unconstrained γ-peptide-H2O complex, which incorporates H2O into both C9 and amide-stacked conformations.

From antiferromagnetic to ferromagnetic exchange in a family of oxime-based Mn(III) dimers: a magneto-structural study.

Abstract: The reaction of Mn(ClO4)2·6H2O, a derivatised phenolic oxime (R-saoH2) and the ligand tris(2-pyridylmethyl)amine (tpa) in a basic alcoholic solution leads to the formation of a family of cluster compounds of general formula [MnIII2O(R-sao)(tpa)2](ClO4)2 (1, R = H; 2, R = Me; 3, R = Et; 4, R = Ph). The structure is that of a simple, albeit asymmetric, dimer of two MnIII ions bridged through one μ-O2− ion and the –N–O– moiety of the phenolic oxime. Magnetometry reveals that the exchange interaction between the two MnIII ions in complexes 1, 3 and 4 is antiferromagnetic, but that for complex 2 is ferromagnetic. A theoretically developed magneto-structural correlation reveals that the dominant structural parameter influencing the sign and magnitude of the pairwise interaction is the dihedral Mn–O–N–Mn (torsion) angle. A linear correlation is found, with the magnitude of J varying significantly as the dihedral angle is altered. As the torsion angle increases the AF exchange decreases, matching the experimentally determined data. DFT calculations reveal that the dyz|π*|dyz interaction decreases as the dihedral angle increases leading to ferromagnetic coupling at larger angles.

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

Abstract: Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.

Analytical Gradients of Hartree-Fock Exchange with Density Fitting Approximations.

Abstract: We extend the local exchange (LK) algorithm [Aquilante, F.; Pedersen, T. B.; Lindh, R. J. Chem. Phys.2007, 126, 194106] to the calculation of analytical gradients with density fitting. We discuss the features of the screening procedure and demonstrate the possible advantages of using this formulation, which is easily interfaced to a standard integral-direct gradient code. With auxiliary basis sets obtained from Cholesky decomposition of atomic or molecular integral blocks with a decomposition threshold of 10(-4)Eh, typical errors due to the density fitting in bond lengths, bond angles, and dihedral angles are 0.1 pm, 0.1°, and 0.5°, respectively. The overall speedup of geometry optimizations is about 1 order of magnitude for atomic natural-orbital-type basis sets but much less pronounced for correlation-consistent basis sets.

On G-arc-regular dihedrants and regular dihedral maps

Abstract: A graph Γ is said to be G-arc-regular if a subgroup G ≤ Aut(Γ ) acts regularly on the arcs of Γ . In this paper connected G-arc-regular graphs are classified in the case when G contains a regular dihedral subgroup D2n of order 2n whose cyclic subgroup Cn ≤ D2n of index 2 is core-free in G. As an application, all regular Cayley maps over dihedral groups D2n, n odd, are classified.