Computational study of thioflavin T torsional relaxation in the excited state

Quantum-chemical calculations of the Thioflavin T (ThT) molecule in the ground S0 and first excited singlet S1 states were carried out. It has been established that ThT in the ground state has a noticeable nonplanar conformation: the torsion angle phi between the benzthiazole and the dimethylaminobenzene rings has been found to be approximately 37 degrees. The energy barriers of the intramolecular rotation appearing at phi = 0 and 90 degrees are quite low: semiempirical AM1 and PM3 methods predict values approximately 700 cm-1 and ab initio methods approximately 1000-2000 cm(-1). The INDO/S calculations of vertical transitions to the S1(abs) excited state have revealed that energy ES1(abs) is minimal for the twisted conformation with phi = 90 degrees and that the intramolecular charge-transfer takes place upon the ThT fragments' rotation from phi = 0 to 90 degrees. Ab initio CIS/RHF calculations were performed to find optimal geometries in the excited S1 state for a series of conformers having fixed phi values. The CIS calculations have predicted a minimum of the S1 state energy at phi approximately 21 degrees; however, the energy values are 1.5 times overestimated in comparison to experimental data. Excited state energy dependence on the torsion angle phi, obtained by the INDO/S method, reveals that ES1(fluor) is minimal at phi = approximately 80-100 degrees, and a plateau is clearly observed for torsion angles ranging from 20 to 50 degrees. On the basis of the calculation results, the following scheme of photophysical processes in the excited S1 state of the ThT is suggested. According to the model, a twisted internal charge-transfer (TICT) process takes place for the ThT molecule in the excited singlet state, resulting in a transition from the fluorescent locally excited (LE) state to the nonfluorescent TICT state, accompanied by torsion angle phi growth from 37 to 90 degrees. The TICT process effectively competes with radiative transition from the LE state and is responsible for significant quenching of the ThT fluorescence in low-viscosity solvents. For viscous solvents or when the ThT molecule is located in a rather rigid microenvironment, for example, when it is bound to amyloid fibrils, internal rotation in the dye molecule is blocked due to steric hindrance, which results in suppression of the LE --> TICT quenching process and in a high quantum yield of fluorescence.     

Conformational structure of gaseous 3-chloropropanoyl chloride by electron diffraction, normal coordinate analysis, and ab initio molecular orbital, and density functional theory calculations

The molecular and conformational structures of 3-chloropropanoyl chloride (CH(2)Cl-CH(2)-C(=O)Cl) have been studied by using gas-phase electron diffraction (GED) data obtained at 22 degrees C (295 K) and ab initio molecular orbital (MO) and density functional theory (DFT) calculations up to the levels of MP4(SDQ) and B3LYP using larger basis sets. Normal coordinate calculations (NCA) taking into account nonlinear vibrational effects were also used in the analyses. The title compound may have up to four low-energy conformers in the gas phase, labeled according to the position of each of the two chlorine atoms in relation to the CCC propanoyl backbone, labeling the carbonyl chlorine torsion angle first: AA, AG, GG, and GA; where A is anti (ideal C-C-C-Cl torsion angle of approximately 180 degrees) and G is gauche (ideal C-C-C-Cl torsion angle of approximately 60 degrees). It has been judged from the experimental GED data and the theoretical calculations, as well as from previously published infrared (IR) studies on the molecule in both the liquid phase and in argon-trapped matrices at 10 K, that the gas phase consists of a mixture of at least three conformers: AA (most stable), AG, and GG, with the possibility of a smaller contribution (<10%) from the higher-energy GA form. The GA conformer cannot be ruled out by the GED experimental data. Relevant structural parameter values obtained from the GED least-squares refinements, with calculated ab initio MO MP2/6-31+G(2d,p) values used as constraints, were as follows (AA values with estimated 2sigma uncertainties): Bond lengths (r(h1)): r(C-C(=O)) = 1.505(4) A, r(C-CH(2)Cl) = 1.520(4) A, r(C=O) = 1.197(4) A, r(C(=O)-Cl) = 1.789(3) A, and r(C-Cl) = 1.782(3) A. Bond angles (angle(h1)): angle CCC = 111.5(11) degrees , angle CCO = 127.0(5) degrees, angle CC(O)Cl = 112.5(3) degrees, and angle CCCl = 110.3(3) degrees. Torsion angles (phi(C-C) = phi(ClCCC)): for AA, phi(1)(C-C(O)) = phi(2)(C-CH(2)Cl) = 180 degrees (assumed for true C(s) symmetry); for AG, phi(1)(C-C(O)) = -140(5) degrees, phi(2)(C-CH(2)Cl) = 76(13) degrees; for GG, phi(1)(C-C(O)) = 46(8) degrees, phi(2)(C-CH(2)Cl) = 77(14) degrees; for GA, phi(1)(C-C(O)) = 67.9 degrees (assumed), phi(2)(C-CH(2)Cl) = 177.8 degrees (assumed). The non-AA conformers all have chiral C(1) symmetry with twice the statistical weight (multiplicity) of C(s). The MP2/6-31+G(2d,p) calculated composition (%) based on the zero-point energy (ZPE) corrected energy differences, and the statistical weights for conformers: AA/AG/GG/GA = 28/35/28/9 was assumed in the final GED refinement. The more recent literature concerning the title molecule, as well as for several related molecules, has been examined and a survey has been attempted in the present article. The new experimental results for 3-chloropropanoyl chloride are discussed and compared with the previously published findings.     

Determination of the intermolecular potential energy surface for (HCl)2 from vibration--rotation--tunneling spectra

An accurate and detailed semiempirical intermolecular potential energy surface for (HCl)2 has been determined by a direct nonlinear least-squares fit to 33 microwave, far-infrared and near-infrared spectroscopic quantities using the analytical potential model of Bunker et al. [J. Mol. Spectrosc. 146, 200 (l99l)] and a rigorous four-dimensional dynamical method (described in the accompanying paper). The global minimum (De= -692 cm-1) is located near the hydrogen-bonded L-shaped geometry (R=3.746 angstroms, theta1=9 degrees, theta2=89.8 degrees, and phi=180 degrees). The marked influence of anisotropic repulsive forces is evidenced in the radial dependence of the donor-acceptor interchange tunneling pathway. The minimum energy pathway in this low barrier (48 cm-1) process involves a contraction of 0.1 angstroms in the center of mass distance (R) at the C2h symmetry barrier position. The new surface is much more accurate than either the ab initio formulation of Bunker et al. or a previous semiempirical surface [J. Chem. Phys. 78, 6841 (1983)].     

How the central torsion angle affects the rates of nonradiative decay in some geometrically restricted p-quaterphenyls

A small series of p-quaterphenyl derivatives has been prepared in which the dihedral angle (phi) for the two central rings is constrained by dialkoxy spacers of varying length. The photophysical properties of these compounds remain comparable, but there is a clear correlation between the rate constants for nonradiative decay of both singlet and triplet excited states and phi in fluid solution. The rates tend toward a minimum as phi approaches 90 degrees . These effects are attributed to the general phenomenon of extended delocalization and can be traced to a combination of changes in the Huang-Rhys factor and the electron-vibrational coupling matrix element, both relating to displacement of the relevant potential energy surfaces and to the medium-frequency vibronic mode coupled to decay. The latter effect arises because of different levels of conjugation in the ground-state molecule. Such findings might have important implications for the design of improved light-emitting diodes. A similar angle dependence is noted for the yield of the pi-radical cation formed on photoionization in a polar solvent, but here, the effect is due to variations in the respective energy gaps between the relevant excited states.     

Al-C60-Al分子结电子输运特性的第一性原理计算

利用基于密度泛函理论的格林函数方法, 计算了Al-C60-Al分子结的电子输运特性. 考虑了C60分子在铝电极表面的原子结构弛豫, 计算结果表明共振传导是Al-C60-Al分子结电子输运的主要特征, 在费米能级附近的电导约为1.14G0 (G0=2e2/h). 投影态密度(PDOS)分析表明, Al-C60-Al分子结的电子输运主要通过C60分子的最低空分子轨道(LUMO)和次低空分子轨道(LUMO+1)进行. 讨论了C60分子和铝电极之间距离的变化对其电子输运特性的影响.     

DFT study of the conductance of molecular wire:The effect of coupling geometry and intermolecular interaction on the transport properties

The density functional theory (DFT) combining with the non-equilibrium Green functions (NEGF) method is applied to the study of the electronic transport properties for a Di-thiol-benzene (DTB) molecule coupled to two Au(111) surfaces. The dependence of the transport properties on the bias, the coupling geometry of the molecule-electrode interface, and the intermolecular interaction are examined in detail. The results show that the existence of the hydrogen atom at the end of the DTB molecule would significantly decrease the transmission coefficients, and then the differential conductance (dI/dV). By changing the position of the DTB molecule located between two electrodes a maximum value of calculated current is observed. It is also found that the intermolecular interaction will strongly influence the transport properties of the system studied.     

Gas-phase structure and conformational properties of 3,3,6,6-tetramethyl-1,2,4,5-tetroxane

The geometric structure and conformational properties of 3,3,6,6-tetramethyl-1,2,4,5-tetroxane (diacetone diperoxide) have been studied by gas electron diffraction and quantum chemical calculations (MP2 and B3LYP methods with 6-31G(d,p) and 6-311+G(2df,p) basis sets). The molecule possesses a chair conformation with C2h symmetry and the following geometric parameters for the six-membered ring (rh1 values) have been determined: O-O = 1.463(5) A, C-O = 1.432 (4) A, O-C-O = 108.2(7) degrees, C-O-O = 107.7(4) degrees, phi(C-O-O-C) = 63.7(4) degrees, and phi(O-O-C-O) = -63.9(4) degrees. A small contribution of less than 3.5% of a twist conformer with C2 symmetry cannot be excluded. Quantum chemical calculations predict a contribution between 1 and 2%. Additional calculations for the parent compound 1,2,4,5-tetroxane (diformaldehyde diperoxide) demonstrate that methyl substitution at the carbon atoms has a minor effect on the ring geometry but a strong effect on the conformational properties. Methyl substitution reduces the energy difference between twist and chair conformers by more than 5 kcal/mol.     

Preparation and properties of methoxycarbonylsulfenyl isocyanate, CH(3)OC(O)SNCO

Pure methoxycarbonylsulfenyl isocyanate, CH3OC(O)SNCO, is quantitatively prepared by the metathesis reaction between CH3OC(O)SCl and AgNCO. This novel species has been obtained in its pure form and characterized by 1H and 13C NMR, UV-vis, FTIR, and FT-Raman spectroscopy. The conformational properties of the gaseous molecule have been studied by vibrational spectroscopy and quantum chemical calculations (B3LYP and MP2 methods). The compound exhibits a conformational equilibrium at room temperature having the most stable form CS symmetry with the C=O double bond synperiplanar with respect to the S-N single bond. A second form was observed in the IR spectrum and corresponds to a conformer possessing the C-S bond antiperiplanar with respect to the N=C double bond of the isocyanate group. The structure of a single crystal of CH3OC(O)SNCO was determined by X-ray diffraction analysis at low temperature using a miniature zone melting procedure. The crystalline solid (triclinic, P1, a = 8.292(6) A, b = 9.839(7) A, c = 11.865(8) A, alpha = 67.290(2) degrees , beta = 71.5570(10) degrees , gamma = 83.4850(10) degrees and Z = 6) shows the presence of molecules having exclusively a synperiplanar conformation with respect to the three phi(CO-C=O), phi(O=C-SN), and phi(CS-N=C) dihedral angles.     

Chlorination-methylation of the hydrogen-terminated silicon(111) surface can induce a stacking fault in the presence of etch pits

Recently, we reported STM images of the methylated Si(111) surface [prepared through chlorination-alkylation of the Si(111)-H surface] taken at 4.7 K, indicating that the torsion angle of the methyl group with respect to the subsurface silicon layer is phi = 23 +/- 3 degrees . Repulsions between H atoms in adjacent methyl groups are minimized at 30 degrees , while repulsions between H atoms and second layer Si atoms are minimized at 60 degrees . The experimental result of 23 degrees is surprising because it suggests a tendency of the methyl group toward the eclipsed configuration (0 degrees ) rather than staggered (60 degrees ). In contrast, extensive fully periodic quantum mechanical Density Functional Theory studies of this surface give an equilibrium torsion angle of 37.5 degrees , indicating a tendency toward the staggered configuration. This discrepancy can be resolved by showing that the CH3 on the step edges and etch pits interacts repulsively with the CH3 on the surface terraces unless a stacking fault is introduced between the first and second silicon layers of the Si(111)-CH3 surface terraces. We propose that this could occur during the chlorination-alkylation of the Si(111)-H surface. This stacking fault model predicted phi = 22.5 degrees measured with respect to the bulk (corresponding to phi = 37.5 degrees with respect to the second layer Si atoms). This model can be tested by measuring the orientation of the CH3 within the etch pits, which should have phi = 37.5 degrees , or by making a surface without etch pits, which should have phi = 37.5 degrees .     

Origin of rotational barriers of the N-N bond in hydrazine: NBO analysis

Hydrazine passes through two transition states, TS1 (phi = 0 degrees ) and TS2 (phi = 180 degrees ), in the course of internal rotation around its N-N bond. The origin of the corresponding rotational barriers in hydrazine has been extensively studied by experimental and theoretical methods. Here, we used natural bond orbital (NBO) analysis and energy decomposition of rotational barrier energy (DeltaE(barrier)) to understand the origin of the torsional potential energy profile of this molecule. DeltaE(barrier) was dissected into structural (DeltaE(struc)), steric exchange (DeltaE(steric)), and hyperconjugative (DeltaE(deloc)) energy contributions. In both transition states, the major barrier-forming contribution is DeltaE(deloc). The TS2 barrier is lowered by pyramidalization of nitrogen atoms through lowering DeltaE(struc), not by N-N bond lengthening through lowering DeltaE(steric). Higher pyramidality of nitrogen atoms of TS2 than that of TS1 explains well why the N-N bond of TS2 is longer than that of TS1. Finally, the steric repulsion between nitrogen lone pairs does not determine the rotational barrier; nuclear-nuclear Coulombic repulsion between outer H/H atoms in TS1 plays an important role in increasing DeltaE(struc). Taken together, we explain the reason for the different TS1 and TS2 barriers. We show that NBO analysis is a useful tool for understanding structures and potential energy surfaces of compounds containing the N-N bond.     

A study of the dielectric behaviour and the liquid structure of a ternary solvent system

The static dielectric constant of the [DMF(1) + ME(2) + DME(3)] ternary mixtures was measured as a function of temperature (25 < or = t/degrees C < or = 80) and composition, over the whole mole fraction range 0 < or = chi,chi2,chi3 < or = 1. The experimental values were processed by an empirical equation accounting for the dependence epsilon = epsilon(T, phi(i)), where phi(t) is the volume fraction of the components. A comparison between calculated and experimental data shows that this fitting relationship can be effectively employed to predict epsilon values in correspondence to experimental data gaps. Starting from the experimental measurements, some derived quantities such as molar polarisation (P), and excess counterpart (PE) were obtained. Both the excess properties, epsilonE and PE, take values partly positive and partly negative under all experimental conditions. The values of the excess quantities are indicative of the presence of specific interactions among different components in the mixtures.     

Ordering in asymmetric block copolymer films by a compressible fluid

We examine the morphological structures of asymmetric poly(ethylene oxide)-b-poly(1,1'-dihydroperflurooctyl methacrylate) (PEO-b-PFOMA) thin films upon annealing in a compressible fluid, supercritical CO2 (Sc-CO2). The strong affinity between PFOMA and CO2 is found to induce phase segregation when annealing PEO-b-PFOMA films at the same temperature as compared with vacuum. In vacuum, PEO-b-PFOMA films remain disordered from 80 to 180 degrees C, whereas, in Sc-CO2 at 13.9 MPa, an upper order-disorder transition (UODT) between 116 and 145 degrees C is found. In Sc-CO2, the observed ordered structure is layers of PEO spheres embedded in the matrix of PFOMA, followed by a brush layer, in which PEO wets the substrate. The swelling isotherms of PFOMA and PEO in CO2 are correlated with the Sanchez-Lacombe equation of state (SLEOS) to estimate the interaction parameters, XPFOMA-CO2 and XPEO-CO2. The phase segregation (order) induced by CO2 relative to vacuum at a given temperature is explained in terms of two factors: (1) copolymer volume fraction upon dilution with CO2, phi, and (2) the relative interaction parameter, DeltaX= XPEO-CO2 - XPFOMA-CO2. The latter factor favors order and is dominant at low temperatures over the phi factor, which always favors disorder. At high temperatures (above the T(ODT)), the preferential swelling of PFOMA by CO2 is less pronounced ( DeltaX decreases), and the copolymer is disordered.     

Torsional angular dependence of 1J(Se,Se) and Fermi contact control of 4J(Se,Se): analysis of nJ(Se,Se) (n=1-4) based on molecular orbital theory

(n)J(Se,Se) (n=1-4) nuclear couplings between Se atoms were analyzed by using molecular orbital (MO) theory as the first step to investigating the nature of bonded and nonbonded (n)J(Se,Se) interactions between Se atoms. The values were calculated by employing Slater-type triple xi basis sets at the DFT level, which were applied to structures optimized with the Gaussian 03 program. The contribution from each occupied MO (psi(i)) and psi(i)-->psi(a) (psi(a)=unoccupied MO) transition was evaluated separately. 1J(Se,Se) was calculated for the MeSeSeMe model compound, which showed a typical dependence on the torsion angle (phi(C(Me)SeSeC(Me))). This dependence explains the small values (< or =64 Hz) of 1Jobsd(Se,Se) observed for RSeSeR' and large values (330-380 Hz) of 1Jobsd(Se,Se) observed for 4-substituted naphtho[1,8-c,d]-1,2-diselenoles, which correspond to synperiplanar diselenides. The HOMO-->LUMO and HOMO-1-->LUMO transitions contribute the most to 1J(Se,Se) at phi=0 and 180 degrees to give large values of 1J(Se,Se), whereas various transitions contribute and cancel each other out at phi=90 degrees to give small values of 1J(Se,Se). Large 4Jobsd(Se,Se) values were also observed in the nonbonded Se...Se, Se...Se=O, and O=Se...Se=O interactions at naphthalene 1,8-positions. The Fermi contact (FC) term contributes significantly to 4J(Se,Se), whereas the paramagnetic spin-orbit (PSO) term contributes significantly to 1J(Se,Se). 2J(Se,Se) and 3J(Se,Se) were analyzed in a similar manner and a torsional angular dependence was confirmed for 3J(Se,Se). Depending on the structure, the main contribution to (n)J(Se,Se) (n=2, 3) is from the FC term, with a lesser contribution from the PSO term. Analysis of each transition enabled us to identify and clearly visualize the origin and mechanism of the couplings.     

Conformations of N-acetyl-L-prolinamide by two-dimensional infrared spectroscopy

Femtosecond two-dimensional infrared (2D IR) spectroscopy has been applied to study the conformations of a model dipeptide, N-acetyl-L-prolinamide (AcProNH2) in deuterated chloroform (CDCl3). Spectral features in the amide-I and -II regions are obtained by rephasing (R), nonrephasing (NR), and reverse photon echo (RPE) pulse sequences with two polarization conditions. The 2D spectra obtained by the RPE and NR sequences with (0, 0, 0, 0) polarization reveal new spectral features associated with the multiple conformers of AcProNH2 that are difficult to discern using R sequence and linear-IR spectroscopy. The high resolving power of the RPE sequence comes from destructive interference between the positive and negative peaks of nearby vibrators, similar to the NR sequence. The RPE response functions that are useful for 2D spectral simulations are evaluated, including the effects of vibrational frequency correlations. The 2D spectra obtained with (45, -45, 90, 0) polarization exhibit clear cross-peak patterns in the off-diagonal region for the R and RPE sequences but in the diagonal region for the NR sequence. These patterns, free from strong diagonal contributions, are crucial for structure determination. DFT calculations, normal-mode analysis, Hessian matrix reconstruction, and vibrational exciton Hamiltonian diagonalization yield molecular parameters needed for quantitative simulations of 2D spectra: angles between transition dipoles, coupling constants, and off-diagonal anharmonicities of the amide-I and -II modes are obtained for solvated trans-C7 and cis structures and for gas-phase trans conformers in the region of phi = -120 degrees to 0 degrees and psi = -100 degrees to 180 degrees in the Ramachandran space. Systematic simulations based on a 4:1 population ratio of the solvated trans-C7 and cis structures reproduce well the 2D spectral features obtained at both polarization conditions. However, better agreement between the experimental and simulated cross-peak patterns can be reached if the dihedral angles of the major trans conformer are close to (phi, psi) = (-80 degrees , 100 degrees ). Our results suggest that the major conformer of AcProNH2 in CDCl3 deviates from the gas-phase global minimum, the trans-C7 form, to an extended intermediate between the C7 and polyproline-II structure. These results are discussed in relationship with earlier findings obtained by NMR, transient IR studies, and MD simulations.     

Molecular structure and conformations of para-methylbenzene sulfonamide and ortho-methylbenzene sulfonamide: gas electron diffraction and quantum chemical calculations study

The molecular structure and conformational properties of para-methylbenzene sulfonamide (4-MBSA) and ortho-methylbenzene sulfonamide (2-MBSA) have been studied by gas electron diffraction (GED) and quantum chemical methods (B3LYP/6-311+G** and MP2/6-31G**). Quantum chemical calculations predict the existence of two conformers for 4-MBSA with the S-N bond perpendicular to the benzene plane and the NH2 group either eclipsing or staggering the S-O bonds of the SO2 group. Both conformers possess CS symmetry. The eclipsed form is predicted to be favored by DeltaE = 0.63 kcal/mol (B3LYP) or 1.00 kcal/mol (MP2). According to the calculations, the S-N bond in 2-MBSA can possess planar direction opposite the methyl group (phi(C2C1SN) = 180 degrees ) or nonplanar direction (phi(C2C1SN) approximately 60 degrees ). In both cases, the NH2 group can adopt eclipsed or staggered orientation, resulting in a total of four stable conformers. The nonplanar eclipsed conformer (C1 symmetry) and the planar eclipsed form (CS symmetry) are predicted to be favored. According to the GED analysis, the saturated vapor over solid 4-MBSA at T = 151(3) degrees C consists as mixture of the eclipsed (78(19) %) and staggered (22(19) %) forms. The saturated vapor over solid 2-MBSA at T = 157(3) degrees C consists as a mixture of the nonplanar eclipsed (69(11) %) and planar eclipsed (31(11) %) forms.     

Gel to glass transition in simulation of a valence-limited colloidal system

We numerically study a simple model for thermoreversible colloidal gelation in which particles can form reversible bonds with a predefined maximum number of neighbors. We focus on three and four maximally coordinated particles, since in these two cases the low valency makes it possible to probe, in equilibrium, slow dynamics down to very low temperatures T. By studying a large region of T and packing fraction phi we are able to estimate both the location of the liquid-gas phase separation spinodal and the locus of dynamic arrest, where the system is trapped in a disordered nonergodic state. We find that there are two distinct arrest lines for the system: a glass line at high packing fraction, and a gel line at low phi and T. The former is rather vertical (phi controlled), while the latter is rather horizontal (T controlled) in the phi-T plane. Dynamics on approaching the glass line along isotherms exhibit a power-law dependence on phi, while dynamics along isochores follow an activated (Arrhenius) dependence. The gel has clearly distinct properties from those of both a repulsive and an attractive glass. A gel to glass crossover occurs in a fairly narrow range in phi along low-T isotherms, seen most strikingly in the behavior of the nonergodicity factor. Interestingly, we detect the presence of anomalous dynamics, such as subdiffusive behavior for the mean squared displacement and logarithmic decay for the density correlation functions in the region where the gel dynamics interferes with the glass dynamics.     

Influences of the molecule–electrode interface structure on the conducting characteristics of the gold-4,4 bipyridine-gold molecular junction

Two popular models of the gold-4,4 bipyridine (44BPD)-gold molecular junction, i.e., the direct contact of the 44BPD molecule with the Au(1 1 1) surface and the intermediary contact through one extra gold atom on each side, were studied using density functional theory calculations under periodic boundary conditions. The relative position of the Fermi level is changed by the extra gold atom from well below the LUMO (lowest unoccupied molecular orbital) of the 44BPD molecule in the direct contact model to within the energy range of the LUMO in the intermediary contact model, indicating that the local structure of the contact can significantly affect the conducting characteristics of the junction. The dependence of the molecule–electrode interaction on the interface structure was also investigated in details.     

Is styrene planar in liquid phases?

The proton NMR spectra of two (13)C-labeled isotopomers of styrene dissolved in two liquid crystalline solvents have been obtained and analyzed to yield four sets each of 24 dipolar couplings. These couplings were then used to investigate the structure of the ring and the ene fragments of the molecule, and the position of the maximum, phi(0), in the ring-ene bond rotational probability distribution. To do this, the effect on the dipolar couplings of small-amplitude vibrational motion was taken into account using vibrational wave functions calculated by molecular orbital and density functional methods. It is concluded that the NMR data are consistent with the ring fragment, averaged over the ring-ene rotation, planar, while the ene fragment is not. The value of phi(0) is found to be 18.0 degrees +/-0.2 degrees for the two solutions, compared with a value of 27 degrees calculated by the molecular method MP2/6-31G(*).     

Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods

Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.     

Synthesis, conformation, and chemical properties of new mini parallel double-stranded peptides conjugated with -Phe-Phe- and -Phe-Phe-X-sequences

To investigate the chemical conformations and functions of the -Phe-Phe-Val- or -Phe-Phe- sequences contained in the Alzheimer's disease related beta-amyloid peptide, a series of mini parallel double-stranded peptides conjugated with two peptide residues to one spacer were designed and prepared. The structure of the compounds was elucidated by circular dichroism (CD) spectrum and NMR two dimensional (2D) nuclear Overhauser enhancement and exchange spectroscopy (NOESY) measurments. The structure of 1,2-ethano-bis(L-Phe-L-Phe-L-Leu), 1,12-dodecano-bis(L-Phe-L-Phe-L-Leu), 1,12-dodecano-bis(L-Phe-L-Phe-L-Val), and 1,12-dodecano (D-Phe-D-Phe-D-Leu) conjugated with L-Leu and L-Val residues show a beta-turn-like nucleation. The dihedral angles (theta = +75 degrees, omega = +180 degrees, phi = +90 degrees, phi = -87 degrees, psi = +180 degrees) obtained from experimental coupling constant (J) data, etc. support that 1,12-dodecano-bis(L-Phe-L-Phe) adopts beta-turn mimic nucleation. The 1,12-dodecano- bis(L-Leu-L-Leu-L-Phe), 1,12-dodecano-bis(L-lle-L-Phe-L-Leu), and 1,12-dodecano-bis(L-Phe-L-Val-L-Leu), etc. adopt most probably a random structure by CD studies. It was found by titration spectrum that an inclusion complex of 1:1 ratio (association constant; azobenzene (guest, Ka=1.0 x 10(4)M-1) is formed between 1,12-dodecano-bis(L.-Phe-L-Phe-L-Leu) and [L0]=1.758 x 10(-5)M-1). Moreover, the stability of the complexes was increased in order of 1,12-dodecano-bis(L-Phe-L-Phe-L-Leu) x azobenzene> 1,12-dodecano-bis(L-Phe-L-Phe-L-Val) x azobenzene> 1,12-dodecano-bis(L-Phe-L-Val-L-Leu) azobenzene. The data show that X-Phe-L-Phe-L-spacer(S)-L-Phe-L-Phe-X (X=amino acids; S = 1,2-ethano- and 1,12-dodecano-) plays an important role as a binding site of the artificial receptor. The hydrophobic interaction of the four Phes in the two strands is a very interesting issue in the physiological action of proteins as well as the conformation of the backbone of X-L-Phe-L-Phe-spacer(S)-iL-Phe-l.-Phe-X.