Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

Benzene carboxylic acids and Benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by H-1, C-13 and N-15 NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations. (C) 2012 Elsevier B.V. All rights reserved.

Novel tetranuclear distorted open-cubane copper complex containing oximate bridges: Synthesis, crystal structure, DNA binding and cleavage activity

The synthesis, molecular structure, DNA binding and nuclease activity of Cu4O4 open-cubane tetranuclear copper(II) complex with 3-2-(ethyl amino)ethyl]imino]-2-butanoneoxime (HL) are reported for the first time. The neutral tetranuclear Cu4L4(ClO4)(4)] complex crystallizes in tetragonal space group P (4) over bar2(1)c with the unit cell parameters; a = 13.798(4) angstrom, b = 13.798(4) angstrom, c = 14.119(6) angstrom, V = 2688(16) angstrom(3), Z = 8, R = 0.0636. Symmetrically equivalent copper atoms exhibit a CuN3O3 elongated distorted octahedral coordination environment, with three nitrogen atoms of the L ligand and one oxime-oxygen atom of second L ligand at equatorial positions, one oxime-oxygen atom of the third L ligand and perchlorate oxygen at axial positions. The complex shows quasireversible cyclic voltammetric response at 0.805 V (Delta E-p = 277 mV) at 100 mV s (1) in DMF for the Cu(II)/Cu(I) redox couple. The binding study of the complex with calf-thymus DNA has been investigated using absorption spectrophotometry. The complex shows strong nuclease activity on stranded pBR 322 plasmid DNA in the presence of hydrogen peroxide and marginal nuclease activity in the presence of reducing agent (dithiothreitol). (C) 2012 Elsevier B. V. All rights reserved.

Synthesis, Spectral Characterization, Crystal Structure and Thermal Behavior of Tert-butyl 2,2-bis(2,4-dinitrophenyl)ethanoate

Tert-butyl 2,2-bis(2,4-dinitrophenyl)ethanoate was prepared from the ethanolic solution of 1-chloro-2,4-dinitrobenzene, tert-butyl 3-oxobutanoate and triethylamine. Acetyl group in tert-butyl 3-oxobutanoate has cleaved off during the formation of the title molecule. UV-VIS, IR, 1H NMR, 13C NMR, Proton-Proton COSY data and single crystal XRD results support the proposed structure. Flammability test, impact sensitivity test and TG/DTA studies at different heating rates on the synthesized molecule imply that it is an insensitive high energy density material.

Critical investigation on hydrogen bonding by Fourier transform infrared spectroscopy in hydrogenated amorphous silicon thin films

Fourier Transform Infrared (FTIR) spectroscopic analysis has been carried out on the hydrogenated amorphous silicon (a-Si:H) thin films deposited by DC, pulsed DC (PDC) and RF sputtering process to get insight regarding the total hydrogen concentration (C-H) in the films, configuration of hydrogen bonding, density of the films (decided by the vacancy and void incorporation) and the microstructure factor (R*) which varies with the type of sputtering carried out at the same processing conditions. The hydrogen incorporation is found to be more in RF sputter deposited films as compared to PDC and DC sputter deposited films. All the films were broadly divided into two regions namely vacancy dominated and void dominated regions. At low hydrogen dilutions the films are vacancy dominated and at high hydrogen dilutions they are void dominated. This demarcation is at C-H = 23 at.% H for RF, C-H = 18 at.% H for PDC and C-H = 14 at.% H for DC sputter deposited films. The microstructure structure factor R* is found to be as low as 0.029 for DC sputter deposited films at low C-H. For a given C-H, DC sputter deposited films have low R* as compared to PDC and RF sputter deposited films. Signature of dihydride incorporation is found to be more in DC sputter deposited films at low C-H.

Effect of quantum nuclear motion on hydrogen bonding

This work considers how the properties of hydrogen bonded complexes, X-H center dot center dot center dot Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H center dot center dot center dot O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4-3.0 angstrom, i.e., from strong to weak hydrogen bonds. The position of the proton (which determines the X-H bond length) and its longitudinal vibrational frequency, along with the isotope effects in both are described quantitatively. An analysis of the secondary geometric isotope effect, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of bending modes is also considered: their quantum effects compete with those of the stretching mode for weak to moderate H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several trends. (C) 2014 AIP Publishing LLC.

I. The crystal structure of trimesic acid. II. Topics in crystallographic calculations

I. Trimesic acid (1, 3, 5-benzenetricarboxylic acid) crystallizes with a monoclinic unit cell of dimensions a = 26.52 A, b = 16.42 A, c = 26.55 A, and β = 91.53° with 48 molecules /unit cell. Extinctions indicated a space group of Cc or C2/c; a satisfactory structure was obtained in the latter with 6 molecules/asymmetric unit - C₅₄O₃₆H₃₆ with a formula weight of 1261 g. Of approximately 12,000 independent reflections within the CuK_α sphere, intensities of 11,563 were recorded visually from equi-inclination Weissenberg photographs.

The structure was solved by packing considerations aided by molecular transforms and two- and three-dimensional Patterson functions. Hydrogen positions were found on difference maps. A total of 978 parameters were refined by least squares; these included hydrogen parameters and anisotropic temperature factors for the C and O atoms. The final R factor was 0.0675; the final "goodness of fit" was 1.49. All calculations were carried out on the Caltech IBM 7040-7094 computer using the CRYRM Crystallographic Computing System.

The six independent molecules fall into two groups of three nearly parallel molecules. All molecules are connected by carboxylto- carboxyl hydrogen bond pairs to form a continuous array of sixmolecule rings with a chicken-wire appearance. These arrays bend to assume two orientations, forming pleated sheets. Arrays in different orientations interpenetrate - three molecules in one orientation passing through the holes of three parallel arrays in the alternate orientation - to produce a completely interlocking network. One third of the carboxyl hydrogen atoms were found to be disordered.

II. Optical transforms as related to x-ray diffraction patterns are discussed with reference to the theory of Fraunhofer diffraction.

The use of a systems approach in crystallographic computing is discussed with special emphasis on the way in which this has been done at the California Institute of Technology.

An efficient manner of calculating Fourier and Patterson maps on a digital computer is presented. Expressions for the calculation of to-scale maps for standard sections and for general-plane sections are developed; space-group-specific expressions in a form suitable for computers are given for all space groups except the hexagonal ones.

Expressions for the calculation of settings for an Eulerian-cradle diffractometer are developed for both the general triclinic case and the orthogonal case.

Photographic materials on pp. 4, 6, 10, and 20 are essential and will not reproduce clearly on Xerox copies. Photographic copies should be ordered.

Crystal structure and characterization of a new μ-oxo bridged iron porphyrin

Comunicacion a congreso: Póster presentado en VIII Reunión Científica de Bioinorgánica – Bioburgos 2013 (Burgos, 7 al 10 de julio de 2013)

Kinetics of picosecond laser pulse induced charge separation and proton transfer in bacteriorhodopsin

Bacteriorhodopsin (BR) films oriented by an electrophoretic method are deposited on a transparent conductive ITO glass. A counterelectrode of copper and gelose gel is used to compose a sandwich-type photodetector with the structure of ITO/BR film/gelose gel/Cu. A single 30-ps laser pulse and a mode-locked pulse train are respectively used to excite the BR photodetector. The ultrafast failing edge and the bipolar response signal are measured by the digital oscilloscope under seven different time ranges. Marquardt nonlinear least squares fitting is used to fit all the experimental data and a good fitting equation is found to describe the kinetic process of the photoelectric signal. Data fitting resolves six exponential components that can be assigned to a seven-step BR photocycle model: BR-->K-->KL-->L-->M-->N-->O-->BR. Comparing tests of the BR photodetector with a 100-ps Si PIN photodiode demonstrates that this type of BIR photocletector has at least 100-ps response time and can also serve as a fast photoelectric switch. (C) 2003 Society of Photo-Optical Instrumentation Engineers.

Effect of block sequence and block length on the stimuli-responsive behavior of polyampholyte brushes: hydrogen bonding and electrostatic interaction as the driving force for surface rearrangement

Diblock polyampholyte brushes with different block sequences (Si/SiO2/poly(acrylic acid)-b-poly (2-vinylpyridine) (PAA-b-P2VP) brushes and Si/SiO2/P2VP-b-PAA brushes) and different block lengths were synthesized by sequent surface-initiated atom transfer radical polymerization (ATRP). The PAA block was obtained through hydrolysis from the corresponding poly(tert-butyl acrylate). The polyampholyte brushes demonstrated unique pH-responsive behavior. In the intermediate pH region, the brushes exhibited a less hydrophilic wetting behavior and a rougher surface morphology due to the formation of polyelectrolyte complex through electrostatic interaction between oppositely charged blocks. In the low pH and high pH regions, the rearrangement of polyampholyte brushes showed great dependence on the block sequence and block length. The polyampholyte brushes with P2VP-b-PAA sequence underwent rearrangement during alternative treatment by acidic aqueous solution (low pH value) and basic aqueous solution (high pH value).

Hydrothermal synthesis, crystal structure and electrochemical properties of a novel 3D Dawson-type polyoxometalate supramolecular network

A novel Dawson-type polyoxometalate supramolecular architecture of the formula [4,4'-H(2)bipy](2.5)center dot[4,4'-Hbipy]center dot[P2W18O62]center dot 6.25H(2)O (4,4'-bipy = 4,4'-bipyridine) has been hydrothermally synthesised and characterised by means of elemental analysis, IR, CV and X-ray single-crystal diffraction. X-ray crystallography indicates that the title compound consists of Dawson-type polyoxoaions [P2W18O62](6-), water molecules and 4,4'-bipy units. The polyoxoanion clusters together with 4,4'-bipy units and water molecules to construct the three-dimensional supramolecular network through hydrogen bonds. The crystal structure analyses reveal that water molecules and 4,4'-bipy units play the important role on the packing arrangements of crystals. Cyclic voltammetry shows that the title compound exhibits three chemically reversible steps

Hydrothermal synthesis and crystal structure of a sulfur-bridged binuclear copper(II) coordination polymer generated by a spontaneous reduction

A simultaneous reduction SO42- to S2- by 2,5-pyridinedicarboxylate under hydrothermal conditions produced a new binuclear copper(II) coordination polymer [CuS(4,4'-bipy)](n) (4,4-bipy = 4,4'-bipyridine) (1). Single crystal X-ray analysis revealed that compound I consisted of sulfur-bridged binuclear copper(II) units with Cu-Cu bonding which were combined with 4,4-bipy to generate a three-dimensional network constructed from mutual interpenetration of two-dimensional (6,3) nets. Crystal data for 1:C10H8CuN2S, tetragonal 14(1)/acd, a = 14.0686(5) Angstrom, b = 14.0686(5) Angstrom, c = 38.759(2) Angstrom, Z = 32. Other characterizations by elemental analysis, IR, EPR and TGA analysis were also described in this paper.

Synthesis, crystal structure, and magnetic properties of {[Cu(oxbe)]Mn(H2O)[Cu(oxbe)(DMF)]}(n)center dot nDMF center dot nH(2)O: From dissymmetrical mononuclear entities to a 3D heterometallic supramolecular coordination polymer

Self-assembly of the building block [Cu(oxbe)](-) with Mn(II) led to a novel coordination polymer {[Cu(oxbe)]Mn(H2O)(Cu(oxbe)(DMF)]}(n).nDMF.nH(2)O, where H(3)oxbe is a new dissymmetrical ligand N-benzoato-N'-(2-aminoethyl)-oxamido and DMF = dimethylformamide. The crystal forms in the triclinic system, space group P(1)over-bar, with a = 9.260(4) angstorm, b = 12.833(5) angstrom, c = 15.274(6) angstrom , alpha = 76.18(3)degrees, beta = 82.7(3)degrees, gamma = 82.31(3)degrees, and Z = 2. The crystal structure of the title complex reveals that the two-dimensional bimetallic layers are constructed of (CuMnII)-Mn-II-Cu-II chains linked together by carboxylate bridge and hydrogen bonds help to produce a novel three-dimensional channel-like structure. The magnetic susceptibility measurements (5-300 K) were analyzed by means of the Hamiltonian (H)over-cap = -2J(S)over-cap (Mn)((S)over-cap(Cu1) + (S)over-cap(Cu2)), leading to J = -17.4 cm(-1).

From dissymmetrical mononuclear entities to centrosymmetrical heterotrinuclear complex with 2D supramolecular structure: synthesis, characterization, crystal structure, and magnetic properties

A new centrosymmetrical heterotrinuclear complex, {[Cu(oxbe)](2)Co(H2O)(2)}.2DMF.DMA with 2D supramolecular structure, has been obtained by the self-assembly of a dissymmetrical building block [Cu(oxbe)](-) with bivalent metal ion Co2+, where H(3)oxbe is dissymmetrical ligand N-benzoato-N'-(2-aminoethyl)oxamido, DMF = dimethylformamide, DMA = dimethylamine. Its structure was determined by single crystal X-ray analysis. The molecular structure is centrosymmetrical with the cobalt atom lying on an inversion center. Through the hydrogen bonds and d-pi stacking interactions, a 2D supramolecular structure is formed. This study exemplifies a new method for the assembly of supramolecular structure using a dissymmetrical brick. Magnetic susceptibility measurements (5-300 K) indicate that the central cobalt and terminal copper metal ions are antiferromagnetically coupled with J = -23.1 cm(-1).

Oxamido-bridged heterobinuclear copper(II)-nickel(II) complex and homotrinuclear nickel(II) complex with 2D supramolecular structure: synthesis, crystal structure, magnetic and spectroscopic properties

The oxamido-bridged heterobinuclear copper(II)-nickel(II) complex, [Cu(oxbe)Ni(phen)(2)]ClO4.3H(2)O (1) and homotrinuclear nickel(11) complex {[Ni(oxbe)](2)Ni(H2O)(2)}.2.5DMF (2) have been synthesized and characterized by means of elemental analysis, IR, EPR. and electronic spectra and magnetic susceptibility, where H(3)oxbe is dissymmetrical ligand N-benzoato-N'-(2-aminoethyl)ox-amido, phen = 1.10-phenanthroline, DMF = dimethylformamide. Complex I has an extended oxamido-bridged structure consisting of planar copper(II) and octahedral nickel(II) ions. The chi(M) and mu(eff) versus T plots of 1 is typical of an antiferromagnetically coupled Cu(II)-Ni(II,) pair with a spin-doublet ground state, and magnetic analysis leads to J = -57.1 cm(-1). The molecular structure of 2 is centrosymmetrical, with one octahedral nickel atom lying at an inversion center and two terminal Ni(II) atoms in approximately square planar environment. Through the hydrogen bonds and pi- pi stacking interactions, a 2D supramolecular structure is formed.