Acid–Base Interactions in the Dichloroacetic Acid–N,N-Dimethylformamide System as Found from IR Spectroscopic Data

Ion–molecule interactions in the dichloroacetic acid–N,N-dimethylformamide system in the concentration range from pure acid to pure base at 30°C were investigated by multiple attenuated total internal reflectance IR spectroscopy. It was found that, depending on the ratio between components in solution, 1 : 1 or 2 : 1 acid–base complexes with strong hydrogen bonds are formed. With an excess of the acid, protonation of the base does not occur. The intensity of continuous absorption at 2000 cm^–1 is characteristic of quasi-ionic pairs with strong symmetrical hydrogen bonds. However, along with a continuous component, the spectra exhibited individual sharp peaks, which are typical of molecular complexes.     

An electrostatic model for hydrogen bonds in alcohols

We have measured the Raman spectra of liquid methanol at temperatures between 50° and –77°C. The weak O–H stretching bands appear, under amplification, more and more asymmetric as the temperature is lowered. They can be decomposed into three Gaussian components centered at about 3220, 3310, and 3400 cm^–1. The former, predominant at low temperature, corresponds to single, linear hydrogen bonds (LHB) between two molecules. The other two are assigned to branched hydrogen bonds, respectively bifurcated (BHB), between three molecules, and trifurcated (THB), between four molecules. We conclude that the molecular structure of liquid alcohols is not chain-like, as presumed so far, but a three-dimensional network featuring a mixture of single (LBH), and multiple hydrogen bonds (BHB, and THB). They are mainly electrostatic in nature, their relative proportions and geometry governed by the packing conditions for minimum energy. They form distinct trimers and tetramers in dilute solutions of alcohols in inert solvents and frozen matrices, and the latter even in the vapor.Deceased December 25, 1987.     

An S N2-Model for Proton Transfer in Hydrogen-Bonded Systems

A new mechanism of proton transfer in donor–acceptor complexes with long hydrogen bonds is suggested. The transition is regarded as totally adiabatic. Two closest water molecules that move synchronously by hindered translation to and from the reaction complex are crucial. The water molecules induce a shift of the proton from the donor to the acceptor with simultaneous breaking/formation of hydrogen bonds between these molecules and the proton donor and acceptor. Expressions for the activation barrier and kinetic hydrogen isotope effect are derived. The general scheme is illustrated with the use of model molecular potentials, and with reference to the excess proton conductivity in aqueous solution.     

Diffuse-Reflectance IR Spectra of ortho-Hydrogen and para-Hydrogen Adsorbed on Zeolite BaX at 77 K and Their Interpretation in Terms of the Stark Effect

The vibrational and vibrational–rotational spectra of hydrogen adsorbed on zeolite BaX at 77 K were examined by diffuse-reflectance IR spectroscopy over a wide range of wavenumbers. The use of hydrogen enriched in the para isomer and of molecular deuterium allowed us to reliably assign the absorption bands to orthohydrogen and para-hydrogen and compare the experimentally observed band splitting with the theoretically calculated shifts of the corresponding levels resulted from the Stark effect. In the calculations, an adsorption site was simulated as a positive point charge. Although this approximation is rough, the IR spectra of adsorbed hydrogen and deuterium are adequately described in terms of the Stark effect. A decrease in the frequency of stretching vibrations of H–H (D–D) bonds in the molecules coordinated to Ba²⁺ cations, a decrease in the intensity of vibrational–rotational absorption bands, and the band splitting in the spectra of adsorbed para-hydrogen and orthohydrogen were explained.     

A Bloembergen–Purcell–Pound <Superscript>13</Superscript>C NMR relaxation study of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

The molecular structure and rotational motion of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) were studied over a wide temperature range using the Bloembergen–Purcell–Pound ¹³C NMR spin–lattice relaxation method and NOE factors. Examination of the spin–lattice relaxation times (T ₁) and the rates (R ₁=1/T ₁) of the 1-butyl-3-methylimidazolium cation reveals the relative motions of each carbon in the imidazolium cation. The rotational characteristics of the [BMIM] cation are supported by ab-initio molecular structures of [BMIM][PF6] using density functional theory (DFT) and Hartree–Fock (HF) methods. The ab-initio gas phase structures of [BMIM][PF6] indicate that the 1-butyl-3-methylimidazolium C2 hydrogen, the ring methyl group, and the butyl side-chain hydrogen atoms form hydrogen bonds with the hexafluorophosphate anion.     

Synthesis and Crystal Structures of [(Nicotinic Acid)2H]+I-, [(2-Amino-6-methylpyridine)H]+(NO3)-, and the 1:1 Complex Between 1-Isoquinoline Carboxylic Acid (Zwitter Ion) and L-Ascorbic Acid Assembled via Hydrogen Bonds

Summary. Three new complexes, namely [(nicotinic acid)₂H]⁺I^–, [(2-amino-6-methylpyridine)H]⁺ (NO₃)^–, and the 1:1 complex between 1-isoquinoline carboxylic acid (zwitter ion form) and L-ascorbic acid were synthesized. The IR spectra revealed different types of hydrogen bonds in these compounds. The X-ray structure determination has shown the first compound to consist of a packing of [(nicotinic acid)₂H]⁺ cations and I^– anions. In the dimeric cation the two nicotinic acid molecules (zwitter ions) are connected through hydrogen bonds (O–HO). Each dimer is further engaged in other hydrogen bonds with adjacent dimers giving 2D layers. The I^– ion is located at the inversion center. In the second compound the cation and anion are connected via hydrogen bonds formed between oxygen atoms of the NO₃ ^– anion and NH and NH₂ of the cation generating a layer structure. All atoms are coplanar on mirror planes. In the 1:1 complex the two molecules are connected through hydrogen bonds formed between the two oxygen atoms of the carboxylate group of 1-isoquinoline carboxylic acid (zwitter ion) and the oxygen atoms of the two adjacent hydrogen groups of the L-ascorbic acid molecule. These complex molecules are engaged in other hydrogen bonds with each other forming a 2D system normal to the long b-axis of the unit cell.     

Synthesis and Crystal Structures of [(Nicotinic Acid)2H]+I-, [(2-Amino-6-methylpyridine)H]+(NO3)-, and the 1:1 Complex Between 1-Isoquinoline Carboxylic Acid (Zwitter Ion) and L-Ascorbic Acid Assembled via Hydrogen Bonds

Three new complexes, namely [(nicotinic acid)₂H]⁺I^–, [(2-amino-6-methylpyridine)H]⁺ (NO₃)^–, and the 1:1 complex between 1-isoquinoline carboxylic acid (zwitter ion form) and L-ascorbic acid were synthesized. The IR spectra revealed different types of hydrogen bonds in these compounds. The X-ray structure determination has shown the first compound to consist of a packing of [(nicotinic acid)₂H]⁺ cations and I^– anions. In the dimeric cation the two nicotinic acid molecules (zwitter ions) are connected through hydrogen bonds (O–HO). Each dimer is further engaged in other hydrogen bonds with adjacent dimers giving 2D layers. The I^– ion is located at the inversion center. In the second compound the cation and anion are connected via hydrogen bonds formed between oxygen atoms of the NO₃ ^– anion and NH and NH₂ of the cation generating a layer structure. All atoms are coplanar on mirror planes. In the 1:1 complex the two molecules are connected through hydrogen bonds formed between the two oxygen atoms of the carboxylate group of 1-isoquinoline carboxylic acid (zwitter ion) and the oxygen atoms of the two adjacent hydrogen groups of the L-ascorbic acid molecule. These complex molecules are engaged in other hydrogen bonds with each other forming a 2D system normal to the long b-axis of the unit cell.     

Analysis of IR Spectra and Hydrogen Bonds of Uracil and N1,N3-deuterouracil

The in-plane vibrations and IR spectrum intensities of monomeric uracil and N₁,N₃-deuterouracil and their associates in the polycrystalline state were calculated and analyzed in the valence-optical approximation of vibration theory. The obtained data on the variations of the parameters of the molecular models is used to analyze hydrogen bonds. It is shown that in the polycrystalline state uracil forms hydrogen bonds of two types: bonds involving N–H groups (C₄=O...HN₁, C₄=O...HN₃) and those involving the C–H group (C₂=O...HC₅).     

Blue-shifted hydrogen-bonded complexes. II. CH3F(HF)1 n 3 and CH2F2(HF)1 n 3

The equilibrium structures, binding energies, and vibrational spectra of the clusters CH₃F(HF)_{1 n 3} and CH₂F₂(HF)_{1 n 3} have been investigated with the aid of large-scale ab initio calculations performed at the Møller–Plesset second-order level. In all complexes, a strong C–FH–F halogen–hydrogen bond is formed. For the cases n = 2 and n = 3, blue-shifting C–HF–H hydrogen bonds are formed additionally. Blue shifts are, however, encountered for all C–H stretching vibrations of the fluoromethanes in all complexes, whether they take part in a hydrogen bond or not, in particular also for n = 1. For the case n = 3, blue shifts of the ν(C–H) stretching vibrational modes larger than 50 cm⁻¹ are predicted. As with the previously treated case of CHF₃(HF)_{1 n 3} complexes (A. Karpfen, E. S. Kryachko, J. Phys. Chem. A 107 (2003) 9724), the typical blue-shifting properties are to a large degree determined by the presence of a strong C–FH–F halogen–hydrogen bond. Therefore, the term blue-shifted appears more appropriate for this class of complexes. Stretching the C–F bond of a fluoromethane by forming a halogen–hydrogen bond causes a shortening of all C–H bonds. The shortening of the C–H bonds is proportional to the stretching of the C–F bond.     

Caffeine interactions with nucleic acids. Molecular mechanics calculations of model systems for explanation of mechanisms of biological actions

To understand the molecular mechanisms of the influence of caffeine (CAF) on DNA functioning, molecular mechanics calculations of the interaction energy of CAF with nucleic acid bases and base pairs have been performed. The calculations reveal three types of mutual CAF–base (and CAF–base pair) arrangements corresponding to minima of the interaction energy. Besides well-known stacking mutual positions of the molecules, two other types of arrangements are revealed and studied. One of these arrangements corresponds to the nearly in-plane position of CAF and base (or base pair) and the formation of a single hydrogen bond. Another type of minimum corresponds to nearly perpendicular arrangements of the molecular planes and the formation of intermolecular hydrogen bonds. These two arrangements are possible both for individual nucleic acid monomers and for DNA duplexes. The calculations suggest the molecular mechanisms of the influence of CAF on DNA interactions with other biologically active molecules.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 20002).     

Structure ofN S-butyl-N O-phenyl(thiooxamide)

The molecular and crystal structure of N^S-butyl-N^O-phenyl(thiooxamide) (1) has been established by X-ray structural analysis. The thiooxamide fragment and the phenyl ring are coplanar. The conformation of 1 is stabilized by NH...O and NH...S hydrogen bonds. No conjugation between the thioamide and the oxamide fragments of the molecule occurs. In the crystal, the centrosymmetrically related molecules 1 are linked in dimers through NH ... O' intermolecular hydrogen bonds.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 485–487, February, 1996     

Reactions of proton transfer and exchange with the participation of OH,SH, and CH acids and amines

A comparison of proton exchange reactions between OH, SH, and CH acids and the NH groups of trialkylammonium ions showed that regardless of the nature of the acid XH, the mechanism of exchange includes transfer of a proton in the ion pair N-H⁺ ... X^– as the slow step. At the fast steps of proton exchange XH- N⁺H, i.e., molecular exchange with breaking of a hydrogen bond X-H ... N and transfer of a proton along these bonds, differences appear in the properties of XH acids. In the sequence from OH to SH and CH acids, the hydrogen bonds X-H ... N are weakened. As a result of this, in the same sequence the kinetic acidity (k₂) decreases but the rate of molecular exchange (k_H) increases. The ratio between the values of k₂ and k_H is inverted when the strong bonds O-H ... N (k₂/k_H 1) are replaced by weak bonds C-H ... N (k₂/k_H 1). It was also established that the kinetic stability of the anions increases as the oxygen atoms are replaced by sulfur in the series RCOO^– < RCOS^– < R₂PSS^– as a result of the more effective delocalization of the negative charge on the diffuse orbitals of sulfur.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 23, No. 4, pp. 471–475, July–August 1987.     

Interaction of carboxyl-containing polymers with deoxypeganine

Polymeric complexes of deoxypeganine hydrochloride with a number of carboxyl-containing polymers have been synthesized and investigated. It has been found that in the interaction of polymers with deoxypeganine both hydrogen bonds and electrostatic bonds arise.Translated from Khimiya Prirodnykh Soedinenii, Vol. 33, No. 1, pp. 87–90, January–February, 1997.     

Crystal and molecular structure of (r-2, c-4)-3-benzyl-2,4,5,5-tetraphenyl1,3-thiazolidine, intramolecular C–HS hydrogen bonds

The crystal and molecular structures of (r-2, c-4)-3-benzyl-2,4,5,5-tetraphenyl-1,3-thiazolidine are investigated showing the existence of C(sp²)–HS and C(sp²)–HN intramolecular contacts. The analysis of geometrical parameters shows that C–HS contacts may be treated as hydrogen bonds but C–HN do not fulfil the geometrical criteria of the existence of H-bonds. The B3LYP/6-311+G* single point calculations were performed to obtain wave functions applied later for ‘atoms in molecules’ (AIM) study. The analysis of bond critical points based on the Bader theory (AIM) supports the existence of intramolecular C–HS H-bonds.     

Effect of intermolecular =C–HO interaction on the crystal structure and vibrational properties of 2,6-dimethyl-4-nitropyridine N-oxide

The crystal structure of 2,6-dimethyl-4-nitropyridine N-oxide (DMNPO) has been determined at ambient temperature. The compound crystallizes as a monoclinic structure, space group P2/n, with 12 molecules per unit cell. The unit cell contains three non-equivalent formula units. The nitro group is not coplanar with the pyridine ring. Through a system of =C–HO hydrogen bonds the molecules are arranged into a two-dimensional network of layers parallel to the axc plane.The IR and Raman spectra, measured in the 3500–100 cm⁻¹ region at ambient temperature, are correlated with X-ray structural data. The assignment of IR and Raman bands is given. The appearance of characteristic vibrational features in the spectra of this compound and the observed shifts of the =C–H and N–O IR active stretching modes, when the sample is dissolved in CCl₄, is discussed in terms of the relatively strong =C–HO hydrogen bonds present in this crystal.     

Thermodynamic Properties of Aqueous Solution of 2-Isopropoxyethanol at 25°C

Excess enthalpy, excess isobaric heat capacity, density, and speed of sound for aqueous 2-isopropoxyethanol solutions were measured at 25°C. The density was also measured at 20°C. The excess enthalpy was –800 J-mol^–1 at the minimum (mole fraction alcohol, x = 0.2), showing that the hydrogen bonds formed between unlike molecules are stronger than those in both pure liquid states. The excess volume also was large and negative, more than –1.2 cm³-mol^–1 at the minimum (x = 0.35). Excess isentropic and isothermal compressibilities are extremely negative. These results suggest that breaking the hydrogen bond network in water and forming the stronger hydrogen bonds between unlike molecules reduces the volume of the solution and makes the solution less compressible. The excess isobaric heat capacity is positive and large, up to 10 J-K^–1-mol^–1 and shows anomalous behavior in the neighborhood of x = 0.15.     

Molecular Structure of Complexes with Bifurcated Hydrogen Bond: II. Theoretical Study of Solvate H-Complexes Formed by the Cyclic Dimer of N-Methyltrifluoromethanesulfonamide

According to the DFT calculations (B3LYP/6-31G*), the structure of solvate complexes formed by N-methyltrifluoromethanesulfonamide with phosgene, formaldehyde, and DMSO and the mode of hydrogen bonding therein (two-center or bifurcate three-center) depend on the proton affinity of the onium base and composition of the complex. The 1 : 1 cyclic dimer–phosgene complex and 1 : 2 cyclic dimer–formaldehyde complex are stabilized by one or two bifurcated hydrogen bonds, respectively.     

Anisotropy of the van der Waals Configuration of Atoms in Complex,Condensed, and Gas-Phase Molecules

Anisotropic van der Waals (vdW) radii of 5b–7bsubgroup elements were determined from structures of gas-phase van der Waals complexes and crystal molecular compounds. The anisotropy of the van der Waals configuration of atoms was shown to decrease when going from isolated molecules to the condensed state. Variations in intermolecular distances, which are usually explained in terms of the formation of hydrogen bonds, are substantially governed by the anisotropic effect.     

Semi-empirical calculations on the structure of the oxonium ion in various crystal sites and relative acidity scale

The structure of the H₃O⁺ ion embedded in a solid environment (H₃O⁺X^–, X^– = Cl^–, NO ₃ ^– , ClO ₄ ^– ) is studied using a modified version of CNDO/2. In this calculation the effect of the first shells of nearest neighbours is taken into account and the effects of second nearest neighbours are introduced by a simulation procedure. Electronic effects are also included. The ion structure is more planar in nitrate than in perchlorate environment and the hydrogen bonds are slightly bent. Trends in structural parameters are compared with chemical properties of the hydrogen bonds and parallels the Hammett acidity scale HNO₃ < HCl < HClO₄.     

Cluster structures for water adsorbed on SiO2

The MO LCAO SCF method has been used in the MNDO approximation to examine the electronic structures and formation energies for adsorption complexes for water on SiO₂ stabilized by hydrogen and coordination bonds. Stabilization by several hydrogen bonds cannot explain the high initial heats of adsorption for dehydrated silica. H₂O coordination complexes give higher energies, and hydroxylated silicon atoms on SiO₂ are considered as primary water-adsorption centers.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 24, No. 5, pp. 532–545, September–October, 1988.