H-bonded Dimers Research Articles

Dipole-bound anions of ethylene glycol dimers. Theoretical ab initio study

Ab initio calculations have been performed to determine the electron affinity of the ethylene glycol molecule and its dimer. Although, as determined, the glycol molecule has only a marginal ability to bind an excess electron, the three glycol H-bonded dimers, whose structures were found in the calculations, have much higher electron affinity values. In all cases the excess electron is bound by the dipole field of the complex. The attachment of the excess electron lowers the relative energy differences between the three complexes, making their coexistence more probable.

Phenomenology of Polymorphism, III:p,TDiagram and Stability of Piracetam Polymorphs

The nootropic drug Piracetam is known to crystallize in three phases. In order to obtain their stability hierarchy from sublimation pressure inequalities, the drawing of a topologicalp,Tdiagram was attempted. For such a purpose and also for quality control, crystallographic and thermodynamic data were required. Powder X-ray diffractometry (XRD) and differential scanning calorimetry (DSC) were used. Molecular energy calculations were performed. Phase I melts at 426K (ΔfusH(I) = +180 J·g−1). Phase II transforms into Phase I at 399K (Δ(II→I)H= +24 J·g−1). Phase III transforms into phase I at 392K (Δ(III→I)H= +28 J·g−1) or melts at 412K (ΔfusH(III) = +210 J·g−1). Thep,Tdiagram shows that phase I is stable at higher temperature and phase II at lower temperature, like phase III, which is stable under high pressure. At room temperature, phase II is the more stable form, and phase I the less stable one. This agrees with the spontaneous I → II transformation observed at 298K within a few hours, and with lattice energies, calculated previously. Molecular energy calculations and crystal structure comparison show how intermolecular hydrogen bonds and H-bonded dimers, in phases II and III, may stabilize conformations higher in energy than those of the isolated molecule and of phase I.

Ab Initio Molecular Orbital Analysis of Dimers of cis-Formic Acid. Implications for Condensed Phases

The gas phase structure of cis-formic acid dimers is investigated by high-level correlated ab initio molecular orbital methods using large basis sets augmented with both polarization and diffuse functions (up to MP2/D95++(d,p) level). Seven stable dimer structures were located on the potential energy hypersurface of the dimer configurational space with two H-bonding interactions. No stable dimer with only one H-bond was found. The heat of dimerization (10.7−11.3 kcal/mol) of the most stable, C2h cyclic dimer is in excellent agreement with more recent experimental measurements. Beside the dimer with two equivalent O−H···OC H-bonds, there exist two local minima with significant stabilization from C−H···O interactions. The three weakest of the seven complexes contain exclusively C−H···O H-bonding interactions. The dimers can interconvert to each other by rotation, disrupting one of their H-bonds. The saddle points and the local minima are anticipated not to play important roles in the gas phase but can have dominant influence on liquid dynamics. The interaction energies of the complexes allow us to assess the relative importance and approximate energetic contributions of the individual H-bonds to the overall stability of the dimers. It is illustrated that, in addition to the inferred stabilization of two separate O−H···OC H-bonds, the most stable C2h complex is stabilized by about 0.4−0.6 kcal/mol internal cooperative effect, less than in the similar acetic acid dimer. The C−H H-bonding dimers display contraction of the C−H bond lengths and positive frequency shift of the ν(C−H) stretching modes relative to the noninteracting monomer. We also show that the effect of BSSE on the intermolecular potential surface of the dimers and, in particular, on the location of the true potential minimum only negligibly influences the interaction energy, but significantly distorts the intermolecular equilibrium geometry.

Strong-coupling mechanism for interpretation of the IR spectra of the hydrogen bonded imidazole crystal

In this work we have attempted to provide a new interpretation of some complex spectral effects, recently observed in the high frequency region of the IR spectra of hydrogen bonded imidazole crystals. The subjects of our interest were effects corresponding to the intensity distribution, the linear dichroism, the influence of temperature and the isotopic substitution of deuterium in imidazole molecules, measured in the v NH and the v ND band ranges in the crystalline spectra. Based on model calculations it was shown that the “strong-coupling” model was able to quantitatively reproduce the v NH and v ND band shapes in the spectra of the imidazole crystal. This fact can be considered as a basis for an explanation of the isotopic, polarization and temperature effects in the spectra. The Fermi resonance effects have been found to be of a minor importance. The key property of the crystal responsible for the abnormal spectral properties of its H-bonds seems to be the statistical disorder in the crystalline lattice, due to bending of the H-bonds. This structural effect, along with the very specific selection rules in the IR for the centrosymmetric H-bonded dimers and the correlation field interactions in the crystal, were considered to be the main source of the spectral effects analyzed.

Strong-coupling mechanism for interpretation of the IR spectra of the hydrogen bonded imidazole crystal

In this work we have attempted to provide a new interpretation of some complex spectral effects, recently observed in the high frequency region of the IR spectra of hydrogen bonded imidazole crystals. The subjects of our interest were effects corresponding to the intensity distribution, the linear dichroism, the influence of temperature and the isotopic substitution of deuterium in imidazole molecules, measured in the νN H and the ν N D band ranges in the crystalline spectra. Based on model calculations it was shown that the “strong-coupling” model was able to quantitative reproduce the ν N H and ν N D band shapes in the spectra of the imidazole crystal. This fact can be considered as a basis for an explanation of the isotopic, polarization and temperature effects in the spectra. The Fermi resonance effects have been found to be of a minor importance. The key property of the crystal responsible for the abnormal spectral properties of its H-bonds seems to be the statistical disorder in the crystalline lattice, due to bending of the H-bonds. This structural effect, along with the very specific selection rules in the IR for the centrosymmetric H-bonded dimers and the correlation field interactions in the crystals, were considered to be the main source of the spectral effects analyzed.

Synthesis and structure of chiral diazacoronands derived from L-tartaric acid1

Abstract Six chiral di-N-p-toluenesulphonyl diazacoronands derived from L-tartaric acid were synthesized by the modified Richman Atkins procedure. The deprotection of isopropylidene acetal led to the formation of compounds 7 possessing an 1,2-diol subunit. 1H and 13C NMR, UV and MS techniques were used for structure assignment. The determination of the X-ray structure of compounds 6a and 7b pointed to a variety of ring conformations. The shape of the molecules is to a great extent determined by a system of intra- and intermolecular hydrogen bonds of a O…O and C…O nature. Compound 7b was found to form a supramolecular assembly (H-bonded dimers) both in solution and in solid state. Complexation studies of this group of compounds suggest that this process is mediated by the hydroxyl and sulfonyl group oxygen atoms.

The vibrational frequency of the donor OH group in the H-bonded dimers of water, methanol and silanol. Ab initio calculations including anharmonicities

The equilibrium structures of the three dimers are determined using quantum chemical ab initio techniques. The anharmonic vibrational frequencies are determined by one-dimensional numerical integration. Second-order Møller-Plesset perturbation theory (MP2) is used with valence triple-ζ basis sets augmented by first and second polarization functions, VTZ(2df, 2p), and corrections are made for the basis set superposition error. This level of approximation yields frequencies for the monomers that are too high (by 30 to 40 cm −1) and frequency shifts that are too large. Complete fourth-order perturbation theory (MP4-SDTQ) reproduces observed OH frequencies in the monomers and in the dimer with an error of ± 10 cm −1, but has been applied to the water dimer only. The MP4 results support a recent assignment of the 3601 cm −1 band in the IR spectrum of water clusters to the donor OH group of the dimer. Combination of the MP4 results on the water dimer with the MP2 results on all three systems leads to estimated OH frequency shifts of −126 and −175 cm −1 in the methanol and silanol dimers, respectively.

An infrared study on matrix-isolated benzoic acid

The infrared spectra of benzoic acid and deuterobenzoic acid embedded in Ar matrices were obtained. The only benzoic acid conformer with syn position of O-H and CO groups was found to fix in the matrices. We have demonstrated that both a raise of benzoic acid concentration and a matrix annealing lead to formation of H-bonded benzoic acid dimers. The results of semiempirical AM1 calculations allowed us to determine probable structures of the dimers observed. The interpretation of the experimental IR spectra was carried out by normal-coordinate analysis for benzoic acid monomer and dimer.

On the intermolecular vibrational modes of the guanine⋯cytosine, adenine⋯thymine and formamide⋯formamide H-bonded dimers

Harmonic force fields, frequencies, and IR and Raman intensities of the intermolecular vibrational modes in the cyclic formamide dimer and the guanine-cytosine and adenine-thymine DNA base pairs were calculated using several ab initio methods, including Hartree-Fock, MP2 and gradient-corrected density functional theory (DFT), with various basis sets. A polar environment was modeled using the polarizable continuum model (SCRF). The effect of electron correlation upon calculated Raman intensities was investigated using DFT. The normal coordinate analysis was carried out in internal coordinates observing C2h symmetry of the formamide dimer. These coordinates were also generalized for the DNA base pairs, allowing force constants, frequencies and intensities of the characteristic intermolecular vibrational modes to be compared among the H-bonded complexes studied. In addition, coordinates defined in this way are directly related to standard DNA interbase structural parameters as pseudodyad, tilt and propeller twist angles. Extensive coupling of the intramolecular wagging vibrations of the amino groups participating in H-bonding with the tilt and propeller twist vibrations was obtained for the lowest frequency normal modes.

Investigation of stearic acid and manganese stearate films obtained by Langmuir-Blodgett and vacuum deposition methods

The molecular structure and morphology of 1–100 nm films, prepared by vacuum deposition of stearic acid (HSt) and manganese stearate (MnSt2) on Si, NaCl and C/NaCl substrates, have been investigated by Fourier transform IR spectroscopy, scanning electron microscopy and transmission electron diffraction techniques and compared with characteristics of Langmuir-Blodgett films on Si. Contrary to previous work, more emphasis is placed on films a few nanometres thick. The parameters (frequencies and intensities) of the Davydov splitting components in IR spectra are evaluated to determine the molecular orientation and intermolecular interaction in these films. HSt shows a three-dimensional growth in vacuum-deposited films on all substrates studied which is evidence of a weak interaction of H-bonded HSt dimers and the substrate. MnSt2 is found to deompose upon evaporation, resulting in stearone (C17 H35)2CO formation and deposition. The orientation of these molecules depends on the substrate type. A Stranski-Krastanov growth mechanism is realized owing to the strong interaction of polar stearone molecules with the substrates. The possible reasons for the distinction of the HSt and the stearone interactions with the substrates are discussed. The Langmuir-Blodgett films exhibit a higher thickness uniformity but lower molecular ordering than vacuum-deposited films do.

Bis(bidentate) complexes of iminobis(diphenylphosphine chalcogenides)[M{N(XPPh2)2-X,X′}2](X = S or Se; M = Ni, Pd or Pt)

The compound NH(SePPh2)2 has been synthesised from NH(PPh2)2 and selenium in refluxing toluene. A range of complexes [M{N(XPPh2)2-X, X′}2](X = Se, M = Pt 1 or Pd 2; X = S, M = Pt 3, Pd 4 or Ni 5) of the monoanions derived from NH(SePPh2)2 and its sulfur analogue have been prepared. The new compounds have been characterised by microanalysis, NMR and IR spectroscopy. The crystal structures of NH(SePPh2)2, 1, 2 and 5 were determined. The neutral NH(SePPh2)2 crystallised as H-bonded dimer pairs with a noticeable difference in the hydrogen bonded and non-hydrogen bonded PSe bond lengths. The PSe groups are approximately anti. On complexation the anionic ligands are bidentate and in all cases the resulting MX2P2N rings are distinctly puckered.

From Racemic Mixtures of Chiral .pi.-Donor Molecules to Mixed Stacks of H-Bonded Centrosymmetrical Dimers of Cation and Anion Radicals with Singlet-Triplet Excitations: The Example of [(.+-.)-Me3TTF-C* H(Me)OH.bul.+]2[TCNQ.bul.-]2 (TTF = Tetrathiafulvalene; TCNQ = Tetracyanoquinodimethane)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFrom Racemic Mixtures of Chiral .pi.-Donor Molecules to Mixed Stacks of H-Bonded Centrosymmetrical Dimers of Cation and Anion Radicals with Singlet-Triplet Excitations: The Example of [(.+-.)-Me3TTF-C* H(Me)OH.bul.+]2[TCNQ.bul.-]2 (TTF = Tetrathiafulvalene; TCNQ = Tetracyanoquinodimethane)Anne Dolbecq, Marc Fourmigue, Patrick Batail, and Claude CoulonCite this: Chem. Mater. 1994, 6, 8, 1413–1418Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://doi.org/10.1021/cm00044a045RIGHTS & PERMISSIONSArticle Views174Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (699 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts

1,1- Bis(diphenylphosphinoyl)ethanol. Synthesis and complexes with neodymium and copper nitrates

A preparative method for the synthesis of 1,1-bis(diphenylphosphinoyl)ethanol (1) has been elaborated. In CHCl3 and MeCN solutions compound1 is associated into H-bonded dimers (-ΔH ≈ 12 kcal mol−1). Complexes of compound1 with NdIII, CuII, and CuI nitrates have been studed. The H-bonded dimers are retained upon complexing.

Strong dynamic coupling effects in the IR spectra of H-bonded 2-mercaptoquinoline

Abstract In this paper we attempt to reproduce quantitatively the IR spectra of 2-mercaptoquinoline in the ν NH and ν ND band frequency regions. The investigated spectra were quantitatively interpreted within the limits of the “strong-coupling” theory for the hydrogen bond vibrations in centrosymmetric H-bonded dimers, including the observed isotopic effect. The observed, very nonregular, spectral properties of 2-mercaptoquinoline were found to be connected with the “strong-coupling” mechanism as well as with the electronic properties of the H-bonds in the molecular associates.

A new approach to the problem of the hydrogen bond spectra of the adipic acid crystal: the polarization and temperature effects

This paper attempts to provide a new interpretation of some complex spectral effects observed in the IR spectra of the hydrogen bond in the adipic acid crystal. The subjects of our interest are the effects corresponding to the abnormal linear dichroism, the influence of temperature, and the isotopic substitution of deuterium in the H-bonds, measured in the v OH and the v OH band ranges in the crystalline spectra. In this paper a critical review of some recent solutions to the problem is given, and a new “strong coupling” approach for the crystalline spectral properties proposed. Based on the model calculations it is shown that the “strong coupling” model is able to quantitatively reproduce the v OH and v OD band shapes in the spectra of the adipic acid crystal, a fact which can be considered as a basis for an explanation of the isotopic, polarization and temperature effects in the spectra. The key property of the crystal responsible for the abnormal spectral properties of the hydrogen bonds seems to be the statistical disorder in the crystalline lattice. The H-bonds bent up or down with respect to the ring formed by the two linked COOH groups are considered to be the main source of the spectral effects analyzed, along with the very specific selection rules in the IR for the centrosymmetric H-bonded dimers.

Structure and bonding in 2-methyl-cinnolin-3-one. A study by X-ray crystallography, 14N nuclear quadrupole resonance and ab initio calculations

The X-ray crystallographic structure of the title compound shows the short and long bond pattern expected for the quinonoid classical structure. The corresponding equilibrium structure, from ab initio SCF calculations with a double zeta basis set is in close agreement, with differences generally less than 0.02 Å. The 14N nuclear quadrupole coupling constants, obtained by level-crossing and cross relaxation NQR spectroscopy, are assigned from the calculated electric field gradients. These show that N 1 and N 2 have tensor elements similar to pyridine and pyrrole respectively. One of the tensor elements at N 1 lies relatively close to the NN bond direction, but the principal value is radial to the ring, a classical lone-pair situation. At N 2, the principal value lies in the out-of-plane direction, with the in-plane tensor element values calculated to lie well away from the bond axes. Attempts to solve the structure of the unmethylated compound, which is expected to consist of H-bonded dimers, have so far been unsuccessful; this failure may result from the presence of a disordered tautomeric mixture in the lattice. The equilibrium structure of the unmethylated molecule shows a very similar quadrupole coupling pattern to the 2-methyl derivative. Neither populations or field gradients are significantly affected by all-valence electron CI, for either molecule.

Synthesis, purification and spectroscopic characterization of potential impurities of hexamethylmelamine

The syntheses and spectroscopic properties (ir, 1 H nmr, 13 C nmr, uv and ms) of pure samples of 2-chloro-4,6-bis(dimethylamino)-s-triazine 1, 4,6-dichloro-2-dimethylamino-s-triazine 2, 4,6-bis(dimethylamino)-s-triazin-2(1H)-one 3, 4-chloro-6-dimethylamino-s-triazin-2(1H)-one 4, 6-dimethylamino-s-triazine-2,4(1H,3H)- dione 5, and 2,4,6-tris(dimethylamino)-s-triazine (altretamine, HMM) are reported. Evidence for enol-keto equilibria are also presented for 3, in which the enol form exhibits as an H-bonded dimer structure similar to the dimer of organic carboxylic acids

Quantum-chemical studies of hydrogen bonding involving thioxoketones, thienols, thioformaldehyde and hydrogen sulfide with specific reference to the strength of intramolecular hydrogen bonds

The results of ab initio quantum-chemical calculations are reported for rotamers of S(CH)3OH (thioxoketone) and HS(CH)3O (thienol), several complexes of these with H2O and H2S as well as a range of other hydrogen-bonded complexes involving H2S, H2O, H2CS and H2CO. The calculations were performed largely at the SCF level of theory using bases of triple zeta plus polarization functions quality yielding equilibrium geometries and energies. Correlation corrections to the energies were obtained using second-order Moller–Plesset (MP2) perturbation theory. The results demonstrate that both thioxoketone and thienol are capable of forming fairly strong hydrogen bonds with H2O and H2S and can also form intramolecular hydrogen bonds. In order to estimate the strengths of such intramolecular H bonds so that comparison with H-bonded dimers is meaningful we propose the use of appropriate, well chosen reference structures. Detailed analysis of the results obtained indicates that enhanced delocalization in thioxoketone gives rise to a strong H bond. Such a mechanism seems to be absent in thienol where the H bond is very weak.

Reactions of PO(NCS)3 with 4-Hydroxy-1,3-dioxanes. Crystal Structure of rel-(2S,4R,5S,6S)-2,6-Diethyl-5-methyl-4-(N'-benzylthioureido)-1,3-dioxane

Substituted 4-hydroxy-1,3-dioxanes II react rapidly with PO(NCS)3 to give 4-isothiocyanato-1,3-dioxanes III. The 1H NMR spectra showed that in the isothiocyanate IIIa the predominant stereoisomer has its NCS group in axial position. The addition of benzylamine to the isothiocyanates IIIa and IIIb gave uniform thioureas IVa and IVb with equatorial alkyl groups at 2 and 6 positions and axial thioureido group at 4 position. On the other hand, the isothiocyanate IIIc reacts with benzylamine to give a mixture of three stereoisomeric thioureas V,VI, and VIII. The structure of VI was proved by means of X-ray diffraction analysis; in crystalline form the molecules of VI are present as H-bonded dimers (N-H...O).

Crystallinity of uniform oligo(oxyethylene) mono-alkyl ethers studied by Raman spectroscopy

Low-frequency Raman spectra have been recorded for two series of uniform oligo(oxyethylene) mono-n-alkyl ethers: α-alkyl,ω-hydroxyoligo(oxyethylene)s, H(CH2)n(OCH2CH2)mOH, and α-alkyl,ω-methoxyoligo(oxyethylene)s, H(CH2)n(OCH2CH2)mOCH3. LAM-1 frequencies were identified and compared with those determined previously for n-alkanes, oligo(oxyethylene) di-n-alkyl ethers and oligo(oxyethylene) dimethyl ethers. On the basis of the linear crystal model of Minoni and Zerbi (J. Phys. Chem., 1982, 86, 4791), non-linear relationships between whole-chain LAM-1 frequency and reciprocal chain length have been explained as effects of end masses and end forces. Prominent bands in the spectra of the α-alkyl,ω-hydroxyoligo(oxyethylene)s were assigned to LAM-1 and LAM-3 of the H-bonded dimer crystallised in a bilayer structure.