Theoretical interpretation of the line shape of the gaseous acetic acid cyclic dimer

A general quantum theoretical approach of the nu(X-H) IR line shape of cyclic dimers of weakly H-bonded species in the gas phase is proposed. In this model, the adiabatic approximation (allowing to separate the high frequency motion from the slow one of the H-bond bridge), is performed for each separate H-bond bridge of the dimer and a strong nonadiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. The present model reduces satisfactorily to many models in the literature dealing with more special situations. It has been applied to the cyclic dimers (CD(3)CO(2)H)(2) and (CD(3)CO(2)D)(2) in the gas phase. It correctly fits the experimental line shape of the hydrogenated compound and predict satisfactorily the evolution in the line shapes, to the deuterated one by reducing simply the angular frequency of the H-bond bridge and the anharmonic coupling parameter by the factor 1/ square root of 2.     

Theoretical interpretation of the infrared lineshape of liquid and gaseous acetic acid

We have applied a model used recently [P. Blaise, M.J. Wojcik, O. Henri-Rousseau, J. Chem. Phys. 122 (2005) 64306] to unpolarized ν_X–H infrared lineshapes of cyclic (CH₃COOH)₂ in liquid and gaseous phases and (CD₃COOH)₂ in gaseous phase and taking into account the IR A_g forbidden transition. This model incorporates (i) the anharmonic coupling between the high frequency mode and the H-bond bridge, (ii) the Davydov coupling between the excited states of the two moieties, (iii) the quantum direct and indirect dampings. The approach reproduces satisfactorily the main features of the experimental lineshapes by using a minimum number of independant parameters.     

Unraveling the structure of hydrogen bond stretching mode infrared absorption bands: an anharmonic density functional theory study on 7-azaindole dimers

The structure of the linear infrared absorption spectrum of the N-H stretching mode in 7-azaindole dimers is analyzed by quartic anharmonic vibrational force field calculations based on density functional theory. It is demonstrated that a multiple Fermi resonance model including contributions from 12 fingerprint vibrational modes, most of them containing considerable contributions of N-H bending motions, combined with a single low-frequency mode satisfactorily explains the complex line shape of N-H stretching mode absorption band.     

液晶二聚体

液晶二聚体作为半柔性主链型液晶聚合物的简化模型, 通过对其液晶性质的研究, 有助于理解更复杂聚合物体系的液晶行为. 另外, 液晶二聚体作为一类特殊的液晶也有其自身的相结构和相行为. 以分子结构与液晶态的相互关系为主线, 系统介绍了目前文献报道的对称及非对称棒状液晶二聚体(线形、H形、U形、T形)、盘状液晶二聚体(对称的盘-盘状液晶二聚体和非对称的盘-棒状液晶二聚体)和香蕉形液晶二聚体(对称的香蕉-香蕉形液晶二聚体和非对称的香蕉-棒状液晶二聚体)等各种不同类型的液晶二聚体的研究进展, 以期为新型液晶二聚体的分子设计提供一些借鉴.     

Investigation of H-bonds in 1,1-diphenylethanol by IR spectra measurements

The parameters of stretching vibrations nu(OH) (frequencies and integral intensities) have been calculated from IR spectra of a large number of H-complexes of 1,1-diphenylethanol [(C(6)H(5))(2)C(CH(3))OH] with solvents of various proton accepting strength which were not regularly reported. The data has been used to estimate the formation enthalpies of H-complexes and the proton-donor action of the mentioned alcohol. Also, correlations between those spectral characteristics have been investigated. The H-bonds in 1,1-diphenylethanol (DPE) have been investigated depending on concentrations in CCl(4) and temperature by means of infrared (IR) absorption spectra measurements. It has been found that the hydrogen bonds of the crystalline DPE are formed in the manner of cyclic tetramer, while in solutions with the concentration 0.5 mol/l, cyclic dimers are formed, which in higher concentrations change into cyclic tetramers.     

Molecular structure and hydrogen bonds in solid dimethylol propionic acid (DMPA)

The H-bonds in dimethylol propionic acid (DMPA) are investigated through the spectra changes between -150 and 180 degrees C, the spectra comparison before and after the pendent carboxylic group was neutralized as well as after DMPA was partly deuterated. Vibrational bands assignment is proposed based on the group frequency, band shape, intensity and the crystal structure. It was found that the highly crystallized DMPA is also highly H-bonded with the obvious crystal relating bands besides the typical H-bonded characteristic bands of both alcohols and carboxylic acids. The packing mode of carboxylic acid is similar to long-chain polymers to some extent but possesses the dimer spectra characteristic, especially still showing the prominent out-of-plane bending vibrational band gammaOH. The three hydroxyls, including the carboxylic hydroxyl, are all in the different H-bond states, showing three H-bonded hydroxyl bands with different frequencies. The frequency, intensity and shape of nuOH relates not only to OH bond length, but also to H-bond length as well as the bond angle. The H-bond in carboxylic hydroxyl is more sensitive to temperature changes and deuteration whereas the two primary hydroxyls form another H-bond pattern after DMPA was neutralized. It was also found that the possible overtone of gammaOH appears at lower temperature.     

Experimental and theoretical study of the polarized infrared spectra of the hydrogen bond in 3‐thiophenic acid crystal

This article presents the results of experimental and theoretical studies of the v_{O H} and v_{O D} band shapes in the polarized infrared spectra of 3‐thiophenic acid crystals measured at room temperature and at 77 K. The line shapes are studied theoretically within the framework of the anharmonic coupling theory, Davydov coupling, Fermi resonance, direct and indirect damping, as well as the selection rule breaking mechanism for forbidden transitions. The adiabatic approximation allowing to separate the high‐frequency motion from the slow one of the H‐bond bridge is performed for each separate H‐bond bridge of the dimer and a strong nonadiabatic correction is introduced via the resonant exchange between the fast‐mode excited states of the two moieties. The spectral density is obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The approach correctly fits the experimental line shape of the hydrogenated compound and predicts satisfactorily the evolution in the line shapes with temperature and the change in the line shape with isotopic substitution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Unveiling the "booster effect" of fluorinated alcohol solvents: aggregation-induced conformational changes and cooperatively enhanced H-bonding

The influence of conformation and aggregation on the hydrogen bond donor ability of fluorinated alcohol solvents [1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and 1-phenyl-2,2,2-trifluoroethanol (PhTFE)] was explored theoretically (DFT) and experimentally (NMR, kinetics, crystal structure analyses). The detailed DFT analysis revealed a pronounced dependence of the H-bond donor ability on the conformation along the CO-bond of the monomeric alcohols. The donor orbital energy (sigma*(OH)) decreases and the molecular dipole moment (mu) increases drastically from the antiperiplanar (ap) to the synperiplanar (sp) H(C)COH conformation. The kinetics of olefin epoxidation with H(2)O(2) in HFIP indicate higher order solvent aggregates (2-3 monomers) to be responsible for the activation of the oxidant. Single-crystal X-ray analyses of HFIP and PhTFE confirmed the existence of H-bonded aggregates (infinite helices, ribbons, and cyclic oligomers) and the predominance of sc to sp conformations of the fluoroalcohol monomers. These aggregate structures served as the basis for a DFT analysis of the H-bond donor ability at the terminal hydroxyl group of HFIP mono- to pentamers. Both the LUMO energy and the natural charge of the terminal hydroxyl proton indicated a substantial cooperative influence of dimerization and trimerization on the H-bond donor ability. We therefore conclude that dimers and trimers, with the individual monomers in their sc to sp conformation, play a crucial role for the solvolytic and catalytic effects exerted by HFIP, rather than monomers.     

Heteronuclear intermolecular resonance-assisted hydrogen bonds. The structure of pyrrole-2-carboxamide (PyCa)

The crystal and molecular structure of pyrrole-2-carboxamide (PyCa) determined by single crystal X-ray diffraction is presented. Molecular conformations of PyCa are also analyzed by FT-IR and NMR techniques. Additionally DFT calculations at the B3LYP/6-311++G(d,p) level of approximation are performed for dimers of PyCa and for related species. The existence of two tautomeric forms for the analyzed dimers differing in H-bond motifs, N-H...O or O-H...N, is studied. The geometrical and energetic features of such H-bonds show that these interactions may be classified as intermolecular resonance-assisted hydrogen bonds. Additionally the Bader theory is applied to determine and to analyze bond critical points.     

A matrix infrared study of association of formamide

The association of formamide has been studied in argon. In the spectral region from 800 to 200 cm⁻¹ several characteristic bands due to association were found and assigned to the out-of-plane bending modes of the NH group. The widths of these low-frequency bands are of the same order of magnitude as those of the fundamental bands of the monomer. By comparing the spectra of self-associated species with spectra of heteroassociated species between formamide and N,N-dimethyl formamide, it was possible to assign association bands to the open dimers as well as to the cyclic dimers. A band appearing upon warming at about 230 cm⁻¹ has been assigned to a H-bond stretching mode. The results indicate that dimers trapped from the gas phase are predominantly open, and that both open and cyclic structures are formed upon diffusion-controlled association in the matrix.     

Tight Xenon Confinement in a Crystalline Sandwich‐like Hydrogen‐Bonded Dimeric Capsule of a Cyclic Peptide

A cyclic hexapeptide with three pyridyl moieties connected to its backbone forms a hydrogen‐bonded dimer, which tightly encapsulates a single xenon atom, like a pearl in its shell. The dimer imprints its shape and symmetry to the captured xenon atom, as demonstrated by ¹²⁹Xe NMR spectroscopy, single‐crystal X‐ray diffraction, and computational studies. The dimers self‐assemble hierarchically into tubular structures to form a porous supramolecular architecture, whose cavities are filled by small molecules and gases.     

主体分子2,2′-二羟基-1,1′-二萘与客体分子乙酸乙酯晶态包结物的研究

用X射线单晶衍射分析法研究主体分子2，2’-二羟基-1，l’-二萘与客体分子乙酸乙酯（3：1）晶态包结物的晶体结构。其化学式为C64H50O8，Mr=947．08。晶体属三斜晶系，空间群为P1。晶胞参数：个独立衍射点，5823个可观察点（F≥3σF）。2，2’-二羟基-1，1’-二萘与乙酸乙酯形成以氢键联系的包结物3个主体分子中的6个羟基形成21环的氢键体系。     

Supramolecular chemistry in the structure direction of microporous materials from aromatic structure-directing agents

A combination of fluorescence spectroscopy, thermogravimetric analysis, and molecular mechanics calculations has been used to study the structure-directing effect of the aromatic benzylpyrrolidine (BP) molecule (and its monofluorinated derivatives), and (S)-(-)-N-benzylpyrrolidine-2-methanol (BPM) in the synthesis of the microporous AFI structure. The results clearly show that, while all molecules form supramolecular aggregates in concentrated water solution, BPM molecules have a much more pronounced trend to aggregate as dimers within the AFI structure due to the development of interdimer H-bond interactions. Instead, BP (and its ortho- and meta-fluorinated derivatives) SDAs tend to incorporate in the AFI structure as monomers but with the simultaneous occlusion of water molecules, while para-fluorinated BP derivatives do not form compact dimers able to be accommodated in the AFI structure. We propose a crystallization mechanism where the presence of dimers is required for the nucleation step to occur, while crystal growth takes place through the simultaneous occlusion of SDA monomers and water (when the synthesis is performed with BP and derivatives) or through the occlusion of SDA dimers (in the synthesis with BPM).     

Side-Chain Interactions in d/l Peptide Nanotubes: Studies by Crystallography,NMR Spectroscopy and Molecular Dynamics

Our understanding of the factors affecting the stability of cyclic d/l peptide (CP) nanotubes remains underdeveloped. In this work, we investigate the impact of side chain alignment, hydrophobicity and charge on CP nanotube stability through X-ray crystallography, NMR spectroscopy and molecular dynamics (MD) simulations. We characterise the distinct CP-CP alignments that can form and identify stable and unstable dimers by MD simulation. We measure H-bond half-lives of synthesised CPs by ¹H−D exchange experiments and find good correlation with predicted CP-CP stabilities. We find that hydrophobic amino acids improve CP dimer stability but experimentally reduce solubility. Charged amino acids either increase or decrease CP dimer stability depending on the relative orientation and composition of charged groups. X-ray crystal structures are solved for two CPs, revealing non-tubular folded conformations. Ultimately, this work will assist the educated design of stable tubular structures for potential applications in biomedicine.     

Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system

The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.     

OH…O Out-of-Plane Bending Band [γ(OH)] and Its Overtone Band of Dimethylol Propionic Acid(DMPA)

In the present paper are reported the OH…O out-of-plane bending band[γ(OH)] between 900-950 cm-1 of dimethylol propionic acid(DMPA), its dependence upon temperature and its overtone band investigated via FTIR spectroscopy. It has been found based on the crystal structure that the band [γ(OH)] may not certainly be the characteristic band of carboxylic dimers, it can also result from another H-bond formed between carboxylic carbonyl and the primary hydroxyl. In addition, the band [γ(OH)] is very sensitive to temperature change but its overtone band can only appear at a low temperature.     

Two size regimes of methanol clusters produced by adiabatic expansion

Free neutral methanol clusters produced by adiabatic expansion have been studied by photoelectron spectroscopy and line shape modeling. The results show that clusters belonging to two distinct size regimes can be produced by changing the expansion conditions. While the larger size regime can be well described by line shapes calculated for clusters consisting of hundreds of molecules, the smaller size regime corresponds to methanol oligomers, predominantly of cyclic structure. There is little contribution from dimers to the spectra.     

The associative behaviour of saturated alcohols with reference to the molecular structure in the OH proximity. An FT-IR temperature study.

The IR absorption pattern of the OH stretching vibration has been determined for six aliphatic alcohols in the temperature range 100–293 K. Differences found for the bandmaximum and shape have been related with the intramolecular structure in the OH proximity. It is shown that the tendency to self-associate upon temperature lowering decreases with increased shielding of the OH group.Beside the formation of linear dimers evidence is found for cyclic associates most likely dimers.     

A crystalline H-bond cluster of hexafluoroisopropanol (HFIP) and piperidine: Structure determination by X ray diffraction

Piperidine and 1,1,1-3,3,3 hexafluoro-2-propanol (HFIP) have been co-crystallized and X-ray crystal structure has been explored. Single-crystal X-ray analysis displays the existence of hydrogen bonding aggregates through dimers 1 of the complex (one piperidine/two HFIP) where the heteroatoms form a six-center ring. In this cluster 1, each heteroatom (N, O) is multiple H-bond donor and acceptor. Surprisingly the strongest H-bond of the network is where HFIP acts as an acceptor from the amine. In this complex HFIP adopts a conformation different from that of HFIP aggregates. The supramolecular architecture is also based on discrimination between polar and hydrophobic parts that allows the alignment of molecules and the formation of parallel channels. NMR experiments show that strong interactions between piperidine and HFIP are maintained in solution.     

Preparation,crystal structure and characterization of 2,4,6-trinitro-3,5-dimethylbenzoic acid monohydrate

In the present work, we synthesized 2,4,6-trinitro-3,5-dimethylbenzoic acid (TNDMBA). Single crystal of TNDMBA·H₂O was cultured from aqueous solution using a slow evaporation method at 30°C. The crystal structure was determined by X-ray single-crystal diffraction analysis. The crystal belongs to the monoclinic system with space group P2(1)/c having unit cell parameters of a = 17.24(3) Å, b = 6.032(1) Å, and c = 16.359(4) Å. There are two kinds of intermolecular H-bond interactions between H₂O and TNDMBA, which is different from typical carboxylic acids that form H-bond dimers across crystallographic centers of inversion. The title compound was characterized by FT-IR, DSC, and TG-DTG technologies, and calculated by using density functional theory (DFT) method. The calculated results show that the structural parameters from the theory are close to those of the crystal structure from the experiments. The compound is composed of three nitro groups and one carboxyl group, and it can be used as a potential energetic combustion catalyst in industry.