Improper Hydrogen Bonds Research Articles

Theoretical investigation on the improper hydrogen bond in κ-carrabiose⋯Y (Y = HF, HCl, HBr, NH3, H2O, and H2S) complexes.

The nature of H-bonds in κ-carrabiose⋯Y (Y = HF, HCl, HBr, NH3, H2O, and H2S) complexes was studied. For this aim, the structure of isolated κ-carrabiose was optimized using three global hybrids functional: B3LYP, PBE0, and M06-2X combined with 6-311G** basis set. Subsequently, the κ-carrabiose in the presence of HF, HCl, HBr, NH3, H2O, and H2S was optimized using the CBS-4M method. NBO analyses were then carried out at the MP2/6-311G** level of theory. A particular interest was focused on C(18)-H(34)⋯Y bond. The results reveal that the C(18)-H(34)⋯Y bond is an improper H-bond since a significant contraction of C(18)-H(34) was observed during the complexation leading to a significant blueshifted stretching frequency. The NBO analyses have shown that the formation of the improper H-bonds C(18)-H(34)⋯Y (Y = F, Cl, Br, N, O, and S) is principally due to the increase of the s-character of the hybrid orbital in carbon atom (rehybridization) in κ-carrabiose⋯Y complexes. Regarding the polarization, it was proved that more the H-bond center (carbon in C(18)-H(34)⋯Y) becomes less positive, the hydrogen more positive, and Y more negative; more the contraction of the C(18)-H(34) bond is important. It was also confirmed for intramolecular H-bonds in κ-carrabiose⋯Y complexes that the rehybridization is responsible for H-bonds nature either proper or improper.

Theoretical Investigations of Hydrogen Bonding Interactions of (E)-1-(1H-Benzo[d]imidazol-2-yl)-3-Phenylprop-2-en-1-one Momoners and Dimers: NBO, QTAIM and NCI Study

Hydrogen bonding is an essential interaction in nature and plays a crucial role in many formations of materials and biological processes, requiring a deeper understanding of its formation. Benzimidazole is an important structural unit found in a large number of natural and pharmacologically active molecules. In the present work, the electronic structures and properties and relatives stabilities of a series of (E)-1-(1H-benzo[d]imidazol-2-yl)-3-phenylprop-2-en-1-one monomers and dimers have been studied by density functional theory using B3LYP 6-31+G (d, p) calculation level. the strengths of the noncovalent interactions have been analyzed in terms of the QTAIM analysis, NCI analysis and natural bond orbital approaches. It was found that the dimers are formed by double N-H⋯O hydrogen bond. QTAIM analysis proved the presence of intramolecular hydrogen bond in monomers and coexistence of intramolecular and intermolecular hydrogen bond in dimers. Frequency analysis show that intermolecular N-H⋯O interactions are proper hydrogen bond while intramolecular C-H⋯N, C-H⋯O, C-H⋯H-C interactions are improper hydrogen bond. NBO and NCI analyses confirm the existence of hydrogen bonds in the studied monomers and dimers. The presence of weakly electron acceptor group on benzene ring favor the total interaction energy of dimerization.

Theoretical investigation on hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

The interaction of diketo and keto-enol form of thymine and uracil tautomers with acridine (Acr), phenazine (Phen), benzo[c]cinnoline (Ben), 1,10-phenanthroline (1,10-Phe), and 4,7-phenenthroline (4,7-Phe) intercalating drug molecules was studied using density functional theory at B3LYP/6-311++G** and M05-2×/6-311++G** levels of theory. From the interaction energy, it is found that keto-enol form tautomers have stronger interaction with intercalators than diketone form tautomers. On complex formation of thymine and uracil tautomers with benzo[c]cinnoline the drug molecules have high interaction energy values of -20.14 (BenT3) and -20.55 (BenU3) kcal mol-1, while phenazine has the least interaction energy values of -6.52 (PhenT2) and -6.67 (PhenU2) kcal mol-1. The closed shell intermolecular type interaction between the molecules with minimum elliptical value of 0.018 and 0.019 a.u at both levels of theory has been found from topological analysis. The benzo[c]cinnoline drug molecule with thymine and uracil tautomers has short range intermolecular N-H…N, C-H…O, and O-H...N hydrogen bonds (H-bonds) resulting in higher stability than other drug molecules. The proper hydrogen bonds N-H..N and O-H..N have the frequency shifted toward the lower side (red shifted) with the elongation in their bond length while the improper hydrogen bond C-H...O has the frequency shifted toward the higher side (blue shifted) of the spectral region with the contraction in their bond length. Further, the charge transfer between proton acceptor and donor along with stability of the bond is studied using natural bond orbital (NBO) analysis. Graphical abstract Hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

Structural and vibrational investigations of a neurotransmitter molecule: Serotonin (5-hydroxy tryptamine)

Structural and vibrational studies have been carried out for the most stable conformer of serotonin (5-HT) at the DFT/B3LYP/6-311++G** level using the Gaussian 09 software. In light of the computed vibrational parameters the observed IR and Raman frequencies have been analyzed. To help assign the vibrational fundamentals the GAR2PED software has been used to compute PEDs. Several of the fundamentals are drastically changed in going from indole to serotonin. The two NH bonds of the NH2 group are slightly different possibly due to bonding of the two H atoms of the NH2 group with different atoms. The rocking and wagging modes of the NH2 groups show mixing with the other modes while the remaining four modes are pure group modes. The Kekule phenyl ring stretching mode is found to remain almost unchanged. The HOMO-LUMO energy gap supports to pharmacological active property of the serotonin molecule. The HOMO and LUMO study suggests the existence of charge transfer within the molecule. The NBO analysis has been carried out to gather information regarding the proper and improper hydrogen bonds.

Proper and improper hydrogen bonds in liquid water

The total lifetime distributions for hydrogen bonds in snapshots of molecular dynamics simulations of water serve as a basis to identify a class of proper hydrogen bonds. Proper bonds emerge and break up when restructuring the surrounding area of the hydrogen bond networkwhich weakly depend on the properties of this individual bond, i.e., almost randomly. Therefore, the distribution of the bond lifetimes is described by an exponential function similar to the distribution of the mean free path time in gas. It is shown that proper hydrogen bonds are strong, long-lived, and tetrahedrally oriented bonds. They account for about 80% of the bonds in each snapshot. Thus, these bonds form the basis or framework of the hydrogen bond network of water. The other, improper bonds have a substantially shorter lifetime; these are weak, bifurcated, and quickly switching bonds.

NMR spectral properties of the tetramantanes - nanometer-sized diamondoids.

Tetramantanes, and all diamondoid hydrocarbons, possess carbon frameworks that are superimposable upon the cubic diamond lattice. This characteristic is invaluable in assigning their (1)H and (13)C NMR spectra because it translates into repeating structural features, such as diamond-cage isobutyl moieties with distinctively complex methine to methylene signatures in COSY and HMBC data, connected to variable, but systematic linkages of methine and quaternary carbons. In all tetramantane C22H28 isomers, diamond-lattice structures result in long-range (4)JHH, W-coupling in COSY data, except where negated by symmetry; there are two highly symmetrical and one chiral tetramantane (showing seven (4)JHH). Isobutyl-cage methines of lower diamondoids and tetramantanes are the most shielded resonances in their (13)C spectra (<29.5 ppm). The isobutyl methylenes are bonded to additional methines and at least one quaternary carbon in the tetramantanes. W-couplings between these methines and methylenes clarify spin-network interconnections and detailed surface hydrogen stereochemistry. Vicinal couplings of the isobutyl methylenes reveal positions of the quaternary carbons: HMBC data then tie the more remote spin systems together. Diamondoid (13) C NMR chemical shifts are largely determined by α and β effects, however γ-shielding effects are important in [123]tetramantane. (1)H NMR chemical shifts generally correlate with numbers of 1,3-diaxial H-H interactions. Tight van der Waals contacts within [123]tetramantane's molecular groove, however, form improper hydrogen bonds, deshielding hydrogen nuclei inside the groove, while shielding those outside, indicated by Δδ of 1.47 ppm for geminal hydrogens bonded to C-3,21. These findings should be valuable in future NMR studies of diamondoids/nanodiamonds of increasing size.

DFT and Vibrational Spectroscopic Study on 3-alkyl-4-amino-6-aryl-1, 2, 4-triazin-5-one Herbicide

Density functional theory and vibrational analysis of 3-alkyl-4-amino-6-aryl-1,2,4-triazin-5-one herbicide has been carried out. The geometry has been optimized by B3LYP level of theories using 6-311G (df, p) basis set using Gaussian 09 program and compared with the crystal data. NBO and structural analysis has been carried out on the compound. Theoretical methods have been used to study the proper and improper hydrogen bonds, considering the hydrogen bond length and charge transfer. The Mulliken population analysis on atomic charges and the HOMO-LUMO energy were also calculated.

Spectroscopic analysis and charge transfer interaction studies of 4-benzyloxy-2-nitroaniline insecticide: A density functional theoretical approach

A widespread exploration on the intra-molecular charge transfer interaction through an efficient π-conjugated path from a strong electron-donor group (amino) to a strong electron-acceptor group (nitro) has been carried out using FTIR, FT-Raman, UV–Vis, fluorescence and NMR spectra on insecticide compound 4-benzyloxy-2-nitroaniline. Density functional theory method is used to determine optimized molecular geometry, harmonic vibrational wavenumbers and intensities using 6-311G(d,p) basis set by means of Gaussian 09W program suit. A comprehensive investigation on the sp2 to sp3 hybridization and non-planarity property has been performed. Natural bond orbital analysis is used to study the existence of C–H⋯O, N–H⋯O and C–H⋯π proper and improper hydrogen bonds. The HOMO and LUMO analysis reveals the possibility of charge transfer within the molecule. A complete assignment of the experimental absorption peaks in the ultraviolet region has also been performed. Isotropic chemical shifts of 13C, 1H, 15N and 18O NMR and nuclear spin–spin coupling constants have been computed using the gauge-invariant atomic orbital method. The biological activity of substituent amino and nitro groups are evident from the hydrogen bonds through which the target amino acids are linked to the drug as evidenced from molecular docking.

Turn-Directed α-β Conformational Transition of α-syn12 Peptide at Different pH Revealed by Unbiased Molecular Dynamics Simulations

The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at both pH values are β-hairpin but with different turns and hydrogen bonds. Turn9-6 and four hydrogen bonds (HB9-6, HB6-9, HB11-4 and HB4-11) are formed at physiological pH; turn8-5 and five hydrogen bonds (HB8-5, HB5-8, HB10-3, HB3-10 and HB12-1) are formed at acidic pH. A common folding mechanism is observed: the formation of the turn is always before the formation of the hydrogen bonds, which means the turn is always found to be the major determinant in initiating the transition process. Furthermore, two transition paths are observed at physiological pH. One of the transition paths tends to form the most-clustered turn and improper hydrogen bonds at the beginning, and then form the most-clustered hydrogen bonds. Another transition path tends to form the most-clustered turn, and turn5-2 firstly, followed by the formation of part hydrogen bonds, then turn5-2 is extended and more hydrogen bonds are formed. The transition path at acidic pH is as the same as the first path described at physiological pH.

The influence of cation-π and anion-π interactions on the strength and nature of N⋯H hydrogen bond

The influence of cation-π and anion-π interactions on the strength and nature of N⋯H hydrogen bond has been investigated by quantum chemical calculations in s-triazine⋯(HF)3 complex. Ab initio calculations were performed at MP2(FC)/6-311++G(d,p) level of theory. The natural bond orbital (NBO) analysis and the Bader’s quantum theory of atoms in molecules (AIMs) were also used to elucidate the interaction characteristics of these complexes. Some bonding parameters were calculated by natural resonance theory (NRT) to investigate the changes in the geometrical parameters upon complexion. The N⋯H hydrogen bonds can be putted in the categories weak to medium in investigated systems. In addition, both proper and improper hydrogen bonds, which depend on the charge/radius of ion, are seen among interactions.

Effects of sugar ring puckering, anti-syn interconversion and intramolecular interactions on N-glycosidic bond cleavage in 3-methyl-2′-deoxyadenosine and 2′-deoxyadenosine

The effects of structural parameters and intramolecular interactions on N-glycosidic bond length in 3-methyl-2′- deoxyadenosine (3MDA) and 2′-deoxyadenosine (DA) were investigated employing quantum mechanical methods. All calculations were performed at B3LYP/6-311++G** level in the gas phase. The N-glycosidic bond length strongly depends on sugar configuration; it is shorter in syn conformation relative to anti in many cases where they have the same sugar ring configuration. The sugar conformation can influence the N-glycosidic bond through interaction with the O4′ atom. The impact of intramolecular improper hydrogen bonds and H-H bonding interactions on N-glycosidic bond length was investigated in DA and 3MDA and their modeled structures. Improper hydrogen bonds decrease N-glycosidic bond length while H-H bonding interactions increase it.

Hydrogen-bonding studies of amino acid side-chains with DNA base pairs

The interactions of the amino acid side-chains arginine (ARG), aspartic acid (ASP), asparagine (ASN), lysine (LYS) and serine (SER) with nucleic acid base pairs have been investigated using theoretical methods. The interaction energy of the short intermolecular N–H ··· N, N–H ··· O, O–H ··· O, O–H ··· N, C–H ··· O and C–H ··· N hydrogen bonds present in both isolated base pairs and complexes and its role in providing stability to the complexes have been explored. The homonuclear interactions are found to be stronger than the heteronuclear interactions. An improper hydrogen bond has been observed for some of the N–H ··· O and N–H ··· N hydrogen-bond interactions with the contraction of the N–H bond varying from 0.001 to 0.0260 Å and the corresponding blue shift of the stretching frequency by 4–291 cm−1. Localized molecular orbital energy decomposition analysis (LMOEDA) reveals that the major contributions to the energetics are from the long-range polarization (PL) interaction, and the short-range attractive (ES, EX) and repulsive (REP) interactions. The Bader's atoms in molecules (AIM) theory shows good correlation for the electron density and its Laplacian at the bond critical points (BCP) with the N–H ··· N and N–H ··· O hydrogen-bond lengths in the complexes, and gives a proper explanation for the stability of the structure. The charge-transfer from the proton acceptor to the antibonding orbital of the X–H bond in the complexes was studied using natural bond orbital (NBO) analysis.

Computational study of proper and improper hydrogen bonding in methanol complexes

The bulk properties of alcohols, like those of aqueous solutions, are governed mostly by hydrogen bonding; however, in contrast with water molecules, the chemical structure of a simple alcohol such as methanol offers an opportunity to explore the effects of both proper and improper hydrogen bonding on a single hydrogen donor. The presence of the hydroxyl group generally gives rise to a strong proper hydrogen bond, while the methyl group of methanol is likely involved in the weaker improper hydrogen bond, among other weak non-covalent interactions. The effects of the two types of hydrogen bonds on the stability, geometric parameters, and properties of electron density of methanol complexes are examined while considering different geometrical arrangements of the methanol dimer and the binary complexes of methanol with water, acetonitrile, and chloromethane. Subsequently, potential conclusions about the nature of improper hydrogen bonding and the origin of the C–H bond contraction that results upon complex formation are discussed. Quantum theory of atoms in molecules and natural bond orbital methods were used in the analysis; all calculations were performed at the MP2(full)/6-311++G(d,p) level of theory.

Solvent effects on blue shifted improper hydrogen bond of C–H⋯O in deoxycytidine isomers

Vibrational spectra of 2′-deoxycytidine (2′-dC) and 3′-deoxycytidine (3′-dC) are simulated with a number of polar and non-polar solvents. Significant spectral changes of the isomers indicate the unique hydrogen bond networks and their interactions with solvents. Vibrations such as C(4′)–H stretch undergo improper blue shift of 103 cm −1 (vacuum), when associated with the C–H⋯O hydrogen bond network. Solvents red shift the IR spectra with respect to vacuum and reduce the improper blue shift, but do not change the nature of the shift (red or blue). Polarity of the solvents affects the spectral shift in a non-linear manner but the spectral shift becomes saturated in strong polar solvents.

Blue shifted intramolecular C−H···O improper hydrogen bonds in conformers of zidovudine

Blue shifted C–H stretch vibrations caused by C–H···O intramolecular improper hydrogen bonds in zidovudine (or AZT) conformers are employed to differentiate its conformers. Two sugar–sugar C–H···O (5′) improper hydrogen bonds, existing in conformers of AZT with apparent drug potency, are related to their unique sugar puckering, showing C (3′)- exo or - endo orientations. Aqueous solution causes a global red shift in IR spectra, but remains reduced blue shifted C–H stretch frequencies. Molecular electrostatic potentials (MEPs) of the conformers and orbitals such as 40a of AZT-B and 37a of AZT-C, which are found to be responsible for the intramolecular improper hydrogen bonds, are also given in this study.

Polarised IR and Raman spectra of monoglycine nitrate single crystal

Polarised Raman spectra of the monoglycine (monoglycinium) nitrate (hereafter MGN) single crystal are reported. Additionally, the polarised specular reflection spectra for the (1 0 0) single crystal sample (E|| Y( b) and E|| Z( c)) were measured in the region 3600–80 cm −1. The spectra of the imaginary parts of the refractive indices are computed by the Kramers–Kronig transformation (Opus). The polarised spectra are discussed with respect to the diffraction crystal structure and recent literature data on normal co-ordinate analysis for the glycinium cation ( +NH 3CH 2COOH). The stretching vibrations of the NH 3 + groups are explained by considering their hydrogen bonds. The intensity of the Raman bands arising from the stretching vibrations of the CH 2 group are explained assuming that each C H bond stretches independently. This finding is unusual and suggests that the C(2) H(5) bond is involved in the hydrogen bonding (improper hydrogen bond). The deformation vibrations of the CH 2 group are explained assuming scissoring, twisting, wagging and rocking type of vibrations. The band at 871 cm −1 exhibits the CC stretching character of the CCN skeleton, whereas the band at ca. 1050 cm −1 shows the ν aCCN character. The stretching νOH vibrations of the C O H⋯O hydrogen bond gives rise to a band at ca. 3087 cm −1, clearly seen in the Y( xx) Z Raman spectrum. Its γOH mode appears at 896 cm −1. The δOH vibration is coupled to other vibrations, although the IR band at ca. 1375 (E|| Y) likely arises from this mode. It was impossible to define a character of the glycinium cations deformation vibrations giving rise to the bands observed in between 680 and 490 cm −1, on the basis of their polarisation properties. The polarisation properties of the internal modes of the nitrate ions are discussed.

Red-, Blue-, or No-Shift in Hydrogen Bonds: A Unified Explanation

We provide a simple explanation for X-H bond contraction and the associated blue shift and decrease of intensity in IR spectrum of the so-called improper hydrogen bonds. This explanation organizes hydrogen bonds (HBs) with a seemingly random relationship between the X-H bond length (and IR frequency and its intensity) to its interaction energy. The factors which affect the X-H bond in all X-H...Y HBs can be divided into two parts: (a) The electron affinity of X causes a net gain of electron density at the X-H bond region in the presence of Y and encourages an X-H bond contraction. (b) The well understood attractive interaction between the positive H and electron rich Y forces an X-H bond elongation. For electron rich, highly polar X-H bonds (proper HB donors) the latter almost always dominates and results in X-H bond elongation, whereas for less polar, electron poor X-H bonds (pro-improper HB donors) the effect of the former is noticeable if Y is not a very strong HB acceptor. Although both the above factors increase with increasing HB acceptor ability of Y, the shortening effect dominates over a range of Ys for suitable pro-improper X-Hs resulting in a surprising trend of decreasing X-H bond length with increasing HB acceptor ability. The observed frequency and intensity variations follow naturally. The possibility of HBs which do not show any IR frequency change in the X-H stretching mode also directly follows from this explanation.

Glycine–methanesulfonic acid (1:1) and glycine– p-toluenesulfonic acid (1:1) crystals: Comparison of structures, hydrogen bonds, and vibrations

The crystal structures of glycine–methanesulfonic acid (1:1) and glycine– p-toluenesulfonic acid (1:1) have been investigated by X-ray diffraction at 293 K. They belong to centrosymmetric: (i) P2 1/ n space group of monoclinic system and (ii) Pbca space group of orthorhombic system, respectively. Both crystals consist of glycinium–sulfonate dimers (methane- or p-toluenesulfonate, respectively) with medium-strong and very similar O–H⋯O hydrogen bonds. N–H⋯O bonds connect glycinium–sulfonate dimers into infinite chains. Both sulfonic acids reveal very similar acidic properties. In glycine– p-toluenesulfonic acid (1:1) crystal very weak, C–H⋯π improper hydrogen bonds are formed. Vibrational spectra of the crystals are related to their structures.

Characterization of conformers of non-ionized proline on the basis of topological and NBO analyses: Can nitrogen be a donor of hydrogen bond?

A detailed population analysis of 10 most stable conformers of neutral proline was undertaken by the natural bond orbitals (NBO) and the atoms in molecules (AIM) methods. The optimized geometries (at MP2/6-311++G(d,p) level) were employed to perform the NBO analysis and also to obtain the suitable wave function files for the AIM analysis. With the exception of OH⋯NH and CH⋯OH hydrogen bond critical points, corresponding to four conformers, the BCPs can be observed just for those which located at the interatomic paths that are defined by the covalent bonds. The charge transfer energy of n ( N ) → σ O – H ∗ interactions are 18.31 and 15.63 kcal/mol which are related to conformers that exhibit the OH⋯NH hydrogen bonds. Similar interactions higher than 0.5 kcal/mol threshold limit do not observe for other conformers. Thus, the NBO and AIM analyses do not confirm the presence of N–H⋯O C and N–H⋯O–H hydrogen bonds in the conformers of proline. On the other hand, improper hydrogen bonds (C–H⋯O–H) reveal in two conformers.

Liquid NMA: A surprisingly realistic model for hydrogen bonding motifs in proteins

The structure of liquid N-methylacetamide is examined using a combination of classical and ab initio molecular dynamics. Polymeric hydrogen bonded (N–H⋯O C) chain motifs having complex topologies emerge as the dominant structural features. Interchain associations, reminiscent of β-sheets in proteins, are also evident and may be stabilized by improper (methyl-donated) hydrogen bonds. Both ab initio and classical simulations lead to a consistent picture of local structure, including the presence of close contacts between oxygen and methyl hydrogen atoms. Liquid NMA, therefore, exhibits a surprisingly complex structure, and possesses two clear bonding motifs relevant to the stability of protein secondary structure.