Specific Intermolecular Interactions of Nitrogenated and Bioorganic Compounds

The hydrogen bond is caused by an additional interaction between a covalently bonded hydrogen atom and a more electronegative atom of the same group or any other molecule. Thus, the purely covalent bond leads to a situation of equal sharing of electrons by the interacting hydrogen atoms in an Н₂ molecule; only in this case the degree of socialization is 50 % [1]. Preferential shifting of the electron density to the atom of the element interacting with the hydrogen atom, i.e. polarization, provides the molecule with an ionic component. Acting in the covalent bond, the electric forces of the nuclear electron interaction and the magnetic forces, together with electrostatic forces of atoms attractingwith opposite charges, correlate with interatomic distances of atoms in the molecule (in the X–H bond distance), and this is observed in the fundamental X–H stretching vibration frequencies [2]. A practically similar definition of the hydrogen bond is given in Pauling’s monograph titled “The Nature of the Chemical Bond” [3].

Among modern ideas, controversies on the n-orbital of the ammonia molecule are reflected on the photoelectron spectra of amino-derivative compounds [1–3]. Violation of the nuclear framework of the molecules of noncyclic alkyl compounds in the range of the trigonal pyramid to plane ones with removal of the n-electron leads to a wide oscillatory circuit of the first FE-bands, which appears at the intramolecular and intermolecular interactions. As a result a change in the coordinating ability of the nitrogen atom takes place and the specific interactions gain thermal stability . Despite the great number of papers on photoelectron spectra the best conformity with inclusion of the vertical ionization potential Iv has been established for the mono-substituted methylamine. It means that the maximum value in thermodynamic construction and specificity of the intermolecular interaction should be reflected precisely in this connection. It was shown above that all linked vacancies of the molecules close to the environment in liquid ammonia are realized in a coordinated state with six nitrogen atoms with the location of the hydrogen atoms on top of the trigonal pyramid (Fig. 2.1), forming a similar structure at the interaction of the nitrogen atom of the ammonia molecule in contact. Hydrogen atoms or alkyl groups of the pyramid base of the interacting molecules are located at maximum distance, which is never reached because their locations relative to each other are not symmetrical. Regarding the productivity of this approach we note that for reliable determination of changes of Н-cohesion of a molecule in condensed condition one should indicate changes in coordination when changing the structure of ammonia and all amino-derivative compounds on planar structure with the nitrogen atom, acting as coordinating center in, for example, hydrazones . The equivalence of all six hydrogen bonds of one type and its gap in the transition of the ammonia molecule to steam allows the use of enthalpy characteristics of the corresponding process to determine the energy of the hydrogen bonds in the condensed state. It follows that the energy of the Н-bond N–H•••N is equal to the quotient of the sublimation enthalpy and evaporation of the number of realized hydrogen bonds [4–6]. The results of the calculation performed show reduced stability of the hydrogen bond, formed by the nitrogen atom of the ammonia molecule with the structure of a trigonal pyramid (4.23 and 3.86 kJ mol⁻¹), being less stable compared with coordination of the four hydrogen atoms (6.34 and 5.91 kJ mol⁻¹) with planar structure of the molecule in solid and liquid states, respectively.

The thermodynamic properties of processes of vaporization of cyclic compounds with saturated and unsaturated cycles and nitrogen atoms in the functional group, established at a standard temperature, are known for a limited number of compounds (Table 3.1). Nevertheless it allows us to find the role of the specific interactions Н₂С → СН₂, Н₂С → H–СН, НС → СН and НС → Н–С, formed by relevant groups СН₂, СН of the carbon-hydrogen cycles in the energy of the formed specific interaction D≡N → C≡ by the cyanide group –C≡N and the hydrogen bond of the amino group.

In Sect. 3.1 we mentioned that the amino В3МО shows an antibonding influence, which destabilizes its N2s-H1s overlap [1]. At the same time, transmission of the electron density from the 3p_z-orbital of the nitrogen atom to the 1s-orbital of hydrogen atom or, for a significantly undivided 2s² electron pair of carbon atoms, respectively, a corresponding reduction in its charges, and the stability of specific interactions reflects the manifestation of the reverse dative bond.

Piperidine molecules and their derivatives with methylene groups and hetero cyclic nitrogen atoms, connected with the hydrogen atom, are influenced by the latter by the shifting of the electron density in comparison with pyridines. The nitrogen atom of piperidine gets electron density from the hydrogen atom of the amino group and contacting by carbon atoms С(2)Н₂ and С(6)Н₂, reducing its negative charge and reaching the increased electron density at its own 3p_z-orbital [1–5]. However, the further formation by the same nitrogen atom of the reverse dative bond is accompanied by the transmission of part of the electron density from this orbital to the essentially unshared 2s² electron pair of the carbon atoms. As a result, there appears a reduction of its own negative charge and relative enrichment of the electron density of the carbon atoms С(2) and С(6) of the methylene groups, of which charges differ from the charges of the carbon atoms С(3), С(5) and, of course, С(4). It follows that the nitrogen atom contributes to a definite change in the charges of all five carbon atoms of the piperidine molecule. Thus, each of the five free bond vacancies of the essentially unshared 2s² electron pair of the carbon atoms of the methylene group of piperidine forms the specific interaction D–H₂C → CH₂, contributing to the vaporization enthalpy being equal to the contribution of the СН₂ group, the energy value (5.70 kJ mol⁻¹) of which is identical to the energy of the realized similar specific interaction in liquid cyclopentane (Table 3.​1). This value of the energy of the specific interaction formed by the methylene group is slightly higher than the energy of the specific interaction formed by the benzene СH-group (5.63 kJ mol⁻¹). It directs attention to the fact that differences of the structure of МО pyridine С₅Н₅N as regards symmetry positions are insignificant compared to the electron structure of the benzene molecule and, consequently, cyclohexane, splitting e(σ) –MO at a ₁ + b ₂, e(π) – at а ₂ + b ₁ and transforming one а ₁ (σ) –orbital of radial type to the n-orbital [6, 7]. It follows that the accepted assumption of the energy contribution by the methylene group of cyclohexane for conducting thermodynamic calculations of the energies of the specific interactions of piperidine, piperazine, and their derivatives is correct and grounded. The rule of using the energy contributed by the СН group of benzene to the enthalpy characteristics of the vaporization process of pyridine and its derivatives is also correct.

Methoxyamines and ethoxyamines are the simplest hetero compounds with two hetero atoms of oxygen and nitrogen. The thermodynamic properties are known for a small number of these acyclic and cyclic compounds; however, one is interested in the diversity of the realized types of specific interactions in their condensed condition. Shifting of the electron density at the carbon atoms of the methyl groups leads to an insignificant negative charge [1–3], reducing the positive value as a result of the intermolecular reverse dative bond [4–8]

The simplest oxazole molecules and its derivatives with two hetero atoms in the cycle exclude the possibility of understanding the specificity of the formed interactions with the use of ideas of sp³-hybridization [1–7]. The increased ability of the oxygen atom to shift of the electron density predetermines the increased positive charge of the carbon atom, at location С(2), located between these atoms. Therefore, the interaction of the oxygen atom with carbon atoms at locations С(2) and С(5) leads to the four interactions of one type, D–O → CH, in the structure of liquid oxazole with the network of specific interactions with increased stability

According to modern ideas about the configuration N,N-hydroxylamine and its derivatives n_N(5a′)-nσ (2a″)-orbital are orthogonal [1], which reflects the character of n_N- and nσ-electrons of vibration band contours. The replacement of the hydrogen atom by the methyl group pushes n-orbitals up to the values of the vertical ionization potentials 1.45 and 1.83 eV, leading to convergence of ОН-groups up to 0.47 eV [1–3]. Such significant changes in the electron configuration of the alkyl derivatives of hydroxylaminе should be expressed at the energies of the hydrogen bonds and the formed specific interactions and are supposed to be at higher energies of D–N•••H–N connections in H₂N–OH in comparison with the realized specific interactions of D–N → CH₃–N. As we mentioned earlier, that an insignificant reduction of the electron density at the nitrogen atom when replacing a hydrogen atom with the ethyl group was found using X-ray electron spectroscopy [4, 5].

The thermodynamic properties of important proteins amino acids have been studied a little in recent decades and the enthalpy and entropy values of the vaporization processes are still known for only a few (Table 9.1). These properties, along with the melting temperature carry important information because the process of phase transformation, with its chemical nature [1–3], is interconnected with the number of severe bonds and their energies. Therefore, even the melting temperature reflects the depth of the transformation of the crystal structure and its difference from the structure of the liquid condition [1–3]. On the basis of these ideas we have reasons to discuss the increase of the melting temperature of alanine at 2° in comparison with the same property of glycine amino acetic acid connected with stabilization of the same type of specific interaction. This stabilization is caused by the contribution to the structure of alanine of the methyl group, implementing the functional properties of the isostructural group, participating in the redistribution of the electron density in the molecule. Further replacement of the methyl group by the fragment СН₃(СН)СН– in the molecule of l-valine and СН₃(СН)СН–СН₂– in the molecule of d-(l)-leucine is accompanied by stabilization of the specific interaction, formed by these fragments with the oxygen atom of the hydroxyl group of the glycine fragment D–O → CH₃(CH₃)CH– < D–O → CH₃(CH₃)CH–CH₂–. Such a sharp reduction of the melting temperature of isoleucine points to the implementation of theethyl ligand with regard the functional properties of the isostructural group. Reduced melting temperatures of diacids l-ashartic and l-glutamic acids reflect the reduction of the energies of the hydrogen bonds with an increasing number of carboxyl groups and the significant change in the difference in the charges at the oxygen and hydrogen atomsof the hydroxyl groups. The hydrogen bonds introduced in a new type at asparagine and glutamine with reduced energy values, formed by the amide group D–O•••H–N > D–N•••H–N, and methylene groups, fringed by the amide groups, are responsible for the reduction of the melting temperature. In turn, the increasing number of methylene groups, fringed by the same amide groups, causes the reduction of the melting temperatures of the mentioned diacids in the sequence asparagine – glutamine. Similar changes in the energies of the specific interactions formed of crystalline and liquid dl-threonine, l-cysteine, l-arginine, and other compounds reflect the melting temperature of important protein amino acids. The insolubility of α-amino acids in hydrocarbons and ethers points to the high stability of the hydrogen bonds formed and the water solubility of most acids in this range indicates the comparability of the energies of the hydrogen bonds with a similar bond with water molecules (10.99 kJ mol⁻¹) [6].

Derivatives of amino acids are used as model compounds, reflecting the nature of polypeptides and proteins [1–3]. Therefore the analog of structures of these acids, simple peptides, dipeptides, and polypeptides, allow us to conduct a correct thermodynamic analysis of each series of compounds, using the enthalpy characteristics of the processes of vaporization and sublimation to obtain the energies of the hydrogen bonds and the specific interactions, formed in its liquid and crystalline conditions.

The derivatives of the β-tautomer (isourea) are characterized by strong basic properties, forming ions H₂NCON₃ ⁺ and H₂NC(NH)O⁻ in a water environment [1]. “Pure” crystalline urea is a mixture of mono crystals with a tetragonal system, the lattice constants of which belong to the structural class P42₁m, Z = 2(mm²), and have the values a = 0.5645, b = 0.5645, and c = 0.4704 nm [2]. The crystalline structures of urea have the shapes of needles and stratiforms, the layers of which consist of plane prisms, formed by peptide (amide) bonds >С=О•••Н–N< [1]. The urea molecule has a planar structure with a sufficiently strong electric moment of dipole μ = 4.6 D or ≈ 15.3•10⁻³⁰ cm at 298 K [3] owing to the asymmetric distribution of the density of n- and π-bonding electrons.