Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

The complexes formed via hydrogen bonding interactions between cysteine and propanoic acid have been studied at the density three-parameter hybrid functional DFT-B3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis was employed to elucidate the interaction characteristics in cysteine–propanoic acid (Cys–Prop) complexes. More than 10 kinds of hydrogen bonds (H-bonds) including intra- and inter-molecular H-bonds have been found in Cys–Prop complexes. The results show that both the strength of H-bonds and the deformation are important factors for the stability of Cys–Prop complexes. The strongest H-bonds (O2H^A···O1^B and O2H^A···O1^B) exist in the most stable Cys–Prop complex. The stronger H-bonds formed between hydroxyl and O (or N) atom usually stronger than those involve C (or S) atom. Relationships between the electron density (ρ) of BCP and H-bond length as well as the Fock matrix element (F _ij) has also been investigated and used to study the nature of H-bonds. Moreover, the results show that the change of the bond length linearly correlates with the corresponding frequency shift.     

Hydrogen-Bonding Interaction in a Complex of Amino Acid with <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dimethylformamide Studied by DFT Calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine and leucine) and N,N-dimethylformamide (DMF) in gas phase have been carried out using density functional theory (DFT) and ab initio calculations at the B3LYP/6-311++G** and MP2/6-311++G** theory levels. The structures, binding energy, stretching frequency and bond characteristics of the mentioned complexes were calculated. The NH₂ and COOH groups of amino acids form different types of hydrogen bonds with the DMF molecule, as well as alkyl side chains. High binding energy suggests multiple hydrogen bonds present in one complex. The nearly linear OH???O and NH???O contacts are stronger than a conventional hydrogen bond interaction with their H???O separation between 1.74 and 2.14 Å. The weaker CH???O H-bond is also discussed as being a crucial interaction in biological systems involving amino acids. The formation of this interaction results in a blue shift in the CH stretching frequency.     

Theoretical study on dimers of 2,6-diamino-3,5-dinitropyridine and its <Emphasis Type="Italic">N</Emphasis>-oxide

First-principle calculations are performed on the dimers of 2,6-diamino-3,5-dinitropyridine (ANPy) and its N-oxide (2,6-diamino-3,5-dinitropyridine-1-oxide, ANPyO). The dimers as well as the monomers are fully optimized by the DFT-B3LYP and HF methods in conjunction with 6-311G**, 6-311++G**, and cc-pVDZ basis sets. The N-O bond length of the pyridine N-oxide moiety decreases in the ANPyO dimer in the dimerization process, which results in a larger deformation energy of the ANPyO submolecule. This deformation prevents the submolecules from further close contact and the formation of strong H-bonds between the nitro and amino groups. The optimized intermolecular distances of the ANPyO dimer are in good agreement with the corresponding experimental values. There is a weak C-H...O hydrogen bond in the ANPyO dimer; the B3LYP method underestimates its binding energy. On the contrary, for the ANPy dimer, the binding energy obtained at the B3LYP level is larger than that obtained at the HF level. The individual O...H strength is stronger in the ANPy dimer than that in ANPyO, which is consistent with the O...H distance. The O...H-C type of the H-bond is stronger in the ANPyO dimer than the ordinary O...H-C bond due to the N-oxide oxygen atom bearing larger negative charges. The corrected binding energy for each hydrogen bond between nitro oxygen and amino hydrogen is about −5 kJ/mol in the ANPy dimer, which is stronger than that in the ANPyO dimer.     

Density functional theory and topological analysis on the hydrogen bonding interactions in N-protonated adrenaline–DMSO complexes

In this study, complexes formed via hydrogen bond interactions between N-protonated adrenaline (AdH⁺) and DMSO have been studied by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the hydrogen bonds (H-bonds) have been systematically investigated. The natural bond orbital (NBO) and the quantum theory of atoms in molecule (QTAIM) analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. The H-bonds involving amino or hydroxyls as H-donor are dominant H-bonds in complexes and are attributed to strong H-bonds. The weak H-bonds, such as π H-bonds and H-bonds involving methyl (DMSO) or methenyls (C2H6 and C5H7 of AdH⁺) as H-acceptors, were found in complexes as well. The complexes in which the dominant H-bond involves amino of AdH⁺ as H-donor are more stable than those with the dominant H-bond involving hydroxyls as H-donor. Some relationships between various properties of QTAIM, NBO, geometry as well as frequency were also investigated.     

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH<Subscript>3</Subscript>OH)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 2–8) clusters

The (CH₃OH) _n (n = 2–8) clusters formed via hydrogen bond (H-bonds) interactions have been studied systemically by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the intermolecular OH···O H-bonds have been investigated. The quantum theory of atoms in molecule (QTAIM) and natural bond orbital (NBO) analysis have also been applied to understand the nature of the hydrogen bonding interactions in clusters. The results show that both the strength of H-bonds and the deformation are important factors for the stability of (CH₃OH) _n clusters. The weakest H-bond was found in the dimer. The strengths of H-bonds in clusters increase from n = 2 to 8, moreover, the strengths of H-bonds in (CH₃OH) _n (n = 4–8) clusters are remarkably stronger than those in (CH₃OH) _n (n = 2, 3) clusters. The small differences of the strengths of H-bonds among (CH₃OH) _n (n = 6–8) clusters indicate that a partial covalent character is attributed to the H-bonds in these clusters. The linear relationships between the electron density of BCP (ρ_b) and the H···O bond length of H-bonds as well as the second-perturbation energies E(2) have also been investigated and used to study the nature of H-bonds, respectively.     

Interaction and Scale of Mixing in Cellulose Acetate/Poly(<Emphasis Type="Italic">N</Emphasis>-vinyl Pyrrolidone-co-vinyl Acetate) Blends

Binary blends and pseudo complexes of cellulose acetate (CA) with vinyl polymers containing N-vinyl pyrrolidone (VP) units, poly(N-vinyl pyrrolidone) (PVP) and poly(N-vinyl pyrrolidone-co-vinyl acetate) [P(VP-co-VAc)], were prepared, respectively, by casting from mixed polymer solutions in N,N-dimethylformamide as good solvent and by spontaneous co-precipitation from solutions in tetrahydrofuran as comparatively poor solvent. The scale of miscibility and intermolecular interaction were examined for the blends and complexes by solid-state ¹³C-NMR spectroscopy. It was revealed that the formation of complexes was due to a higher frequency of hydrogen-bonding interactions between the residual hydroxyl groups of CA and the carbonyl groups of VP residues in the vinyl polymer component. From measurements of CP/MAS spectra and proton spin-lattice relaxation times (T_1ρ^H) in the NMR study, the existence of the hydrogen-bonding interaction was also confirmed for the miscible blends and the homogeneity of the mixing was estimated to be substantially on a scale within a few nanometers.     

Crystal structures of [Hg(<Emphasis Type="Italic">N</Emphasis>-ethylthiourea)<Subscript>2</Subscript>(CN)<Subscript>2</Subscript>] and [Hg(<Emphasis Type="Italic">N</Emphasis>-propylthiourea)<Subscript>2</Subscript>(CN)<Subscript>2</Subscript>]

Two mercury(II) cyanide complexes of N-ethylthiourea (Ettu) and N-propylthiourea (Prtu) ligands, [Hg(Ettu)₂(CN)₂] (1) and [Hg(Prtu)₂(CN)₂] (2), were prepared and their crystal structures were determined by X-ray crystallography. In both structures, the mercury atom is coordinated to two sulfur atoms of thioureas and two cyanide carbon atoms in a pseudo-tetrahedral mode with the bond angles in the range of 90.52(11)–162.2(3)°. The structures are stabilized by N-H—S, N-H—N, and C-H—N intramolecular and intermolecular hydrogen bonds.     

Interaction of <Emphasis Type="Italic">L</Emphasis>-cysteine with selenious and selenic acids: A study by the density functional theory method

Using the density functional theory method at the B3LYP/6-31G(d,p) theory level, the formation of hydrogen bonded complexes of L-cysteine with selenious and selenic acids is studied. In both cases, complexes formed through the carboxyl group of cysteine mostly arise, their enthalpy of formation being of -19kcal/mol to -21 kcal/mol and the free energy of -6kcal/mol to -9kcal/mol. The primary act of interaction in the system of hydroxyl-containing selenium compound — α-aminoacid, including the mutual orientation of reactant molecules and the formation of intermolecular hydrogen bonds is likely to a serve as prerequisite for the thiol group to be able to participate in the next stages (including deeper chemical transformations) of biologically significant reactions.     

Intermolecular interactions in orthophosphoric acid-<Emphasis Type="Italic">N,N</Emphasis>-dimethylformamide system according to viscometric data

The viscosity of an orthophosphoric acid—N,N-dimethylformamide system was measured in the whole region of compositions at 298–338 K. An excess viscosity of the system was analyzed by the data obtained using different model concepts. Calculations suggested that strong intermolecular interactions and the formation of complexes (H₃PO₄)₂·DMF occur in the system. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2252–2256, October, 2005.     

A New Rare-Earth Metal Coordination Polymer Constructed from <Emphasis Type="Italic">N</Emphasis>-hetero Aromatic Multicarboxylate Ligand

Abstract  

The hydrothermal reaction of Gd(NO₃)₃·6H₂O with 2,2′-bipyridyl-4,4′-dicarboxylic acid(H₂BPDC) ligand results in the formation of a new Gd(III) polymer: {[Gd₂(BPDC)₃(H₂O)₃]·H₂O} _n..(1). The central gadolinium ion is coordinated by eight oxygen atoms to give a dicapped triangular prism geometry. Based on the versatile coordination modes of BPDC²⁻ ligand, together with hydrogen bonds and π···π stacking interactions, a 3-D network is presented. DFT calculation was executed to probe the electronic structure of 1.     

Redox Behavior of Neptunium(V) in Tributyl Phosphate and <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dihexyl Octanamide Extractants Dissolved in <Emphasis Type="Italic">n</Emphasis>-Dodecane

Spectrophotometric investigations have been carried out on the disproportionation of Np(V) to form Np(IV) and Np(VI) in 1.1 mol⋅L⁻¹ solutions of tributyl phosphate (TBP) and in N,N-dihexyl octanamide (DHOA) in n-dodecane medium. The Np(V) was found to coordinate with Np(IV) in 1.1 mol⋅L⁻¹ TBP solution in n-dodecane to form a mixed valence “cation–cation” complex by bonding through an axial oxo group on Np(V). By contrast, this interaction was less prominent in the case of 1.1 mol⋅L⁻¹ DHOA solutions. The effect of 1-octanol, added as phase modifier, on the disproportionation behavior of Np(V) was also investigated. An attempt was made to calculate the disproportionation/reduction rate constants for Np(V) under the conditions of these studies. Absorbance measurements on the Np stripped from organic phases revealed the occurrence of Np(V) in the aqueous phase.     

<Emphasis Type="Italic">Z</Emphasis>-and <Emphasis Type="Italic">E</Emphasis>-conformers of <Emphasis Type="Italic">N</Emphasis>-chloroacetylcytisine

N-Chloroacetylcytisine was synthesized by acylation of (–)-cytisine. Stable Z- and E-conformers with respect to rotational isomerism around the N-12–CO bond were found in PMR spectra at room temperature. The point at which PMR resonances of the Z- and E-conformers coalesced upon heating was measured. The transition barrier between the conformers was estimated.     

Synthesis and properties of <Emphasis Type="Italic">O,O</Emphasis>-dialkyl [1-hydroxy-3-(dialkylamino)-2,2-dimethylpropyl]phosphonates

O,O-Dialkyl [1-hydroxy-3-(dialkylamino)-2,2-dimethylpropyl]phosphonates were prepared for the first time. By means of NMR ¹H, IR spectroscopy and quantum-chemical calculations the presence in them of various H-bonds was established. In the crystalline state P=O…HO intermolecular hydrogen bonds favor the formation of cyclic dimer associates D _P=O. In the liquid state and concentrated solutions P=O…HO and N…HO intermolecular hydrogen bonds cause the formation of cyclic dimer associates D _P=O and D_N, and intramolecular hydrogen bonds provide the existence of different conformations of the monomer form MN, the most stable among them with the non-strained six-membered …NCCCOH… ring.     

Conformational Polymorphism in Racemic 2,4-Di-<Emphasis Type="Italic">o</Emphasis>-Benzoyl-6-<Emphasis Type="Italic">o</Emphasis>-Tosyl <Emphasis Type="Italic">myo</Emphasis>-Inositol 1,3,5-Orthoacetate

The title compound, C₂₉H₂₆O₁₀S, yields two conformational polymorphs concomitantly from dichloromethane-methanol mixture; the major polymorph grows as plates (Form I, monoclinic, P2₁/n) and the minor polymorph grows as needles (Form II, triclinic, P-1). The two forms differ mainly in orientation of the tosyl group. In Form I, sulfonyl oxygen of the tosyl group makes intermolecular C −H…O interactions, whereas the same group in Form II is involved in an intramolecular short dipolar S=O…C=O (sulfonyl-carbonyl) contact. The molecular organization and the influence of various weak non-covalent interactions that stabilize these conformers in the crystal lattices are discussed.     

Synthesis,characterization and X-ray crystal structures of <Emphasis Type="Italic">N</Emphasis>-2-pyridinyl carbonyl-2-pyridine carboximidate copper(II) complexes

Two copper complexes, [Cu(bpca)(4,4′-bpyH)(H₂O)(ClO₄)]ClO₄·H₂O (1) and [Cu₄(bpca)₄(mpba)]·3H₂O (2) [bpca = N-2-pyridinylcarbonyl-2-pyridine-carboximidate; mpba = 1,3-phenylenebis(oxamate)] were synthesized and characterized by physico-chemical and spectroscopic techniques. Complex 1 crystallizes in the Triclinic P-1 space group while complex 2 is in the Monoclinic space group C2/c. Bpca acts as a tridentate ligand through its three nitrogen atoms in these species. They exhibit 2D supramolecular architectures through hydrogen bonds and short-distance intermolecular interactions. Magnetic measurements in the range 2–300 K have shown weak antiferromagnetic interactions between the adjacent copper ions in complex 2. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Studies on a New Binuclear Tungsten(IV)-pterin Complex Showing Reactivity Towards Trimethylamine <Emphasis Type="Italic">N</Emphasis>-oxide

The new compound [W₂^IVOCl₂L₂] · DMF (2) has been synthesized by a redox reaction between WOCl₄ and 2-pivaloylamino-6-acetonylisoxanthopterin (H₂L, 1) in DMF medium. It bas been characterized by elemental analysis, spectroscopy and electrochemistry. Its reactivity towards Me₃N → O has been followed both kinetically and stoichiometrically. The reaction follows substrate saturation kinetics and a large negative entropy of activation value points towards involvement of an associative mechanism. ¹H-n.m.r. and c.v. data throw light on the role of a redox ‘non-innocent’ pterin ligand (1), in conferring reducing properties on the W(IV) atoms of (2).     

Composition and structure of heteroassociates formed in the HF-<Emphasis Type="Italic">N,N</Emphasis>-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.     

Thermal decomposition of new ruthenium(II) complexes containing <Emphasis Type="Italic">N</Emphasis>-alkylphenothiazines

Thermal decomposition of chlorpromazine hydrochloride (CP·HCl), trifluoperazine dihydrochloride (TF·2HCl) and thioridazine hydrochloride (TR·HCl), and the ruthenium complexes with dimethyl sulfoxide (dmso) of composition [RuCl₂(dmso)₄] and L[RuCl₃(dmso)₃]·xEtOH, L = CP·HCl, TF·2HCl or TR·HCl is described. The phenothiazines are stable to temperature range of 200–280 °C with an increasing stability order of TF·2HCl < CP·HCl < TR·HCl. The decomposition of all the compounds takes place in superposing steps. For detection of chlorides and sulfides, EGD analysis was performed. The decomposition pattern of the complexes, due to their similar structure, is similar. The thermal data unambiguously resolve the contradiction between the elemental analysis and X-ray structural data for (TF·2HCl)[RuCl₃(dmso)₃]Cl·EtOH. The compound crystallizes with one EtOH, evaporating in part at room temperature.     

Aggregation in isomeric imides: analysis of the weak interactions in six <Emphasis Type="Italic">N</Emphasis>-(benzoyl)-<Emphasis Type="Italic">N</Emphasis>-(2-pyridyl)benzamides

Crystal structures of 4-chloro-N-(4-chlorobenzoyl)-N-(2-pyridyl)benzamide (I) Clpod, 3-chloro-N-(3-chlorobenzoyl)-N-(2-pyridyl)benzamide (II) Clmod and 2-chloro-N-(2-chlorobenzoyl)-N-(2-pyridyl)benzamide (III) Clood together with three methylated analogues, Mpod, Mmod and Mood, are presented herein. The Clxod acyclic imides are produced from reacting the 4-/3-/2-chlorobenzoyl chlorides (Clx) with 2-aminopyridine (o), respectively, together with their benzamide analogues Clxo; the Mxod/Mxo triad are produced similarly and in good yield. The five Clxod, Mpod and Mmod structures adopt the open transoid conformations as expected, but Mood crystallises with cisoid oriented benzoyl groups, and this conformation was unexpected, though not unknown. Halogen bonding contacts and weak hydrogen bonding C-H···N/O/π contacts are noted in the structures lacking strong hydrogen bonding donor atoms/groups but possessing a variety of strong and weaker acceptor atoms/groups. For Clxod, contact studies show that both hydrogen and carbon account for a high percentage of elements (70–75%) on the molecular surface and being the most abundant have C···H forming 26–30% of the contacts. Contact enrichment ratios are an indicator of the likelihood of chemical species to form intermolecular interactions with themselves and other species. The C-H···N and C-H···O are the most enriched (with E_HN?>?2.15), indicating that these weak hydrogen bonds are the driving force in the Clxod crystal packing formation. For Mxod, the C···H contact type at 40–52% is the most abundant contact type and C-H···O and C-H···N weak hydrogen bonds dominate with enrichment values in the 1.48–1.78 range. In Mxod, N/O···N/O contacts are effectively absent, except for Mpod (0.2%, N···N contacts) and both H···H and C···C non-polar contacts are moderately impoverished while the C···H interactions are slightly enriched (E?=?1.1–1.21).     

Thermochemical study on ternary complex of dysprosium <Emphasis Type="Italic">m</Emphasis>-nitrobenzoic acid with <Emphasis Type="Italic">o</Emphasis>-phenanthroline

A ternary binuclear complex of dysprosium chloride hexahydrate with m-nitrobenzoic acid and 1,10-phenanthroline, [Dy(m-NBA)₃phen]₂·4H₂O (m-NBA: m-nitrobenzoate; phen: 1,10-phenanthroline) was synthesized. The dissolution enthalpies of [2phen·H₂O(s)], [6m-HNBA(s)], [2DyCl₃·6H₂O(s)], and [Dy(m-NBA)₃phen]₂·4H₂O(s) in the calorimetric solvent (V_DMSO:V_MeOH = 3:2) were determined by the solution–reaction isoperibol calorimeter at 298.15 K to be \Updelta_\texts H_\textm^q \Updelta_{\text{s}} H_{\text{m}}^{\theta } [2phen·H₂O(s), 298.15 K] = 21.7367 ± 0.3150 kJ·mol⁻¹, \Updelta_\texts H_\textm^q \Updelta_{\text{s}} H_{\text{m}}^{\theta } [6m-HNBA(s), 298.15 K] = 15.3635 ± 0.2235 kJ·mol⁻¹, \Updelta_\texts H_\textm^q \Updelta_{\text{s}} H_{\text{m}}^{\theta } [2DyCl₃·6H₂O(s), 298.15 K] = −203.5331 ± 0.2200 kJ·mol⁻¹, and \Updelta_\texts H_\textm^q \Updelta_{\text{s}} H_{\text{m}}^{\theta } [[Dy(m-NBA)₃phen]₂·4H₂O(s), 298.15 K] = 53.5965 ± 0.2367 kJ·mol⁻¹, respectively. The enthalpy change of the reaction was determined to be \Updelta_\textr H_\textm^q = 3 6 9. 4 9 ±0. 5 6   \textkJ·\textmol ^{- 1} . \Updelta_{\text{r}} H_{\text{m}}^{\theta } = 3 6 9. 4 9 \pm 0. 5 6 \;{\text{kJ}}\cdot {\text{mol}}^{ - 1} . According to the above results and the relevant data in the literature, through Hess’ law, the standard molar enthalpy of formation of [Dy(m-NBA)₃phen]₂·4H₂O(s) was estimated to be \Updelta_\textf H_\textm^q \Updelta_{\text{f}} H_{\text{m}}^{\theta } [[Dy(m-NBA)₃phen]₂·4H₂O(s), 298.15 K] = −5525 ± 6 kJ·mol⁻¹.