Infrared intensity analysis of hydroxyl stretching modes in carboxylic acid dimers by means of the charge–charge flux–dipole flux model

The Charge‑Charge Flux‑Dipole Flux (CCFDF) model in terms of multipoles from the quantum theory of atoms in molecules (QTAIM) was used to investigate the variations in infrared intensities of hydroxyl (O H) stretching modes during the dimerization of carboxylic acids. The hydrogen bond formation in these systems results into bathochromic shifts of vibrational frequencies for all the O H stretching modes along with huge infrared intensity increments for some of them. These bands become more intense on dimerization due mainly to changes in the cross-term contribution between charge and charge flux. In addition, interaction energies for the pair of atoms directly involved in individual hydrogen bonds (O…H) are linearly correlated to electron densities at their bond critical points (BCPs). Therefore, the hydrogen bonds between the carbonyl group (CO) of acetic acid and the hydroxyl group of halogenated monomers show the largest electron density values at their BCPs. The formation of these intermolecular interactions is also accompanied by ionic character enhancements of O H bonds and electron density decrements at their BCPs. We finally noticed that the hydrogen atom belonging to the hydroxyl group loses electronic charge, while the oxygen from the CO end becomes more negatively charged during dimerization. © 2019 Wiley Periodicals, Inc.     

Comparative estimation of the energies of intramolecular C-H…O,N-H…O,and O-H…O hydrogen bonds according to the QTAIM analysis and NMR spectroscopy data

The energies of intramolecular C-H…O, N-H…O, and O-H…O hydrogen bonds in model compounds are empirically estimated based on the values of the hydrogen bond induced weak-field shift of the bridging hydrogen atom signal in the ¹H NMR spectrum. It is supported by a theoretical estimation of these energies based on the electron density value at the hydrogen bond critical point calculated within the QTAIM method. Good agreement between the empirical and theoretical estimates is found, which gives evidence of their reliability. It is shown that from the standpoint of their strength the intramolecular N-H…O and O-H…O hydrogen bonds can be classified as moderate whereas the intramolecular C-H…O hydrogen bonds must be classified as very weak interactions similar in their energy significance to van der Waals interactions.     

The effect of hydrogen bonding on structural parameters ii. an ab initio study of the monohydrated formamide molecule

Four hydrogen-bonded formamide-water complexes have been studied by ab initio calculations, two where the amino group acts as a donor and two where the carbonyl oxygen is an acceptor. The results indicate that the effect on the conjugated NCO fragment depends on both the type and the energy of the hydrogen bond formed. Although, in all cases the formation of a hydrogen bond leads to increased conjugation, expressed as a shortening of the CN bond and a corresponding lengthening of the CO bond, there is a significant difference in the effect of the two types of hydrogen bonds. This difference may be explained by changes in the electron populations. In two of the complexes the effect of varying the hydrogen bond length has been studied in some detail. It is found that the effect on the conjugated system depends on the length of the hydrogen bond, and analytical expressions have been found for the variations of the CO and CN bond lengths with changes in the hydrogen bond length. Potential functions for the N-H β O and O-H β O hydrogen bonds have also been derived.     

Recurrence of carboxylic acid-pyridine supramolecular synthon in the crystal structures of some pyrazinecarboxylic acids.

X-ray crystal structures of pyrazinic acid 1 and isomeric methylpyrazine carboxylic acids 2-4 are analyzed to examine the occurrence of carboxylic acid-pyridine supramolecular synthon V in these heterocyclic acids. Synthon V, assembled by (carboxyl)O-H...N(pyridine) and (pyridine)C-H...O(carbonyl) hydrogen bonds, controls self-assembly in the crystal structures of pyridine and pyrazine monocarboxylic acids. The recurrence of acid-pyridine heterodimer V compared to the more common acid-acid homodimer I in the crystal structures of pyridine and pyrazine monocarboxylic acids is explained by energy computations in the RHF 6-31G* basis set. Both the O-H.N and the C-H...O hydrogen bonds in synthon V result from activated acidic donor and basic acceptor atoms in 1-4. Pyrazine 2,3- and 2,5-dicarboxylic acids 10 and 11 crystallize as dihydrates with a (carboxyl)O-H...O(water) hydrogen bond in synthon VII, a recurring pattern in the diacid structures. In summary, the carboxylic acid group forms an O-H...N hydrogen bond in pyrazine monocarboxylic acids and an O-H...O hydrogen bond in pyrazine dicarboxylic acids. This structural analysis correlates molecular features with supramolecular synthons in pyridine and pyrazine carboxylic acids for future crystal engineering strategies.     

The dynamic behavior of a liquid ethanol-water mixture: a perspective from quantum chemical topology

Quantum Chemical Topology (QCT) is used to reveal the dynamics of atom-atom interactions in a liquid. A molecular dynamics simulation was carried out on an ethanol-water liquid mixture at its azeotropic concentration (X(ethanol)=0.899), using high-rank multipolar electrostatics. A thousand (ethanol)(9)-water heterodecamers, respecting the water-ethanol ratio of the azeotropic mixture, were extracted from the simulation. Ab initio electron densities were computed at the B3LYP/6-31+G(d) level for these molecular clusters. A video shows the dynamical behavior of a pattern of bond critical points and atomic interaction lines, fluctuating over 1 ns. A bond critical point distribution revealed the fluctuating behavior of water and ethanol molecules in terms of O-H···O, C-H···O and H···H interactions. Interestingly, the water molecule formed one to six C-H···O and one to four O-H···O interactions as a proton acceptor. We found that the more localized a dynamical bond critical point distribution, the higher the average electron density at its bond critical points. The formation of multiple C-H···O interactions affected the shape of the oxygen basin of the water molecule, which is shown in three dimensions. The hydrogen atoms of water strongly preferred to form H···H interactions with ethanol's alkyl hydrogen atoms over its hydroxyl hydrogen.     

Density functional theory study of the hydrogen bond interaction between lactones, lactams, and methanol

The structure and relative stability of methanol complexes with various cyclic ketones, lactones, lactams, and N-methyl lactams from three- to seven-membered rings have been investigated using the density functional theory method. The geometries, harmonic frequencies, and energies were calculated at the B3LYP/6-311+G(d,p) level. Three stable structures, cis-a, cis-b, and trans, with respect to the ring oxygen (nitrogen) atom, were found to be local minima of the potential energy surface. For lactones and N-methyl lactams, the most stable structure is trans; it is stabilized, as in cyclic ketones, through the conventional hydrogen bond (HB) interaction between the basic carbonyl oxygen and the acidic methanolic hydrogen and an unconventional HB interaction between the methanolic oxygen and the CH hydrogen, in the alpha position of the carbonyl group. For unsubstituted lactams, the cis-a structure, stabilized through a HB interaction between the NH group and the methanol oxygen in addition to the conventional HB interaction, is the most stable. The topological properties of the electron density ratify the existence of conventional (N,O-H. . .O) and unconventional (C-H. . .O) hydrogen bonding. A good correlation was found between the HB distances and the electron density at the HB critical point. The unsubstituted lactams yield more stable complexes with methanol than N-methyl lactams, lactones, and cyclic ketones. In the most stable complexes, both components behave simultaneously as a HB donor and as a HB acceptor.     

Interaction of alcohols with 2-fluoro- and 4-fluorophenylacetylenes: infrared-optical double resonance spectroscopic and computational investigation

Alcohol complexes of 4-fluorophenylacetylene and 2-fluorophenylacetylene were investigated using IR-UV double resonance spectroscopy. Methanol forms a cyclic complex with both the fluorophenylacetylenes incorporating C-H···O and O-H···π hydrogen bonds, the structure of which is similar to that of the corresponding water complex but different from that of a phenylacetylene-methanol complex. The anti conformer of ethanol also binds in a similar fashion to both the fluorophenylacetylenes. Additionally, the gauche conformer of ethanol binds to 2-fluorophenylacetylene in a distinctly different structural motif that incorporates C-H···F and O-H···π hydrogen bonds. The OH group of trifluoroethanol interacts primarily with the π electron density of the C≡C bond. The π electron density of the C≡C bond is the principal point of interaction between the alcohols and both the fluorophenylacetylenes. The present results are indicative of the fact that fluorine substitution on the phenyl ring is sufficient to eliminate the subtle hydrogen bonding behavior of phenylacetylene.     

Proton-coupled electron transfer versus hydrogen atom transfer in benzyl/toluene,methoxyl/methanol,and phenoxyl/phenol self-exchange reactions

Degenerate hydrogen atom exchange reactions have been studied using calculations, based on density functional theory (DFT), for (i) benzyl radical plus toluene, (ii) phenoxyl radical plus phenol, and (iii) methoxyl radical plus methanol. The first and third reactions occur via hydrogen atom transfer (HAT) mechanisms. The transition structure (TS) for benzyl/toluene hydrogen exchange has C(2)(h)() symmetry and corresponds to the approach of the 2p-pi orbital on the benzylic carbon of the radical to a benzylic hydrogen of toluene. In this TS, and in the similar C(2) TS for methoxyl/methanol hydrogen exchange, the SOMO has significant density in atomic orbitals that lie along the C-H vectors in the former reaction and nearly along the O-H vectors in the latter. In contrast, the SOMO at the phenoxyl/phenol TS is a pi symmetry orbital within each of the C(6)H(5)O units, involving 2p atomic orbitals on the oxygen atoms that are essentially orthogonal to the O.H.O vector. The transferring hydrogen in this reaction is a proton that is part of a typical hydrogen bond, involving a sigma lone pair on the oxygen of the phenoxyl radical and the O-H bond of phenol. Because the proton is transferred between oxygen sigma orbitals, and the electron is transferred between oxygen pi orbitals, this reaction should be described as a proton-coupled electron transfer (PCET). The PCET mechanism requires the formation of a hydrogen bond, and so is not available for benzyl/toluene exchange. The preference for phenoxyl/phenol to occur by PCET while methoxyl/methanol exchange occurs by HAT is traced to the greater pi donating ability of phenyl over methyl. This results in greater electron density on the oxygens in the PCET transition structure for phenoxyl/phenol, as compared to the PCET hilltop for methoxyl/methanol, and the greater electron density on the oxygens selectively stabilizes the phenoxyl/phenol TS by providing a larger binding energy of the transferring proton.     

Radical-induced aromatic substitution between benzoyl peroxide and benzenediols in the gas phase characterized by mass spectrometry

A radical-induced aromatic substitution mechanism for the reaction between benzoyl peroxide and benzenediols in the gas phase was characterized by mass spectrometry. The benzoyloxy radical produced from the homolysis of benzoyl peroxide associates at its carbonyl group with the phenolic hydroxyl group. The pairing tendency of the unpaired electron on the oxygen of the radical induces electron transfer along the hydrogen bond, which results in the rupture of the O? H bond of the phenol and aromatic substitution at the ortho position of the benzoyloxy radical. Supporting evidence for the mechanism was obtained by isotope labelling.     

Structure of dihydrochalcones and related derivatives and their scavenging and antioxidant activity against oxygen and nitrogen radical species

Quantum mechanical calculations at B3LYP/6-31G** level of theory were employed to obtain energy (E), ionization potential (IP), bond dissociation enthalpy (O-H BDE) and stabilization energies (DE(iso)) in order to infer the scavenging activity of dihydrochalcones (DHC) and structurally related compounds. Spin density calculations were also performed for the proposed antioxidant activity mechanism of 2,4,6-trihydroxyacetophenone (2,4,6-THA). The unpaired electron formed by the hydrogen abstraction from the phenolic hydroxyl group of 2,4,6-THA is localized on the phenolic oxygen at 2, 6, and 4 positions, the C? and C? carbon atoms at ortho positions, and the C? carbon atom at para position. The lowest phenolic oxygen contribution corresponded to the highest scavenging activity value. It was found that antioxidant activity depends on the presence of a hydroxyl at the C2 and C4 positions and that there is a correlation between IP and O-H BDE and peroxynitrite scavenging activity and lipid peroxidation. These results identified the pharmacophore group for DHC.     

Molecular structure and antioxidant properties of delphinidin

Density functional theory calculations were performed to evaluate the antioxidant activity of delphinidin, taking into account its acid/base equilibrium. The conformational behavior of both the isolated and the aqueous solvation species (simulated with the polarizable continuum model) were analyzed at the B3LYP/6-31++G(d,p) level, considering the cationic, neutral, and anionic forms, the latter two forms consisting of diverse tautomers. The analysis of their electron density distributions, using the quantum theory of atoms in molecules, reveals several facts that are not in line with their usual Lewis structures. The prototropic preferences observed in the gas phase and in solution are similar. Thus, in both phases, most stable tautomer of neutral delphinidin is obtained by deprotonating the hydroxyl at C4', and the most stable tautomer of the anion is obtained by deprotonating the hydroxyls at C4' and C5. All the planar conformers obtained display an intramolecular hydrogen bond (IHB) between O3 and H6'. Furthermore, the most stable tautomers of the neutral and anionic forms display two IHBs between O4' and H3' and H5'. To obtain ionization potentials (IPs) and homolytic O-H bond dissociation enthalpies (BDEs), the corresponding radical species were optimized at the UB3LYP level. Heterolytic O-H bond dissociation enthalpies (proton dissociation enthalpies, PDEs) were also computed. The expected important antioxidant activity can be justified from these results. IP, O-H BDE, and O-H PDE values suggest that one-step H atom transfer rather than sequential proton loss-electron transfer or electron transfer-proton transfer would be the most favored mechanisms for explaining the antioxidant activity of delphinidin in nonpolar solvents as well as in aqueous solution.     

Hydrogen bond, dimerization and vibrational modes in 2-chloro-3-hydroxybenzaldehyde and 3-chloro-4-hydroxybenzaldehyde from vibrational and ab initio studies

Ab initio conformers and dimers have been computed at RHF and B3LYP/6-31G* levels for isomers 2-chloro-3-hydroxybenzaldehyde and 3-chloro-4-hydroxybenzaldehyde to explain the observed infrared absorption and Raman vibrational spectral features in the region 3500-50 cm(-1). The position of the chlorine in ortho position with respect to aldehyde group in 2-chloro-3-hydroxybenzaldehyde yields four distinct conformers; whereas the chlorine in meta position in 3-chloro-4-hydroxybenzaldehyde yields effectively only three conformers. Major spectral features as strong absorptions near 3160-80 cm(-1), down-shifting of the aldehydic carbonyl stretching mode and up-shifting of hydroxyl group's in-plane bending mode are explained using ab initio evidence of O-H?O bond-aided dimerization between the most stable conformers of each molecule. Absorption width of about 700 cm(-1) (～8.28 kJ/mol) of O-H stretching modes suggests a strong hydrogen bonding with the ab initio bond lengths, O-H?O in the range of 2.873-2.832 ?. A strong Raman mode near 110-85 cm(-1) in each molecule is interpreted to be coupled vibrations of pseudo-dimeric trans and cis structures.     

Hydrogen bonding mediated by key orbital interactions determines hydration enthalpy differences of phosphate water clusters

Electronic structure calculations have been carried out to provide a molecular interpretation for dihydrogen phosphate stability in water relative to that of metaphosphate. Specifically, hydration enthalpies of biologically important metaphosphate and dihydrogen phosphate with one to three waters have been computed with second-order M?ller-Plesset perturbation and density functional theory (B3LYP) with up to the aug-cc-pvtz basis set and compared to experiment. The inclusion of basis set superposition error corrections and supplemental diffuse functions are necessary to predict hydration enthalpies within experimental uncertainty. Natural bond orbital analysis is used to rationalize underlying hydrogen bond configurations and key orbital interactions responsible for the experimentally reported difference in hydration enthalpies between metaphosphate and dihydrogen phosphate. In general, dihydrogen phosphate forms stronger hydrogen bonds compared to metaphosphate due to a greater charge transfer or enhanced orbital overlap between the phosphoryl oxygen lone pairs, n(O), and the antibonding O-H bond of water. Intramolecular distal lone pair repulsion with the donor n(O) orbital of dihydrogen phosphate distorts symmetric conformations, which improves n(O) and sigma*(O-H) overlap and ultimately the hydrogen bond strength. Unlike metaphosphate, water complexed to dihydrogen phosphate can serve as both a hydrogen bond donor and a hydrogen bond acceptor, which results in cooperative charge transfer and a reduction of the energy gap between n(O) and sigma*(O-H), leading to stronger hydrogen bonds. This study offers insight into how orbital interactions mediate hydrogen bond strengths with potential implications on the understanding of the kinetics and mechanism in enzymatic phosphoryl transfer reactions.     

低阶煤中氢键作用的色散校正密度泛函理论研究

本研究以苯酚…苯酚、苯酚…苯、苯酚…二苯醚、苯酚…喹啉和苯甲酸…苯甲酸为对象，采用色散校正的密度泛函理论分别研究褐煤中自缔合OH、OH-π、OH-醚O、OH-N和COOH-COOH之间形成的氢键。此外，还研究了氢键供体中取代基(CH₃-、CH₃O-、OH-、NH₂-、COOH-和NO₂-)对氢键的影响。对上述复合物进行了几何优化，并计算了能量、Mulliken电荷分布及振动频率。从优化的结构中可以看出上述复合物之间都存在氢键，所有复合物中O-H键键长都比苯酚中自由羟基的长，这表明这些复合物之间存在相互作用。其中，羧酸…羧酸复合物中O-H键的键长最长。此外，通过Mulliken电荷分布可看出上述复合物之间存在电荷转移。基于振动频率分析，所有的O-H键伸缩振动都发生了红移，尤其是羧酸…羧酸和苯酚…喹啉复合物，这可为煤中羟基振动的红外光谱分析提供依据。根据键能不同氢键强度按以下顺序依次递减：COOH-COOH>OH-N > 自缔合OH≈OH-醚O > OH-π，这与振动频率的分析结果一致。此外，不同取代基对氢键作用的影响不同。     

Direct determination of hydrogen-bonded structures in resonant and tautomeric reactions using ultrafast electron diffraction

We elucidate the keto-enol tautomeric equilibrium in acetylacetone, the structure of both keto and enol forms, and the nature of the intramolecular O-H...O HB in enolic acetylacetone using our ultrafast electron diffraction apparatus, thereby shedding new light on the nature of the hydrogen bond in resonant tautomeric structures. The enolic structure exhibits some pi-resonance delocalization; however, this delocalization is not strong enough to give a symmetric skeletal geometry. The long O...O distance in the refined structure renders the homonuclear O-H...O hydrogen bond in acetylacetone localized and asymmetric.     

The conformers of phenylglycine

The neutral form of the unnatural amino acid phenylglycine was vaporized by laser ablation, and the presence of two conformers was detected in a supersonic expansion by Fourier transform microwave spectroscopy. Both conformers were unequivocally identified by comparison of their experimental rotational and quadrupole coupling constants with those calculated ab initio. The most stable conformer is stabilized by intramolecular hydrogen bonds N-H...O=C, N-H...pi (with the closest C-C bond in the aromatic ring), and a cis-COOH interaction. The other conformer exhibits a O-H...N hydrogen bond between the hydrogen atom of the hydroxyl group and the lone pair at the nitrogen atom.     

A survey of O-H⋯O hydrogen bond geometries determined by neutron diffraction

An analysis of the geometries of one hundred O-H?O hydrogen bonds observed by neutron diffraction in 24 crystal structures shows the following results. Twenty-Five of the hydrogen bonds can be described as bifurcated, indicating that this form of association is more common than previously supposed. Of the linear hydrogen bonds, those engaged in cooperative, or self associated, arrangements have a mean bond length of 1.805(9) Å, compared with 1.869(23) Å for the non-cooperative hydrogen bonds. This difference is significant at the 99.5 percent level. The mean O-H?O valence angle is 167.1(8)°, and there is evidence at the 92.5 percent significance level that the shorter O?H bonds are more linear. There is a preferred direction of hydrogen bonding with respect to the acceptor oxygen atom, which is in, or close to, the plane containing the oxygen lone pair orbitals, but there is no evidence of a preferred direction within that plane.     

Complexes of atmospheric alpha-dicarbonyls with water: FTIR matrix isolation and theoretical study

The complexes of glyoxal (Gly), methylglyoxal (MGly), and diacetyl (DAc) with water have been studied using Fourier transform infrared (FTIR) matrix isolation spectroscopy and MP2 calculations with 6-311++G(2d,2p) basis set. The analysis of the experimental spectra of the Gly(MGly,DAc)/H2O/Ar matrixes indicates formation of one Gly...H2O complex, three MGly...H2O complexes, and two DAc...H2O ones. All the complexes are stabilized by the O-H...O(C) hydrogen bond between the water molecule and carbonyl oxygen as evidenced by the strong perturbation of the O-H, C=O stretching vibrations. The blue shift of the CH stretching vibration in the Gly...H2O complex and in two MGly...H2O ones suggests that these complexes are additionally stabilized by the improper C-H...O(H2) hydrogen bonding. The theoretical calculations confirm the experimental findings. They evidence the stability of three hydrogen-bonded Gly...H2O and DAc...H2O complexes and six MGly...H2O ones stabilized by the O-H...O(C) hydrogen bond. The calculated vibrational frequencies and geometrical parameters indicate that one DAc..H2O complexes, two Gly...H2O, and three MGly...H2O ones are additionally stabilized by the improper hydrogen bonding between the C-H group and water oxygen. The comparison of the theoretical frequencies with the experimental ones allowed us to attribute the calculated structures to the complexes present in the matrixes.     

Oxo,sulfido, and tellurido Mo-enedithiolate models for xanthine oxidase: understanding the basis of enzyme reactivity

The active site of the mononuclear molybdenum enzyme xanthine oxidase has an LMoOS(OH) center that catalyzes the hydroxylation of substrate (L representing an enedithiolate ligand contributed by a pterin cofactor in the enzyme). Reaction of the enzyme with cyanide results in the replacement of the Mo=S group with a second Mo=O group, which results in loss of enzyme activity. To understand the basis for this loss of activity, we have computationally examined the interaction of a model for the LMoO2(OH) as well the LMoOTe(OH) congener of the enzyme with formamide (a substrate for the enzyme). Our electronic structure calculations for the oxo congener indicate a reduced electron density on the hydrogen being transferred from substrate in the course of the reaction, a shorter O-H bond in the transition state, and a longer nascent O-C bond of product, factors which combine to account for the loss of reactivity in the LMoO2(OH) species. Interestingly, our calculations indicate that the Te congener is characterized by an increased electron density on the hydrogen species being transferred, a longer Te-H bond in the transition state, and a shorter O-C nascent bond in the product and suggest that a Te congener of xanthine oxidase, were it to be prepared experimentally, should exhibit catalytic activity.