306 resultados para Hydrogen Bond


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Experimental and theoretical charge density analyses on 2,2-dibromo-2,3-dihydroinden-1-one have been carried out to quantify the topological features of a short CBr....O halogen bond with nearly linear geometry (2.922 angstrom, angle CBr....O = 172.7 degrees) and to assess the strength of the interactions using the topological features of the electron density. The electrostatic potential map indicates the presence of the s-hole on bromine, while the interaction energy is comparable to that of a moderate OH....O hydrogen bond. In addition, the energetic contribution of CH.....Br interaction is demonstrated to be on par with that of the CBr....O halogen bond in stabilizing the crystal structure.

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Solvent effects play a vital role in various chemical, physical, and biological processes. To gain a fundamental understanding of the solute-solvent interactions and their implications on the energy level re-ordering and structure, UV-VIS absorption, resonance Raman spectroscopic, and density functional theory calculation studies on 9,10-phenanthrenequinone (PQ) in different solvents of diverse solvent polarity has been carried out. The solvatochromic analysis of the absorption spectra of PQ in protic dipolar solvents suggests that the longest (1n-pi(1)*; S-1 state) and the shorter (1 pi-pi(1)*; S-2 state) wavelength band undergoes a hypsochromic and bathochromic shift due to intermolecular hydrogen bond weakening and strengthening, respectively. It also indicates that hydrogen bonding plays a major role in the differential solvation of the S-2 state relative to the ground state. Raman excitation profiles of PQ (400-1800 cm(-1)) in various solvents followed their corresponding absorption spectra therefore the enhancements on resonant excitation are from single-state rather than mixed states. The hyperchromism of the longer wavelength band is attributed to intensity borrowing from the nearby allowed electronic transition through vibronic coupling. Computational calculation with C-2 nu symmetry constraint on the S-2 state resulted in an imaginary frequency along the low-frequency out-of-plane torsional modes involving the C=O site and therefore, we hypothesize that this mode could be involved in the vibronic coupling. (C) 2015 AIP Publishing LLC.

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The structure of a new cysteine framework (-C-CC-C-C-C) ``M''-superfamily conotoxin, Mo3964, shows it to have a beta-sandwich structure that is stabilized by inter-sheet cross disulfide bonds. Mo3964 decreases outward K+ currents in rat dorsal root ganglion neurons and increases the reversal potential of the Na(V)1.2 channels. The structure of Mo3964 (PDB ID: 2MW7) is constructed from the disulfide connectivity pattern, i.e., 1-3, 2-5, and 4-6, that is hitherto undescribed for the ``M''-superfamily conotoxins. The tertiary structural fold has not been described for any of the known conus peptides. NOE (549), dihedral angle (84), and hydrogen bond (28) restraints, obtained by measurement of (h3)J(NC') scalar couplings, were used as input for structure calculation. The ensemble of structures showed a backbone root mean square deviation of 0.68 +/- 0.18 angstrom, with 87% and 13% of the backbone dihedral (phi, psi) angles lying in the most favored and additional allowed regions of the Ramachandran map. The conotoxin Mo3964 represents a new bioactive peptide fold that is stabilized by disulfide bonds and adds to the existing repertoire of scaffolds that can be used to design stable bioactive peptide molecules.

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The survival protein SurE from Salmonella typhimurium (StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of beta-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167 degrees. New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11 degrees between the B chains upon superposition of the A chains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.

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A new, phenoxo-bridged Cu-II dinuclear complex Cu-2(L)(2)(DMF)(2)] (1) has been obtained by employing the coumarin-assisted tridentate precursor, H2L, benzoic acid(7-hydroxy-4-methyl-2-oxo-2H-chromen-8-ylmethylene)-hydrazide]. Complex 1 has been systematically characterized by FTIR, UV-Vis, fluorescence and PR spectrometry. The single crystal X-ray diffraction analysis of 1 shows that the geometry around each copper ion is square pyramidal, comprising two enolato oxygen atoms belonging to different ligands (which assemble the dimer bridging the two metal centers), one imine-N and one phenolic-O atoms of the Schiff base and one oxygen atom from the DMF molecule. The temperature dependent magnetic interpretation agrees with the existence of weak ferromagnetic interactions between the bridging dinuclear Cu(II) ions. Both the ligand and complex 1 exhibit anti-mycobacterial activity and considerable efficacy towards M. tuberculosis H37Rv ATCC 27294 and M. tuberculosis H37Ra ATCC 25177 strains. The cytotoxicity study on human adenocarcinoma cell lines (MCF7) suggests that the ligand and complex 1 have potential anticancer properties. Molecular docking of H2L with the enoyl acyl carrier protein reductase of M. tuberculosis H37R(v) (PDB ID: 4U0K) is examined and the best docked pose of H2L shows one hydrogen bond with Thr196 (1.99 angstrom).

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Experimental charge density analysis combined with the quantum crystallographic technique of X-ray wavefunction refinement (XWR) provides quantitative insights into the intra-and intermolecular interactions formed by acetazolamide, a diuretic drug. Firstly, the analysis of charge density topology at the intermolecular level shows the presence of exceptionally strong interaction motifs such as a DDAA-AADD (D-donor, A-acceptor) type quadruple hydrogen bond motif and a sulfonamide dimer synthon. The nature and strength of intra-molecular S center dot center dot center dot O chalcogen bonding have been characterized using descriptors from the multipole model (MM) and XWR. Although pure geometrical criteria suggest the possibility of two intra-molecular S center dot center dot center dot O chalcogen bonded ring motifs, only one of them satisfies the ``orbital geometry'' so as to exhibit an interaction in terms of an electron density bond path and a bond critical point. The presence of `s-holes' on the sulfur atom leading to the S center dot center dot center dot O chalcogen bond has been visualized on the electrostatic potential surface and Laplacian isosurfaces close to the `reactive surface'. The electron localizability indicator (ELI) and Roby bond orders derived from the `experimental wave function' provide insights into the nature of S center dot center dot center dot O chalcogen bonding.

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The photochemistry of aromatic ketones plays a key role in various physicochemical and biological processes, and solvent polarity can be used to tune their triplet state properties. Therefore, a comprehensive analysis of the conformational structure and the solvent polarity induced energy level reordering of the two lowest triplet states of 9,10-phenanthrenequinone (PQ) was carried out using nanosecond-time-resolved absorption (ns-TRA), time-resolved resonance Raman (TR3) spectroscopy, and time dependent-density functional theory (TD-DFT) studies. The ns-TRA of PQ in acetonitrile displays two bands in the visible range, and these two bands decay with similar lifetime at least at longer time scales (mu s). Interestingly, TR3 spectra of these two bands indicate that the kinetics are different at shorter time scales (ns), while at longer time scales they followed the kinetics of ns-TRA spectra. Therefore, we report a real-time observation of the thermal equilibrium between the two lowest triplet excited states of PQ assigned to n pi* and pi pi* of which the pi pi* triplet state is formed first through intersystem crossing. Despite the fact that these two states are energetically close and have a similar conformational structure supported by TD-DFT studies, the slow internal conversion (similar to 2 ns) between the T-2(1(3)n pi*) and T-1(1(3)pi pi*) triplet states indicates a barrier. Insights from the singlet excited states of PQ in protic solvents J. Chem. Phys. 2015, 142, 24305] suggest that the lowest n pi* and pi pi* triplet states should undergo hydrogen bond weakening and strengthening, respectively, relative to the ground state, and these mechanisms are substantiated by TD-DFT calculations. We also hypothesize that the different hydrogen bonding mechanisms exhibited by the two lowest singlet and triplet excited states of PQ could influence its ISC mechanism.

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Highly conserved residues in enzymes are often found to be clustered close to active sites, suggesting that functional constraints dictate the nature of amino acid residues accommodated at these sites. Using the Plasmodiumfalciparum triosephosphate isomerase (PfTIM) enzyme () as a template, we have examined the effects of mutations at positions 64 and 75, which are not directly involved in the proton transfer cycle. Thr (T) occurring at position 75 is completely conserved, whereas only Gln (Q) and Glu (E) are accommodated at position 64. Biophysical and kinetic data are reported for four T75 (T75S/V/C/N) and two Q64 (Q64N/E) mutants. The dimeric structure is weakened in the Q64E and Q64N mutants, whereas dimer integrity is unimpaired in all four T75 mutants. Measurement of the concentration dependence of enzyme activity permits an estimate of K-d values for dimer dissociation (Q64N=73.79.2nm and Q64E=44.6 +/- 8.4nm). The T75S/V/C mutants have activities comparable to the wild-type enzyme, whereas a fourfold drop is observed for T75N. All four T75 mutants show a dramatic fall in activity between 35 degrees C and 45 degrees C. Crystal structure determination of the T75S/V/N mutants provides insights into the variations in local interactions, with the T75N mutant showing the largest changes. Hydrogen-bond interactions determine dimer stability restricting the choice of residues at position 64 to Gln (Q) and Glu (E). At position 75, the overwhelming preference for Thr (T) may be dictated by the imperative of maintaining temperature stability of enzyme activity.

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Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and A beta peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH <= 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR.

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A combined experimental (infrared, Raman and NMR) and theoretical quantum chemical study is performed on the charge-transfer complex hydroxyethylammonium picrate (HEAP). The infrared (IR) spectra for HEAP were recorded at various temperatures, ranging from 16 K to 299 K, and the Raman spectrum was recorded at room temperature. A comparison of the experimental IR and Raman spectra with the corresponding calculated spectra was done, in order to facilitate interpretation of the experimental data. Formation of the HEAP complex is evidenced by the presence of the most prominent characteristic bands of the constituting groups of the charge-transfer complex e.g., NH3+, CO- and NO2]. Vibrational spectroscopic analysis, together with natural bond orbital (NBO) and theoretical charge density analysis in the crystalline phase, was used to shed light on relevant structural details of HEAP resulting from deprotonation of picric acid followed by formation of a hydrogen bond of the N-H center dot center dot center dot OC type between the hydroxyethylammonium cation and the picrate.C-13 and H-1 NMR spectroscopic analysis are also presented for the DMSO-d(6) solution of the compound revealing that in that medium the HEAP crystal dissolves forming the free picrate and hydroxyethylammonium ions. Finally, the electron excitation analysis of HEAP was performed in an attempt to determine the nature of the most important excited states responsible for the NLO properties exhibited by the compound. (C) 2015 Elsevier B.V. All rights reserved.

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Reaction of a ditopic urea ``strut'' (L-1) with cis-(tmen)Pd(NO3)(2) yielded a 3+3] self-assembled molecular triangle (T)L-1 = 1,4-di(4-pyridylureido)benzene; tmen = N,N,N',N'-tetrame-thylethane-1,2-diamine]. Replacing cis-(tmen)Pd(NO3)(2) in the above reaction with an equimolar mixture of Pd(NO3)(2) and a clip-type donor (L-2) yielded a template-free multicomponent 3D trigonal prism (P) decorated with multiple urea moieties L-2 = 3,3'-(1H-1,2,4-triazole-3,5-diyl)dipyridine]. This prism (P) was characterized by NMR. spectroscopy, and the structure was confirmed by X-ray crystallography. The P was employed as an effective hydrogen-bond-donor catalyst for Michael reactions of a series of water-insoluble nitro-olefins in an aqueous medium. The P showed better catalytic activity compared to the urea based ligand L-1 and the triangle T. Moreover, the confined nanospace of P in addition to large product outlet windows makes this 3D architecture a perfect molecular vessel to catalyze Diels-Alder reactions of 9-hydroxymethylanthracene with N-substituted maleimide in the aqueous medium. The present results demonstrate new observations on catalytic aqueous Diels-Alder and Michael reactions in heterogeneous fashion employing a discrete 3D architecture of Pd(II). The prism was recycled by simple filtration and reused several tithes without significant loss of activity.

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One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

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The Zeeman effect of chlorine nuclear quadrupole resonance in polycrystalline samples of 2,6-, 2,5 and 3,5-dichlorophenol has been investigated at room temperature in order to study the effect of hydrogen bonding on the electric field gradient asymmetry parameter n. While the two n.q.r. lines in 3,5-dichlorophenol gave an asymmetry parameter of 10%, those in 2,6- and 2,5-dichlorophenol gave different values of n for the two chlorines. The chlorine atom which is ortho to the OH group and involved in hydrogen bonding (i.e., corresponding to the low frequency line) gave an asymmetry parameter of 0.21 in 2,6-dichlorophenol and 0.17 in 2,5-dichlorophenol while the other chlorine (i.e., corresponding to the high frequency line) gave a lower value of 0.12 in 2,6-dichlorophenol and 0.11 in 2,5-dichlorophenol. These values of n are discussed in terms of hydrogen bonding and bond parameters.

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The perturbation treatment previously given is extended to explain the process of hydrogen abstraction from the various hydrogen donor molecules by the triplet nπ* state of ketones or the ground state of the alkyl or alkoxy radical. The results suggest that, as the ionization energy of the donor bonds is decreased, the reaction is accelerated and it is not influenced by the bond strength of the donor bonds. The activation barrier in such reactions arises from a weakening of the charge resonance term as the ionization energy of the donor bond increases.

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The perturbation treatment previously given is extended to explain the process of hydrogen abstraction from the various hydrogen donor molecules by the triplet nπ* state of ketones or the ground state of the alkyl or alkoxy radical. The results suggest that, as the ionization energy of the donor bonds is decreased, the reaction is accelerated and it is not influenced by the bond strength of the donor bonds. The activation barrier in such reactions arises from a weakening of the charge resonance term as the ionization energy of the donor bond increases.