Potential Hydrogen Bond Donor Research Articles

Crystal structure of 2,4-di-amino-5-(4-hy-droxy-3-meth-oxy-phen-yl)-8,8-dimethyl-6-oxo-6,7,8,9-tetra-hydro-5H-chromeno[2,3-b]pyridine-3-carbo-nitrile-di-methyl-formamide-water (1/1/1).

In the structure of the title compound, C22H22N4O4·C3H7NO·H2O, the entire tricyclic system is approximately planar except for the carbon atom bearing the two methyl groups; the meth-oxy-phenyl ring is approximately perpendicular to the tricycle. All seven potential hydrogen-bond donors take part in classical hydrogen bonds. The main mol-ecule and the DMF combine to form broad ribbons parallel to the a axis and roughly parallel to the ab plane; the water mol-ecules connect the residues in the third dimension.

Probing molecular interactions in mixed system of green solvent ethyl lactate with oligomers of polyethylene glycol

Polyethylene glycol and its oligomers are potential hydrogen bond donors that act as a green, effective, non-toxic, non-corrosive and recyclable molecular component for extractive desulfurization of liquid fuels and variety of other applications. The aim of this investigation is to explore the molecular interactions via variations in viscosity that occur on mixing these glycols with green solvent ethyl lactate. Dynamic viscosities (η) for pure solvents and binary mixtures of ethyl lactate and glycols oligomers (mono/di/tri/tetra-ethylene glycol) were measured at varying temperatures T/(K) = (298.15–313.15; with an interval of 5). Viscosity deviations (Δη) along with excess thermodynamic parameters of activation for viscous flow as Gibbs free energy (ΔG∗E), Enthalpy (ΔH∗E) and Entropy (ΔS∗E) were derived from experimental data. The Δη and ΔG∗E values were further correlated using Redlich-Kister polynomial expression. The experimentally obtained viscosity values were compared with 10 generalised literature models (Arrhenius, Kendall, Kendall-Monroe, Grunberg-Nissan, Hind, Katti-Chaudhri, Heric, McAllister three-body, McAllister four-body and Jouyban-Acree models). The average standard deviation percentages (ASD %) were calculated for all the models to compare the quality of correlation with experimental data. The minimal ASD % for McAllister four-body and Jouyban-Acree models in the working systems indicate that the multiparameter relations have the best capability of reproducing the experimental values. The temperature induced variations were also discussed together with molecular interactions. Further, quantum mechanical density-functional theory and graph theoretical approaches were used to explore the extent of interactions among the components.

Development of quantitative structure-property relationship to predict the viscosity of deep eutectic solvent for CO2 capture using molecular descriptor

Transport properties of deep eutectic solvent (DES), such as viscosity, are essential for selecting and designing processes based on these “green solvents” for CO2 capture and separation. Although experimental values for the viscosity of DES are available for a large number of systems, the number of potential hydrogen bond acceptors and hydrogen bond donors to form eutectic mixtures make the experimental characterization and screening of these systems impractical. A computational method able to predict the viscosity of DES would be highly valuable. The present study is aimed to develop a method to predict the viscosity of DESs using interaction energy descriptors derived from Conductor like Screening Model for Real Solvent (COSMO-RS). The stepwise multiple linear regression was implemented to select the optimal number of molecular descriptors and temperature based on an extensive database covering 947 viscosity data points for a wide range of DESs. The new model showed a good correlation between experimental and predicted values, with R-squared (R2) and average absolute relative deviation (AARD) of 0.9734 and 15.22%, respectively, for the overall dataset. In addition, the model showed that the viscosity of DES was significantly influenced by the hydrogen bonding between the anion of the hydrogen bond acceptor and the hydrogen bond donor molecules. The electrostatic-misfit and van der Waals forces were shown to have a marginal impact on the viscosities. In conclusion, the developed model provides an effective tool to predict the viscosity of DES and allows a fundamental understanding of the molecular level interactions on this property.

Double Free: A Promising Route toward Moisture-Stable Hypotoxic Hybrid Perovskites

Double Free: A Promising Route toward Moisture-Stable Hypotoxic Hybrid Perovskites

Thiols as Hydrogen Bond Acceptors and Donors: Spectroscopy of 2-Phenylethanethiol Complexes.

Evidence and understanding of sulfur-centered hydrogen bonding, especially where the donor is a thiol, lags far behind that for conventional OH interactions. To help address this deficiency, conformer specific IR spectra of 2-phenylethanethiol (PET) and associated 1:1 solvent complexes have been measured in SH, OH, and CH stretch regions using resonant-two-photon-ionization (R2PI) and IR-UV ion dip spectroscopic techniques. The aromatic and aliphatic CH stretch regions show signature differences between anti and gauche conformers. Supported by ab initio calculations, a PET-water cluster with an OH···S arrangement and a PET-diethyl ether cluster expressing an SH···O interaction were identified. The SH stretch band of the SH···O complex is red-shifted and undergoes significant intensity enhancement compared to the bare molecule, which is characteristic of hydrogen bonding. These findings offer insight into the nature of the thiol functional group as a potential hydrogen bond donor and acceptor.

Stereoselective Ammonium-Directed Epoxidation in the Asymmetric Syntheses of Dihydroconduramines (–)-A-2, (–)-B-2, (–)-C-3 and (+)-F-3

Epoxidation of racemic trans-2-(N,N-dibenzylamino)cyclohex-3-en-1-ol, upon treatment with Cl3CCO2H then m-CPBA, proceeded with poor diastereoselectivity (ca. 60:40 dr), whilst epoxidation of racemic trans-2-(N-benzylamino)cyclohex-3-en-1-ol under the same conditions proceeded with high diastereoselectivity (>95:5 dr) and was followed by completely regioselective and stereospecific ring-opening in situ to give, after methanolysis of the intermediate trichloroacetate ester, (1RS,2SR,3SR,4SR)-2-(N-benzylamino)cyclohexane-1,3,4-triol. Use of aq HBF4 as the acid protecting agent gave the amino triol directly. The differing diastereoselectivities of these epoxidation reactions may be due to a predilection towards formation of an intramolecular hydrogen-bond in the former substrate disrupting the ability of the in situ formed ammonium moiety to act as a directing group for the incoming oxidant; the presence of two potential hydrogen-bond donors (i.e., two N–H bonds) in the latter substrate circumvents this limitation. With the criterion for a highly diastereoselective (ammonium-directed) epoxidation in this system established, a synthesis of enantiopure trans-2-(N-benzylamino)cyclohex-3-en-1-ol (>99% ee) was developed and the ammonium-directed epoxidation was then employed as a key synthetic step to facilitate the asymmetric syntheses of enantiopure dihydroconduramines (–)-A-2, (–)-B-2, (–)-C-3 and (+)-F-3 (>98% ee in each case) from 1,3-cyclohexadiene.

Vibrational spectroscopy and density functional theory study of ninhydrin

In this paper, ninhydrin was designed as a model molecule for theoretical and experimental studies of the molecule structure. Density functional theory (DFT) calculations have been performed to predict the IR and Raman spectra for the molecule. In addition, Fourier transform infrared (FTIR) and Raman spectra of the compound have been obtained experimentally. Based on the modeling results obtained at the B3LYP/6-311++G** level, all FTIR and Raman bands of the compound obtained experimentally were assigned. Our calculated vibrational frequencies are in good agreement with the experimental values. The molecular electrostatic potential surface calculation was performed and the result suggested that the ninhydrin had two potential hydrogen bond donors and four potential hydrogen bond acceptors. HOMO–LUMO gap was also obtained theoretically at B3LYP/6-311++G** level.

Propeller-Shaped Self-Assembled Molecular Capsules: Synthesis and Guest Entrapment

Molecular containers or supramolecular capsules are a subject of great interest because of their potential utilizations in various fields of chemistry, medicine, and nanoscience. They have been utilized as nanovessels for reactions and targeted drug delivery in recent years. Cyclotricatechylene (CTC) is a bowl-shaped molecule in its crown structure. It has six phenolic groups as potential hydrogen bond donors. In this work, we utilize this hydrogen bonding capability of CTC to generate supramolecular complexes with hydrogen bond acceptors such as 4,4′-bipyridine, pyrazine, 2,2′-bipyridine, and phenanthroline. These supramolecular entities were studied in the solid state by X-ray crystallography and scanning electron microscopy. They are not soluble in low polar solvents. Therefore, the hydrogen bonding behavior in solution could not be studied by NMR. Except in the case of pyrazine, capsular supramolecular assemblies were formed in all the cases. One of these capsules was studied for guest entrapment. Pla...

H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin

The ferric form of truncated hemoglobin II from Thermobifida fusca (Tf-trHb) and its triple mutant WG8F-YB10F-YCD1F at neutral and alkaline pH, and in the presence of CN− have been characterized by resonance Raman spectroscopy, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations. Tf-trHb contains three polar residues in the distal site, namely TrpG8, TyrCD1 and TyrB10. Whereas TrpG8 can act as a potential hydrogen-bond donor, the tyrosines can act as donors or acceptors. Ligand binding in heme-containing proteins is determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. Since both the RR Fe–OH− and Fe–CN− frequencies are very sensitive to the distal environment, detailed information on structural variations has been obtained. The hydroxyl ligand binds only the WT protein giving rise to two different conformers. In form 1 the anion is stabilized by H-bonds with TrpG8, TyrCD1 and a water molecule, in turn H-bonded to TyrB10. In form 2, H-bonding with TyrCD1 is mediated by a water molecule. Unlike the OH− ligand, CN− binds both WT and the triple mutant giving rise to two forms with similar spectroscopic characteristics. The overall results clearly indicate that H-bonding interactions both with distal residues and water molecules are important structural determinants in the active site of Tf-trHb. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

Multicomponent pharmaceutical cocrystals: furosemide and pentoxifylline

The combination of the active pharmaceutical ingredients furosemide [4-chloro-2-(furan-2-ylmethylamino)-5-sulfamoylbenzoic acid] and pentoxifylline [3,7-dimethyl-1-(5-oxohexyl)-3,7-dihydro-1H-purine-2,6-dione] produces a 1:1 cocrystal, C(12)H(11)ClN(2)O(5)S·C(13)H(18)N(4)O(3), (I), a 1:1 cocrystal hydrate, C(12)H(11)ClN(2)O(5)S·C(13)H(18)N(4)O(3)·H(2)O, (II), and a 1:1 cocrystal acetone solvate, C(12)H(11)ClN(2)O(5)S·C(13)H(18)N(4)O(3)·C(2)H(6)O, (III). These structures exhibit the presence of a rarely encountered synthon with the graph set R(2)(2)(7). All potential hydrogen-bond donors of furosemide participate in hydrogen-bond formation in (I)-(III). However, only two hydrogen-bond acceptors of furosemide are active in (I) and (II), and only one is active in (III). Four hydrogen-bond acceptors of pentoxifylline are active in (II), three in (I) and two in (III). These observations are in good agreement with the calculated packing indexes of 69.5, 69.6 and 68.8% for (II), (I) and (III), respectively.

42 salt forms of tyramine: structural comparison and the occurrence of hydrate formation

The single-crystal diffraction structures of 38 salt forms of the base tyramine (4-hydroxyphenethylamine) are reported for the first time. Together with literature examples, these structures are discussed with respect to cation conformation, cation packing, hydrogen bonding and hydrate formation. It is found that isostructural cation packing can occur even with structurally different anions, with different hydration states and with different hydrogen bonding. Hydrate formation is found to be more likely both (i) when there is an increase in the total number of potential hydrogen bond acceptor and donor atoms; and (ii) when the ratio of potential hydrogen bond donor to acceptor atoms is low.

UNAC tetraloops: to what extent do they mimic GNRA tetraloops?

The structures of four small RNAs each containing a different version of the UNAC loop were determined in solution using NMR spectroscopy and restrained molecular dynamics. The UMAC tetraloops (where M is A or C) exhibited a typical GNRA fold including at least one hydrogen bond between the first U and fourth C. In contrast, UGAC and UUAC tetraloops have a different orientation of the first and fourth residues, such that they do not closely mimic the GNRA fold. Although the UMAC tetraloops are excellent structural mimics of the GNRA tetraloop backbone, sequence comparisons typically do not reveal co-variation between the two loop types. The limited covariation is attributed to differences in the location of potential hydrogen bond donors and acceptors as a result of the replacement of the terminal A of GNRA with C in the UMAC version. Thus, UMAC loops do not readily form the common GNRA tetraloop-receptor interaction. The loop at positions 863-866 in E. coli 16S ribosomal RNA appears to be a major exception. However, in this case the GNRA loop does not in fact engage in the usual base to backbone tertiary interactions. In summary, UMAC loops are not just an alternative sequence version of the GNRA loop family, but instead they expand the types of interactions, or lack thereof, that are possible. From a synthetic biology perspective their inclusion in an artificial RNA may allow the establishment of a stable loop structure while minimizing unwanted long range interactions or permitting alternative long-range interactions. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 617-628, 2012.

Molecular design and density functional theory investigation of novel low‐band‐gap benzobisthiadiazole‐based systems: from monomer to polymer

AbstractThe electronic structure and properties of benzobisthiadiazole‐based alternating donor–acceptor conjugated oligomers and their periodic copolymers of donor and acceptor units with ratios of 1:1 and 2:1 were investigated systematically using the density functional theory method. The donors include thiophene, thieno[3,2‐b]thiophene and pyrrole. The ratio of donor to acceptor units (D:A ratio) plays a very important role in the geometric and electronic properties. The intramolecular charge transfer increases and the bond length alternation decreases with an increase in the D:A ratio for these oligomers and polymers. Moreover, an increase in D:A ratio can greatly reduce the band gap and effective mass of holes and electrons for these alternating donor‐acceptor conjugated copolymers. The unusually large intramolecular charge transfer caused by intramolecular hydrogen bonds reveals that pyrrole is not only a strong electron donor but also a potential hydrogen bond donor. The theoretical results suggest those copolymers possessing a D:A ratio of 2:1 are better candidates for conducting materials compared to those with a D:A ratio of 1:1. The almost zero band gap, large bandwidth and small effective mass of holes and electrons of poly(4,8‐bis(thieno[3,2‐b]thiophene‐2‐yl)benzo[1,2‐c:4,5‐c′]bis[1,2,5]thiadiazole) indicate that it is a very good candidate for an electrically conductive material. Copyright © 2010 Society of Chemical Industry

Synthesis of Enantiopure Planar-Chiral Thiourea Derivatives

An efficient access to enantiopure pseudo-geminally substituted 4-amino-13-bromo[2.2]paracyclophane is described. The aminobromide was employed in cross-coupling reactions to yield arylated 4-amino[2.2]paracyclophanes. The amines were converted into enantiopure planar-chiral thioureas, which are potential hydrogen-bond donors for enantioselective organocatalysis.

Arginine/lysine–methyl/methyl switches: biochemical role of histone arginine methylation in transcriptional regulation

Post-translational modifications (PTMs) are commonly used to modify protein function. Modifications such as phosphorylation, acetylation and methylation can influence the conformation of the modified protein and its interaction with other proteins or DNA. In the case of histones, PTMs on specific residues can influence chromatin structure and function by modifying the biochemical properties of key amino acids. Histone methylation events, especially on arginine- and lysine-residues, are among the best-characterized PTMs, and many of these modifications have been linked to downstream effects. The addition of a methyl group to either residue results in a slight increase in hydrophobicity, in the loss of a potential hydrogen-bond donor site and, in the alteration of the protein interaction surface. Thus far, a number of protein domains have been demonstrated to directly bind to methylated lysine residues. However, the biochemical mechanisms linking histone arginine methylation to downstream biological outputs remain poorly characterized. This review will focus on the role of histone arginine methylation in transcriptional regulation and on the crosstalk between arginine methylation and other PTMs. We will discuss the mechanisms by which differentially methylated arginines on histones modulate transcriptional outcomes and contribute to the complexity of the 'histone code'.

Aryl azo imidazoles assisted assembly of anion/anion–water through salt formation

Aryl azo dyes containing imidazole group can act as an acid or base. They are also potential hydrogen bond donor and acceptor. The imidazolium form of these dyes can form salts with various inorganic anions. The effect of the anion shape (linear, planner, spherical) on higher-dimensional supramolecular assembles of these salts has been analyzed and rationalized. Ligand assisted anion or anion–water assembly formation has been discussed. The presence of water in the crystal structure plays a vital role in the formation of higher dimensional networks. All supramolecular networks of salt 1–5 are guided by various noncovalent interactions, especially directional hydrogen bonds, halogen bonds and π-stacking interactions. The interaction of anions with the ligands in the solution phase was also investigated by absorption and fluorescent spectra.

Isothermal Titration Calorimetry Study of the Interaction of Sweeteners with Fullerenols as an Artificial Sweet Taste Receptor Model

A fullerenol-based synthetic sweetness receptor model, consisting of polyhydroxy groups for potential hydrogen bond donor along with a spherical hydrophobic center, was proposed according to the widely accepted sweetness hypothesis. An isothermal titration calorimetry (ITC) technique was used to study mimetic interaction of this sweet receptor model with a series of sweeteners having increasing sweetness intensity. The results showed that ITC is an effective method to provide thorough and precise characterization of the energies of molecular complex formation. Binding of all of the studied sweeteners with fullerenols was found through two sets of site models. More heat was released from sweeter synthetic compounds binding with fullerenols than from less sweet carbohydrates. The results imply that hydrogen bond formation is necessary for the sweeteners to bind to the fullerenol receptor in the first stage, whereas hydrophobic effect and conformation changes that lead to favorable entropy changes occur in most cases. The preliminary results of this study help to cover the lack of information about the thermodynamic basis of understanding of the initiation of the sweet sensation. It also adds complementary physicochemical measurements available for comparison with the sweetness hypothesis. On the other hand, a correlation between the thermodynamic parameters and sweetness intensity has been made as well, which exhibits potential as a useful tool in sensory analysis.

Redetermination and invariom refinement of 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-4-ium-1-yl)-1,4-dihydroquinoline-3-carboxylate hexahydrate at 120 K

The structure of the title compound, C17H18FN3O3·6H2O, has been redetermined at 120 K. An invariom refinement, a structural refinement using aspherical scattering factors from theoretically predicted multipole population parameters, yields accurate geometry and anisotropic displacement parameters, including hydrogen-bonding parameters. All potential hydrogen-bond donors and acceptors are involved in hydrogen bonding, forming an intricate three-dimensional network of N—H⋯O and O—H⋯O bonds.

Dimethyl 6-[1,2-bis(methoxycarbonyl)-2-(triphenyl-λ5-phosphanylidene)ethylideneamino]-2-methylsulfanyl-3,4-pyridinedicarboxylate forms a chain of hydrogen-bonded rings

In the title compound, C(34)H(31)N(2)O(8)PS, the intramolecular distances provide evidence for polarization of the molecular-electronic structure. The molecules are linked into complex chains of rings by three independent C-H...O hydrogen bonds. The significance of this study lies in its finding that two of the four carbonyl O atoms play no role in the hydrogen bonding, despite the large excess of potential hydrogen-bond donors present.

Similar sulfonamides with different crystal structures: sulfasymazine and sulfatriazine

The crystal structures of 4-amino-N-(4,6-diethyl-1,3,5-triazin-2-yl)benzenesulfonamide, C13H17N5O2S, and 4-amino-N-(4,6-dimethoxy-1,3,5-triazin-2-yl)benzenesulfonamide, C11H13N5O4S, also known as sulfasymazine and sulfatriazine, respectively, are dominated by hydrogen-bond interactions. All three potential hydrogen-bond donors are employed in each case, resulting in a three-dimensional network for sulfasymazine, while an entirely different hydrogen-bonded layer structure is obtained for sulfatriazine. This study demonstrates the versatile nature of the hydrogen-bonding capabilities in sulfonamides, even in structurally very similar molecules.