Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

Stabilisation of unusual simultaneous binding of four cytosine nucleobases to copper(II) by a novel network of bifurcated hydrogen bonding

The crystal structure of tetrakis(cytosine)copper(II) perchlorate dihydrate has been determined. All the hydrogen atoms were obtained from Fourier-difference synthesis. The geometry around. copper is a bicapped octahedron (4 + 2 + 2*). The adjacent cytosine rings are oriented head-to-tail with respect to each other and are roughly at right angles to the co-ordination plane. The exocyclic oxo groups form an interligand, intracomplex hydrogen-bonding network above and below the co-ordination plane with the exocyclic amino groups of alternate cytosine bases. The EPR and electronic spectra are consistent with the retention of the solid-state structure in solution. The steric effect of the C(2)=O group of cytosine is offset by the presence of the intracomplex hydrogen-bonding network. The trend in Ei values of Cu-II-Cu-I couples for 1.4 complexes of cytosine, cytodine, pyridine, 2-methylpyridine and N-methylimidazole suggests that both steric effects and pi-delocalization in imidazole and pyridine ligands and the steric effect of C(2)=O in pyrimidine ligands are important in stabilising Cu-I relative to Cu-II.

Molecular self-assembly of cadmium-triazolate complexes via hydrogen bonding: Synthesis, structures and photoluminescent properties

Two new cadmium coordination polymers namely Cd(HAmTrz-COO)(4)(NH4+)(2)] 1; and Cd(HAmTrz)(2)I-2](n) 2; (HAmTrz-COOH = 3-amino-1,2,4-triazole-5-carboxylic acid), have been prepared based on HAmTrz-COOH as ligand. The crystal structures of 1 and 2 have been determined by single-crystal X-ray diffraction technique. In coordination-complex 1 four triazole ligands coordinate via N1 nitrogen leading to a tetrahedral geometry around cadmium ion, while in 2 the ligand prefers to coordinate to the metal in a bidentate bridging mode. The structures of both the coordination polymers can be envisaged as 3D hydrogen bonded networks. Thermogravimetric analysis shows that 2 is more stable than 1 owing to different coordination numbers of cadmium atoms. Photoluminescence properties of both the compounds have been investigated in the solid state. (C) 2011 Elsevier B.V. All rights reserved.

Crystal packing and melting temperatures of small oxalate esters: the role of C-H center dot center dot center dot O hydrogen bonding

The simple dialkyl oxalates are generally liquids at room temperature except for dimethyl and di-tert-butyl oxalate which melt at 327 and 343 K. The crystal structures of diethyl, di-iso-propyl, di-n-butyl, di-tert-butyl and methyl ethyl oxalates were determined. The liquid esters were crystallized using the cryocrystallization technique. A comparison of the intermolecular interactions and packing features in these crystal structures was carried out. The crystal structure of dimethyl oxalate was redetermined at various temperatures. The other compounds were also studied at several temperatures in order to assess the attractive nature of the hydrogen bonds therein. A number of moderate to well defined C-H center dot center dot center dot O interactions account for the higher melting points of the two solid esters. Additionally, a diminished entropic contribution Delta S(m) in di-tert-butyl oxalate possibly increases the melting point of this compound further.

Intra-molecular hydrogen bonding with organic fluorine in the solution state: Deriving evidence by a two dimensional NMR experiment

The direct evidence for the existence of intra-molecular C-F center dot center dot center dot H-N hydrogen bond in organofluorine molecules, in the liquid state, is derived using NMR spectroscopy by the detection of long range interactions among fluorine, nitrogen and hydrogen atoms. The present study reports the determination of the relative signs and magnitudes of through space and through bond couplings to draw unambiguous evidence on the existence of weak molecular interactions involving organic fluorine. It is a simple, easy to implement, N-15 natural abundant two dimensional heteronuclear N-15-H-1 double quantum-single quantum correlation experiment. The existence of intra-molecular hydrogen bond is conclusively established in the investigated molecules. (C) 2011 Elsevier B.V. All rights reserved.

Homo- or Heterosynthon? A Crystallographic Study on a Series of New Cocrystals Derived from Pyrazinecarboxamide and Various Carboxylic Acids Equipped with Additional Hydrogen Bonding Sites

Four new cocrystals of a well studied active pharmaceutical ingredient (API), namely, pyrazinecarboxamide (PZA), with various monocarboxylic acids equipped with additional hydrogen bonding sites such as vanillic acid (VA), gallic acid (GA), 1-hydroxy-2-naphthoic acid (1HNA), and indole-2-carboxylic acid (I2CA) have been successfully prepared and characterized by FTIR, H-1 NMR, differential scanning calorimetry (DSC), and single crystal and powder X-ray diffraction (SXRD and PXRD, respectively) techniques. In the majority of the cases, preferential occurrence amide amide and acid acid homosynthons has been observed. Since the heterosynthon is energetically preferred to homosynthon, such unusual occurrence of homosynthon in these cocrystals is intriguing.

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.

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.

ENDOR studies of hydrogen bonding of the AsO44- centre in x-ray irradiated KH2AsO4

We here report what we believe to be an important method for studying hydrogen bonding in systems containing a paramagnetic centre. The technique of electron-nuclear double resonance ( ENDOR) has been applied to study the hydrogen-bond network around the AsO44-. centre in X-ray irradiated KH2AsO4. ENDOR transitions from several sets of hydrogen nuclei surrounding the centre were observed at 4.2 degrees K and the spectra for two sets of neighbouring nuclei are identified. The angular dependences for these spectra are fitted with a spin-Hamiltonian to obtain the isotropic and anisotropic magnetic hyperfine constants. The results are discussed in terms of the available spectroscopic and crystallographic data on KH2AsO4 and the order-disorder model of ferroelectrictricity in this class of crystals.

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.

Hydrogen-Bond-Driven Controlled Molecular Marriage in Covalent Cages

A supramolecular approach that uses hydrogen-bonding interaction as a driving force to accomplish exceptional self-sorting in the formation of imine-based covalent organic cages is discussed. Utilizing the dynamic covalent chemistry approach from three geometrically similar dialdehydes (A, B, and D) and the flexible triamine tris(2-aminoethyl)amine (X), three new 3+2] self-assembled nanoscopic organic cages have been synthesized and fully characterized by various techniques. When a complex mixture of the dialdehydes and triamine X was subjected to reaction, it was found that only dialdehyde B (which has OH groups for H-bonding) reacted to form the corresponding cage B3X2 selectively. Surprisingly, the same reaction in the absence of aldehyde B yielded a mixture of products. Theoretical and experimental investigations are in complete agreement that the presence of the hydroxyl moiety adjacent to the aldehyde functionality in B is responsible for the selective formation of cage B3X2 from a complex reaction mixture. This spectacular selection was further analyzed by transforming a nonpreferred (non-hydroxy) cage into a preferred (hydroxy) cage B3X2 by treating the former with aldehyde B. The role of the H-bond in partner selection in a mixture of two dialdehydes and two amines has also been established. Moreover, an example of unconventional imine bond metathesis in organic cage-to-cage transformation is reported.

Explosives Sensing by Using Electron-Rich Supramolecular Polymers: Role of Intermolecular Hydrogen Bonding in Significant Enhancement of Sensitivity

We demonstrate here that supramolecular interactions enhance the sensitivity towards detection of electron-deficient nitro-aromatic compounds (NACs) over discrete analogues. NACs are the most commonly used explosive ingredients and are common constituents of many unexploded landmines used during World WarII. In this study, we have synthesised a series of pyrene-based polycarboxylic acids along with their corresponding discrete esters. Due to the electron richness and the fluorescent behaviour of the pyrene moiety, all the compounds act as sensors for electron-deficient NACs through a fluorescence quenching mechanism. A Stern-Volmer quenching constant determination revealed that the carboxylic acids are more sensitive than the corresponding esters towards NACs in solution. The high sensitivity of the acids was attributed to supramolecular polymer formation through hydrogen bonding in the case of the acids, and the enhancement mechanism is based on an exciton energy migration upon excitation along the hydrogen-bond backbone. The presence of intermolecular hydrogen bonding in the acids in solution was established by solvent-dependent fluorescence studies and dynamic light scattering (DLS) experiments. In addition, the importance of intermolecular hydrogen bonds in solid-state sensing was further explored by scanning tunnelling microscopy (STM) experiments at the liquid-solid interface, in which structures of self-assembled monolayer of the acids and the corresponding esters were compared. The sensitivity tests revealed that these supramolecular sensors can even detect picric acid and trinitrotoluene in solution at levels as low as parts per trillion (ppt), which is much below the recommended permissible level of these constituents in drinking water.

Dissociation Constants of Weak Acids from ab Initio Molecular Dynamics Using Metadynamics: Influence of the Inductive Effect and Hydrogen Bonding on pK(a) Values

The theoretical estimation of the dissociation constant, or pK(a), of weak acids continues to be a challenging field. Here, we show that ab initio CarParrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pK(a) value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pK(a). We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pK(a) values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pK(a) values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pK(a) values.

Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide

Longitudinal relaxation due to cross-correlation between dipolar ((HN-1H alpha)-H-1) and amide-proton chemical shift anisotropy (H-1(N) CSA) has been measured in a model tripeptide Piv-(L)Pro-(L)Pro-(L)Phe-OMe. The peptide bond across diproline segment is known to undergo cis/trans isomerization and only in the cis form does the lone Phe amide-proton become involved in intramolecular hydrogen bonding. The strength of the cross correlated relaxation interference is found to be significantly different between cis and trans forms, and this difference is shown as an influence of intramolecular hydrogen bonding on the amide-proton CSA. (C) 2015 Elsevier B.V. All rights reserved.