Nonvalent Interactions Research Articles

The non-covalent interaction between C3N and H2

Non-covalent interactions play an important role in numerous fields, particularly in physical hydrogen storage. The hydrogen storage properties of C3N are investigated by DFT calculations. The results indicated that H2 and C3N form physical adsorption. The electronic structure analysis demonstrates that both the covalent and electrostatic interactions between H2 and C3N are rather weak, while IRI analysis reveals that their interactions belong to non-valent interactions, and the further energy decomposition based on SAPT suggests that the sources of interaction energies differ for the two configurations TCR and TNR. For TCR, the induction energy is the primary contributor, for TNR, the electrostatic interaction dominates. Our comprehensive study not only enhances our understanding of the intricate interactions between H2 and C3N but also serves as a valuable guide for enhancing the adsorption strength in physical hydrogen storage systems.

Dibenzoxanthene-β-lactam hybrids as potential antioxidant and anticancer agents: Synthesis, biological evaluation, and docking study

In this study, we designed and synthesized a series of β-lactam compounds bearing 14-phenyl-14H-dibenzo[a,j]xanthene moiety attached to the N-1 position of the β-lactam ring through a [2 + 2] cycloaddition process. All the synthesized compounds have been characterized by elemental analysis, Fourier-transform infrared (FT-IR) and nuclear magnetic resonance (1H NMR and 13C NMR) spectral analysis. These derivatives were evaluated for their anticancer and antioxidant activities. The in vitro anticancer activity of new compounds was examined against MCF-7 (breast cancer), HepG2 (liver hepatocellular carcinoma), and TC-1 (mouse lung epithelial) cell lines by 3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide (MTT) assay. Notably, compounds 4c, 4e and 4 g demonstrated significant anticancer activity against TC-1 cell line. Additionally, compounds 4c, 4f and 4 g exhibited promising levels of efficacy against the MCF-7 cell line. The diphenylpicrylhydrazyl (DPPH) radical scavenging assay indicated that 4h and 4i are more potent antioxidant agents than the Vitamin C, while 4a, 4b, 4c, and 4j exhibited moderate antioxidant capabilities. Furthermore, the docking simulations are consistent with the biological assay results, indicating that the hybrids may bind to protein targets through hydrogen bonding and other nonvalent interactions.

How does a biopolymer (protein) fold into a unique 3D structure?

The current state of the problem of folding proteins and other biopolymers is discussed. The concept of a multidimensional potential energy surface and a free energy surface for linear polymers is detailed, taking into account the topology of the configuration space and the presence of symmetry elements with respect to the permutation of identical monomer units. The presence of kinematic bonds for conformational movements in a viscous medium leads to a tendency to form helical structures of linear polymers. The dynamic effects of viscosity also lead to an almost uniform distribution of energy dissipation rates over the chain nodes. The combination of potential energy surface topography and viscosity effects provides a physical basis for the development of the theory of folding in the direction of interpreting various experimental observations and elucidating the principles for the formation of an amino acid code for 3D protein structures. The relationship between the denaturation temperature of the folded state of the biopolymer and the energy of non-valent interactions between monomers in the chain is analyzed.

Intramolecular Re···O Nonvalent Interactions as a Stabilizer of the Polyoxorhenate(VII).

The first polyoxorhenate(VII) compound, pyrazolium polyoxorhenate ((C4N2H5)2Re4O15), and two new rhenium(VII) and technetium(VII) salts have been synthesized and studied. The structure of Tc2O7 has been reinvestigated. The [Re4O15]2- polyoxoanion contains four Re(VII) atoms: one with an octahedral environment and three with a tetrahedral environment. Polyoxorhenate is formed in the presence of a buffering agent, pyrazole, the latter maintaining pH = 2.5 during the formation of crystals. The [Re4O15]2- polyoxoanion has novel stoichiometry and the cis-conformation, likely due to the stabilizing intramolecular nonvalence interactions. For the first time, intramolecular interactions of the Re···O, Re···μ-O, and O···O are described (previously known were only intermolecular ones). In all of the compounds, intermolecular Re···O interactions are observed, which, however, in other compounds, do not lead to the formation of polyoxometalates. The Hirshfeld surface analysis showed that the main contribution to intermolecular interactions is made by the O···H/H···O contacts, van der Waals interactions of the H···H for cations, and the O···O for anions. DFT calculations of the [Re4O15]2- geometry, compared with the crystallographic data, revealed a deviation in the angles. Mass spectroscopy of the red polyoxometalate [Tc20O68]4- was carried out for the first time. Comparison of the results of MALDI and LI for the first known polyoxometalates of the manganese subgroup made it possible to find general patterns of oligomerization for rhenium and technetium compounds. The ESI-MS and LI-MS methods applied to solution and crystals Re compounds made it possible to prove rhenium being able to form not only [Re4O15]2- but also heavier polyoxoanions.

Structural and theoretical study of π-stacking interactions in new complexes based on CuCl2 and 3-sulfonamide-substituted imidazo[2,1-b]thiazoles.

At present, sulfonamides and their metal complexes have received a new impetus for development. Of particular interest is the study of molecular and crystal structures, which takes into account weak non-valent interactions. Despite the low energy of such interactions, in many cases, they act collectively, and the sum of their actions can play a significant role. As a result, the spectrum of medical and biological activity of new metal complexes is expanded. In this regard, the synthesis and study of the molecular and crystal structure of sulfonamides and their metal complexes is of undoubted relevance. In this work, we studied non-valent intra- and intermolecular interactions in ligands of sulfonamide-substituted imidazo[2,1-b]thiazoles and their previously unknown complexes with CuCl2. The performed analysis of the data obtained by X-ray diffraction analysis made it possible to establish the intramolecular π-stacking interaction in imidazothiazole ligands, which is retained in their complexes with CuCl2. Within the framework of QTAIM topological analysis of electron density and DORI analysis, stereoelectronic and topological structures were studied. In the complexes, tetral, chalcogen, and pnycogen new interligand non-valent interactions were established. The energies of all established types of non-valent interactions have been calculated, and their comparative evaluation has been made. X-ray data of new arylsulfonylamino-substituted derivatives of imidazo[2,1-b]thiazoles and their metal complexes with CuCl2 have been studied. To determine the theoretical prerequisites for the occurrence of π-stacking in the molecules under study, the QTAIM method was used in the framework of the DFT/B3LYP/6-311 + G(d) calculation using the GAUSSIAN 09 program. In addition, the DORI electron density region overlap indicator and the Multiwfn program were used to analyze non-valent interactions.

Photoluminescence Behaviors in Self-Assembly Supramolecular Pyridinium Salts

The host–guest supramolecular organic salts would be of great interest due to their excellent optical and electronic properties. Herein, we report three supramolecular materials, o-2MAP, m-3MAP, and p-4MAP, composed of 18-crown-6 and pyridine amine salts, which are crystallized in space groups P1̅, P1̅, and P21/n with a pendulum-like structural variation at room temperature. They all show blue photoluminescence with photoluminescence quantum yields (PLQYs) of 26.85, 77.08, and 32.67%, respectively. The experimental and theoretical analyses reveal that PL emission is associated with strong π–π * and n–π* absorption and charge transition, while hydrogen bond nonvalent interactions affect their structures and cause the enhancement of PLQY. Especially, deep-blue PL materials m-3MAP with the highest PLQY have been used as excellent color conversion media to fabricate ultraviolet light-emitting diodes (UV-LEDs) and anticounterfeiting inks for handwriting and transfer-printing. This work caters to a reliable strategy to design novel optical supramolecular materials and extends their applications for PL materials.

Species of Gold(III) Binding by Binuclear Zinc Dipropyldithiocarbamate: Supramolecular Self-Organization and Thermal Behavior of Ionic Complexes [Au(S2CNPr2)2]2[ZnCl4] and [Au(S2CNPr2)2]2[AuCl4][AuCl2

The reaction of binuclear zinc dipropyldithiocarbamate [Zn2{S2CN(C3H7)2}4] with an AuCl3/2 М HCl solution is studied. The double ionic complex [Au{S2CN(C3H7)2}2]2[ZnCl4] (I) is identified as the main species of gold(III) binding in the heterogeneous system under study and is characterized by 13С and 15N CP-MAS NMR spectroscopy. Single crystals of heterovalent compound [Au{S2CN(C3H7)2}2]2[AuCl4][AuCl2] (II) are sampled as a by-product. The crystal and supramolecular structures of complexes I and II are determined by the direct XRD method (CIF files CCDC nos. 2159171 and 2159170, respectively). The self-organization of the complex pseudopolymeric structures of compounds I and II are shown to be due to the binding of ionic structural units by secondary nonvalent interactions Au⋅⋅⋅S and S⋅⋅⋅Cl and hydrogen bonds C–H⋅⋅⋅Cl. The thermal behavior of the complexes is studied by simultaneous thermal analysis (STA), and the quantitative regeneration of bound gold (I and II) with the partial transformation of released ZnCl2 to ZnS (I) is found.

Thiourea as a Stabilizer of Reduced Forms of Technetium─Tc(III) and Tc(IV): Experimental and Theoretical Studies of Complexes

This paper presents synthetic methods for the preparation of Tc(III) and Tc(IV) coordination compounds with thiourea. We have shown that the main product of the synthesis is the complex [TcTu5X]X2, (Tu = (NH2)2CS, X = Cl, Br) and not [TcTu6]Cl3·4H2O, as previously thought. Tu2[TcX6]X2·3H2O is the main technetium-containing byproduct of the reaction. All reaction products, including byproducts, were characterized by X-ray diffraction analysis. We also measured the solubility for the obtained Tc(III) complexes. This research work considers the process of thermolysis of the obtained Tc(III) complexes and shows that the presence of sulfur atoms in the coordination sphere can inhibit the process of metal formation in an argon-hydrogen medium. The analysis of nonvalent interactions in Tc(III) complexes showed that the main contribution is made by van der Waals interactions of the H···H type (40.8-42.3%) and hydrogen bonds Hal···H/H···Hal and H···S/S···H, which are 41.6-44.5% in total. As the temperature decreases, the proportion of H···H contacts and H bonds decreases, and when the halogen (Cl by Br) is replaced, the proportion of H bonds increases and the proportion of van der Waals interactions decreases.

New O- and N-N-Bridging Complexes of Tc(V), the Role of the Nitrogen Atom Position in Aromatic Rings: Reaction Mechanism, Spectroscopy, DTA, XRD and Hirshfeld Surface Analysis.

In this work, O- and N-N-bridging complexes of technetium (V), previously known only for rhenium, were obtained for the first time. Tc(V) complexes with pyridazine (pyd), 1,2,4-triazole (trz), 3,5-dimethylpyrazole (dmpz) and pyrimidine (pyr) were obtained. In three complexes [{TcOCl2}2(μ-O)(μ-pyd)2], [{TcOCl2}2(μ-O)(μ-trz)2]·Htrz·Cl and [{TcO(dmpz)4}(μ-O)(TcOCl4)] two technetium atoms are linked by a Tc-O-Tc bond, and in the first two, Tc atoms are additionally linked by a Tc-N-N-Tc bond through the nitrogen atoms of the aromatic rings. We determined the role of nitrogen atom position in the aromatic ring and the presence of substituents on the formation of such complexes. For the first time, a reaction mechanism for the formation of such complexes was proposed. This article details the crystal structures of four new compounds. The work describes in detail the coordination of Tc atoms in the obtained structures and the regularities of the formation of crystal packings. The spectroscopic properties of the obtained compounds and their mother solutions were studied. The decomposition temperatures of the described complexes were determined. An assumption was made about the oligomerization of three-bridged complexes based on the results of mass spectrometry. Through the analysis of non-valent interactions in the structures, π-stacking, halogen-π and CH-π interactions were found. An analysis of the Hirshfeld surface for [{TcOCl2}2(μ-O)(μ-pyd)2], [{TcOCl2}2(μ-O)(μ-trz)2] and their rhenium analogues showed that the main contribution to the crystalline packing is made by interactions of the type Hal···H/H···Hal (45.4-48.9%), H···H (10.2-15.8%), and O···H/H···O (9.4-16.5%).

"ANTI-HALOGEN" BONDS AS A FACTOR DETERMINING THE TETRAHEDRAL STRUCTURE OF COPPER IN ITS COMPLEXES WITH (5Z, 5'Z)-2,2'- (ETHANE-1,2-DIYLDISULFANYLDIYL)BIS(5-(2-PYRIDYLMETHYLENE)-3-ALLYL-3,5-DIHYDRO- 4H-IMIDAZOLE-4-ONE)

Analysis of the valence angles of the Si and carbon atoms of the C-S bond in the obtained complexes of CiVg2 c (5Z, 5'Z)-2,2’-(ethane-1,2-diyldisulfanyldiyl)bis(5-(2-pyridylmethylene)-3-allyl-3,5-dihydro-4Нimidazole-4-one) unambiguously indicates the determinant effect of the non-valent interactions of the electron density centroids of the NEP of bromine atoms and sulfur atoms, leading to a change in the plane structure of Cu(II) towards tetrahedral with a likely change in the magnetochemical properties of the copper atom, and the angle of rotation of the planes is almost 900. This interaction is the opposite of what is commonly called a halogen bond. In this case, it is an "anti-halogen" bond.

Interplay of the Ring and Steric Strains in the Highly Substituted Cyclopropanes.

Using the concept of a complete set of homodesmotic reactions for the analysis of molecular energetics of polysubstituted methyl- and fluorocyclopropanes allows assessing the strain energy SE of cyclopropanes, free from interfering effects, in full accordance with the IUPAC definition ("relative to a reference ... hypothetical 'strainless' structure"). The correct SE calculation requires quantifying nonvalence interactions in the products of formal homodesmotic reactions (HDRs) using a routine multiregression analysis. The complete HDR set provides the information necessary for the analysis, namely, the heat effects of HDRs calculated by the G4 composite method and the wide set of reference compounds with various combinations of nonvalence effects. We have found that the SE value for methylcyclopropanes lies in the range from 117.0 (1.1-dimethylcyclopropane) to 146.1 kJ/mol (hexamethylcyclopropane). It is the sum of the ring strain energy RSE = 117.9 ± 0.3 kJ mol, which does not depend on the number of methyl substituents, and the Pitzer strain energy of 4.4±0.1 kJ/mol per one contact (the standard deviation is shown as an error of determination). In the series of fluorocyclopropanes, SE varies from 137.9 (monosubstituted cyclopropane) to 260.0 kJ/mol (hexafluorocyclopropane) and well correlates with the ∑DBCP parameter deduced from the QTAIM analysis of the electron density of the compound, representing the total deviation of bond critical points from geometrical C-C bond lines of CC bonds. The ∑DBCP parameter characterizes the curvature of banana-like bonds in cyclopropanes.

Synthesis and crystal structures of 7,8-bromo (dibromo)-3-tert-butylpyrazolo[5,1-c][1,2,4]triazines.

Single crystal structures in a series of 7-bromo-, 8-bromo-, and 7,8-dibromo-3-tert-butylpyrazolo[5,1-c][1,2,4]triazin-4(1H)-ones have been investigated by X-ray diffraction. Novel 7-bromo- and 7,8-dibromo-3-tert-butylpyrazolo[5,1-c][1,2,4]triazines were synthesized by reduction of triazine carbonyl with dehydrative aromatization in acidic media, and their XRD structural features were compared with that of the 4-oxo analogs. The lengths and bond angles and the packing of molecules in crystals have been considered. Non-valence interactions for some of the studied compounds were observed. Correlations between the presence of bromine atoms at different positions and structural features are determined.Graphical abstract Supplementary InformationThe online version contains supplementary material available at 10.1007/s11224-021-01768-0.

Spatial Structure of the Acth-(6-9)-PGP Molecule

The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

Spatial Structure of the Acth-(6-9)-PGP Molecule

The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

Inhibition of starch digestion: The role of hydrophobic domain of both α-amylase and substrates

The physicochemical mechanism of starch digestion is very complicated since it may be affected by the non-valence interactions of the amylase inhibitor with the substrate or the enzyme. The role of hydrophobic interaction in the process of starch digestion is not clear. In this study, pluronics (PLs) with different hydrophobicity were used as model amphiphilic compounds to study their inhibition on starch digestion using multi-spectroscopic methods. The results showed that the hydrophobic nature of PLs changed starch structure, but it had a greater effect on the structure of α-amylase by exposing more tryptophan residues and increasing α-helix and β-sheet contents. Further investigation by using different chain-length fatty acids confirmed the results. The finding in this study is informative to design and fabricate α-amylase inhibitors for controlling starch digestion at the molecular level.

Structural studies of 3-tert-butyl-8-(methylchalcogenyl)pyrazolo[5,1-c][1,2,4]triazin-4(1H)-ones

Crystal structures of novel 3-tert-butyl-8-(methylchalcogenyl)pyrazolo[5,1-c][1,2,4]triazin-4(1H)-ones, C10H14N4OE (E = S, 3; Se, 4; Te, 5), have been determined. Compound 3 crystalizes in the monoclinic crystal system (P21/c), whereas 4 provides two polymorph modifications, 4a (orthorhombic, Pbca) and 4b (tetragonal, I41/a, merohedral twin), depending on solvent media. Crystal structure of 5 (tetragonal, I41/a) is isomorphous with 4b. The studied structures of pyrazolo[5,1-c][1,2,4]triazin-4(1H)-ones exhibit a planar heterocyclic C5N4O core possessing a conjugated π-electron system, which is partly involved in the conjugation with the chalcogen atom. In general, geometric parameters found by X-ray method and ab initio calculated by density functional theory (DFT) for a single molecule (method PBE1PBE/Def2TZV, gas phase) are in good agreement. The structures form 1D infinite chains in the crystalline lattice via intermolecular NH∙∙∙O/N hydrogen bonding and demonstrate short E···E (3, 4b, 5) and E···C/N (all compounds) interactions among molecules of the neighboring chains. Such non-valence interactions do not perturb much the geometries of 3, 4b, and 5 but move the Se atom out of the C5N4O plane in 4a, compared with geometries calculated by DFT method. Photochemical studies have revealed that UV irradiation induces decomposition of telluride 5, accompanied with the Te-C8 bond cleavage, while sulfide 3 and selenide 4 remain inert under analogous conditions.

Charge States of Sorption Centers in Matrimid

The features of the electronic structure of Matrimid, which are important for assessing the sorption ability of the specified polymer as a membrane material, are considered. Using the density functional theory, the charge states of sorption centers in the Matrimid are calculated. The most probable polymer atoms responsible for nonvalent interactions of polar molecules of gases or liquids when passing through membranes based on this polymer are investigated.

The Problem of Dynamic Process Manifestation in Identification of Organic Compounds by NMR Spectroscopy

The number, shape and position of NMR spectral lines depend on dynamic processes, and this creates certain difficulties in identification of pharmaceutical substances by NMR spectroscopy. The aim of the paper was to study instances of manifestation of intramolecular dynamic processes that affect identification of organic compounds by NMR, and to illustrate the potential of the methods used for their reduction, as well as associated problems.Materials and methods: 1H and 13C spectra of the following pharmaceutical substances: «buserelin acetate», «valsartan», «goserelin acetate», «iopromide», «clopidogrel hydrogensulfate», «omeprazole», «proroxan», «risperidone», «triptorelin acetate», and «enalapril maleate» were used to demonstrate negative effects of dynamic processes. The spatial structures of conformers were established by 1H-1H ROESY experiments. The quantum-chemical calculation of geometric and thermodynamic characteristics of different conformers was carried out by the PM3 method, and electronic characteristics—by the AM1 method with the help of the HyperChem software.Results: the authors analysed intramolecular dynamic processes which are most commonly encountered in expert work: pyramidal inversion of nitrogen in a heterocyclic compound (risperidone, proroxan, clopidogrel), rotation of molecular fragments around the amide bond (valsartan, iopromide, enalapril), prototropic rearrangements (buserelin, goserelin, omeprazole, triptorelin). The change in exchange rates was explained from the perspective of the change in the system of intra- and intermolecular nonvalent interactions.Conclusions: the use of traditional methods for increasing the rate of dynamic processes (increasing the temperature and changing the solvent) does not always eliminate the negative effects of intramolecular transformations. Methods of smoothing the spectral manifestations of dynamic processes have limited application due to strong intramolecular nonvalent interactions which prevent the conversion of the dynamic process rate into fast exchange. Experts and manufacturers should take into account the manifestation of dynamic processes during identification of pharmaceutical substances by NMR spectroscopy.

Intramolecular Nonvalent Interactions in the $${\text{Eu}}_{{\text{2}}}^{{{\text{II}}}}$$EuIII(μ-ORF)2(μ2-ORF)3(μ3-ORF)2(DME)2 Complex

A quantum chemical study of fluorinated europium alcoholate $${\text{Eu}}_{{\text{2}}}^{{{\text{II}}}}$$ EuIII(μ-ORF)2(μ2-ORF)3(μ3-ORF)2(DME)2 (I), where DME is 1,2-dimethoxyethane, is performed. The structure of the complex contains numerous F⋅⋅⋅F, F⋅⋅⋅O, F⋅⋅⋅H, and C–F → Eu interactions. The nature and energy of these nonvalent interactions is studied in the framework of R. Bader’s quantum theory “Atoms in Molecules.” Nonvalent interactions between the negatively charged fluorine atoms in the structure of complex I can occur due to the donation of the electron density from the regions where the electron density is fairly highly concentrated to the regions of its relative depletion. Weaker C–F → Eu interactions are observed by the additional study using the Topos Pro structural topological program package. These interactions are confirmed by the study of the delocalization indices of electrons in the region of potential Eu⋅⋅⋅F interactions.

Inner- and Outer-Sphere Coordination of Acido and Neutral N,O-Donor Ligands in the Rare-Earth Metal Complexes

The data on the rare-earth metal complexes with the anionic (halides, NCS) and neutral N,O-donor ligands are systematized and generalized. The influence of the ionic radius of the complexing agent and the ligand nature (donor characteristics, steric features, nonvalent interactions) on the formation of the coordination sphere with the inner- or outer-sphere position of the ligands is monitored. The transitions of the ligands from the outer-sphere position to the first coordination sphere are considered.