Aminomethylene derivatives of azoles

4-Aminoethylidene and 4-aminomethylene derivatives of 5-imidazolone exist in the enamine form as two isomers that are stabilized by intramolecular hydrogen bonds of the NHN and NHO type. In solution the enamine with a five-membered H ring is gradually converted to the corresponding isomer with a six-membered H ring with an NHO bond. Because of steric hindrance, rotation about the carbon-carbon double bond is realized more slowly in the aminoethylidene derivatives than in the aminomethylene derivatives of 5-imidazolone.See [1] for communication XXI.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1677–1679, December, 1978.     

Crystal and molecular structure analysis of flutamide. Bifurcated helicoidal C-H ⋯ O hydrogen bonds

Crystal structure determination and semiempirical AM1 and PM3 calculations were performed on flutamide {2-methyl-N[4 nitro-3-(trifluoromethyl) phenyl] propamide}, a powerful nonsteroidal androgen antagonist. The molecule is almost planar apart from CF₃, NO₂, and CH₃ groups. The NO₂ plane makes an angle of 36.3(4) with the least-square plane of the phenyl ring. The molecules are intermolecularly linked by one N-H O and one C-H O hydrogen bonds. A bifurcated helicoidal hydrogen bond network is formed by the intermolecular C-H O hydrogen bond together with another intramolecular C-H O hydrogen bond. The calculated structures are in good agreement with the crystallographic conformations. AM1 is more accurate for predicting the intramolecular C-H O hydrogen bond while PM3 gives a better geometry for the crowded nitro group. AM1 and PM3 charges of benzenic hydrogens are used to predict the propensity of these atoms to form hydrogen bonds. The noncentrosymmetric space group of the crystal (Pna2₁), the calculated dipole moment (8.88 D), and the calculated angle between molecular dipoles and the twofold axis (–49) close to the optimal value (54.7) indicate that flutamide might be a possible candidate for nonlinear optical material.     

Hydrogen bond lengths in aqueous hydroxylammonium nitrate as a function of concentration,temperature and pressure

Qualitative and quantitative information about the interspecies distance distributions in aqueous hydroxylammonium nitrate (HAN) is obtained as a function of concentration (7 to 17M), temperature (–120 to 60°C) and pressure (0.1 to 7100 MPa) using isotopic uncoupling techniques for the O-HO and N-HO hydrogen bonds in conjunction with frequency-distance correlations.     

The geometry of intermolecular interactions in some crystalline fluorine-containing organic compounds

The propensity of C-F groups to form C-F H-C interactions with C-H groups on other molecules has been analyzed. Crystal structures of molecules containing only carbon, hydrogen, and fluorine, but no oxygen, nitrogen, or other hydrogen-bond-forming elements, were chosen for an initial study in which the intermolecular interactions in crystal-structure determinations of polycyclic aromatic hydrocarbons and their analogous fluoro derivatives were analyzed. It is found that C-F H-C interactions occur, but they are weak, as judged by the intermolecular distances and the angles involved. In a study of crystal structures of molecules containing other elements in addition to carbon, hydrogen, and fluorine, it was found that when an oxygen atom is in a neighboring position on an interacting molecule, a C-O group is more likely than a C-F group to form a linear interaction to the hydrogen atom of a C-H group. Thus, in spite of the high electronegativity of the fluorine atom, a C-F group competes unfavorably with a C-O^–, C-OH, or C=O group to form a hydrogen bond to an O-H, N-H, or C-H group. It is found, however, particularly for polycyclic aromatic hydrocarbons with substituted CF₃ groups that, in the absence of other functional groups that can form stronger interactions, C-F H-C interactions may serve to align molecules and give a different crystal packing from that in the pure hydrocarbon (where fluorine is replaced by hydrogen). Thus, C-F H-X (X = C, N, O) interactions are very weak, much weaker than C=O H-X interactions, but they cannot be ignored in predictions of modes of molecular packing in complexes and in crystals.     

Molecular and Supramolecular Structures of a Nickel(II)–Copper(II)–Nickel(II) Trinuclear Complex Containing a New Macrocyclic Oxamido Complex Ligand

The title complex, [Cu(NiL)₂(H₂O)₂](ClO₄)₂, has been obtained by self-assembly, where [NiL] is a new macrocyclic oxamido complex ligand. In the crystal, a new kind of supramolecular interaction between the carbon atoms of the oxamido group of each [NiL] complex ligand in a [Cu(NiL)₂(H₂O)₂]^{2 +} cation and the oxygen atom of one of the ester carbonyls of another [Cu(NiL)₂(H₂O)₂]^{2 +} cation, and C—HO, O—HO and interactions are observed and link the trinuclear fragments and perchlorate ions to form a 3D supramolecular network.     

Molecular and crystal structure of 2-para-toluimido-4,4-dimethyl-(4H)-1,3-thiazine

The imino structure of 2-p-toluimido-4,4-dimethyl-(4H)-1,3-thiazine (I) was demonstrated by x-ray diffraction structural analysis. Molecules of I in the crystal are linked by N-HO hydrogen bonds in infinite chains. A shortened SO intramolecular contact was found which corresponds to a secondary interaction. A mechanism was proposed for the thiazoline-thiazine rearrangement.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1638–1643, December, 1984.     

A quantum chemical study of the hydrogen bonding in the CO2⋯HF and N2O⋯HF complexes

Summary Quantum chemical ab initio calculations have been performed for the complex CO₂HF and N₂OHF. The interaction energies were computed through fourth order MBPT and were corrected for basis set superposition errors. Extended polarized basis sets were used which are constructed to give accurate values for electric moments and polarizabilities. The complex NNOHF was found to be bent, while OCOHF is linear, in agreement with experiment. The MBPT calculations give evidence for a second linear isomeric structure FHNNO, a possibility which has also been suggested by recent experimental data. The computed binding energies are: 2.5 kcal/mol for OCOHF, 2.4 kcal/mol for NNOHF, and 3.0 kcal/mol for FHNNO. At the SCF level, the FHNNO complex is less stable than NNOHF, but correlation has a large effect on the geometry and energetics of the latter complex. The NNOHF complex seems to be a system where the positive intramolecular correlation correction prevails over the negative intermolecular component.     

Vibrational spectroscopic,conductivity, and calorimetric studies on tripotassium hydrogen diselenate

Infrared spectra of K₃H(SeO₄)₂ obtained at 300 and 77 K, conform to the pattern expected for a very strong O-H O hydrogen bond. Differential scanning calorimetry (DSC) and electrical conductivity measurements indicate the presence of a phase transition at 388 K to a state having high protonic conductivity.A. W. A. is a recipient of a La Trobe University Postgraduate Research Scholarship.     

Rayleigh and Raman light scattering in hydrogen-bonded acetonitrile–water

The structure, vibrational frequencies, light scattering activities and binding energies of CH₃CNH₂O are obtained from ab initio methods. The hydrogen NH bond distance is calculated as 2.06 Å, the dipole moment as 5.77 D and our best estimate for the binding energy is 3.5 kcal mol^–1 (14.7 kJ mol^–1), after correcting for zero-point vibrations. The calculated average dipole polarizability is 39.67 au and the anisotropy is fairly large, corresponding to 21.78 au. The changes in intramolecular vibrational frequencies are analyzed. The scattering activities and depolarization of the Rayleigh and Raman light scattered are calculated. In the Raman case the depolarization due to the intense NC stretching vibration is increased by 20% after the hydrogen bond. For the OH symmetric stretch of water there is a large redshift of 75 cm^–1 and a great intensification of the Raman scattering activity by a factor of 2 and a considerable increase of the depolarization by a factor of nearly 4.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002)     

On the Oximine Complexes of Transition Metals: Part 110: Spectroscopic and DSC study on some [Fe(Diox·H)2L2] and [Fe(Diox)3(BOR)2] type chelates and clathrochelates

A number of 15 [Fe(Diox#x00B7;H)₂L₂] type chelates and [Fe(Diox)₃(BOR)₂] clathrochelates (Diox#x00B7;H₂ — dimethylglyoxime, glyoxime, propoxime, nyoxime, furyl-dioxime; L-pyridine, alkyl-pyridine derivatives, diethyl-phenyl-phosphine, diethyl-p-tolyl-phosphine) were obtained and characterized by means of far and middle FTIR and Mössbauer spectroscopic methods. Some structural problems were discussed on the basis of the optical data.The DSC measurements show the higher thermal stability of the clathrochelates without O—HO intramolecular hydrogen bonds (with asymmetric octahedral structure), as compared to the [Fe(Diox#x00B7;H)₂L₂] trans, symmetric chelates containing O—HO bonds. The kinetic parameters of the thermal decomposition of the complexes have been derived using the nomogram method.This revised version was published online in November 2005 with corrections to the Cover Date.     

Tryptophan-derived peptides. 1: Crystal structure and solution conformation of Boc-Gly-Trp-Ala-OtBu

The solid-state structure of Boc-Gly-Trp-Ala-OBu^t was determined by single-crystal X-ray diffraction analysis. The tripeptide gave crystals belonging to the orthorhombic systemP2₁2₁2₁ and at 122.0(5) K:a=11.0663(12),b=14.107(2),c=17.275(2) Å,V=2697.0(5) ųZ=4,R(F)=0.0259, andR _w(F)=0.0695. The peptide adopts a type-I-turn in the solid state with a single, rather weak, intramolecular hydrogen bond between the Boc-CO and Ala-NH groups (NO 3.082(1) Å, <NHO 167(1)°). The conformation of the Boc-Gly-Trp-Ala-OBu^t peptide has also been studied by¹H NMR spectroscopy. The solvent and temperature dependencies of NH chemical shifts suggests that this hydrogen bond is broken and that all amide protons are solvent exposed in CDCl₃ and (CD₃)₂SO.     

An ab initio study of the structures and enthalpies of the hydrogen-bonded complexes of the acids H2O,H2S,HCN, and HCl with the anions OH−, SH−, CN−, and Cl−

Ab initio calculations at second-order Møller-Plesset perturbation theory with the 6-31 + G(d,p) basis set have been performed to determine the equilibrium structures and energies of a series of negative-ion hydrogen-bonded complexes with H₂O, H₂S, HCN, and HCl as proton donors and OH^–, SH^–, CN^–, and Cl^– as proton acceptors. The computed stabilization enthalpies of these complexes are in agreement to within the experimental error of 1 kcal mol^–1 with the gas-phase hydrogen bond enthalpies, except for HOHOH^–, in which case the difference is 1.8 kcal mol^–1. The structures of these complexes exhibit linear hydrogen bonds and directed lone pairs of electrons except for complexes with H₂O as the proton donor, in which cases the hydrogen bonds deviate slightly from linearity. All of the complexes have equilibrium structures in which the hydrogen-bonded proton is nonsymmetrically bound, although the symmetric structures of HOHOH^– and ClHCl^– are only slightly less bound than the equilibrium structures. MP2/6-31 + G(d,p) hydrogen bond energies calculated at optimized MP2/B-31 + G(d,p) and at optimized HF/6-31G(d) geometries are similar. Using HF/6-31G(d) frequencies to evaluate zero-point and thermal vibrational energies does not introduce significant error into the computed hydrogen bond enthalpies of these complexes provided that the hydrogen-bonded proton is definitely nonsymmetrically bound at both Hartree-Fock and MP2.     

Mutual Weakening of Hydrogen Bonds Between Hydrogen Fluoride and Proton Donors

The mutual effect of hydrogen bonds in BHF(HHal) _n complexes (Hal = F, Cl, Br, I; B = –, CH₃CN, NH₃; n = 1-3) was examined using the self-consistent field ab initio approach (6-31++G(d,p) and ECP-HW). When two and three equivalent H bonds are formed from the lone electron pairs of the fluorine atom of the HF molecule, the mutual weakening effect is 17% and 28%, respectively. The coefficients of the mutual effects of hydrogen bonds in HF(HHal)₂ and H₂O(HHal)₂ bridges are close in magnitude.     

The influence of Na+ on neighbouring hydrogen bonds of aliphatic amino acid

Summary The influence of Na⁺ on hydrogen bonds of the OH O and NH O type between an aliphatic amino acid (glycine zwitterion) and water is investigated byab initio calculations with minimal Gaussian basis sets. Distortion of the hydration shell caused by Na⁺, and interaction energies contributing to the over-all stabilization are discussed.

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Der Einfluß von Na⁺ auf die benachbarten Wasserstoffbindungen in aliphatischen Aminosäuren

Zusammenfassung Der Einfluß von Na⁺ auf die Wasserstoffbindungen vom OH O- und NH O-Typ in aliphatischen Aminosäuren (Glycin-Zwitterion) und Wasser wurde mittelsab initio Berechnungen mit einem minimalen Gausschen Basissatz untersucht. Die durch Na⁺-Ionen hervorgerufenen Verzerrungen der Hydratationsschale und die zur Gesamtstabilisierung beitragenden Wechselwir-kungsenergien werden diskutiert.

     

Bond Length–Electron Density Relationships: From Covalent Bonds to Hydrogen Bond Interactions

It is possible to treat bond distances of covalent C-H bonds and CH hydrogen bonds simultaneously assuming a logarithmic relationship with the electron density at the bond critical point. Similar relationships have been found for other X-H/XH bonds. The data used for obtaining these equations have been determined theoretically. All the systems have been fully optimized and their electron densities calculated at the B3LYP/6-311 + + G(d,p) level.     

Computational Model of the Complex between GR113808 and the 5-HT4 Receptor Guided by Site-Directed Mutagenesis and the Crystal Structure of Rhodopsin

A computational model of the transmembrane domain of the human 5-HT₄ receptor complexed with the GR113808 antagonist was constructed from the crystal structure of rhodopsin and the putative residues of the ligand-binding site, experimentally determined by site-directed mutagenesis. The recognition mode of GR113808 consist of: (i) the ionic interaction between the protonated amine and Asp^3.32; (ii) the hydrogen bond between the carbonylic oxygen and Ser^5.43; (iii) the hydrogen bond between the ether oxygen and Asn^6.55; (iv) the hydrogen bond between the C-H groups adjacent to the protonated piperidine nitrogen and the electrons of Phe^6.51; and (v) the - aromatic-aromatic interaction between the indole ring and Phe^6.52.This computational model offers structural indications about the role of Asp^3.32, Ser^5.43, Phe^6.51, Phe^6.52, and Asn^6.55 in the experimental binding affinities. Asp^3.32Asn mutation does not affect the binding of GR113808 because the loss of binding affinity from an ion pair to a charged hydrogen bond is compensated by the larger energetical penalty of Asp to disrupt its side chain environment in the ligand-free form, and the larger interaction between Phe^6.51 and the piperidine ring of the ligand in the mutant receptor. In the Phe^6.52Val mutant the indole ring of the ligand replaces the interaction with Phe^6.52 by a similarly intense interaction with Tyr^5.38, with no significant effect in the binding of GR113808. The mutation of Asn^6.55 to Leu replaces the hydrogen bond of the ether oxygen of the ligand from Asn^6.55 to Cys^5.42, with a decrease of binding affinity that approximately equals the free energy difference between the SHO and NHO hydrogen bonds.Because these residues are also present in the other members of the neurotransmitter family of G protein-coupled receptors, these findings will also serve for our understanding of the binding of related ligands to their cognate receptors.     

A study of imidazole by the proton magnetic resonance method

The concentration dependence of the chemical shifts of the protons of imidazole in six polar organic solvents and water has been studied. In aqueous solutions an exchange of the NH protons between the imidazole and the water molecules takes place. In organic solvents, the position and half-width of the NH line of imidazole depend on the concentration. With an increase in the concentration, this line shifts in the downfield direction. The shift (1 ppm for a solution of imidazole in DMSO) may be due to the formation of an ordinary hydrogen bond (> NH N ) between the imidazole molecules.Translated from Khimiya Geterotsiklicheskikh Soedinenii, Vol. 6, No. 6, pp. 810–813, June, 1970.     

The structure and harmonic vibrational frequencies of the weakly bound complexes formed by HF with CO,CO2 and N2O

The structure and harmonic vibrational frequencies of several weakly bound complexes formed by HF are reported. Theab initio MP2 approach is used with large basis sets for the optimisation of geometries and the determination of harmonic frequencies. COHF and OCHF are examined; both are found to be minima, with the latter being the dominant structure. The linear OCOHF andT shaped OCOFH are studied, but only the linear structure is a minimum. N₂OHF has two minima on the surface corresponding to bent NNOHF and linear ONNHF structures.     

Double proton shifts in associates of formic acid with CH4, NH3, H2O,CH3F,NH2F,HOF, and HF molecules

The mechanisms of double synchronous proton transfer in associates of formic acid with solvent molecules of the HC(O)OHX (X = CH₄, NH₃, H₂O, or HF) and HC(O)OHFHY (Y = CH₃F, NH₂F, HOF, F₂, or HF) types have been studied by anab initio (SCF/3G) method. The calculated activation barriers of the reactions are 78.52, 17.72, 9.91, and 7.06 kcal mol^–1 in the former case and 120.1, 259.4, 228.7, 182.8, and 0.35 kcal mol^–1 in the latter case. In the latter case, simultaneously with the double transfer of protons, migration of two fluorine atoms along the chain of the associate occurs.Dedicated to Academician of the RAS N. S. Zefirov (on his 60th birthday).Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1690–1700, September, 1995.The present work was carried out with financial support from the Russian Foundation for Basic Research (Project Nos. 93-03-4972 and 93-03-18692) and the International Science Foundation (Grant ISF RNJ 000).     

Structure of the Molecular Complexes of 18-Crown-6 with 1,2,5-Oxadiazole Derivatives

This paper reports on an X-ray diffraction analysis of host–guest type molecular complexes of 18-crown-6 with 1,2,5-oxadiazole derivatives: ethyl 4-amino-1,2,5-oxadiazole-3-carboxylic ether (1:1) (complex I), 4-(2-chloroethylamino)-1,2,5-oxadiazole-3-carboxylic acid hydrazide (1:2) (complex II), and 4-amino-1,2,5-oxadiazole-3-carboxylic acid amide monohydrate (1:1:1) (complex III). Crystals I are monoclinic with cell parameters a = 8.960(2), b = 18.118(4), c = 14.405(3) , = 106.9(3)°, space group P2₁/n, R = 0.054 for 4082 reflections. The 18-crown-6 and guest molecules are linked by hydrogen bonds of NHO(crown) and CHO(crown) types based on the head-to-tail principle, alternating in infinite chains along the y axis in the crystal. Crystals II are triclinic with cell parameters a = 8.615(2), b = 9.249(2), c = 10.987(2) , = 106.86(3), = 95.25(3), = 97.74(3)°, space group P1, R = 0.046 for 3006 reflections. The guest molecules are united into dimers by N–HO=C hydrogen bonds. The 18-crown-6 molecules and the dimer associates of the guest form chains along [110] in the crystal. Crystals III are monoclinic with cell dimensions a = 13.238(3), b = 19.004(4), c = 8.485(2) , = 100.75(3)°, space group Cc, R = 0.051 for 2032 reflections. The crown ether molecule is disordered over two positions. The NHO=C and NHN type hydrogen bonds link the guest molecules into chains. The water molecules serve to bridge the chains with crown ether molecules, forming ribbons whose axis lies along the z direction in the crystal.