A molecular orbital explanation of bond distance variation caused by hydrogen bond formation

For hydrogen bond systems X–D–HA–Y, a simple molecular orbital model is proposed to understand the mechanism of the bond distance variations caused by the hydrogen bond formation. This model explains the bond distance variations for X–D and A–Y as follows. Electrostatic potential that the electrons in a molecule receive from other molecules causes the changes in atomic orbital energy differences between the bonded atoms. Then, the changes in the orbital energy differences make the bond orders larger or smaller and consequently the bond distances vary. The validity of this model has been confirmed by the effective fragment potential method, using the test systems of (HCOOH)₂, HCONH₂ (formamide) crystal and BF₃·2H₂O crystal.     

The calculation of molecular electrostatic potential from a multipole expansion based on localized orbitals and developed at their centroids: Accuracy and applicability for macromolecular computations

An improvement of a multipole expansion based on localized orbitals and termed LMTP is presented and its ability to generate accurate electrostatic potentials is demonstrated. The possibilities of using this expansion in studying the potential of different conformational states of a molecule without the necessity of recalculating its molecular wavefunction is described and the construction of macromolecular potentials by the superposition of the potentials of subunits is reconsidered.     

Theoretical study of hydrogen bonded clusters of water and cyanic acid: Hydrogen bonding in terms of the molecular structure

Ab initio and density functional calculations were used to analyze the interaction between a molecule of cyanic acid (HOCN) and up to 4 molecules of water at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. The cooperative effect (CE) is increased with the increasing size of the studied clusters. Red shifts of the H–O stretching frequency for complexes involving HOCN as an H-donor were predicted. The strength of the hydrogen bonds in terms of molecular structures could be deduced from a comparison of HOCN–H₂O with HCNO–H₂O, HONC–H₂O and HNCO–H₂O HB clusters. The atom in molecules (AIM) method was used to analyze the cooperative effects on topological parameters.     

Recognition of a dicarboxylic acid with dipicolyl urea in solution and in solid phases: intramolecular hydrogen bond inhibiting both pyridine nitrogens from binding carboxyl groups

Recognition of a dicarboxylic acid in solution as well as in the solid phase by the pyridyl urea based pseudoditopic receptor 1 has been studied. The X-ray structures of both the receptor and its complex with 1,4-phenylenediacetic acid are also presented. Intramolecular hydrogen bonding inhibits both the pyridine ring nitrogens from forming hydrogen bonds with the carboxyl group and force the receptor to behave in a monotopic manner, using the syn urea amide moiety to bind carboxyl group of a dicarboxylic acid to form a 2:1 complex. Binding of receptor 1 with a monocarboxylic acid is also compared.     

The NMR study of hydrogen bond formation in some tris(((-salicylidene)amino)ethyl)amine derivatives in solution and in the solid state

Eight Schiff bases, derived from tris(2-aminoethyl)amine and some aromatic aldehydes have been investigated by heteronuclear NMR methods in solution and in the solid state. Six of those compounds can form intramolecular hydrogen bonds and two remaining imines which do not have hydroxyl substituent in position 2 cannot form such bonds and were chosen as a model compounds for nonbonded structure. The tautomeric equilibrium position of investigated compounds were estimated on the base of nitrogen chemical shifts and nitrogen-proton one bond coupling constants when available. In solution for each compound in all temperatures applied, single symmetrical dynamic averaged structures were found but in the solid state in a few cases mixtures of several nonequivalent or nonsymmetrical structures were observed. Generally at low temperature the –NH– form is more abundant then at room temperature. Similarly in the solid state the proton transfer from oxygen to nitrogen site is more effective in comparison with the solution, except for the 9-formyl-8-hydroxyjulolidine derivative for which different behavior was found.     

Coherent tunneling of proton in the intramolecular hydrogen bond of crystalline bromo-hydroxyphenalenone at low temperature

Infrared absorption spectra of 5-bromo-9-hydroxyphenalenone were measured and analyzed in detail as a function of temperature. An intense and broad peak at 83 cm⁻¹ occurring in the protonated crystal, but not in the deuterated analog, arises from the coherent tunneling motion of the hydrogen in the intramolecular hydrogen bond. Strong temperature dependence of the frequency and width of the tunneling peak determined by fitting the Gaussian or Lorentzian peak shape function is reproduced well by three-parameter functions representing the thermal population of the excited state of the tunneling proton.     

The visible absorbance maximum of 2-hydroxy-1,4-naphthoquinone as a novel probe for the hydrogen bond donor abilities of solvents and solvent mixtures

Summary The electronic absorption spectra of 2-hydroxy-1,4-naphthoquinone (HNQ) in one- and two-component solvents are discussed. The visible absorption of this reagent has been shown to arise from a charge-transfer transition of the zwitterionic tautomer stabilized by a hydrogen bond donating solvent. The formation constant of the 1:1 hydrogen bonded complex with methanol, ethanol, andn-propanol has been determined at 25 °C from the spectral behaviour in mixed solvents. The tautomerization equilibrium ofHNQ in aqueous ethanol is demonstrated and characterized. The dependence of the absorbance maximum ofHNQ on the hydrogen bond donor ability of the solvent in the visible spectrum, as measured by theTaft-Kamlet parameter, has been established. Experimentally derived evidence is supplied to justify the recommendation ofHNQ as a novel probe for hydrogen bond donor ability in pure solvents and in mixed aqueous solvents.

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Das Absorptionsmaximum von 2-Hydroxy-1,4-naphthochinon im sichtbaren Bereich als neues Maß für die Wasserstoffbrückenbindungsbildungsfähigkeit von Lösungsmitteln und Lösungsmittelgemischen

Zusammenfassung Die Absorptionsspektren von 2-Hydroxy-1,4-naphthochion (HNQ) in Ein- und Zweikomponentensystemen werden diskutiert. Die Absorption im sichtbaren Bereich stammt von einemcharge-transfer — Übergang des zwitterionischen Tautomers, das über Wasserstoffbrückenbindungen zum Lösungsmittel stabilisiert wird. Die Bildungskonstanten der binären Komplexe mit Methanol, Ethanol undn-Propanol wurden aus spektroskopischen Daten in Lösungsmittelgemischen bei 25 °C emittelt. Das Tautomeriegleichgewicht vonHNQ in wäßrigem Ethanol wird iskutiert. Die Abhängigkeit des Absorptionsmaximums vonHNQ vond der Wasserstoffbrückenbindungsbildungsfähigkeit des Lösungsmittels wird mittels desT aft-Kamlet — Parameters beschrieben. Experimentelle Ergebnisse ermutigen zur Verwendung vonHNQ als neue Testsubstanzfür die Wasserstoffbrückenbindungsbildungsfähigkeit von reinen und gemischten Lösungsmitteln.

     

Theoretical study of the strong intramolecular hydrogen bond and metal-ligand interactions in group 10 (Ni, Pd, Pt) bis(dimethylglyoximato) complexes

The structural and bonding characteristics of the bis(dimethylglyoximato) complexes of group 10 transition metals ([M(dmg)₂], where M = Ni, Pd and Pt) were investigated by means of quantum chemical computations. The equilibrium geometries, energetic and bonding properties were computed using the B3P86 exchange-correlation density functional in conjunction with a 6-311+(+)G^∗∗ basis set. The computations revealed that the strong O⁻?H-O hydrogen bond exists only in the presence of the metal cations. The free (dmg)₂²⁻ ligand has significantly different geometry in which the O⁻?H-O interaction is replaced by N?O-H bonds. The characteristics of the metal-ligand interactions were determined by natural bond orbital analysis.     

The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: How good is a point charge as a model for a hydrogen bonding atom?

In order to design new ligands for protein-binding sites of unknownstructure, it would be useful to predict the likely sites of hydrogenbonding of an unknown protein fragment to a known molecule. The positions ofmaxima and minima in the electrostatic potential at appropriate distancesfrom the van der Waals surface were calculated for various small molecules,nucleic acid bases, peptide units and amino acid side chains containinggroups which can form the biologically important N-H...O=C andN-H...N hydrogen bonds. Their ability to predict the positions of H andO/N in hydrogen bonded complexes, as predicted by optimising theelectrostatic interactions of pairs of such molecules constrained by themolecular shapes, was assessed. It is shown that extrema in theelectrostatic potential around the isolated molecules give worthwhilepredictions for the locations of hydrogen bonding partners. For moleculesbound by a single N-H...O=C hydrogen bond, the electrostatic maximumassociated with the H is usually less than 1 Å from an acceptor atom,while a C=O electrostatic minimum is generally less than 1.5 Å fromthe hydrogen bond proton. However, a significant number of hydrogen bondsform to the opposite lone pair from the electrostatic minimum, in which casethe separation is up to 3.3 Å. This reflects the broad electrostaticpotential well around a carbonyl oxygen between the lone pair directions.The model predicts when neighbouring atoms drastically change the hydrogenbonding characteristics of an N-H or C=O group. Although the geometries ofhydrogen bonded complexes are influenced by the other van der Waals contactsbetween the molecules, particularly multiple hydrogen bonds, theseinfluences are constant when considering hydrogen bonding to a specificuncharacterised binding site. Hence, the consideration of stericallyaccessible electrostatic extrema will be useful in the design of newligands.     

Effects of dynamical couplings in hydrogen bond systems in the polarized IR spectra of 3-hydroxybenzaldehyde and 4-hydroxybenzaldehyde crystals

This paper presents the investigation results of the polarized IR spectra of 3-hydroxybenzaldehyde and 4-hydroxybenzaldehyde crystals measured at 293 and 77 K. Analysis of the results concerned the linear dichroic, H/D isotopic and temperature effects observed in the spectra of the hydrogen and deuterium bond at the frequency ranges of the ν_O–H and the ν_O–D bands, respectively. The main spectral properties of the crystals were interpreted in terms of the “strong-coupling” theory on the basis of the hydrogen bond dimer model. The spectra revealed that the strongest vibrational exciton coupling involved the closely-spaced hydrogen bonds, each belonging to a different chain of associated molecules. The reason for two different crystalline systems, are characterized by almost identical ν_O–H and ν_O–D band shapes, is explained. It was proved that a random distribution of the protons and deuterons took place in the lattices of the isotopically diluted crystals.     

Polarized IR spectra of the hydrogen bond in acetic acid crystals

The paper presents the results of our investigations of the polarized IR spectra of the hydrogen bond in crystals of acetic acid, CH₃COOH, as well as in crystals of three deuterium isotopomers of the compound: CH₃COOD, CD₃COOH and CD₃COOD. The spectra were measured at 283 K and at 77 K by a transmission method using polarized light. Theoretical analysis of the results concerned the linear dichroic effects, together with the H/D isotopic and temperature effects observed in the solid-state IR spectra of the hydrogen and of the deuterium bond at the frequency ranges of the ν_O–H and the ν_O–D bands, respectively. Basic spectral properties of the crystals can be interpreted satisfactorily in terms of one of the quantitative theories of the IR spectra of the hydrogen bond, i.e. the “strong-coupling” theory or the “relaxation” theory when a hydrogen bond dimer model is used. From the spectra obtained it resulted that the strongest exciton coupling involved the closely spaced hydrogen bonds, belonging to different chains of associated acetic acid molecules. These results contradict the former explanation of the spectra within a model, which assumed a strong vibrational exciton coupling between four hydrogen bonds in a unit cell. On analyzing the spectra of isotopically diluted crystalline samples of acetic acid it has been proved that a non-random distribution of the protons and deuterons takes place in the hydrogen bond lattices. This non-conventional isotopic effect is a result of dynamical co-operative interactions involving hydrogen bonds in the system. Simultaneously it has been also found that in an individual hydrogen bonded chain in the crystals, distribution of the hydrogen isotope atoms H and D was fully random. The H/D isotopic “self-organization” mechanism most probably involves a pair of hydrogen bonds from each unit cell where each hydrogen bond belongs to a different chain.     

Use of the hydrogen bond potential function in a comparative molecular field analysis (CoMFA) on a set of benzodiazepines

Summary The results of the GRID-Comparative Molecular Field Analysis (CoMFA) were compared with those of the SYBYL-CoMFA in a study of benzodiazepines. The results demonstrate that the hydrogen bonding function using the GRID H₂O probe in a CoMFA can successfully describe the hydrophobic effects of substituents without any bias or preconcept of their effects in the development.     

Fluorines in tetrafluoromethane as halogen bond donors: Revisiting address the nature of the fluorine's σhole

It has been demonstrated in several instances that the 0.001 a.u. (electrons per bohr³) isodensity mapped electrostatic surface potentials on the fluorines along the outermost extensions of the C? F covalent bonds in tetrafluoromethane (CF₄) are entirely negative, they are thereby unable to engage in σ_hole bonding interactions with the negative sites on another molecules. In this study, we have attempted at resolving this controversy by performing various high‐level electronic structure calculations with Quadratic Configuration Integrals of Singles and Doubles QCISD(full), second‐order Møller–Plesset MP2(full), and 12 other Density Functional Theory (DFT) based functionals with and without dispersion corrections, all in conjunction with the 6–311++G(2d,2p) basis set. The results achieved with all the levels of theory utilized suggest that the fluorine's σ_holes in CF₄ are positive regardless of the 0.001‐, 0.0015‐, and 0.002‐a.u. isodensity mapped electrostatic surfaces examined. Because of this specific quality, the fluorines in CF₄ have displayed their capacities to form not only 1:1 clusters with the Lewis bases such as water (H₂O), ammonia (NH₃), formaldehyde (H₂C?O), hydrogen fluoride (HF), and hydrogen cyanide (HCN), but also 1:2, 1:3, and 1:4 clusters with the latter three randomly chosen Lewis bases. Various topological and nontopological features obtained from applications of atoms in molecules, noncovalent interaction reduced‐density‐gradient and natural bond orbital analytical tools reveal that the N···F, O···F, and F···F long‐ranged interactions developed between the interacting monomers in H₃N···FCF₃, H₂O···FCF₃, and (Y? D)_n=1–4···F₄C (Y? D = H₂C?O, HCN, and HF) are reminiscent of halogen bonding. The nonadditive cooperative and anticooperative energetic effects emerged on cluster formations are discussed in detail. © 2015 Wiley Periodicals, Inc.     

NiFe2O4 as a magnetically recoverable nanocatalyst for odourless C–S bond formation via the cleavage of C–O bond in the presence of S8 under mild and green conditions

We present green methodologies for one‐pot and odourless syntheses of unsymmetric and symmetric diaryl sulfides via C─O bond activation using NiFe₂O₄ magnetic nanoparticles as a reusable heterogeneous nanocatalyst. The synthesis of unsymmetric sulfides is performed using the cross‐coupling reaction of phenolic esters such as acetates, triflates and tosylates with arylboronic acid/S₈ or triphenyltin chloride/S₈ as thiolating agents in the presence of base and NiFe₂O₄ magnetic nanoparticles as a catalyst in poly(ethylene glycol) as solvent at 60–85°C. Also, the synthesis of symmetric diaryl sulfides from phenolic compounds using S₈ as the sulfur source and NiFe₂O₄ as catalyst in dimethylformamide at 120°C is described. Using these protocols, the syntheses of various unsymmetric and symmetric sulfides become easier than using the available protocols due to the use of a magnetically reusable bimetallic nanocatalyst and avoiding the use of thiols and aryl halides.     

The reactivity of 2,5-diaminoimidazolone base modification towards aliphatic primary amino derivatives: nucleophilic substitution at C5 as a potential source of abasic sites in oxidatively damaged DNA

N5-deoxyribosyl derivatives of 2,5-diaminoimidazolone formed by oxidative damage to the guanine bases in 2-deoxyguanosine and highly polymerized DNA readily undergo nucleophilic substitution at C5 in reaction with primary amines in neutral aqueous solutions at 37–70 °C, as it was found in a kinetic study using reverse-phase HPLC. The reaction of 2-amino-5-[(2′-deoxy-β-D-erythro-pentofuranosyl)amino]-4H-imidazol-4-one (dIz) with excess of ethanolamine, alanine and γ-aminobutyric acid (0.2–1 M) is a pseudo-first-order process that proceeds with 45–80 % yields depending on the nature of the amine, its concentration, and the reaction temperature. In the case of ethanolamine, the corresponding bimolecular rate constant has a pre-exponential factor and activation energy of 1.1 × 10⁵ s^?1 and 47 kJ mol^?1, respectively. The reaction is highly competitive with the previously described hydrolysis of dIz into 2,2-diamino-4-[(2-deoxy-β-D-erythro-pentofuranosyl)amino]-5(2H)-oxazolone under biologically relevant conditions. A similar reaction with the same lesion in polymeric DNA results in the release of a low-molecular-weight analog of dIz, presumably producing an abasic site as the second reaction product. Kinetic characteristics of this process make it a potentially important source of abasic sites in oxidatively damaged DNA, formed through the reaction of 2,5-diaminoimidazolone lesions with naturally abundant DNA-affinic amines and proteins. The release of low-molecular-weight analogs of dIz can potentially be employed for quantification of imidazolone lesions in oxidized DNA. The half-life of imidazolone lesions in double-stranded DNA evaluated using this approach was found to be 154 min at 37 °C.     

The variation of coordination modes of aromatic imines in iron carbonyl complexes: Is there a correlation between bond lengths in organometallic model compounds and the reactivity of the ligands in catalytic C-C bond formation reactions?

The reaction of aromatic imines with Fe₂(CO)₉ proceeds via a two-step reaction sequence. A C-H activation reaction in ortho-position with respect to the exocyclic imine function is followed by an intramolecular hydrogen transfer reaction towards the former imine carbon atom. The resulting dinuclear iron carbonyl complexes show an aza-ferra-cyclopentadiene ligand which is apically coordinated by the second iron tricarbonyl moiety. Comparing the bond lengths of 43 different compounds, which were synthesized and structurally characterized in our group shows that the iron iron bond length correlates with one of the iron carbon bond lengths. The longer the iron carbon bond between the apically coordinated iron atom and the carbon atom next to the former imine carbon atom is, the shorter is the iron iron bond. The same ligands may be used as the substrates in ruthenium catalyzed C-C bond formation reactions. Whereas most of the imines react via the formal insertion of CO and/or ethylene into the C-H bond in ortho-position to the imine function, the ligands that show the longest iron carbon bond lengths in the model compounds under the same reaction conditions produce different types of isoindolones.     

The Phosphorus Bond,or the Phosphorus-Centered Pnictogen Bond: The Covalently Bound Phosphorus Atom in Molecular Entities and Crystals as a Pnictogen Bond Donor

The phosphorus bond in chemical systems, which is an inter- or intramolecular noncovalent interaction, occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a covalently or coordinately bonded phosphorus atom in a molecular entity and a nucleophile in another, or the same, molecular entity. It is the second member of the family of pnictogen bonds, formed by the second member of the pnictogen family of the periodic table. In this overview, we provide the reader with a snapshot of the nature, and possible occurrences, of phosphorus-centered pnictogen bonding in illustrative chemical crystal systems drawn from the ICSD (Inorganic Crystal Structure Database) and CSD (Cambridge Structural Database) databases, some of which date back to the latter part of the last century. The illustrative systems discussed are expected to assist as a guide to researchers in rationalizing phosphorus-centered pnictogen bonding in the rational design of molecular complexes, crystals, and materials and their subsequent characterization.