Heteroassociates Research Articles

Self and hetero-association in Benzaldehyde/Quinoline − Formamide solutions: Time Domain Reflectometry studies

The complex permittivity spectra of binary solutions of Benzaldehyde (PhCHO)/Quinoline (QUI) with Formamide (FMD) have been obtained at different mole fractions of FMD in the frequency range from 10 MHz to 30 GHz using the Time Domain Reflectometry (TDR) technique. The complex permittivity spectra have been fitted with Debye function. Dielectric relaxation time values have been interpreted in terms of the nature and size of the self and hetero associates of the binary solutions. The effective Kirkwood correlation factor (geff) has been correlated with closed and open associates of the solutions. The geff∼0.51 is the characteristic value of closed dimers. It appears that geff∼0.75 signifies the presence of both closed and open dimers. The Excess static dielectric constant (εE) shows negative deviation. The corrective Kirkwood correlation factor (gf) and Bruggeman factor (fB) have been used to investigate the strength of the H-bond interactions. The Geometry optimization has been carried out using Density Functional Theory (DFT) with B3LYP/6–311++G (d, p) basis set. Population analysis on the optimized geometries shows that PhCHO has 53.61 and 46.39 % closed and open geometries, respectively, while FMD has 17.11 % open dimers and remaining are closed dimers.

Glass formation mechanism in aqueous formic acid solutions

The glass-formation mechanism in the HCOOH–H2O system, which occurred at component molar ratios from 1:2 to 3:2, was studied by calorimetry and quantum chemistry. The results were analyzed and interpreted in light of the laws that guide the formation of stable H-bonded hetero associates in binary systems. The thermo analytical curves for 1:2, 1:1, and 3:2 glasses each showed three thermal events due to glass transition at about –130°С, crystallization, and melting of crystals. The structures and energy parameters were calculated in terms of density functional theory for polymeric chain moieties comprised of one or two types of the HCOOH⋅(H2O)2, (HCOOH)2⋅(H2O)2, and (HCOOH)3⋅(H2O)2 hetero associates. Glass formation was shown to occur precisely when [HCOOH]:[H2O] = 1:2–3:2 due to the ability of those hetero associates to be linked into strongly bonded, unlimitedly long polymeric chains. The energy parameters of 1:2, 1:1, and 3:2 samples derived from the calorimetric experiment were compared to those gained from the calculations of moieties that model polymeric structures in these samples, so all experimentally observed thermal events were interpreted at the molecular level. The glass-formation mechanism in the HCOOH–H2O system where the key role is played by hetero associates and not by individual molecules was elucidated.

Composition and Structure of Hydrates Formed in Aqueous Solutions of Formic Acid

IR spectroscopy and quantum chemical methods are used to study the features of hydration and determine concentration structural areas in the HCOOH-H2O system. Data on the composition and structure of stable heteroassociates (HA) formed in HCOOH aqueous solutions are obtained from the joint analysis of the IR spectra of these solutions and the results of quantum chemical calculations of (HCOOH)m·(H2O)n (m = 1−4, 6, n = 1−10, 14) and HCO 2 − ·(H2O)n (n = 2, 6) complexes. The sequence is established in which these complexes form when pure acid is diluted with water. For HCOOH concentrations from 100% to the ratio HCOOH:H2O = 1:1, all water molecules are involved in the most stable cyclic (HCOOH)2· (H2O)2 HAs with the C2 symmetry. The components of the equimolar solution are almost completely bound into such hydrates. For the HCOOH:H2O ratio ranging from 1:1 to 1:2, less stable (by ∼10%) cyclic HCOOH · (H2O)2 HAs form along with the (HCOOH)2 · (H2O)2 complexes. The solution with a twofold water excess consists of these hydrates. A further increase in the water concentration results in further hydration of HCOOH · (H2O)2 HAs.

Equilibrium Compositions of HF Solutions in N,N-Dimethylformamide

For HF solutions in DMF, concentration-dependent fractions of DMF molecules (α(DMF)) that remain unassociated and that enter heteroassociates (HAs) of 1 : 1, 4 : 1, and 12 : 1 molecular stoichiometries were obtained by two independent methods, namely, from an analysis of IR spectra and by calculating the material balance. The experimental way was shown to be enough exact in determining the ratio between the solvent molecules in four different states up to ~83 mol % HF. The equilibrium compositions of HF–DMF solutions were estimated over the entire range of concentrations. Starting with [HF] of ~25 mol %, more than one-half HF molecules are associated, and at [HF] of ~50–92 mol %, at least 90% of the HF molecules are associated. The equilibrium composition of HF–organic solvent (Solv) solutions in which HAs of 1 : 1, 1 : 4, and 1 : 12 molecular stoichiometries are formed, can be described by a single set of α(HF–Solv) versus concentration plots.

Composition and structure of hydrates of CH3COOH molecules and CH3CO2− anions in aqueous solutions

The optimal configurations, energy parameters, and normal vibrational frequencies of hydrates of the acetic acid molecule and anion (CH3COOH·(H2O) n (n = 1-10) and CH3CO2−⋅(H2O) n (n = 1-8, 16)) are calculated by density functional theory (B3LYP/6-31++G(d,p)). The comparison of the calculation results with the known experimental data (Raman, NMR, and so on) gives arguments in favor of the existence of two stable heteroassociates (HAs) in СН3СООН–H2O solutions: previously found CH3COOH·(H2O)2 heterotrimer and CH3COOH·(H2O)8, and three complexes (CH3CO2−⋅(H2O)2, CH3CO2−⋅(H2O)6, and CH3CO2−⋅(H2O)16) in NaCH3CO2−–H2O solutions. Each of them is most stable in a series of isomers, contains unstrained H bonds, and is characterized by the maximum molecular packing density among HAs with similar n values. The structure of the subsequent complex formed in solution uniquely follows the structure of the preceding complex and is based on it.

Structure of hydrogen fluoride complexes with diethylketone in a HF–Et2CO solution

The optimal configurations and the vibrational spectra of heteroassociates (HAs) of hydrogen fluoride and diethylketone molecules with 1:1, 2:2, 4:1, and 8:2 compositions are calculated using the density functional theory (B3LYP/6-31++G(d,p)). A comparison of the results of calculations and the known experimental data reveal that the following stable hydrogen-bonded molecular complexes are formed in HF–Et2CO solutions: the C2h symmetry cyclic heterotetramer (HF)2∙(Et2CO)2 and the tricyclic HA (HF)8∙(Et2CO)2 formed based on the heterotetramer by the binding of two (HF)3 moieties. It is shown that it is appropriate to decompose the spectral curve into the Gaussian functions or the Lorentzian functions to determine the frequencies and the integrated intensities of broad and overlapped IR bands. The first type of the decomposition enables one to estimate more correctly the values of the band frequencies, and the second type makes it possible to find more correctly the band intensities.

Quantum-сhemical analysis of geometric and energetic characteristics of hetero associates m9Ade•m1Ura in main tautomeric form

For the first time, on the quantum-mechanical level of theory MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p), a full set of hydrogen (H)-bonded hetero associates m 9 Ade·m 1 Ura in the main tautomeric forms consisting of 18 different structures was obtained. Their structural and energetical parameters were characterized and basic physical and chemi­cal characteristics of intermolecular H-bonds that stabilize the investigated complexes were described. It was shown that global minimum of Gibbs free energy corresponds to Hoogsteen pair, after it with a small margin follow Watson–Crick pair, inverse Hoogsteen pair and inverse Watson–Crick pair. It was found that in stabilization of identified hetero associates four types of H-bonds – NH...O, NH...N, CH...O and CH...N are involved. In this case non-canonical CH...O and CH...N bonds show a linear dependence of energy on electron density in the corresponding critical point. Obtained data may be useful for experimental interpretation of the features of non-canonical base pairs association by common methods of spectroscopy, including NMR and vibrational spectroscopy. They are also important for understanding the problem of mutational variability that is caused by formation of non-complementary pairs of nucleotide bases whose role is not clear yet. Keywords: quantum chemistry, hetero associates of nucleotide bases, hydrogen bonds, adenine, uracil.

Relationship between variously associated molecules in the HF-Et2CO solution

Data on the relationship between the molecules involved in various heteroassociates (HAs) and “free” molecules in the HF-Et2CO binary liquid system (BLS) are obtained by two independent methods: experimental and computational. The first method is applicable in the 0:1–6:1 molar range provided that the IR spectrum of the solvent molecule contains a band whose frequency and intensity can be measured when this molecule passes from the “free state” to the composition of all Has present in BLS. The second method is based on taking into account the material balance between the “free” molecules and molecules involved in various HAs of the solvent and HF. This method requires the knowledge of stoichiometric ratios of molecules in HAs and concentrations at which they appear in the solution. It is shown that in HF-Et2CO BLS, starting from the molar fraction of HF of ∼0.25, the majority of molecules is involved in the composition of the complexes, and at the molar fraction of HF of ∼0.50–0.92 already 90–100% of molecules of the solution form HAs.

Relationship between free molecules and molecules involved in various heteroassociates in HF-Me2CO solution

The experimental and computational methods to acquire the data on the relationship between free molecules and molecules involved in various heteroassociates (HA) in the HF—organic solvent binary liquid system (BLS) were developed and applied to the series of HF solutions in acetone. The first method is appropriate at the component molar ratios from 0 : 1 to 6 : 1 under the condition that the IR spectrum of the solvent molecule contains a band, whose frequency and intensity can be measured as the molecule passes from the free state to the composition of all HA formed in the BLS. The second method is based on the consideration of the balance between free molecules and molecules involved in HA of the solvent and HF. This method requires the knowledge of molar ratios of the components of the solution at which each HA appears in the solution. It is shown that in an HF-Me2CO solution the main part of the molecules is involved in the HA composition starting from the HF content ∼0.25 molar fraction, whereas 90–100% molecules are associated at an HF content of ∼0.50–0.93 molar fraction.

Structure of heteroassociates formed in the HF-(CH3)2CO binary liquid system

The vibrational spectra of a series of HF solutions in acetone (1:20–8.9:1) are analyzed with the help of special techniques. It is shown that three types of strong heteroassociates (HAs) with 1:1, 4:1, and ≥10:1 stoichiometric ratios of the molecules are formed in the HF-(CH3)2CO binary liquid system. The concentration ranges of the existence of HAs in the solution and the stretching vibrational frequency of their constituent HF molecules are estimated. The density functional method (B3LYP/6-31++G(d,p)) is used to calculate the optimal configurations and IR spectra of the (HF)m·((CH3)2CO)n molecular complexes (m = 1, 2, 4, 8, n = 1, 2) of different structure. The relative stability of the latter is studied. By comparing the calculated and experimental data, the composition (2:2 and 4:1) and structure of two types of HAs are determined.

Composition and structure of heteroassociates formed in the HF-N, N-dimethylformamide binary liquid system

The concentration dependence of the normalized (to the total number of moles of the components per liter) absorbance of HF solutions in DMF in ratios from 1: 12 to 7: 1 was analyzed. In the binary liquid system (BLS) under consideration, there are molecular complexes with stoichiometric ratios of 1: 1 and ≥10: 1 along with heteroassociates (HA) with the HF to DMF ratio of 4: 1, which have been found earlier. For each HA, the concentration range, in which HA is formed in BLS, was estimated, and the positions of the stretching bands of HF were determined. The optimal configurations and the vibrational frequencies of the molecular complexes (HF) m ·(DMF) n (m = 1, 2, 4, 8; n = 1, 2) with different topologies were calculated using the density functional theory (B3LYP/6-31++G(d,p)). The relative stability and structural features of the latter complexes were investigated. The complex formation in the HF-DMF system was analyzed. The structures of HA with stoichiometric ratios of 1: 1 and 4: 1 were determined by comparing the results of calculations and experimental data.

Using IR spectroscopy to determine the number of different heteroassociates in an HF-organic-solvent solution

Using the three binary liquid systems HF-(C2H5)2CO, HF-CH3CN, and HF-HCON(CH3)2 as examples, a simple method is proposed and tested for detecting stable heteroassociates (HAs) in solution and determining the number of various types of these HAs. When the variation of the vibrational frequencies of the multiple bonds of the solvent (Solv) molecules with the concentration of the solution was analyzed, it showed that the formation of various compositions of HAs is spectrally manifested by appreciable displacements (by about 15-170cm−1) of the CO(CN) vibration band. If the shape of this vibration remains approximately constant as the Solv molecule makes a transition from the pure solvent into the composition of the various types of associates, the corresponding frequency shifts have the same sign. A change in the shape of such a vibration when a solvent molecule is incorporated into any of the heterocomplexes can cause this sign to change.

Composition of heteroassociates formed in an HF-diethyl ketone liquid binary system

The IR spectra and solution densities in a binary liquid system (BLS) HF-diethyl ketone were measured for the first time upon variation of the component molar ratio from 1: 12 to 12: 1 and to 27: 1, respectively. Analysis of the concentration dependences of normalized (to the total number of moles of BLS components in 1 L) optical density and excess density of the solutions revealed the presence of 1: 1, 4: 1, and ∼12: 1 heteroassociates (HAs). For each associate, the concentration range in which it forms in the HF-(C2H5)2CO binary mixture was estimated. It was shown that, at component molar ratios from 2: 1 to 9: 1, all three types of HAs are present simultaneously.

Structure of heteroassociates formed in the HF-(C2H5)2O liquid system

The aim of this work was to determine the structure of stable heteroassociates (HAs) with the stoichiometric ratios 1:2, 2:1, and 4:1 of molecules formed in the HF-(C2H5)2O binary liquid system. The stretching frequencies of HF molecules found for each HA using a special procedure for processing IR spectra were compared with the calculated frequencies V HF of the stable molecular complexes (HF)m ((C2H5)2O)n (m = 1, 2, 4, 8; n = 1, 2) with different topologies by the density functional method (B3LYP/6-31++G(d,p)). As a result, it was shown that the most stable (among H-bonded complexes with the same stoichiometric ratio of molecules) HAs HF((C2H5)2O)2, (HF)4 ((C2H5)2O)2, and (HF)8-((C2H5)2O)2 formed in HF solutions in diethyl ether. All of them had a cyclic structure and a common peculiarity of structure: only one lone electron pair of the oxygen atom of the (C2H5)2O molecules is involved in hydrogen bonding.

Composition and structure of heteroassociates formed in a binary liquid system HF-CH3CN

The concentration dependence of normalized absorbance (to the total number of moles of components in one liter) of HF solutions in acetonitrile (1:12–10:1) is analyzed. It is found that in the binary liquid system (BLS) under study molecular complexes with stoichiometric 1:1 and ∼10:1 ratios of molecules occur along with the heteroassociates (HAs) found previously with the ratio HF:CH3CN of 4:1. For each of the HAs the concentration range at which it is formed in BLS is evaluated, and the positions of HF stretching vibrational bands are found. Optimum configurations and vibrational frequencies of molecular complexes (HF)m·(CH3CN)n (m = 1–6, n = 1–2) of various topology are calculated using the density functional method (B3LYP/6-31 ++ G (d, p)). Their relative stability and the structure peculiarities are studied; complexation tendencies in the HF-CH3CN system are revealed. The structure of HAs with 1:1 and 4:1 stoichiometric ratios of molecules is determined by comparing the results of calculations and experiment.

PM6 quantum chemical study of the H-bonded and stacked associates of the adenine and thymine DNA bases: The nature of base stacking

The planar H-bonded adenine-thymine (A • T) base pair and four stacked hetero associates (A/T) of these bases in a cluster containing 200 water molecules were studied by the new semi-empirical PM6 method. The formation of the planar A • T base pair in the water cluster was found to be energetically unfavourable, primarily due to the destabilising contribution of the base-water interactions. Under complete geometry optimisation, the planar A • T base pair converted into a nonplanar propeller-twisted and buckled associate. In contrast, the formation of all stacked dimers studied was found to be favourable, with formation energies ranging from −11 to −20 kcal/mol. The preference for the formation of these stacks results from the favourable change in the water structure and distortion of the paired and isolated bases during the base association reaction.

Composition of heteroassociates formed in HF-pyridine and HF-formamide binary liquid systems

The IR spectra and the densities of solutions in HF-pyridine and HF-formamide binary liquid systems were measured over a wide range of mole ratios HF: Solv (Solv is the organic solvent). The composition of heteroassociates (HA) formed in these systems was determined by analysis of the concentration dependences of normalized (to the total number of moles per 1 L) optical density in the IR region and the excess density of the binary mixtures under study. The HA with the stoichiometric ratio 3: 1 are present in the HF-Py system at all studied mole ratios of the components (from 1: 12 to 20: 1). The 1: 2 HA were found in the dilute solutions, whereas the >6: 1 HA were revealed in the concentrated solutions. The HA with the stoichiometric ratio 4: 1 were found in HF-formamide system. The results obtained were compared with the known data on the composition of HA formed in the binary liquid systems HF-DMF, HF-Me2CO, and HF-MeCN.