Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Conformational Analysis of a 20-Membered Cyclic Peptide Disulfide from Conus virgo with a WPW Segment: Evidence for an Aromatic-Proline Sandwich

A novel peptide containing a single disulfide bond, CIWPWC (Vi804), has been isolated and characterised from the venom of the marine cone snail, Conus virgo. A precursor polypeptide sequence derived from complementary DNA, corresponding to the M-superfamily conotoxins, has been identified. The identity of the synthetic and natural peptide sequence has been established. A detailed analysis of the conformation in solution is reported for Vi804 and a synthetic analogue, (CIWPWC)-W-D ((D)W3-Vi804), in order to establish the structure of the novel WPW motif, which occurs in the context of a 20-membered macrocyclic disulfide. Vi804 exists exclusively in the cis W3P4 conformer in water and methanol, whereas (D)W3-Vi804 occurs exclusively as the trans conformer. NMR spectra revealed a W3P4 typeVI turn in Vi804 and a typeII turn in the analogue peptide, (D)W3-Vi804. The extremely high-field chemical shifts of the proline ring protons, together with specific nuclear Overhauser effects, are used to establish a conformation in which the proline ring is sandwiched between the flanking Trp residues, which emphasises a stabilising role for the aromatic-proline interactions, mediated predominantly by dispersion forces.

Heteronuclear proton double quantum-carbon single quantum scalar correlation in solids

A new NMR experiment that exploits the advantages of proton double quantum (DQ) NMR through a proton DQ-carbon single quantum (SQ) correlation experiment in the solid state is proposed. Analogous to the previously proposed 2D H-1 (DQ)-C-13 refocused INEPT experiment (Webber et al., 2010), the correlation between H-1 and C-13 is achieved through scalar coupling evolution, while the double quantum coherence among protons is generated through dipolar couplings. However, the new experiment relies on C-13 transverse coherence for scalar transfer. The new experiment dubbed MAS-J-H-1 (DQ)-C-13-HMQC, is particularly suited for unlabeled molecules and can provide higher sensitivity than its INEPT counterpart. The experiment is applied to four different samples. (C) 2014 Elsevier Inc. All rights reserved.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative disallowed conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (phi, =180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (c) 2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 21-36, 2015.

Measurement of Large Dipolar Couplings of a Liquid Crystal with Terminal Phenyl Rings and Estimation of the Order Parameters

NMR spectroscopy is a powerful means of studying liquid-crystalline systems at atomic resolutions. Of the many parameters that can provide information on the dynamics and order of the systems, H-1-C-13 dipolar couplings are an important means of obtaining such information. Depending on the details of the molecular structure and the magnitude of the order parameters, the dipolar couplings can vary over a wide range of values. Thus the method employed to estimate the dipolar couplings should be capable of estimating both large and small dipolar couplings at the same time. For this purpose, we consider here a two-dimensional NMR experiment that works similar to the insensitive nuclei enhanced by polarization transfer (INEPT) experiment in solution. With the incorporation of a modification proposed earlier for experiments with low radio frequency power, the scheme is observed to enable a wide range of dipolar couplings to be estimated at the same time. We utilized this approach to obtain dipolar couplings in a liquid crystal with phenyl rings attached to either end of the molecule, and estimated its local order parameters.

Design of symmetric TIM barrel proteins from first principles

Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (alpha/beta)(8) TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T-m of 44 degrees C and a Gibbs free energy of unfolding (Delta G degrees) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C-m of 1.6 M and a Delta G degrees of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Self-assembly of Metallamacrocycles Employing a New Benzil-based Organometallic Bisplatinum(II) Acceptor

A benzil-based semi-rigid dinuclear organometallic acceptor 4,4'-bistrans-Pt(PEt3)(2)(NO3)(ethynyl)]benzil (bisPt-NO3) containing a Pt-ethynyl functionality was synthesized in good yield and characterized by multinuclear NMR (H-1, P-31, and C-13), electrospray ionization mass spectrometry (ESI-MS), and single-crystal X-ray diffraction analysis of the iodide analogue bisPt-I. The stoichiometric (1:1) combination of the acceptor bisPt-NO3 separately with four different ditopic donors (L-1-L-4; L-1 = 9-ethyl-3,6-di(1H-imidazol-1-yl)-9H-carbazole, L-2 = 1,4-bis((1H-imidazol-1-yl)methyl)benzene, L-3 = 1,3-bis((1H-imidazol-1-yl)methyl)benzene and L-4 = 9,10-bis((1H-imidazol-1-yl) methyl)anthracene) yielded four 2 + 2] self-assembled metallacycles M-1-M-4 in quantitative yields, respectively. All these newly synthesized assemblies were characterized by various spectroscopic techniques (NMR, IR, ESI-MS) and their sizes/shapes were predicted through geometry optimization employing the PM6 semi-empirical method. The benzil moiety was introduced in the backbone of the acceptor bisPt-NO3 due to the interesting structural feature of long carbonyl C-C bond (similar to 1.54 angstrom), which enabled us to probe the role of conformational flexibility on size and shapes of the resulting coordination ensembles.

A 1h And 13c Magnetic Resonance And Infrared Spectroscopic Study Of Coordinated 2-Aminocyclopentene-1-Dithiocarboxylic Acid And Its S-Methyl Ester

The ligating properties of 2-aminocyclopentene-1-dithiocarboxylic acid and its S-methyl esters were investigated. Complexes with Zn(II), Cd(II) and Hg(II) halides were synthesized and characterized by infrared and proton and carbon-13 NMR studies. The results are concordant with a bidentate coordination of the -CS2 group to the metal ions

Synthesis and structure of mixed ligand isonitroso-β-ketoiminenickel(II) complexes. Crystal structure of (1-ethoxycarbonyl-2-npropylimino-1-propanoneoximato) (1-methoxycarbonyl-2-imino-1-propanoneoximato)nickel(II)

Mixed ligand complexes of the type Ni(R-AB)(AC') and Ni(R-AC)(AB') where AB/AC denote N-bonded isonitroso- [3-ketoimino ligands, AB'/AC' denote the corresponding Obonded ligands and R = Me, Et, n-Pr are synthesised and characterised. The complexes are neutral with square planar geometry around nickel(II). The bonding isomerism of the isonitroso group is discussed on the basis of i.r. and 1H n.m.r. studies. The crystal structure of the title complex, Ni(n-Pr-IEAI)(IMAI') has been determined from diffractometer data by Patterson and Fourier methods and refined by least squares to R = 0.088 for 2209 observed reflections. Unit cell constants are: a = 11.945(2), b = 22.436(7), c = 13.248(5) ~, [3 = 95.13(2) ~ The space group is P2Jc with Z = 8. Niekel(II) has a square planar coordination of two imine nitrogens, an isonitroso-nitrogen (from n-Pr-IEAI) and another isonitrosooxygen (from IMAI').

Thermally Induced Acyl Migration in Salicylamides. 1. Structures of the Reactants, O-Acetylsalicylamide and O-Benzoylsalicylamide

O-Acetylsalicylamide (Ia), C9H9NO3, M r =179.18, monoclinic, P2Jc, a=8.155(5), b=8.571 (2), c= 13.092 (3)A, fl=99.54 (5) ° , V= 902.4(6)A 3, Z=4, Dm=l.31, Dx=l.319gcm -3, 2(Mo Ka) = 0.71069 A,/~ = 1.08 cm -1, F(000) = 376, T = 295 K, R = 0.076 for 1604 reflections. O-Benzoylsalicylamide (Ib), C14HtlNO 3, M,=241.2, monoclinic, P2t/e, a=9.423(1), b=5.116(1), e= 26.424 (2) A, fl= 103.97 (1)% V= 1236.2 (3)/~3, Z= 4, D~ = 1.28, D x = 1.296 gcm -3, ,;L(Cu Ks) = 1.5418 A, p = 7.71 cm-', F(000) = 504, T= 295 K, R =0.050 for 2115 reflections. The dihedral angles between the amide group and the benzene ring are 39.9 ° (Ia) and 37.9 ° (Ib), whereas between the acyl group and the benzene ring they are 78.1 ° (Ia) and 93.4 ° (Ib). The differences in the packing of the two structures are brought out in terms of the observed hydrogen-bonding patterns. Based on the crystallographic results, an intramolecular mechanism for the migration of the acyl group from the O to the N position is suggested in both compounds.

On Coloration of Polyacrylonitrile: A Nuclear Magnetic Resonance Study

Coloration in polyacrylonitrile can be induced in three distinct ways: by heat treatment, by treatment with base, or during synthesis of the polymer itself using ionic initiators at relatively higher temperatures. The present investigation employing 'H and NMR spectroscopy has revealed some common features in colored polyacrylonitrile irrespective of ita mode of coloration. All colored polyacrylonitriles give an additional peak around S 2.7 in 'H NMR spectra and, except for heat-treated polyacrylonitrile, one extra group of peaks in the region 8 12-16 in 13C NMR spectra. The former peak has been attributed to methine and/or methylene protons in branched and/or cyclized structures, while the latter peak has been attributed to methylene carbon atoms in the branched structure. Colorless polyacrylonitriles have been found to be predominantly heterotactic, while colored polyacrylonitriles have been found to have appreciable isotactic contribution.

Studies of phosphazenes. 12. Reactions of N4P4Cl8 with dibenzylamine- isolation of an unusual "bicyclic" phosphazene, N4P4[N(CH2Ph)2]6(NCH2Ph)

Octachlorocyclotetraphosphazene, N4P4CIa, reacts with dibenzylamine to give the chloro(dibenzy1amino) derivatives, N4P,C18,[N(CH2Ph)2],,, n = 1, 2 (two isomers), and 4 (three isomers). Nongeminal structures have been assigned to these compounds on the basis of ‘H and jlP NMR spectra. The presence of at least two tris(dibenzylamin0) derivatives in some reaction mixtures is also inferred from NMR spectra. Steric effects become important at the tetrakis stage of chlorine replacement, and further substitution by dibenzylamine to give monocyclic tetrameric derivatives does not occur. A “bicyclic” phosphazene, N4P4[N(CH2Ph)2]6(NCHzPh)is, obtained from the reaction of N4P4Claw ith an excess of dibenzylamine in boiling methyl cyanide. The formation of this derivative and its spectroscopic data are discussed.

Complexes of lanthanide iodides with 4-methylpyridine-1-oxide and 2-methylpyridine-1-oxide

Complexes of lanthanide iodides with 4-methylpyridine-1-oxide and 2-methylpyridine-1-oxide of the formulae Ln(4-MePyO)8I3.xH2O (x=0 or 2) and Ln(2-MePyO)5I3.xH2O (x=0, 1 or 3) have been prepared and characterized by analyses, conductance, infrared and proton NMR data. Infrared spectra of the complexes indicate that the coordination of the ligand to the metal ion takes place through the oxygen of the N-O group of the ligand. Proton NMR data for the paramagnetic complexes indicate that both contact and pseudocontact interactions are responsible for the isotropic shifts. Proton NMR spectra of the 2-methylpyridine-1-oxide complexes indicate a restricted rotation of the ligand about the N-O group.