Spectroscopic,X-ray Diffraction and Density Functional Theory Study of Intra- and Intermolecular Hydrogen Bonds in Ortho-(4-tolylsulfonamido)benzamides

The conformations of the title compounds were determined in solution (NMR and UV-Vis spectroscopy) and in the solid state (FT-IR and XRD), complemented with density functional theory (DFT) in the gas phase. The nonequivalence of the amide protons of these compounds due to the hindered rotation of the C(O)–NH₂ single bond resulted in two distinct resonances of different chemical shift values in the aromatic region of their ¹H-NMR spectra. Intramolecular hydrogen bonding interactions between the carbonyl oxygen and the sulfonamide hydrogen atom were observed in the solution phase and solid state. XRD confirmed the ability of the amide moiety of this class of compounds to function as a hydrogen bond acceptor to form a six-membered hydrogen bonded ring and a donor simultaneously to form intermolecular hydrogen bonded complexes of the type N–H···O=S. The distorted tetrahedral geometry of the sulfur atom resulted in a deviation of the sulfonamide moiety from co-planarity of the anthranilamide scaffold, and this geometry enabled oxygen atoms to form hydrogen bonds in higher dimensions.     

Hydrogen bond strength in chromates with kröhnkite-type chains, K2Me(CrO4)2·2H2O (Me = Mg, Co, Ni, Zn, Cd)

Infrared spectra of the title compounds with kröhnkite-type infinite octahedral–tetrahedral chains, K₂Me(CrO₄)₂·2H₂O (Me = Mg, Co, Ni, Zn, Cd), are presented in the regions of the uncoupled O–D stretching modes of matrix-isolated HDO molecules (isotopically dilute samples) and water librations. The strengths of the hydrogen bonds are discussed in terms of the respective O_wO bond distances, the Me–water interactions (synergetic effect), the proton acceptor capability of the chromate oxygen atoms as deduced from Brown's bond valence sum of the oxygen atoms. The spectroscopic experiments reveal that hydrogen bonds of medium strength are formed in the chromates. The hydrogen bond strengths decrease in the order Cd > Zn > Ni > Co in agreement with the decreasing covalency of the respective Me–OH₂ bonds in the same order, i.e. decreasing acidity of the water molecules. The infrared band positions corresponding to the water librations confirm the claim that the hydrogen bonds in K₂Cd(CrO₄)₂·2H₂O are stronger than those formed in K₂Mg(CrO₄)₂·2H₂O on one hand, and on the other—the hydrogen bonds in K₂Ni(CrO₄)₂·2H₂O are stronger than those in K₂Co(CrO₄)₂·2H₂O.     

Ab initio study of the structure and tautomerism of internally hydrogen-bonded aromatic carbonyls: Salicylamide,salicylic Acid,and O-hydroxybenzoyl cyanide

We carried out an ab initio study at the 3–21 G level with full geometric optimization of three compounds with intramolecular hydrogen bonds in their most stable conformations, namely salicylamide, salicylic acid, ando-hydroxybenzoyl cyanide. The energy of the hydrogen bonds was estimated and their structural effects were analyzed. We also studied the stability of the tautomers resulting from a proton transfer between the oxygen atoms by analyzing the potential surfaces of the tautomerization process. The potential surfaces of salicylamide and salicylic acid showed a single minimum, while that of the cyanide showed a double minimum with a scarcely significant inverse barrier (3.01 kJ/mol). Single point calculations at the 6–31+G^* level on salicylic acid showed a trend to appear a second minimum in the potential surface. Both the strength of the hydrogen bond and the occurrence of stable tautomers were found to be clearly correlated with the electron-releasing and electron-withdrawing ability of the organic functions present in each compound (-NH₂,-OH and -CN, respectively).     

Consequences of Strain for the Structure of Aliphatic Molecules

The chemist is accustomed to deriving structures and preferred conformations of organic compounds from rigid molecular models and standard values for bond lengths, bond angles, and torsional profiles. In the case of strained compounds, this rigid structural model has to be abandoned and replaced by a flexible one which takes individual conditions of strain into consideration. It is shown, on the basis of new experimental structure data, that the force field method is suitable and highly reliable for the calculation of structural parameters and preferred conformations of strained compounds. It is, therefore, capable of replacing the rigid molecular model. Furthermore, the systematic analysis of strain induced angle and bond deformation gives a new pivot for the development of a qualitative discussion of deformation in strained molecules and hence for improved conformational analysis. — In the course of this work we were able to isolate two rotamers of D,L -3,4-di(1-adamantyl)-2,2,5,5-tetramethylhexane; this is the first isolation of a rotamer pair of an aliphatic hydrocarbon.     

Docking-based 3D-QSAR study of pyridyl aminothiazole derivatives as checkpoint kinase 1 inhibitors

Checkpoint kinase 1 (Chk1) is a promising target for the design of novel anticancer agents. In the present work, molecular docking simulations and three-dimensional quantitative structure–activity relationship (3D-QSAR) studies were performed on pyridyl aminothiazole derivatives as Chk1 inhibitors. AutoDock was used to determine the probable binding conformations of all the compounds inside the active site of Chk1. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were developed based on the docking conformations and alignments. The CoMFA model produced statistically significant results with a cross-validated correlation coefficient (q²) of 0.608 and a coefficient of determination (r²) of 0.972. The reliable CoMSIA model with q² of 0.662 and r² of 0.970 was obtained from the combination of steric, electrostatic and hydrogen bond acceptor fields. The predictive power of the models were assessed using an external test set of 14 compounds and showed reasonable external predictabilities (r²_pred) of 0.668 and 0.641 for CoMFA and CoMSIA models, respectively. The models were further evaluated by leave-ten-out cross-validation, bootstrapping and progressive scrambling analyses. The study provides valuable information about the key structural elements that are required in the rational design of potential drug candidates of this class of Chk1 inhibitors.     

Strong asymmetric hydrogen bonding in 2‐(oxamoylamino)ethylammonium oxamate–oxamic acid (1/1)

The title compound, C₄H₁₀N₃O₂⁺·C₂H₂NO₃⁻·C₂H₃NO₃, contains at least 11 distinct hydrogen‐bond interactions showing a great variety of bond strengths. The shortest and strongest hydrogen bond [O...O = 2.5004 (12) Å] is found between the uncharged oxamic acid molecule and the oxamate monoanion. The grouping formed by such a strong hydrogen bond can thus be considered as a hydrogen bis(oxamate) monoanion. It lacks crystallographic symmetry and the two oxamate groups have different conformations, showing an asymmetric hydrogen‐bond interaction. Significantly, the asymmetry allows us to draw a direct comparison of site basicity for the two inequivalent carboxylate O atoms in the planar oxamate anion. The constituent molecular ions of (I) form ribbons, where all amide and carboxylate groups are coplanar. Graph‐set analysis of the hydrogen‐bonded networks reveals the R²₂(10) and R²₂(9) homodromic nets as important structure‐directing motifs, which appear to be a common feature of many oxamate‐containing compounds.     

Preparation and Characterization of SiO2-MxOy(M = V, Sn, Sb) Thin Films from Silicic Acid and Metal Chlorides

The preparation of SiO₂-M _x O _y (M = V, Sn, Sb) binary oxide thin films by sol-gel method was investigated. The reaction of silicic acid with metal chloride (M = Sn and Sb) or oxychloride (M = V) formed homogeneous solutions. The dip-coating of slide glass and silicon wafer followed by heat treatment gave oxide films having Si—O—M bond. The changes of FT-IR spectra as a function of heat treatment temperature and molar composition confirmed the Si—O—M bonds. The sheet resistance of films increased with an increase on heat treatment temperature and decrease in the content of metal oxide M _x O _y . X-ray diffraction peaks were observed for the SiO₂-V₂O₅ films with high V₂O₅ contents and heat-treated above 250°C, while the others were amorphous. Oxide films heat treated at 500°C had a thickness between 340–470 nm.     

Investigation of hydrofluorides of the alkaline earth metals by the NMR method

Summary The structure of hydrofluorides with the composition MeF₂ · HF(Me=Sr, Ba) includes two anions: F^– and HF₂ ^– with a linear hydrogen bond. In SrF₂ · HF, the hydrogen bond is characterized by a more asymmetrical position of the proton than in BaF₂ · HF.Increasing the number of added HF molecules leads to the formation of two bifluoride ions in the compounds CaF₂ · 2HF and SrF₂ · 2.5HF. The hydrogen bond in this case is also nonsymmetrical, and the average F–H distance is equal to 1.17 A. Thus, the hydrogen bond in these compounds is of the same order as in KF · 2HF (r_F–F=2.33 A) [12],i.e., weaker than in KF · HF (r_F–F=2.26 A) [13], but stronger than in solid HF (r_F–F=2.49 A) [14].A structure with two polyfluoride anions evidently corresponds to the compound BaF₂ · 3HF.Institute of Inorganic Chemistry, Siberian Branch of the Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 9, No. 2, pp. 202–206, March–April, 1968.     

Fluoroindenes. 13. Transformations of polyfluorinated indenes and 1-alkylideneindans in the H2O2-HF-SbF5 system

The reaction of perfluorinated indene, 3-methylindene, and 1-methylene- and 1-ethylideneindans with hydrogen peroxide in the hydrogen fluoride—antimony pentafluoride medium takes place at the multiple bond of the substrate and leads to the oxo derivatives of indan. The process probably takes place through the electrophilic addition of HO⁺. The C=C bond in perfluoro-3-methylindenone is not affected. In this compound and also in perfluoro-2-indanone and perfluoro-1-methyl-2-indanone the carbonyl group is involved in reaction with hydrogen peroxide in the HF-SbF₅ system, and six-membered oxygen-containing heterocyclic compounds are formed.For Communication 12, see [1].Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 6, pp. 1412–1419, June, 1992.     

Ab initio studies of structural features not easily amenable to experiment. 18. Conformational analysis and molecular structure of glycine methyl ester

The structures of four conformations of the methyl ester of glycine were determined by standard single-determinant molecular orbital (MO ) calculations using Pulay's force method and the 4-21G basis set. The most stable conformation of this compound has a symmetry plane which contains all the heavy atoms; it is stabilized by hydrogen bonds between the NH₂ group and the carbonyl oxygen; it corresponds to the most stable, stretched form of free glycine. The structural parameters in the different conformations can vary significantly (bond distance by more than 0.02 Å and bond angles by up to 15°). The structural changes which are caused in glycine by esterification are discussed and some of them are interpreted in terms of hyperconjugative π-electron delocalization.     

Design of Peptides with α,β-Dehydro Residues: Synthesis,Crystal Structure and Molecular Conformation of a Peptide N-Boc-Phe-ΔPhe-Ile-OCH<Subscript>3</Subscript>

To develop a complete set of design rules with α,β-dehydro residues, a tripeptide N-Boc-Phe-ΔPhe-Ile-OCH₃ was synthesized. The synthesis was carried out in solution phase using azlactone procedure. The three-dimensional structure of the peptide was determined by X-ray diffraction method and refined to an R-factor of 0.085. The structure contains three peptide molecules in the asymmetric unit. In all the three crystallographically independent molecules ΔPhe residue adopts one of the three conformations that have been reported for a ΔPhe residue. The overall conformations of three peptide molecules in the asymmetric unit are not similar. Two out of three crystallographically independent molecules adopt type II β-turn conformations whereas the third molecule is found having the characteristic S-shaped conformation in which the values of dihedral angles φ, ψ have opposite signs alternately. One of these two types of conformations has been observed when a ΔPhe is introduced at (i+2) position of a tetrapeptide. The β-turn conformation is stabilized by a 4→1 hydrogen bond where the hydrophobic side chains of residues at (i+1) and (i+3) positions stabilized the unfolded conformation with van der Waals interactions. The three independent molecules are locked together by three hydrogen bonds between molecules A and B and two hydrogen bonds between molecules B and C.     

Recoordination of a metal ion in the cavity of a crown compound: a theoretical study. 1. Conformers of arylazacrown ethers and their complexes with Ca2+ cation

Photoinduced recoordination of Ca²⁺ complexes of the photochromic azacrown ethers is studied by the density functional method. The study included model arylazacrown ethers containing various acceptor groups in the aromatic ring in the para position to the azacrown ether moiety and a real azacrown-containing styryl dye. It is found that both free azacrown ethers and their complexes can adopt two types of conformations: (1) axial conformations, in which the aromatic ring axis passing through the crown ether nitrogen N_cr and the opposite atom of the aromatic ring is perpendicular to the root-mean-square (RMS) plane of the crown ether (least-squares fitted plane for all the crown ether atoms), and (2) equatorial conformations, in which the aromatic ring axis only slightly deflects from the RMS plane of the crown ether. In the equatorial conformers, the metal cation is coordinated only to the O atoms of the azacrown ether cycle, the metal—nitrogen bond is broken, and N_cr is conjugated with the aromatic ring. In the axial conformers, the metal cation is additionally coordinated to N_cr. It is found that the presence of an acceptor group bearing a formal positive charge decreases the relative energy of the equatorial conformer and favors metal—nitrogen bond dissociation, which results in the recoordination of the metal cation. However, a long distance between the charged group and N_cr has the reverse effect. The photoinduced recoordination observed in the alkaline-earth metal complexes of the photochromic azacrown ethers is explained by the transitions between the axial and equatorial conformers facilitated by the charge transfer in the excited state of the complex.     

Intramolecular Nonbonded Interactions Between Oxygen and Group VIA Elements: An Ab Initio Molecular Orbital and Density Functional Theory Investigation of the Structures of HX—CH2—COOH (X=S,Se, and Te)

Ab initio molecular orbital and density functional methods have been used to study the potential energy surfaces of the substituted acetic acids HX—CH₂—COOH, where X is one of the Group VIA Chalcophiles S, Se, or Te. The various conformers adopted by these compounds provide information regarding the energetic importance of nonbonded and hydrogen bonding interactions involving oxygen atoms with different hybridizations. Density functional and ab initio molecular orbital methods yield similar structural and energetic trends for these compounds. Calculations show that the structure of the lowest-energy conformer of each of these acids has the X—C—C—O backbone substantially twisted from planarity, similar to that previously observed for the corresponding aldehydes, HX—CH₂—CHO. In the twisted acid structures the shortest distance is within about 0.1 Å of the sum of the X and O van der Waals radii, which reduces overcrowding of the lone pairs of electrons on these atoms. In conformers where the heavy atom backbone is planar, one of the distances is significantly shorter than the sum of the van der Waals radii, and the total molecular energy of these conformers is higher than that of the twisted forms. The variation of X—H vibrational frequencies among conformers reflects the extent of X—H hydrogen bonding, and indicates that formation of this hydrogen bond is not the dominant factor in determining the lowest-energy conformation. When X is oxygen (HO—CH₂—COOH), the lowest-energy conformer is also nonplanar, whereas for the corresponding aldehyde, HO—CH₂—CHO, the lowest-energy conformer is a planar structure with C_S symmetry. The conformational preferences of these simple species provide reference points for inter- and intramolecular interactions in more complex systems of biological interest.     

H2-induced CO adsorption and dissociation over Co/Al2O3 catalyst

The activation of adsorbed CO is an important step in CO hydrogenation. The results from TPSR of pre-adsorbed CO with H2 and syngas suggested that the presence of H2 increased the amount of CO adsorption and accelerated CO dissociation. The H2 was adsorbed first, and activated to form H＊ over metal sites, then reacted with carbonaceous species. The oxygen species for CO2 formation in the presence of hydrogen was mostly OH^＊, which reacted with adsorbed CO subsequently via CO^＊＋OH^＊ → CO2^＊＋H^＊; however, the direct CO dissociation was not excluded in CO hydrogenation. The dissociation of C-O bond in the presence of H2 proceeded by a concerted mechanism, which assisted the Boudourd reaction of adsorbed CO on the surface via CO^＊＋2H^＊ → CH^＊＋OH^＊. The formation of the surface species （CH） from adsorbed CO proceeded as indicated with the participation of surface hydrogen, was favored in the initial step of the Fischer-Tropsch synthesis.     

Synthesis and study of organometallic complexes of octaphenyltetraazaporphyrinatoindium(iii)

Five-coordinate organometallic complexes RIn(TAPPh₈) (R = Ph, Bu) were synthesized by the reactions of chloro(octaphenyltetraazaporphyrinato)indium(iii) ClIn(TAPPh₈) with organolithium and organomagnesium compounds. The optical, IR, and ¹H NMR spectra of the complexes were studied. In the presence of pyridine, the photochemical insertion of CO₂ occurs at the In—C bond to form the carboxylate complexes (RCOO)In(TAPPh₈). A study of the kinetics of this reaction showed a higher stability of the In—C bond in the aryl PhIn(TAPPh₈) complex than that in the alkyl complex BuIn(TAPPh₈). The mechanism of the reaction was proposed.     

Orthorhombic polymorphs of two trans‐4‐aminoazoxybenzenes

The two isomeric compounds 4‐amino‐ONN‐azoxy­benzene [or 1‐(4‐amino­phenyl)‐2‐phenyl­diazene 2‐oxide], i.e. the α isomer, and 4‐amino‐NNO‐azoxy­benzene [or 2‐(4‐amino­phenyl)‐1‐phenyl­diazene 2‐oxide], i.e. the β isomer, both C₁₂H₁₁N₃O, crystallized from a polar solvent in orthorhombic space groups, and their crystal and molecular structures have been determined using X‐ray diffraction. There are no significant differences in the bond lengths and valence angles in the two isomers, in comparison with their monoclinic polymorphs. However, the conformations of the mol­ecules are different due to rotation along the Ar—N bonds. In the α isomer, the benzene rings are twisted by 31.5 (2) and 14.4 (2)° towards the plane of the azoxy group; the torsion angles along the Ar—N bond in the β isomer are 24.3 (3) and 23.5 (3)°. Quantum‐mechanical calculations indicate that planar conformations are energetically favourable for both isomers. The N—H?O hydrogen bonds observed in both networks may be responsible for the deformation of these flexible mol­ecules.     

Ba2In2O4(OH)2: Proton sites, disorder and vibrational properties

The structure of Ba₂In₂O₄(OH)₂ is analysed by the explicit full optimization of a large number of possible proton arrangements using periodic density functional theory. It is shown that the experimental assignments in which protons appear to be located at high symmetry positions with unphysical bond lengths do not correspond to minima on the potential energy hypersurface. The apparent sites are averages of a number of possible proton locations involving a set of possible local structural environments in which the internuclear separations are more realistic. Such problems with structural refinements are common where profile refinement programs place the atoms at the average position due to dynamic and/or static disorder. Thus while the calculations support a previous neutron diffraction analysis of the structure in that the average structure contains two different proton sites, they also reveal substantial information about the local environments of the protons. In all optimizations, the protons moved from the average positions suggested in the neutron diffraction study with calculated O–H and OHO distances consistent with those observed in other oxides. The energies of different proton distributions vary significantly so the protons are not randomly distributed. We also present an analysis of the vibrational properties of the O–H bonds. Since the strength of the hydrogen bonds is closely related to the local structural environments of the protons, a range of vibrational frequencies is obtained providing a prediction of the vibrational spectra. In O–HO linkages, O–H stretching modes soften with increasing HO hydrogen bond strength, while the in-plane and out-of-plane bending or libration modes stiffen. Together, our results show how modern theoretical methods can provide a clearer understanding of the structure and dynamics of a complex inorganic material.     

The x-ray structural investigation of alkaloids I. Molecular structure and absolute configuration of (+)-cocculine

Summary An x-ray structural investigation of the alkaloid (+)-cocculine in the form of the hydrobromide has been performed. The bond lengths and valence angles are the usual ones. The conformations of the rings are: A — envelope⁴E; B — half-chair⁹T₅; C — half-chair¹⁰H₅. The absolute configuration 3R,5S has been established.Institute of Heteroorganic Compounds, Academy of Sciences of the USSR. Institute of the Chemistry of Plant Substances, Academy of Sciences of the Uzbek SSR. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 395–400, May–June, 1975.     

New heteroorganic betaines containing the (+)E15—C—E14—X(–) and (+)E15—C—E14(–) structural fragments (E15 = P,As; E14 = Si,Ge, Sn; X = C,S, O,NR)

The review surveys the data on the reactions of phosphorus and arsenic ylides with compounds containing E=X bonds (E = C, Si, Ge, or Sn; X = C or S), cyclic oligomers (R₂ES)_n (n = 2 or 3), and heavier analogs of carbenes. These reactions give rise to two new classes of heteroorganic betaines containing the ⁽⁺⁾E¹⁵—C—E¹⁴—X^(–) (I) and ⁽⁺⁾E¹⁵—C—E^14(–) (II) (E¹⁵ = P or As; E¹⁴ = Si, Ge, or Sn; X = C or S) structural fragments. Procedures for the synthesis of these compounds, their reactivities, the X-ray diffraction structures, and the electronic structures established by high-level quantum-chemical calculations are considered in detail. The carbon analogs of betaines of type I, viz., compounds bearing the ⁽⁺⁾P—C—C—X^(–) fragment (III), are also discussed. The latter were long considered as possible intermediates in the reactions of compounds containing the polar C=X bond (X = C, O, S, NR, etc.) with phosphorus ylides (classical Wittig and Corey—Chaykovsky reactions and related processes).