Hydrogen Bond Lengths Research Articles

A density functional theory and quantum theory of atoms in molecules study on hydrogen bonding interaction between paracetamol and water molecules

To consider the hydrogen bonding interactions between paracetamol and water molecules, probable complexes of paracetamol from three active sites (carbonyl oxygen atom, hydroxyl oxygen atom, and nitrogen atom) with H2O molecule were formed. The optimized geometries and total energies have been obtained at the B3PW91/6-31+G(d, p) level of theory. Comparison of hydrogen bond lengths and the energies of complexes showed hydrogen bond that form between the oxygen atom of the carbonyl group and hydrogen atom is stronger than others. Moreover, an increase in the number of hydrogen bonds increases stability of paracetamol-water complexes. At the end, the QTAIM was applied to explain the nature of the hydrogen bonds and confirm the more stability by complexation.

The Crystal Structure and Behavior of Fenamic Acid-Acridine Complex Under High Pressure

The crystal structure of fenamic acid-acridine complex is determined by X-ray diffraction. The strong OHN hydrogen bond linking the complex components and other interactions responsible for packing of the molecules into a crystal are investigated within the Quantum Theory of Atom in Molecule theory. The crystal structure is compared with the structure optimized at B3LYP/6-311++G** level and with the theoretical structures optimized under systematically changed pressure. Analysis of the lattice constants, hydrogen bond lengths, and angles of the inter- and intramolecular hydrogen bond under compression is performed. The structural transformation observed at 5 GPa is connected with a change in the intermolecular OHN hydrogen bond. The proton shifts to acceptor and a new interaction in the crystal appears.

IN-SILICO ANALYSIS

ntroduction: Different pathogen reducing technologies are being implementedwhich includes S-303. CD-61 is important receptor for clotting. Pathogen reducing agents arebeing studied extensively to probe its effects. Objective: We conducted this study to reviewthe docking of S-303 at CD-61, to look into the effect of S-303 on function of platelets. StudyDesign: This was an observational study. Setting: In-silico study. Period: March 2015 toAugust 2015. Method: The study was carried out in-silico. PDB (Protein data bank) code ofTirofiban bound to CD-61 was 2vdm. CD-61 was docked with Tirofiban using online dockingtools i.e. Patchdock and Firedock. Then, S-303 and CD-61 were also docked. Best dockingposes to active sites of 2vdm were found. Interactions of ligands and CD-61 were obtained.Then comparison of Hydrogen Bonds, Hydrogen Bond Lengths, Hydrophobic bonds of 2vdmmolecule and best poses of docking results were done. Patchdock and Firdock results of bestposes were also analyzed using SPSS-16. Results: The Hydrogen bonds and Hydrogen bondlength and hydrophobic bonds of docking results were compared to 2vdm. 2 best poses wereobtained for docking of tirofiban to CD-61. No docking to active site was observed in Patchdockand firedock for S-303to CD-61. Conclusion: S-303 did not bind to the active site of CD-61. Wecan assume that S-303 doe

Two-dimensional molecular simulations using rose potentials

Molecular simulations of two-dimensional (2D) systems can provide behavior and insight analogous to three-dimensional systems, often with reduced complexity and computational cost. We describe here an approach for molecular dynamics simulation of single point particles using rose potentials for orientation dependent pairwise interactions. Modifying both the shape and range of a 3-petal rose function, we construct an efficient and dynamical mimic of the 2D Mercedes Benz (MB) water model. This rose water model is structurally similar to MB water and demonstrates the same water-like anomalous properties. When given a mass distribution similar to real water, we observe rose water to diffuse at a faster rate, only with longer lived “hydrogen-bonds”. This is likely due to the use of the significantly expanded acceptable hydrogen-bond length relative to the particle size parameter, resulting in more free volume for translation coupled with relatively strong hydrogen-bonds. We also show how one can extend the rose potential to generate alternate models with varying numbers of interacting arms.

Synthesis, spectroscopic (FT-IR, FT-Raman, NMR, UV–Visible), first order hyperpolarizability, NBO and molecular docking study of (E)-1-(4-bromobenzylidene)semicarbazide

The compound (E)-1-(4-bromobenzylidene)semicarbazide(4BSC) was synthesized and characterized by FT-IR, FT-Raman, UV–Visible, 1HNMR and 13CNMR spectra. The optimized molecular geometry(bond length, bond angle), the complete vibrational frequency, the infrared intensities and the Raman scattering activities were calculated by using density functional theory(DFT) B3LYP method with the help of 6–311++G(d,p) basis set. From the recorded UV–Visible spectrum, the electronic properties such as excitation energies, wavelength, band gap and oscillator strength are evaluated by TD-DFT in DMSO solution and gas phase methods using 6-311++G(d,p) basis set. The calculated HOMO - LUMO band gap energies confirm that charge transfer occurs within the molecule. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the gauge-independent atomic orbital (GIAO) method and compared with experimental results. The hyperconjugative interaction energy E(2) and electron densities of donor (i) and acceptor (j) bonds were calculated using NBO analysis. Besides NLO and MEP were also calculated and interpreted. To study the biological activity of the investigation molecule, molecular docking was done to identify the hydrogen bond lengths and binding energy with different antimicrobial protein. Thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations the heat capacity (C), entropy (S) and enthalpy changes (H) and temperatures.

Effect of phenolic radicals on the geometry and electronic structure of DNA base pairs: computational study

In this paper, we show the reaction of a hydroxyl, phenyl and phenoxy radicals with DNA base pairs by the density functional theory (DFT) calculations. The influence of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. The results showed that hydroxyl, phenyl and phenoxy radicals increase the length of the nearest hydrogen bond of adjacent DNA base pair which is accompanied by decrease in the length of furthest hydrogen bond of DNA base pair. Also, hydroxyl, phenyl and phenoxy radicals influenced the dihedral angle between DNA base pairs. According to the results, hydrogen bond lengths between AT and GC base pairs in water solvent are longer than vacuum. All of presented radicals influenced the structure and geometry of AT and GC base pairs, but phenoxy radical showed more influence on geometry and electronic properties of DNA base pairs compared with the phenyl and hydroxyl radicals.

Parallel β-Sheet Structure of Alanine Tetrapeptide in the Solid State As Studied by Solid-State NMR Spectroscopy.

The structural analysis of alanine oligopeptides is important for understanding the crystalline region in silks from spiders and wild silkworms and also the mechanism of cellular toxicity of human diseases arising from expansion in polyalanine sequences. The atomic-level structures of alanine tripeptide and tetrapeptide with antiparallel β-sheet structures (AP-Ala3 and AP-Ala4, respectively) together with alanine tripeptide with parallel β-sheet structures (P-Ala3) have been determined, but alanine tetrapeptide with a parallel β-sheet structure (P-Ala4) has not been reported yet. In this article, first, we established the preparation protocol of P-Ala4 from more stable AP-Ala4. Second, complete assignments of the (13)C, (15)N, and (1)H solid-state NMR spectra were performed with (13)C- and (15)N-labeled Ala4 samples using several solid-state NMR techniques. Then, the structural constraints were obtained, for example, the amide proton peaks of P-Ala4 in the (1)H double-quantum magic-angle spinning NMR spectrum were heavily overlapped and observed at about 7.4 ppm, which was a much higher field than that of 8.7-9.1 ppm observed for AP-Ala4, indicating that the intermolecular hydrogen-bond lengths across strands (N-H···O═C) were considerably longer for P-Ala4, that is, 2.21-2.34 Å, than those reported for AP-Ala4, that is, 1.8-1.9 Å. The structural model was proposed for P-Ala4 by NMR results and MD calculations.

A DFT-D Study on Structural, Electronic, Thermodynamic, and Mechanical Properties of HMX/MPNO Cocrystal under High Pressure

ABSTRACTAn investigation on the structural, electronic, thermodynamic, and mechanical properties of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/2-methylpyridine-N-oxide (MPNO) cocrystal was carried out from 0 to 100 GPa by using a dispersion-corrected density functional theory (DFT-D) method. Our calculated crystal structure is in excellent agreement with experimental results at ambient pressure. Based on the analysis of lattice parameters, lattice angles, bond lengths, bond angles, and dihedral angles under high pressure, we observe that HMX molecules in the cocrystal bulk are seriously distorted but MPNO molecules remain relatively unchanged. Hydrogen bond lengths are greatly shortened under high pressure. In addition, with the increase in pressure, the bandgap decreases gradually. However, it increases suddenly at 70 GPa. Some important hydrogen bonds between HMX and MPNO are also observed in the density of states spectrum. According to the thermodynamic analysis, this cocrystal is more easily prepared under low pressure. Finally, we characterized its mechanical properties and the results show that this cocrystal is malleable in nature. We expect that this research can provide a fundamental basis for further HMX cocrystal design and preparation.

NMR properties of hydrogen-bonded glycine cluster in gas phase

Density Functional Theory (DFT) calculations have been performed to study the effect of the hydrogen bond formation on the Nuclear Magnetic Resonance (NMR) parameters of hydrogen-bonded clusters of glycine molecules in gas-phase. DFT predicted isotropic chemical shifts of H, C, N and O of the isolated glycine with respect to standard reference materials are in reasonable agreement with available experimental data. The variations of isotropic and anisotropic chemical shifts for all atoms constituting these clusters containing up to four glycine molecules have been investigated systematically employing gradient corrected hybrid B3LYP functional with three different types of extended basis sets. The clusters are mainly stabilized by a network of strong hydrogen bonds among the carboxylic (COOH) groups of glycine monomers. The formation of hydrogen bond influences the molecular structure of the clusters significantly which, on the other hand, gets reflected in the variations of NMR properties. The carbon (C) atom of the COOH group, the bridging hydrogen (H) and the proton-donor oxygen (O) atom of the OH bond suffer downfield shift due to the formation of hydrogen bond. The hydrogen bond lengths and the structural complexity of the clusters are found to vary with the number of participating monomers. A direct correlation between the hydrogen bond length and isotropic chemical shift of the bridging hydrogen is observed in all cases. The individual variations of the principal axis elements in chemical shift tensor provide additional insight about the different nature of the monomers within the cluster.

Hydrogen bonding at C=Se acceptors in selenoureas, selenoamides and selones.

In recent years there has been considerable interest in chalcogen and hydrogen bonding involving Se atoms, but a general understanding of their nature and behaviour has yet to emerge. In the present work, the hydrogen-bonding ability and nature of Se atoms in selenourea derivatives, selenoamides and selones has been explored using analysis of the Cambridge Structural Database and ab initio calculations. In the CSD there are 70 C=Se structures forming hydrogen bonds, all of them selenourea derivatives or selenoamides. Analysis of intramolecular geometries and ab initio partial charges show that this bonding stems from resonance-induced C(δ+)=Se(δ-) dipoles, much like hydrogen bonding to C=S acceptors. C=Se acceptors are in many respects similar to C=S acceptors, with similar vdW-normalized hydrogen-bond lengths and calculated interaction strengths. The similarity between the C=S and C=Se acceptors for hydrogen bonding should inform and guide the use of C=Se in crystal engineering.

Spectroscopic investigation, molecular interactions and molecular docking studies on 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine

Vibrational spectroscopy is an essential tool for the structural investigation of the organic molecules. Benzodiazepines and their polycyclic derivatives are chief class of bioactive compounds. They are frequently used as anticonvulsant, hypnotic, analgesic, anti-inflammatory and anti depressive agents. The alprazolam is a derivative of benzodiazepine. The IUPAC name of alprazolam is 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine. Its molecular formula is C17H13ClN4. Theoretical calculations are used to analyse the vibrational frequencies of alprazolam. The Fourier Transform infrared spectrum of the compound is recorded between 400–4000cm−1 in solid phase. The electronic properties like HOMO and LUMO energies are determined. Mulliken charges of the sample are determined along with NBO charges. The 13C and 1H NMR chemical shifts are calculated and compared with experimental values. Chemical shifts are reported in parts per million relative to tretramethylsilane. To study the biological activity of the investigation molecule, molecular docking (ligand-protein) stimulations are performed using the web server SWISSDOCK. The full fitness score, binding energy, delta G and hydrogen bond lengths values are determined.

The Trimethylamine-Formic Acid Complex: Microwave Characterization of a Prototype for Potential Precursors to Atmospheric Aerosol.

The reactions of amines and carboxylic acids have recently received attention for their possible role in the formation of atmospheric aerosol. Here, we report a microwave study of the trimethylamine-formic acid hydrogen-bonded complex, a simple prototype in which to study amine-carboxylic acid interactions. Spectra of three isotopologues of the system have been observed using a tandem cavity and chirped-pulse Fourier transform microwave spectrometer. The complex has a plane of symmetry, with the acidic proton of the formic acid directed toward the lone pair of the nitrogen. The zero-point-averaged hydrogen bond length is 1.702 Å, and the O-H···N angle is 177°. (14)N nuclear quadrupole hyperfine structure has been used to assess the degree of proton transfer from the formic acid to the trimethylamine. Experimental results are supplemented with density functional theory calculations. M06-2X/6-311++G(3df,3pd) calculations indicate a binding energy of 16.8 kcal/mol with counterpoise correction (17.4 kcal/mol without counterpoise correction).

Differential Potency of 2,6-Dimethylcyclohexanol Isomers for Positive Modulation of GABAA Receptor Currents.

GABAA receptors meet all of the pharmacological requirements necessary to be considered important targets for the action of general anesthetic agents in the mammalian brain. In the following patch-clamp study, the relative modulatory effects of 2,6-dimethylcyclohexanol diastereomers were investigated on human GABAA (α1β3γ2s) receptor currents stably expressed in human embryonic kidney cells. Cis,cis-, trans,trans-, and cis,trans-isomers were isolated from commercially available 2,6-dimethylcyclohexanol and were tested for positive modulation of submaximal GABA responses. For example, the addition of 30 μM cis,cis-isomer resulted in an approximately 2- to 3-fold enhancement of the EC20 GABA current. Coapplications of 30 μM 2,6-dimethylcyclohexanol isomers produced a range of positive enhancements of control GABA responses with a rank order for positive modulation: cis,cis > trans,trans ≥ mixture of isomers > > cis,trans-isomer. In molecular modeling studies, the three cyclohexanol isomers bound with the highest binding energies to a pocket within transmembrane helices M1 and M2 of the β3 subunit through hydrogen-bonding interactions with a glutamine at the 224 position and a tyrosine at the 220 position. The energies for binding to and hydrogen-bond lengths within this pocket corresponded with the relative potencies of the agents for positive modulation of GABAA receptor currents (cis,cis > trans,trans > cis,trans-2,6-dimethylcyclohexanol). In conclusion, the stereochemical configuration within the dimethylcyclohexanols is an important molecular feature in conferring positive modulation of GABAA receptor activity and for binding to the receptor, a consideration that needs to be taken into account when designing novel anesthetics with enhanced therapeutic indices.

Changing Hydrogen-Bond Structure during an Aqueous Liquid-Liquid Transition Investigated with Time-Resolved and Two-Dimensional Vibrational Spectroscopy.

We investigate the putative liquid-liquid phase transition in aqueous glycerol solution, using the OD-stretch mode in dilute OD/OH isotopic mixtures to probe the hydrogen-bond structure. The conversion exhibits Avrami kinetics with an exponent of n = 2.9 ± 0.1 (as opposed to n = 1.7 observed upon inducing ice nucleation and growth in the same sample), which indicates a transition from one liquid phase to another. Two-dimensional infrared (2D-IR) spectroscopy shows that the initial and final phases have different hydrogen-bond structures: the former has a single Gaussian distribution of hydrogen-bond lengths, whereas the latter has a bimodal distribution consisting of a broad distribution and a narrower, ice-like distribution. The 2D-IR spectrum of the final phase is identical to that of ice/glycerol at the same temperature. Combined with the kinetic data this suggests that the liquid-liquid transformation is immediately followed by a rapid formation of small (probably nanometer-sized) ice crystals.

Effect of Chemical Radicals on the Geometry of DNA: Computational Study

To understand the effect of chemical radicals on DNA base pairs, we investigate the mechanism for the reaction of a hydroxyl radical to the GC and AT base pairs, by the density functional theory (DFT) calculations. The effect of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. We find that, radical structure increasing the length of the nearest hydrogen bond of adjacent base pair, accompanied by decreasing the length of furthest hydrogen bond. According to the results, hydrogen bond lengths between AT an GC base pairs in water solvent are longer than vacuum.

Factor Analysis of Conformations and NMR Signals of Rotaxanes: AIMD and Polarizable MD Simulations.

The interlocked ⟨rod | ring⟩ structures of pseudorotaxanes and [2]rotaxanes are usually maintained by the complex hydrogen-bonding (H-bonding) network between the rod and ring. Ab initio molecular dynamics (AIMD) using generalized energy-based fragmentation approach and polarizable force field (polar FF)-based molecular dynamics (MD) simulations were performed to investigate the conformational changes of mechanically interlocked systems and to obtain the ensemble-averaged NMR chemical shifts. Factor analysis (FA) demonstrates that the ring H-donor (2,6 pyridinedicarboxamide group) plays an important role in the ring-rod recognition. In comparison to the conventional fixed-charge force field, the polarization effect is crucial to account for the H-bonding interactions in supramolecular systems. In the hybrid scheme, the polar FF-based MD simulations are used to generate different initial states for the AIMD simulations, which are able to give better prediction of ensemble-averaged NMR signals for chemically equivalent amide protons. The magnitude of the deshielding shift of NMR signal is correlated with the length of hydrogen bond. The polar FF model with variable charges shows that the dipole-dipole interactions between the flexible diethylene glycol chain of ring and polar solvents induce the upfield shifts of NMR signals of rod H-donors and the directional distribution of the neighboring CH3CN solvents.

Rotational spectra and gas phase structure of the maleimide – Formic acid doubly hydrogen bonded dimer

Rotational transitions were measured for the maleimide – formic acid doubly hydrogen bonded dimer using a Flygare–Balle type pulsed-beam Fourier transform microwave spectrometer. No splittings caused by possible concerted double proton tunneling motion were observed. Experimental rotational constants (MHz), quadrupole coupling constants (MHz), and centrifugal distortion constants (kHz) were determined for the parent and three deuterium substituted isotopologues. The values for the parent are A=2415.0297(10), B=784.37494(38), C=592.44190(33), DJ=0.0616(64), DJK=−0.118(35), DK=−1.38(15), 1.5χaa=2.083(14), and 0.25(χbb–χcc)=1.1565(29). The hydrogen bond lengths were determined using a nonlinear least squares structure fitting program. Rotational constants for this complex are consistent with a planar structure, with an inertial defect of Δ=−0.528amuÅ2. The B3LYP calculation yielded rotational constants within 0.1% of the experimental values.

Rotational spectra and nitrogen nuclear quadrupole coupling for the cyanoacetylene dimer: H[sbnd]C[tbnd]C[sbnd]C[tbnd]N⋯H[sbnd]C[tbnd]C[sbnd]C[tbnd

The rotational spectra of cyanoacetylene dimer, HCCCN⋯HCCCN, were recorded using Balle–Flygare type Fourier transform microwave (FTMW) spectrometers. The low J transitions were measured down to 1.3GHz at very high resolution, FWHM∼1kHz. The spectral hyperfine structure due to the 14N nuclear quadrupole coupling interactions is well-resolved below 4GHz using a low frequency spectrometer at the University of Arizona. The experimental spectroscopic constants were fitted as: B0=339.2923310(79)MHz, DJ=32.152(82)Hz, H=−0.00147(20)Hz, eqQ(14N1)=−3.9902(14)MHz, and eqQ(14N2)=−4.1712(13)MHz. The vibrationally averaged dimer configuration is HCCCN⋯HCCCN. Using a simple linear model, the vibrational ground state and the equilibrium hydrogen bond lengths are determined to be: r0(N⋯H)=2.2489(3)Å and re(N⋯H)=2.2315Å. The equilibrium center-of-mass distance between the two HCCCN subunits is rcom=7.0366Å. Using the rigid precession model, the vibrational ground state center-of-mass distance and the pivot angles which HCCCN subunits make with the a-axis of HCCCN⋯HCCCN are rc.m.=7.0603Å, θ1=13.0°, and θ2=8.7°, respectively. The calculated hydrogen bond energy of HCCCN⋯HCCCN is 1466cm−1 using the MP2/aug-cc-PVTZ method in present work.

Quantifying cooperativity in water clusters: an attempt towards obtaining a generalised equation

The current study describes the development of a general equation of cooperativity energy (CE) for an n-mer system based on the difference between interaction energy of the system and the sum of interaction energy of its dimeric subunits. The counterpoise corrected generalised CE equation of n-mer system has also been developed. In order to validate these two generalised equations, we have considered four different kinds of water clusters, viz. W1D, W2D, W2D-H and W3D, ((H2O)n: n = 3–10), with the increasing cluster size as well as changing arrangements. The CE obtained from the two generalised equations follow the trend W3D > W2D-H > W2D > W1D. The deviation at n = 6 for W3D clusters in the plot of CE with cluster size has also been observed for O–H stretching frequencies, electron density and the Laplacian of the electron density plots. The contrastingly higher CE for cyclic pentamer compared to hexamer is in accordance with earlier observations as well as computed average hydrogen bond lengths. We have observed that the average charge value is more on oxygen atoms of pentamer than hexamer resulting in the shortening of hydrogen bond in pentamer and hence the CE values are more for pentamer than hexamer. We have shown that CE has the capability to quantify the cooperativity effect in water clusters.

Local Mode Approach to OH Stretch Spectra of Benzene–(H2O)n Clusters, n = 2–7

Isomer-specific resonant ion-dip infrared spectra are presented for benzene-water (Bz-(H2O)n) clusters with two to seven water molecules. Local mode Hamiltonians based on scaled M06-2X/6-311++G(2d,p) density functional calculations are presented that accurately model the spectra across the entire OH stretch region (3000-3750 cm(-1)). The model Hamiltonians include the contribution from the water bend overtone and an empirical parameter for the local OH stretch-bend Fermi coupling. The inclusion of this coupling is necessary for accurate modeling of the infrared spectra of clusters with more than three water molecules. For the cyclic water clusters (n = 3-5), the benzene molecule perturbs the system in a characteristic way, distorting the cycle, splitting degeneracies, and turning on previously forbidden transitions. The local OH stretch site frequencies and H···OH hydrogen bond lengths follow a pattern based on the each water monomer's proximity to benzene. The patterns observed for these cyclic water clusters provide insight into benzene's effects on the three-dimensional hydrogen-bonded networks present in water hexamer and heptamer structures, which also have their spectra dramatically altered from their pure water counterparts.