Non-conventional Hydrogen Bonds Research Articles

Stabilization of Branched Oligosaccharides: Lewisx Benefits from a Nonconventional C–H···O Hydrogen Bond

Although animal lectins usually show a high degree of specificity for glycan structures, their single-site binding affinities are typically weak, a drawback which is often compensated in biological systems by an oligovalent presentation of carbohydrate epitopes. For the design of monovalent glycomimetics, structural information regarding solution and bound conformation of the carbohydrate lead represents a valuable starting point. In this paper, we focus on the conformation of the trisaccharide Le(x) (Gal[Fucα(1-3)]β(1-4)GlcNAc). Mainly because of the unfavorable tumbling regime, the elucidation of the solution conformation of Le(x) by NMR has only been partially successful so far. Le(x) was therefore attached to a (13)C,(15)N-labeled protein. (13)C,(15)N-filtered NOESY NMR techniques at ultrahigh field allowed increasing the maximal NOE enhancement, resulting in a high number of distance restraints per glycosidic bond and, consequently, a well-defined structure. In addition to the known contributors to the conformational restriction of the Le(x) structure (exoanomeric effect, steric compression induced by the NHAc group adjacent to the linking position of L-fucose, and the hydrophobic interaction of L-fucose with the β-face of D-galactose), a nonconventional C-H···O hydrogen bond between H-C(5) of L-fucose and O(5) of D-galactose was identified. According to quantum mechanical calculations, this C-H···O hydrogen bond is the most prominent factor in stabilization, contributing 40% of the total stabilization energy. We therefore propose that the nonconventional hydrogen bond contributing to a reduction of the conformational flexibility of the Le(x) core represents a novel element of the glycocode. Its relevance to the stabilization of related branched oligosaccharides is currently being studied.

Can a C–H···O Interaction Be a Determinant of Conformation?

Whether nonconventional hydrogen bonds, such as the C-H···O interaction, are a consequence or a determinant of conformation is a long-running and unresolved issue. Here we outline a solid-state and quantum mechanical study designed to investigate whether a C-H···O interaction can override the significant trans-planar conformational preferences of α-fluoroamide substituents. A profound change in dihedral angle from trans-planar((OCCF)) to cis-planar((OCCF)) observed on introducing an acceptor group for a C-H···O hydrogen bond is consistent with this interaction functioning as a determinant of conformation in certain systems. This testifies to the potential influence of the C-H···O hydrogen bond and is consistent with the assignment of this interaction as a contributor to overall conformation in both model and natural systems.

Raman spectroscopy study on the [formula omitted] Fermi resonance of liquid carbon disulfide in binary solutions: Effect of the weak hydrogen bond formation on the Fermi resonance

We have measured the Raman spectra of liquid CS2 at different volume concentrations in CHCl3 and CH2Cl2 solutions. With decreasing the volume concentration of CS2, a noticeable growth in the 2ν2 band frequency was observed, while the ν1 band location remained practically unchanged. This asymmetric wavenumber shift phenomenon of the Fermi doublet ν1 and 2ν2 of CS2 has been ascribed to weak, non-conventional hydrogen bonds formed between the CS2 and the solvent molecules. These weak hydrogen bonds were also responsible for significant decreases in the C–H bond symmetric stretching vibration band frequencies of CHCl3 and CH2Cl2. The values of the ν1-2ν2 FR parameters of CS2 in CH2Cl2 and CHCl3 at different volume concentrations were calculated according to the FR theory. The magnitude of the FR coupling coefficient W of CS2 increases upon dilution with CH2Cl2 and CHCl3, indicating that the vibrational anharmonicity is relatively sensitive to variations in the weak hydrogen bonding. Compared with the changing tendencies of Fermi coupling coefficient W of CS2 in CH2Cl2 and CHCl3 at different volume concentrations, we discussed the effect of the weak hydrogen bond formation on the FR and the asymmetric wavenumber shift phenomenon of the Fermi doublet ν1 and 2ν2 of CS2.

Intermolecular interactions between gold clusters and selected amino acids cysteine and glycine: a DFT study

The intermolecular interactions between Au(n) (n = 3-4) clusters and selected amino acids cysteine and glycine have been investigated by means of density functional theory (DFT). Present calculations show that the complexes possessing Au-NH(2) anchoring bond are found to be energetically favored. The results of NBO and frontier molecular orbitals analysis indicate that for the complex with anchoring bonds, lone pair electrons of sulfur, oxygen, and nitrogen atoms are transferred to the antibonding orbitals of gold, while for the complex with the nonconventional hydrogen bonds (Au···H-O), the lone pair electrons of gold are transferred to the antibonding orbitals of O-H bonds during the interaction. Furthermore, the interaction energy calculations show that the complexes with Au-NH(2) anchoring bond have relatively high intermolecular interaction energy, which is consistent with previous computational studies.

Calculation of the Binding Energies of Different Types of Hydrogen Bonds Using GGA Density Functional and Its Long-Range, Empirical Dispersion Correction Methods

We investigated eleven exchange-correlation energy density functionals including generalized gradient approximation (GGA) (PBE, PW91), meta-GGA (M06-L), hyper-GGA (M06-2X, B3LYP, X3LYP), LC-DFT methods (CAM-B3LYP, LC-ωPBE, ωB97X), and density functional theory with dispersion corrections (DFT-D) methods (ωB97X-D, B97-D) for their performance in describing systems with conventional and non-conventional hydrogen bonds. After comparing the results using the benchmark CCSD(T)/aug-cc-pVQZ approach we found that the M06-2X and ωB97X-D functionals provided the most accurate and reliable results for the fifteen systems studied in this work with strong, moderate, and weak hydrogen bonds. It is important to employ an appropriate basis set to predict the binding energy of hydrogen bonds for all DFT methods and we found that the basis set of 6-311++G(2d, 2p) or aug-cc-pVDZ is adequate. The effect of the basis set superposition error (BSSE) is relatively small for the DFT methods tested. All the methods except for ωB97X and ωB97X-D were found to produce equally accurate or even more accurate results without BSSE correction.

Non-conventional hydrogen bonds: pterins-metal anions

In this paper, we present an analysis of the interaction of metal ions (Cu, Ag and Au) with three different pterins (pterin, isoxanthopterin and sepiapterin) to provide insights concerning the formation of conventional and non-conventional H bonds. Density functional theory calculations were performed in order to reveal the optimized structures of pterin molecules, dimers and tetramers compounds, both with and without metal anions (M). The interaction with small metal clusters (M(3)) is also considered. The formation of different systems is characterized in terms of the structural parameters and hydrogen binding energies (HBE). The HBE values for pterin-M systems presented in this study lie between 22 and 60 kcal mol(-1) and can therefore be classified as strong conventional and strong non-conventional hydrogen bonds. The HBE with small metal clusters (pterin-M(3)) are smaller than the HBE with metal atoms. Vertical electron detachment energies (VEDEs) are also reported in order to analyze the influence of the hydrogen bond on electronic properties. A direct correlation between VEDEs and HBE was found for pterin-M and pterin-M(3) complexes; i.e. as the VEDEs increase, the HBE also augment. The only exception is with Ag(3). The main conclusion derived from this study is that the strong non-conventional hydrogen bonds formed between pterins, dimers and tetramers do not affect the formation of conventional hydrogen bonds between pterins but they do influence the VEDEs.

Identification of Modular Chiral Bisphosphines Effective for Cu(I)-Catalyzed Asymmetric Allylation and Propargylation of Ketones

New modular chiral phosphines effective for two distinct Cu(I)-catalyzed asymmetric tetrasubstituted-carbon-forming reactions, namely, allylation and propargylation of ketones, were identified. The optimized phosphine 8 was readily synthesized on a gram scale in high yield via three facile transformations (O-alkylation, bisaminal formation, and phosphination) from commercially available materials. In both reactions, excellent enantioselectivity (up to 98% ee) was produced from a range of substrates, including aromatic and aliphatic ketones, using 0.1-5 mol % catalyst loading. Specifically, catalytic enantioselective propargylation was the first example, affording synthetically useful chiral building blocks that have not been easily accessed to date. In addition to the enantioselectivity, the high catalytic activity of the CuOAc-8 complex is noteworthy. Preliminary studies to elucidate the structure-catalyst activity relationship suggested that the high catalytic activity of the Cu-8 complex is due to the extraordinarily wide bite angle ( angleP-Cu-P = 137.8 degrees ), leading to the stabilization of the active monomeric catalytically active species. Furthermore, mechanistically intriguing nonconventional hydrogen bonds existed between the acetate ligand of Cu and the bisaminal hydrogen atoms, stabilizing the distorted tetrahedral coordination state of the Cu atom.

Isolation of 1,4-Li2-C6H4 and its reaction with [(Ph3P)AuCl

The difficulty in generating 1,4-Li2-C6H4 utilising the lithium halogen exchange reaction on 1,4-Br2-C6H4, 1,4-I2-C6H4 and 1-Br-4-I-C6H4 is revisited and only on treatment of 1,4-I2-C6H4 with 2 molar equivalents of n-BuLi can 1,4-Li2-C6H4 1 be isolated in excellent yield. Treatment of 1 with two equivalents of [ClAu(PPh3)] gives [1,4-(Ph3PAu)2-C6H4] 2a in excellent yield. Subsequent treatment of 2a with 2.5 molar equivalents of PPh2Me, PPhMe2 or PMe3 affords the PPh3 substituted compounds [1,4-(LAu)2-C6H4] (L = PPh2Me 2b, PPhMe2 2c, PMe3 2d) in essentially quantitative yields. On treatment of 1,4-Br2-C6H4 or 1-Br-4-I-C6H4 with 2 molar equivalents of n-BuLi only mono-lithiation takes place to give 1-Br-4-Li-C6H4 3 as shown through the isolation of essentially 1:1 molar equivalents of Ph2PC6H4-4-Br and Ph2PBu on treatment with 2 molar equivalents of ClPPh2. Treatment of 3, prepared by lithium/iodine exchange on 1-Br-4-I-C6H4, with [ClAu(PPh3)] affords [(Ph3P)Au(C6H4-4-Br)] 4 as expected and in addition [(Ph3P)Au(n-Bu)(C6H4-4-Br)2] 5, indicating the straightforward chloride/aryl exchange at gold may proceed in competition with oxidative addition of the n-BuI, generated in the initial lithium/iodine exchange reaction, to some aurate complex Li[Au(C6H4-4-Br)2] 6 formed in situ followed by reductive elimination of Br-C6H4-4-n-Bu in a manner that mimics lithium diorganocuprate chemistry. All of the gold-containing compounds have been spectroscopically characterised by 1H and 31P-{1H} NMR and in addition compounds 2a-d and 5 by single crystal X-ray diffraction studies. The solid state structures observed for 2a-d are dictated by non-conventional hydrogen bonding and the packing requirements of the phosphine ligands. For 2a and 2b there is no close Au...Au approach, however for 2c and 2d the reduction in the number of phenyl rings allows the formation of Au...Au contacts. For 2c and 2d the extended structures appear to be helical chains with Au...Au contact parameters of 3.855(5) A and C-Au-Au-C 104.1(3)degrees for 2c and 3.139(4) A and C-Au-Au-C -92.0(2)degrees for 2d. The Au...Au approach in 2c is longer than is normally accepted for an AuAu contact and is dictated by ligand directed non-conventional hydrogen bonding to the aurated benzene ring and the pi-stacking requirements of the phosphine ligand. By comparison of the structures 2a-2d with other structures in the database it is evident that the aurophilic interaction is a poor supramolecular synthon in the presence of non-conventional hydrogen bond donors. Searches of the CCDC database suggest that the observed parameters for the Au...Au contact in 2c sit close to the cut-off point for observing this type of contact. In addition to aurophilic contacts and non-conventional hydrogen bonds there are a number of halogenated solvent C-Cl...Au contacts observed in the structures of 2a and 2d. The nature of these contacts have implications for the accepted van der Waals radius of gold which should be extended to 2 A.

Contribution of unconventional C-H…O bonds to the structural stability of Antimicrobial peptides

The native structure of Antimicrobial peptides is stabilized by a large number of individually weak forces; a complete understanding of folding implies the need to evaluate the contribution of each of these, including nonconventional hydrogen bonds. In this work, we have analyzed the influence of C-H...O interactions in the structural stability of Antimicrobial peptides by comparison with conventional hydrogen bond. There are a number of amino acid residues that can form hydrogen bonds via their side chains in addition to their peptide group. Perhaps highest contribution in this category is polar residue (Cys) and charged residues such as Lys and Arg. A total of 2513 C-H...O interactions were found in a data set of 53 Antimicrobial peptides. Among the 2513 nonconventional interactions observed in the data set, 40% of interactions are bonded to alpha carbon. This is consistent with the fact that the hydrogens are more acidic than others. Most prominent were side-chain to main-chain C-H...O interactions (SM-C-H...O). 92% of the stabilizing centers in the Antimicrobial peptides were found to be involved in C-H...O interactions. These interactions are mainly formed by short range contacts. Moreover, the study shows that, there is an average of more than one C-H...O interactions observed for every single residue in the Antimicrobial peptides data set. It is concluded that the C-H...O interaction can, indeed, be categorized as a true stabilizing force like hydrogen bond in Antimicrobial peptides.

Combined Experimental and Theoretical Study on Hydrogen-Bonded Complexes between Cyclic Ketones, Lactones, and Lactams with 3,4-Dinitrophenol

The interaction of 3,4 dinitrophenol (DNP) with cyclic ketones, lactones, and lactams was investigated by UV-visible spectroscopy and density functional theory (DFT) methods. Equilibrium constants K(HB) for 1:1 hydrogen bonded complexes were determined in solution in CCl(4) and C(6)H(12). For the entire range of studied bases, the pK(HB) scale, varying between 2.92 for beta-propiolactone to 5.53 for 1-methyl-epsilon-caprolactam, indicates that the basicity increases with the ring size. Geometries, energies, and vibrational characteristics of complexes were obtained by means of DFT calculations. For lactones and lactams, the energy difference between the two most stable conformers, cis and trans, with respect to the ring oxygen (nitrogen) atom, is relatively small, suggesting that the complex observed in solution is probably an equilibrium mixture of both forms. The good correlation between Gibbs free energies in solution and in the gas phase, computed at the B3LYP/6-311++G(3df,2p) level of theory, confirms the reliability of our results. The electron density of the complexes has been analyzed by means of the atoms in molecules (AIM) theory and the natural bond orbital (NBO) method have been used to characterize the orbital interactions. Our theoretical survey shows that the 1:1 complexes are stabilized by a network of conventional and/or nonconventional intermolecular hydrogen bonds.

Silylene Defect at the Dihydrogen Terminated (100) Si Surface

Density functional calculations for both periodic slabs and different size cluster models of the hydrogen-terminated (100) surface of silicon are used to study a new configuration, formed by a silylene center interacting with vicinal silicon dihydrides through nonconventional hydrogen bonds. A comparison between slab-model and cluster-model approaches to modeling surface silylene defect formation processes is presented. The cluster models are used to analyze the structure and bonding of the silylene with a Lewis acid and base, showing the Zwitterionic nature of the defect. The silylene is also demonstrated to behave as a strong Brønsted acid. The stabilization of the silylene defect via interaction with species unavoidably present in the HF(aq)-etching solution is investigated. Finally, the negative chemical shift observed by X-ray photoelectron spectroscopy in the HF(aq)-etched (100) Si surface is attributed to the occurrence of silylene defect.

Adenine–Au and adenine–uracil–Au. Non-conventional hydrogen bonds of the anions and donator–acceptor properties of the neutrals

This is a study of adenine–Au and adenine–uracil–Au (neutral, anionic and cationic), applying the B3LYP density-functional approach. In these systems, the interaction is directly related to the charge; so that as the metal atomic charge increases, the bond strength also increases. Neutral molecules are weakly bonded, the interaction in the case of cations is mainly electrostatic and in the case of the anions, the extra electron is localized on the metal atom and consequently, non-conventional hydrogen bonds are formed. In the case of adenine–Au (anion), the H dissociation energy is similar to the electron dissociation energy, and therefore both reactions may be possible. Moreover, the Au anionic atom modifies the hydrogen bonds of the uracil–adenine base pair. This may be significant in the study of point mutations that may occur in the Watson–Crick dimmer of nucleic basis. The electron-donator properties of these compounds are analyzed with the aid of the donator–acceptor map (DAM), previously described. Adenine–Au, uracil–Au and adenine–uracil–Au are more effective electron donors, but poorer electron acceptors than adenine, uracil and adenine–uracil. If the electron acceptor properties of carotenoids such as β-carotene and astaxanthin are compared, there are indications that astaxanthin may act as an oxidant instead of an antioxidant with the uracil–adenine base pair. The oxidation of nucleic acid bases by carotenoids may have important consequences, as oxidative damage of DNA and RNA appears to be linked to cancer. This is something that demands further studies and for this reason, work concerning the reactivity of carotenoids with DNA-nitrogen bases is in progress.

Comparison of halogen bonding and van der Waals and π–π interactions in 4,5-dibromo-2-hexyloxyphenol

The title compound, C(12)H(16)BrO(2), is an interesting case of a simple organic molecule making use of five different types of intra- and intermolecular interactions (viz. conventional and nonconventional hydrogen bonds, and pi-pi, Br...Br and Br...O contacts), all of them relevant in the molecular and crystal structure geometry. The molecules are strictly planar, with an intramolecular O-H...O hydrogen bond, and associate into two-dimensional structures parallel to (201) through two different types of halogen bonding. The planar structures, in turn, stack parallel to each other interlinked by C-H...pi and pi-pi contacts. Also discussed are the relevant structural features leading to the rather low melting point of the compound.

Do Anionic Gold Clusters Modify Conventional Hydrogen Bonds? The Interaction of Anionic Aun (n = 2−4) with the Adenine−Uracil Base Pair

Density functional approximation (B3LYP) calculations have been used in order to analyze the interaction of gold anionic clusters (Au(n) with n = 2-4) with uracil ([uracil-Au(n)](-1)), adenine ([adenine-Au(n)](-1)), and the adenine-uracil base pair ([uracil-adenine-Au(n)](-1)). It was found that there is only one stable isomer for [uracil-Au(2)](-1) and [uracil-Au(3)](-1), whereas there are two or more stable structures for [uracil-Au(4)](-1), [adenine-Au(n)](-1), and [uracil-adenine-Au(n)](-1). For all these systems, nonconventional hydrogen bonds are formed. Strengthening the bond between anionic gold clusters and the nitrogen base pair weakens the conventional hydrogen bond of the adenine-uracil base pair. This destabilization is not very strong (2-4 kcal/mol) and is at the limits of calculations, but anionic gold clusters bound in between the uracil-adenine base pair indicate that gold anionic clusters may dissociate it. These results will be useful for further experimental studies and may be important for future applications.

Nonconventional Hydrogen Bonds: A Theoretical Study of [uracil-L]−(L = F, Cl, Br, I, Al, Ga, In) Complexes

The interaction of L (-) (L = F, Cl, Br, I, Al, Ga and In) with a uracil molecule has been studied with B3LYP density-functional geometry optimizations and electron-propagator calculations of vertical electron detachment energies. Because the extra electron of the anion is localized on L, nonconventional hydrogen bonds are formed. The interactions of halide anions with uracil are similar to the interactions of uracil with Cu (-), Ag (-) and Au (-) that were reported previously. Whereas halide and transition metal anion complexes with uracils are singlets, the anions formed with Al, Ga and In are triplets. Vertical electron detachment energies (VEDEs) are higher for (uracil-L) (-) than the analogous values for isolated L (-) anions. Predicted VEDEs are assigned to Dyson orbitals that may be localized on L (-) or uracil.

Experimental Measurement of Carbohydrate–Aromatic Stacking in Water by Using a Dangling‐Ended DNA Model System

Protein-carbohydrate recognition is of fundamental importance for a large number of biological processes; carbohydrate-aromatic stacking is a widespread, but poorly understood, structural motif in this recognition. We describe, for the first time, the measurement of carbohydrate-aromatic interactions from their contribution to the stability of a dangling-ended DNA model system. We observe clear differences in the energetics of the interactions of several monosaccharides with a benzene moiety depending on the number of hydroxy groups, the stereochemistry, and the presence of a methyl group in the pyranose ring. A fucose-benzene pair is the most stabilizing of the studied series (-0.4 Kcal mol(-1)) and this interaction can be placed in the same range as other more studied interactions with aromatic residues of proteins, such as Phe-Phe, Phe-Met, or Phe-His. The noncovalent forces involved seem to be dispersion forces and nonconventional hydrogen bonds, whereas hydrophobic effects do not seem to drive the interaction.

Theoretical Study of Neutral, Anionic, and Cationic Uracil−Ag and Uracil−Au Systems: Nonconventional Hydrogen Bonds

The interaction of Ag and Au with uracil has been studied using the B3LYP density-functional approach. Neutral, cationic, and anionic systems were analyzed in order to study the influence of the atomic charge on bond formation. This interaction becomes stronger as the charge increases. In the case of neutral systems, a weak association is present. In the case of cations, the interaction is mainly electrostatic. The extra electron of the anions is localized on the metal atom. Consequently, nonconventional hydrogen bonds are formed. The ionization energy of uracil-Ag and uracil-Au is lower than the corresponding values for the metal atoms and uracil molecule, while the electron affinity is higher for uracil-Ag and uracil-Au than the analogous values for the isolated Ag, Au, and uracil. This might have significance for further experiments and possibly for applications, where the movement of the electrons is important. In the case of uracil-Ag and uracil-Au (anions), it may be possible to induce the detachment of one electron from the anion and also to remove a single hydrogen atom. It is possible that tight competition exists between the H dissociation and electron aloofness.

Theoretical Study of Cytosine−Al, Cytosine−Cu and Cytosine−Ag (Neutral, Anionic and Cationic)

The binding of cytosine to Al, Cu and Ag has been analyzed using the hybrid B3LYP density functional theory method. The three metals all have open shell electronic configuration, with only one unpaired valence electron. Thus it is possible to study the influence of electronic configuration on the stability of these systems. Neutral, cationic and anionic systems were analyzed, in order to assess the influence of atomic charge on bond formation. We argue that in the case of anions, nonconventional hydrogen bonds are formed. It is generally accepted that the hydrogen bond A-H...B is formed by the union of a proton donor group A-H and a proton acceptor B, which contains lone-pair electrons. In this study, we found that in the case of (Cu-cytosine)(-1) and (Ag-cytosine)(-1), N-H...Cu and N-H...Ag bonds are geometrically described as nonconventional hydrogen bonds. Their binding energies fall within the range of -20.0 to -55.4 kcal/mol (depending on the scheme of the reaction) and thus they are classified as examples of strong (>10 kcal/mol) hydrogen bonds.

Where gold meets a hydrogen bond?

This is a short survey of the area of the hydrogen bonding where the noble and coinage metal gold enters its manifold of the proton acceptors. It is largely focused on the nonconventional hydrogen bonds that are formed in the complexes of the auride anion Au − with HF, (HF) 2, H 2O, (H 2O) 2, NH 3, and (NH 3) 2, as mostly experimentally investigated to date. A thorough comparison of the experimental and computational data on these nonconventional hydrogen bonds is the main motif of the present work.

Interaction of Gold Atom with Clusters of Water: Few Computational Mise-En-Scènes with Hydrogen Bonding Motif

The present work outlines the fair relationship of the computational model with the experiments on anion photoelectron spectroscopy for the gold-water complexes [Au(H2O)1≤n≤2]- that is established between the auride anion Au- and water monomer and dimer thanks to the nonconventional hydrogen bond where Au- casts as the nonconventional proton acceptor. This work also extends the computational model to the larger complexes [Au(H2O)3≤n≤5]- where gold considerably thwarts the shape of water clusters and even particularly breaks their conventional hydrogen bonding patterns. The fascinating phenomenon of the lavish proton acceptor character of Au- to form at least six hydrogen bonds with molecules of water is computationally unveiled in the present work for the first time.