OHO Hydrogen Bonds Research Articles

Renewed spectroscopic and theoretical research of hydrogen bonding in ascorbic acid

The studies of two isomers of ascorbic acid and their deuteroanalogues, presented in the paper, have been accomplished by vibrational spectroscopy methods and quantum-chemical simulations. The spectroscopic research of L-ascorbic and D-isoascorbic acids have been carried out by the infrared (IR) and Raman (R) techniques. On the basis of the obtained results the spectral interpretation of the hydrogen bonded groups of ascorbic acids has been performed. Car-Parrinello Molecular Dynamics (CPMD) and Density Functional Theory (DFT) have been employed to support spectroscopic experimental findings and shed light onto the bridged proton dynamics in the L- and D- isomers of ascorbic acids. The accurate assignments of the hydrogen bond modes have been accomplished with the application of deuterosubstitution, CPMD-solid state simulations and Potential Energy Distribution (PED) analysis. The spectral and structural results have shown that dependency ν(OH) = f(γ(OH)) is the most common for the OHO hydrogen bond, whereas dependency d(OO) = f(γ(OH)) differs as for the ionic and resonance assisted hydrogen bonds.

Complexes of phosphine oxides with substituted phenols: hydrogen bond characterization based on shifts of PO stretching bands.

In this work IR spectral characteristics of PO groups are used to evaluate the strength of OHO hydrogen bonds. Three phosphine oxides: triphenylphosphine oxide, tributylphosphine oxide and hexamethylphosphoramide are investigated as proton acceptors. The results of the experimental IR study and DFT calculation of 30 complexes formed by phosphine oxides with various substituted phenols or CF3CH2OH in CCl4 solution at room temperature are reported. We show that the PO vibrational frequency changes non-linearly upon hydrogen bond formation and strengthening and that the shift of the PO band could be used for the estimation of hydrogen bond strength in complexes with phosphine oxides. The accuracy of these estimations and the influence of solvation effects on the main characteristics of complexes are discussed.

Theoretical Studies on the Structure and Intramolecular Interactions of Fagopyrins—Natural Photosensitizers of Fagopyrum

Simple SummaryThe study determines the spatial structure and intramolecular interactions of fagopyrins—natural photosensitizers of Fagopyrum species. In silico calculations show many fagopyrin conformers characterized by the formation of strong intramolecular interactions.Compounds characterized by a double-anthrone moiety are found in many plant species. One of them are fagopyrins—naturally occurring photosensitizers of Fagopyrum. The photosensitizing properties of fagopyrins are related to the selective absorption of light, which is a direct result of their spatial and electronic structure and many intramolecular interactions. The nature of the interactions varies in different parts of the molecule. The aim of this study is to determine the structure and intramolecular interactions of fagopyrin molecules. For this purpose, in silico calculations were used to perform geometry optimization in the gas phase. QTAIM and NCI analysis suggest the formation of the possible conformers in the fagopyrin molecules. The presence of a strong OHO hydrogen bond was shown in the anthrone moiety of fagopyrin. The minimum energy difference for selected conformers of fagopyrins was 1.1 kcal∙mol−1, which suggested that the fagopyrin structure may exist in a different conformation in plant material. Similar interactions were observed in previously studied structures of hypericin and sennidin; however, only fagopyrin showed the possibility of brake the strong OHO hydrogen bond in favor of forming a new OHN hydrogen bond.

IR and Raman spectra of strong OHO hydrogen bonds

The work outlines general ideas on how the frequency and the intensity of proton vibrations of O-H⋅⋅⋅O hydrogen bonding are formed as the bond evolves from weak to maximally strong bonding. The Raman spectra of glycinium phosphite and protonated di-methylformamid possessing strong and maximally strong hydrogen bonds were obtained in the temperature region of 5 K – 300 K. It is shown that strong bonding is formed only as a result of a particular chemical state of the donor and the acceptor and that the registration of proton vibrations requires low temperatures or high pressures. The dependence of the proton vibrational frequency is schematically presented as a function of the rigidity of O-H⋅⋅⋅O bonding.

Self-Assembly of Hydrogen-Bonded Cage Tetramers of Phosphonic Acid

The self-association of phosphonic acids with general formula RP(O)(OH)2 in solution state remains largely unexplored. The general understanding is that such molecules form multiple intermolecular hydrogen bonds, but the stoichiometry of self-associates and the bonding motifs are unclear. In this work, we report the results of the study of self-association of tert-butylphosphonic acid using low temperature liquid-state 1H and 31P NMR spectroscopy (100 K; CDF3/CDF2Cl) and density functional theory (DFT) calculations. For the first time, we demonstrate conclusively that polar aprotic medium tert-butylphosphonic acid forms highly symmetric cage-like tetramers held by eight OHO hydrogen bonds, which makes the complex quite stable. In these associates. each phosphonic acid molecule is bonded to three other molecules by forming two hydrogen bonds as proton donor and two hydrogen bonds as proton acceptor. Though the structure of such cage-like tetramers is close to tetrahedral, the formal symmetry of the self-associate is C2.

A two-dimensional crystal formed by pentamers on Au(111).

A new type of two-dimensional crystal comprising supramolecular pentamers on Au(111) is studied using an ultra-high vacuum low-temperature scanning tunnelling microscope. (2E,4E)-3-Methyl-5-(2,6,6-trimethylcyclohex-1-enyl)penta-2,4-dienoic acid molecules form pentamers through five-fold OH-O hydrogen bonds. In ordered arrays, pentamers interact with each other via van der Waals interactions. The impacts of different annealing temperatures and substrates on the formation of pentamer patterns are systemically investigated.

Side-by-Side Comparison of Hydroperoxide and Corresponding Alcohol as Hydrogen-Bond Donors.

Hydroperoxides are formed in significant amounts in the atmosphere by oxidation of volatile organic compounds and are key in aerosol formation. In a room-temperature experiment, we detected the formation of bimolecular complexes of tert-butyl hydroperoxide (t-BuOOH) and the corresponding alcohol tert-butanol (t-BuOH), with dimethyl ether (DME) as the hydrogen-bond acceptor. Using a combination of Fourier-transform infrared spectroscopy and quantum chemical calculations, we compare the strength of the OH-O hydrogen bond and the total strength of complexation. We find that, both in terms of observed red shifts and determined equilibrium constants, t-BuOOH is a significantly better hydrogen-bond donor than t-BuOH, a result that is backed by a number of calculated parameters and can be explained by a weaker OH bond in the hydroperoxide. On the basis of combined experimental and theoretical results, we find that the hydroperoxide complex is stabilized by ∼4 kJ/mol (Gibbs free energy) more than the alcohol complex. Measured red shifts show the same trend in hydrogen-bond strength with trimethylamine (N acceptor atom) and dimethyl sulfide (S acceptor atom) as the hydrogen-bond acceptors.

A butterfly motion of formic acid and cyclobutanone in the 1 : 1 hydrogen bonded molecular cluster.

Upon supersonic expansion, formic acid and cyclobutanone (CBU) form a molecular cluster in which the two constituent molecules, linked by OHO and CHO hydrogen bonds, undergo a rapid interconversion between two equivalent forms. The tunneling motion takes place through the rupture and reformation of the C-HO hydrogen bond between the carbonyl oxygen of HCOOH and one of the two hydrogen atoms of the methylenic group adjacent to the cyclobutanone keto group. From the microwave spectra, tunneling energy splittings (ΔE01) have been determined for the parent (1122.756(3) MHz), DCOOHCBU (1084.538(1) MHz) and HCOODCBU (1180.282(4) MHz) isotopic species. From these splittings, the potential barrier to interconversion has been calculated to be B2 = 39.7(5) cm-1. The tunneling pathway is an asymmetric butterfly-like motion between the two moieties of the adduct, with a barrier at a configuration in which the ring plane of cyclobutanone is coplanar with formic acid.

Spectroscopic studies of the 1:1 complex of piperidine-4-carboxylic acid (isonipecotic acid) with 2,6-dichloro-4-nitrophenol

The 1:1 complex of piperidine-4-carboxylic acid (isonipecotic acid, P4C) with 2,6-dichloro-4-nitrophenol (DCNP), has been investigated by single-crystal X-ray analysis, Raman and FTIR spectroscopy and theoretical calculations. The hydrogen-bonded-ion-pair complex is observed in the crystalline state with the O⋯H⋯OOC hydrogen bond of 2.453(16) Å. FTIR spectrum shows a broad absorption in the 1600–400cm−1 region characteristic of very short OHO hydrogen bond, broken by the Evans holes. The complexes are joined through NH⋯O into a H-bonding network. The NH⋯O mode appears as a broad band in the range of 3100–2000cm−1. In the structure optimized at the B3LYP/6–311++G(d,p) level of theory the proton is transferred from DCNP to P4C, and molecules are joined through the O⋯HOOC hydrogen bond of 2.640Å. The experimental and theoretical infrared spectra are discussed. Detail interpretation of the vibrational spectra has been carried out with the use of computed Potential Energy Distribution (PED).

Copper(II) ion as modulator of the conformation of non-steroidal anti-inflammatory drugs. Theoretical insight into the structure

Complexes of four non-steroidal anti-inflammatory drugs (NSAIDs): phenylobutazone, nimesulide, diclofenac and meloxicam with Cu2+ have been theoretically investigated using B3LYP/6-31G∗∗ method. The potential copper binding sites for the selected drugs have been found. Complexation of the investigated drug with Cu2+ can significantly change of the ligand geometry as for phenylobutazone and nimesulide or conformation of the drug can be persistent during complexation with Cu2+ as for meloxicam. For the last compound presence of Cu2+ influences the intramolecular OHO hydrogen bond. For the lowest energy complexes interaction of Cu2+ with the drug has been investigated in the frame of Atom in Molecule (AIM) theory.

Conformational state of β-hydroxynaphthylamides: Barriers for the rotation of the amide group around CN bond and dynamics of the morpholine ring

Three β-hydroxynaphthylamides (morpholine, pyrrolidine and dimethylamine derivatives) have been synthesized and their conformational state was analyzed by NMR, X-ray and DFT calculations. In aprotic solution the molecules contain intramolecular OHO hydrogen bonds, which change into intermolecular ones in solid state. The energy barriers for the amide group rotation around the CN bond were estimated from the line shape analysis of 1H and 13C NMR signals. A tentative correlation between the barrier height and the strength of OHO bond was proposed. Calculations of the potential energy profiles for the rotations around CC and CN bonds were done. In case of morpholine derivative experimental indications of additional dynamics: chair–chair ‘ring flip’ in combination with the twisting around CC bond were obtained and confirmed by quantum chemistry calculations.

Equilibrium configuration of (H2O)n, for n = 1–3

The equilibrium configurations of water molecule (H2O)n=1, its dimer (H2O)n=2 and trimer (H2O)n=3 have been studied in this paper. The ionic character of the OHO hydrogen bond, formed between the electronegative oxygen atoms, in (H2O)n=2, appears as a change in bond lengths in one of the water molecules while the bond lengths in the other molecule remain same as in (H2O)n=1. The increased hydrogen bond strength, caused by the cooperative effect of three-body forces (H2O)n=3, as compared to (H2O)n=2, results in the equilibrium structure of the water trimer to be much more rigid than that of the dimer. An attempt has been made, from the energy standpoint, to understand the controversy on chemical formula of water as H2O or H1·5O by studying the equilibrium configuration of (H2O) OH, which corresponds to 2H1·5O. The ground-state energy of (H2O) OH is found to be lower than the sum of the ground-state energies of OH and H2O at infinite separation. Calculations also show the ground-state energy of (H2O) OH to be lower than the sum of the energies of the constituent atoms at infinite separation. This shows that the binding energy of (H2O) OH is positive, which indicates that (H2O) OH is relatively stable.

Influence of varying hydrogen bond strength resulting from compositional variation on the vibration spectra of proton glasses: K1−x(NH4)xH2PO4

Single crystal neutron diffraction investigation [Choudhury and Chitra, J. Phys. Condense Matter, 25 (2013) 075902] on four mixed crystals with composition (K1−x(NH4)xH2PO4) where x=0.0, 0.29, 0.67, and 1.0 belonging to the potassium dihydrogen phosphate family of hydrogen bonded ferroelectric crystals had revealed that the compositional variation results in subtle structural differences primarily in the hydrogen bonds of these crystals. The study indicated that there is a change in hydrogen bond strengths with the change in crystal composition. Spectral investigation of the same set of four mixed crystals is undertaken with an intention to study the influence of the varying hydrogen bond strength on the vibrational properties of the crystals. Room temperature Raman spectra for all the four crystals are recorded in the range 100–4000cm−1. This Raman investigation correlates the structural changes observed from neutron diffraction investigations to the changes in the vibration spectra of the crystals. The varying N–H–O hydrogen bond strength in the mixed crystals is found to have an observable effect on the librational frequencies of the molecular components of these crystals. The strong OHO hydrogen bonds in these crystals give rise to four spectral bands in the 1500–3000cm−1 spectral region; this is in accordance with the theoretical prediction from the tunneling model for the very strong OHO hydrogen bonds. These OHO bonds can be described by a low barrier double well potential; the vibrational energy levels of the potential are split due to quantum tunneling effects. It is observed that the varying OHO hydrogen bond strength of these crystals results in a variation in the splitting of the vibrational energy levels of the hydrogen bond potential. It is attempted to correlate the varying OHO hydrogen bond strength with the expected variation in the freezing temperature with composition of these proton glasses.

Structural and energetic properties of the potential HIV-1 reverse transcriptase inhibitors d4A and d4G: a comprehensive theoretical investigation

A comprehensive quantum-chemical investigation of the conformational landscapes of two nucleoside HIV-1 reverse transcriptase inhibitors, 2′,3′-didehydro-2′,3′-dideoxyadenosine (d4A), and 2′,3′-didehydro-2′,3′-dideoxyguanosine (d4G), has been performed at the MP2/6-311++G(d,p)//B3LYP/6-31G(d,p) level of theory. It was found that d4A can adopt 21 conformers within a 5.17 kcal/mol Gibbs free energy range, whereas d4G has 20 conformers within 6.23 kcal/mol at T = 298.15 K. Both nucleosides are shaped by a sophisticated network of specific noncovalent interactions, including conventional (OHO, NHO) and weak (CHO, CHN) hydrogen bonds, as well as dihydrogen (CHHC) contacts. For the OHO, NHO, and CHO hydrogen bonds, natural bond orbital analysis revealed hyperconjugative interactions between the oxygen lone pairs and the antibonding orbital of the donor group. For the CHHC contacts, the electron density migrates from the antibonding orbital, corresponding to the CH group of the sugar residue, to the bonding orbital relative to the same group in the nucleobase. The results confirm the current belief that the biological activity of d4A and d4G is connected with the termination of the DNA chain synthesis in the 5′–3′ direction. Thus, these nucleosides act as competitive HIV-1 reverse transcriptase inhibitors.

Energy Analysis of Competing Non-Covalent Interaction in 1:1 and 1:2 Adducts of Collidine with Benzoic Acids by Means of X-Ray Diffraction

Abstract The hydrogen bond pattern and the types of non-covalent interactions in the crystals of the 1:1 and 1:2 adducts of 2,4,6-trimethylpyridine and benzoic acids are studied using high-resolution X-ray diffraction. The geometries of the hydrogen bonds are estimated using a combined XRD/DFT approach that provides the geometrical parameters within the margin of error of neutron diffraction studies. The energies of the non-covalent interactions are estimated on the base of the experimental electron density distribution function. It is shown that the structures of the adducts are governed by the NOH and OHO hydrogen bonds. In turn, C-H...O contacts and stacking interactions define the packing of the adducts in the crystal. On the other hand, it is important to note that the latter interactions affect the competition of the former hydrogen bonds in some 1:2 adducts.

Solvent and H/D Isotope Effects on the Proton Transfer Pathways in Heteroconjugated Hydrogen-Bonded Phenol-Carboxylic Acid Anions Observed by Combined UV–vis and NMR Spectroscopy

Heteroconjugated hydrogen-bonded anions A···H···X(-) of phenols (AH) and carboxylic/inorganic acids (HX) dissolved in CD2Cl2 and CDF3/CDF2Cl have been studied by combined low-temperature UV-vis and (1)H/(13)C NMR spectroscopy (UVNMR). The systems constitute small molecular models of hydrogen-bonded cofactors in proteins such as the photoactive yellow protein (PYP). Thus, the phenols studied include the PYP cofactor 4-hydroxycinnamic acid methyl thioester, and the more acidic 4-nitrophenol and 2-chloro-4-nitrophenol which mimic electronically excited cofactor states. It is shown that the (13)C chemical shifts of the phenolic residues of A···H···X(-), referenced to the corresponding values of A···H···A(-), constitute excellent probes for the average proton positions. These shifts correlate with those of the H-bonded protons, as well as with the H/D isotope effects on the (13)C chemical shifts. A combined analysis of UV-vis and NMR data was employed to elucidate the proton transfer pathways in a qualitative way. Dual absorption bands of the phenolic moiety indicate a double-well situation for the shortest OHO hydrogen bonds studied. Surprisingly, when the solvent polarity is low the carboxylates are protonated whereas the proton shifts toward the phenolic oxygens when the polarity is increased. This finding indicates that because of stronger ion-dipole interactions small anions are stabilized at high solvent polarity and large anions exhibiting delocalized charges at low solvent polarities. It also explains the large acidity difference of phenols and carboxylic acids in water, and the observation that this difference is strongly reduced in the interior of proteins when both partners form mutual hydrogen bonds.

Comparable Strength of OH–O versus OH−π Hydrogen Bonds in Hydrogen-Bonded 2,3-Benzofuran Clusters with Water and Methanol

Two different types of hydrogen bond, which are classified into a familiar OH-O and a relatively weak OH-π one, have been compared in the 1:1 hydrogen-bonded 2,3-benzofuran clusters with water and methanol molecules. By applying fluorescence-detected infrared spectroscopy and dispersed fluorescence spectroscopy, two isomers having different types of hydrogen bonds are distinguished. From the calculated stabilization energy as well as the frequency shift of the OH stretching vibration in each cluster, these two isomers are almost equally stable, although that of OH-π type is usually thought to be relatively weak. It is suggested that the origin of the weak OH-O hydrogen bond is derived from the lower availability for a hydrogen bond acceptor on the oxygen atom of a heteroaromatic ring, which is attributed to the larger furan aromaticity.

Directionality of Inter- and Intramolecular OHO Hydrogen Bonds: DFT Study Followed by AIM and NBO Analysis

The directionality of inter- and intramolecular OHO hydrogen bonds has been compared. For intramolecular bridges it is determined by an orbital formed in the proton transfer process. For intermolecular bonds, the hydrogen-bonded proton is attached to two lone pairs of the acceptor and the OHO angle is not fixed but can change in a broad range. Depending on the OHO angle, the interaction changes continuously from electrostatic interaction to strong OHO hydrogen bond.

Hydrogen Bond Geometries and Proton Tautomerism of Homoconjugated Anions of Carboxylic Acids Studied via H/D Isotope Effects on 13C NMR Chemical Shifts

Ten formally symmetric anionic OHO hydrogen bonded complexes, modeling Asp/Glu amino acid side chain interactions in nonaqueous environment (CDF(3)/CDF(2)Cl solution, 200-110 K) have been studied by (1)H, (2)H, and (13)C NMR spectroscopy, i.e. intermolecularly H-bonded homoconjugated anions of acetic, chloroacetic, dichloroacetic, trifluoroacetic, trimethylacetic, and isobutyric acids, and intramolecularly H-bonded hydrogen succinate, hydrogen rac-dimethylsuccinate, hydrogen maleate, and hydrogen phthalate. In particular, primary H/D isotope effects on the hydrogen bond proton signals as well as secondary H/D isotope effects on the (13)C signals of the carboxylic groups are reported and analyzed. We demonstrate that in most of the studied systems there is a degenerate proton tautomerism between O-H···O(-) and O(-)···H-O structures which is fast in the NMR time scale. The stronger is the proton donating ability of the acid, the shorter and more symmetric are the H-bonds in each tautomer of the homoconjugate. For the maleate and phthalate anions exhibiting intramolecular hydrogen bonds, evidence for symmetric single well potentials is obtained. We propose a correlation between H/D isotope effects on carboxylic carbon chemical shifts and the proton transfer coordinate, q(1) = ½(r(OH) - r(HO)), which allows us to estimate the desired OHO hydrogen bond geometries from the observed (13)C NMR parameters, taking into account the degenerate proton tautomerism.

Temperature dependence of one-dimensional hydrogen bonding in morpholinium hydrogen chloranilate studied by 35Cl nuclear quadrupole resonance and multi-temperature X-ray diffraction

The temperature dependence of (35)Cl NQR frequencies and the spin-lattice relaxation times T(1) has been measured in the wide temperature range of 4.2-420 K for morpholinium hydrogen chloranilate in which a one-dimensional O-HO hydrogen-bonded molecular chain of hydrogen chloranilate ions is formed. An anomalous temperature dependence of the NQR frequencies was analyzed to deduce a drastic temperature variation of the electronic state of the hydrogen-bonded molecular chain. The hydrogen atom distribution in the OHO hydrogen bond is discussed from the results of NQR as well as multi-temperature X-ray diffraction. Above ca. 330 K, the T(1) showed a steep decrease with an activation energy of ca. 70 kJ mol(-1) and with an isotope ratio (37)Cl T(1)/(35)Cl T(1) = 0.97 ± 0.2. The orientational change of the z axis of electric field gradient tensor in conjunction with the hydrogen transfer between adjacent hydrogen chloranilate ions is suggested as a possible relaxation mechanism.