Hydrogen bonding: How much anharmonicity?

In moderately strong hydrogen bonds, hydrogen bond formation increases the anharmonicity constant of the high frequency stretching vibration, significantly but not dramatically. This increase tends to increase with the strength of the hydrogen bond. The main cause of the fine structure and breadth of this band is, however, coupling with both the low frequency stretching and bending vibrations of the bridge, despite the smallness of the coupling constants. Second–order perturbation theory is sufficient to interpret the observed frequencies in the case of moderately strong hydrogen bonds. HCNHF, O–H:O, O–H:N, and N–H:N hydrogen bonds are considered.     

Hydrogen-bonded complexes involving HF and HCl: the effects of electron correlation and anharmonicity

Calculations on the hydrogen-bonded complexes HCNHF, H₂OHF, ClCNHCl and (CH₃)₂OHCl are reported. SCF harmonic values for the HF and HCl frequency shifts are in considerable disagreement with experiment, by as much as 100 cm^–1. Calculations at the MP2 (harmonic) level yield improved agreement with experiment, reducing discrepancies to the order of 10 cm^–1. We have also calculated all the cubic and quartic force constants for HCNHF at the SCF level, so that the anharmonic constants, x _rs can be evaluated. Although x ₁₁ (v ₁=H-F stretch) is large and negative, it is more than compensated by a positive x ₁₆ (v ₆=NH-F bend), so that the anharmonic correction to v ₁ is small and positive. The validity of these anharmonistudies is examined.     

Overtone spectroscopy of butanol

Overtone spectra of CH and OH stretching vibrations in normal, secondary and tertiary butanol have been studied. A large number of combination and overtone bands, along with the fundamentals have been measured and assigned in the three cases. These data have been used to obtain the vibrational frequency, anharmonicity constant and dissociation energy for the CH and OH stretch motions in the respective molecules. Effect of dilution on the OH fundamental frequency in n-butanol causes a blue shift.     

Structure, conformation and hydrogen bonding of two amino-cycloalkanespiro-5-hydantoins

The crystal structures of 3-amino-cycloheptanespiro-4′-imidazolidine-2′,5′-dione (I) {systematic name: 3-amino-1,3-diazaspiro[4.6] undecane-2,4-dione} and 3-amino-cyclooctanespiro-4′-imidazolidine-2′,5′-dione (II) {systematic name: 3-amino-1,3-diazaspiro[4.7] dodecane-2,4-dione}, have been determined. In both compounds the polar hydantoin groups cause molecules to aggregate via N-H...O and N-H...N interactions, forming a layer structure, in which the cycloalkane rings project outwards from the central, more polar, region. The observed molecular structure is compared with that calculated by density functional theory methods.      

Structural properties of montmorillonite intercalated with tetraalkylammonium cations—Computational and experimental study

Several tetraalkylammonium (TAA) cations intercalated in layered clay mineral montmorillonite were studied by a combination of theoretical approach based on density functional theory (DFT) and infrared spectroscopy. DFT calculations revealed positions of TAA cations in the interlayer space and a dependence of d₀₀₁ parameter on the cation size. A finite difference method and molecular dynamic simulations were used to analyze and interpret vibrational modes observed in the experimental spectra with a specific focus on the CH₃ and CH₂ stretching modes. MD simulations on the tetraethylammonium-montmorillonite (TEA-M) model showed a high sensitivity of the position of the stretching vibrations of the CH₃ and CH₂ groups on the d₀₀₁ value. MD calculations also helped to distinguish vibrations of the parallel and perpendicular CH₃ groups of the tetramethylammonium-montmorillonite (TMA-M) which was not possible from the experimental infrared spectra because of many overlapping broad bands.     

Association of model peptides and dehydropeptides: N-acetyl-l-alanine- and dehydroalanine N′,N′-dimethylamides

The comparative studies on the association of Ac-ΔAla-NMe₂ and Ac-l-Ala-NMe₂ in carbon tetrachloride were performed by the analysis of their average molecular weight, dipole moments and FTIR spectra. To aid spectroscopic interpretation and gain some deeper insight into the nature of associates, the geometries of the minimum energy of the dimers of Ac-ΔAla-NMe₂ and Ac-l-Ala-NMe₂ were calculated by the B3LYP/6-31+G** method. The average molecular weight in the studied concentration range, for the ΔAla and l-Ala peptide, as determined by the osmometric method, did not exceed 1.5 and 1.2 of the monomeric mass, respectively. Accordingly, the percentage of the monomeric form (α) decreased as concentration was increased more significantly for the ΔAla analogue than for its saturated counterpart. In the studied concentrations, the dipole moment of the unsaturated compound decreases and that of its counterpart is almost constant. We identified a wider range of dimeric forms of Ac-ΔAla-NMe₂ than those of Ac-l-Ala-NMe₂. While Ac-ΔAla-NMe₂ mainly forms cyclic dimers, built of open conformers H/F, specific for α,β-dehydroamino acids, Ac-l-Ala-NMe₂ forms cyclic and linear dimers, characteristic for the usual amino acids. Ac-ΔAla-NMe₂ has a greater tendency to associate than its saturated variant, which is the result of stronger hydrogen bonds.     

Cholesterol complexes with some proton acceptors in benzene and toluene solutions

Abstract  Cholesterol complexes with tri-n-butyl phosphate, tri-n-octylamine, N,N-dimethylacetamide, and cyclohexanone in benzene and toluene solutions were studied using conventional IR spectroscopy. The spectra were recorded in the region of fundamental OH stretching (3,700–3,100 cm⁻¹) at 298 K. The experimental spectra were resolved into bands corresponding to the cholesterol monomer and particular oligomeric and complex species. The formation constants of complexes were determined from the-least squares plots of the linearized expressions of Bjerrum’s formation function. The stoichiometry of complexes was also identified in this way. The identification of the particular resolved bands was performed from their location, and from the dependence of their intensity on the cholesterol monomer and free base concentration. Graphical Abstract        

Synthesis and spectroscopic properties of Schiff bases derived from 3-hydroxy-4-pyridinecarboxaldehyde

A series of six new Schiff bases has been prepared by reacting aniline and 4-R-substituted anilines (R=CH₃, OCH₃, Br, Cl, NO₂) with 3-hydroxy-4-pyridinecarboxaldehyde. The ¹H, ¹³C, ¹⁵N and ¹⁷O NMR data of these compounds are used to discuss the tautomerism. ¹⁵N NMR and ¹⁷O NMR chemical shifts established the tautomer existing in solution as the hydroxy/imino. ¹³C CPMAS NMR confirms that the same tautomer is found in the solid state. The stabilities of the tautomeric forms have been approached using density functional calculations (B3LYP/6-31G**) in the gas phase. In all cases the neutral hydroxy/imino with E configuration is more stable than the oxo/enamino form (by ∼22 kJ mol⁻¹) and significantly more stable than the betaine (by ∼75 kJ mol⁻¹).     

Synthesis and properties of p-benzoquinone-fused hexadehydro[18]annulenes

A series of hexadehydro[18]annulenes fused with different numbers of p-benzoquinone, 4-6, were synthesized by stepwise transformation of the p-dimethoxybenzene moiety of the precursor dehydroannulene 3 fused with three 3,6-dimethoxy-4,5-dimethylbenzene units at 1,2-positions into p-benzoquinone using ceric ammonium nitrate. The UV-vis spectra of compounds 4 and 5, which have both electron-donating p-dimethoxybenzene unit(s) and electron-accepting p-benzoquinone unit(s) in the π-systems, showed the maximum absorption bands bathochromically shifted in comparison with 3 having only p-dimethoxybenzene units and 6 having only p-benzoquinone units. However, the solvatochromism expected for 4 and 5 was found to be quite weak possibly because the HOMO and LUMO (B3LYP/6-31G(d)) are not localized but rather delocalized over the whole π-systems.     

Tailor-made naphthyridines: Self-assembling multiple hydrogen-bonded supramolecular architectures from dimer to helix

Stepwise changes of functional oxo and amino groups in 1,8-naphthyridines to modify the supramolecular architecture have been carried out. The first example of a naphthyridine helix has been found and its structure established by X-ray crystallography. The design is based on hydroxy and amido tautomeric naphthyridines which crystallize in dimers or catemers, one of them attaining helicity. The most stable tautomer present in all the compounds discussed in this paper, as well as the formation of hydrogen-bonded dimers or catemers, was established by X-ray crystallography and rationalized with theoretical calculations.     

Geometrical and electronic structures of the dication and ion pair in the geminal dicationic ionic liquid 1,3-bis[3-methylimidazolium-yl]propane bromide

Geminal dicationic ionic liquids (ILs), a new category of IL family, have been developed recently and found to possess unique properties compared to conventional monocationic ILs. To establish a basis for understanding their novel properties, we studied the geometrical and electronic structures of the dication ([(mim)C₃(mim)]²⁺) and the ion pair ([(mim)C₃(mim)]²⁺-2Br⁻) in the geminal dicationic IL 1,3-bis[3-methylimidazolium-yl]propane bromide by performing density functional theory calculations. The geometrical structures and relative stabilities for the dication and the ion pair are discussed, and their electronic properties are analyzed in detail. The intrinsic interaction between the dication and Br anions in the most stable conformer was investigated by performing the natural bond orbital analyses. Results for the dication and the ion pair are compared with those of the corresponding monocation ([C₄mim]⁺) and ion pair ([C₄mim]⁺-Br⁻). ¹H NMR spectroscopy for the most stable ion pair has been calculated and the general trend is found to be in fairly agreement with the experimental data.     

N-H?S hydrogen bonding in 2-mercapto-5-methyl-1,3,4-thiadiazole. Synthesis and crystal structures of mercapto functionalised 1,3,4-thiadiazoles

The synthesis and crystal structures of three mercapto functionalised 1,3,4-thiadiazoles and the crystal structure of 2-mercapto-5-methyl-1,3,4-thiadiazole are described. In the solid state, 2-mercapto-5-methyl-1,3,4-thiadiazole 1 forms a thioamide tautomer as shown by FTIR and Raman spectroscopy as well as X-ray crystallography and as theoretically predicted. The molecules are connected to form chains via N-H?S hydrogen bonds with N?S=328.3 pm. Bis(2-methyl-1,3,4-thiadiazolyl)-5,5′-disulfide 2, the disulfide of 1, as well as 2-(tert-butyldithio)-5-methyl-1,3,4-thiadiazole 3 and 2,5-bis(tert-butyldithio)-1,3,4-thiadiazole 4 have been synthesised and characterised by vibrational spectroscopy and X-ray diffraction.     

有机和生物晶体固态核磁共振参数的准确预测

理论计算有助于复杂的有机和生物系统光谱的鉴定.对于核磁共振光谱,固体结晶中的化学位移和四极耦合常数(QCC)受到邻近的分子和晶格的氢键和范德华作用较大的影响,从而显示出与气态单体分子不同的NMR参数.因此,在固体晶体NMR参数的理论计算中有必要将氢键和范德华作用这两个因素考虑进来.基于周期性方法,本文采用L-Ala-Gly二肽和硝基苯晶体作为模型体系来考察该方法计算NMR参数的精度.研究结果显示周期结构模型能够将分子间的氢键和范德华作用考虑进来,得到的化学位移和QCC值明显优于传统的单分子模型和超分子模型得到的结果,采用该方法计算的结果能够重现NMR实验结果.     

Hydrogen bonds and ionic interactions in Guanidine/Guanidinium complexes: a computational case study

It is frequently said that hydrogen bonds (HBs) are enhanced by ionic interactions and in this article we intend to determine the degree at which this reinforcement happens. Considering our interest in the Guanidine(neutral)/Guanidinium(cation) system and its particular nature, all the possible 1:1 complexes with the Chloride(anion)/Hydrochloric acid(neutral) system have been studied at different levels of computation (B3LYP with 6-31+G* and TZVP basis sets; MP2 with 6-31+G*, 6-311++G** and aug-cc-pVDZ basis sets; CBS-QB3 and G3MP2). The nature of these interactions established in all the systems and, when possible, at all the levels of computation used in this study, has been analyzed using Atoms in Molecules and Natural Bond Orbital methodologies. By examining the interaction energy, the electron density at the bond critical bonds, the atomic energy, the charge transfer, the orbital energy, and the deformation energy we can conclude that HBs are stronger when the ionic interaction is stronger. Thus, both interactions do not work in an independent manner but one reinforces the other to different degrees depending on the nature of the charges present. Several correlations with the interaction energy have been found and a partition of the contributions of both the HB and ionic forces to the total interactions is proposed.     

MNDO calculations on hydrogen bonds. Modified function for core-core repulsion

The MNDO method has been modified to calculate the properties of the structures involving hydrogen bonds X···H—Y, X, Y = N, O and F. A new method (referred to as MNDO/H) has been tested by calculation of a wide range of molecular systems with weak and strong (ionic) hydrogen bonds. The results obtained are in good agreement with the experimental data. In the cases where direct comparisons are possible, the MNDO/H method seems to give more accurate values of hydrogen bond energy than the ab initio method using STO-4-31G basis set.     

A Model of Hydrogen-Bonded Liquids

The orientation defect model can be used for quantitative estimates and for understanding the properties of H-bonded liquids, such as water and alcohol. The defect concentrations can be determined by vibrational spectroscopy, and the applicability of the approximation procedure derives from considering H-bonds as chemical equilibria. Possible extensions of the simple model are critically discussed.