Home – Home – Jornals – Journal of Structural Chemistry 2015 number 7

By means of a structural representation of the chemical reactivity as a condensed graph a model predicting rate constants of the bimolecular elimination reaction is derived for the first time. The model developed enables the prediction of rate constants of reactions proceeding in different solvents or water-organic mixtures at different temperatures. It demonstrates a good predictive performance: a mean square deviation of predicted values from experimental ones is less than 0.7 logarithmic units. An outlier analysis shows that prediction errors are mainly due to the imperfection of the training data containing unique reactions. The model is available for users at arsole.u-strasbg.fr.

Selenium containing amino acids are known to play numerous key biological roles in various life-supporting processes. In the current theoretical investigation DFT(B3LYP) and MP2 methods are used to study the gas phase conformers of the selenomethionine molecule in view of their relative stabilities, theoretically predicted harmonic frequencies, HOMO-LUMO energy gaps, rotational constants, and dipole moments. The number and type of intramolecular H-bond interactions existing in the selenomethionine conformers, which play key roles in determining the energy of the conformers, are also analyzed. The predicted geometries as well as the relative stabilities of the conformers suggest that the structural aspects and energies of the conformers may depend on the level of theory and the size of the basis set used. A comparison of the vibrational frequencies furnished in this study with the previous experimental and theoretical results obtained at MP2/6-31++G( d , p ) and B3LYP/6-311++G( d , p ) levels promotes the interpretation of the vibrational spectroscopy data on biologically relevant molecules.

The structural characterization of fused thiazolopyrimidine 1 (C₂₄H₂₄N₂O₄S) is performed using the single crystal X-ray study, the DFT calculation, and the Hirshfeld surface analysis. The molecular packing of the crystal is mainly stabilized by C-H…O and C-H…p interactions. A DFT calculated HOMO-LUMO energy gap of 3.90 eV indicates a high kinetic stability of the compound. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots are investigated for short contact interactions. The relative contribution of different interactions to the Hirshfeld surface indicates that the H…H, C…H, and O…H contacts account for about 83.4% of the total Hirshfeld surface area.

The titled imidazo compound can exist as three tautomers: OH, CH, and NH forms. Firstly, the OH tautomer is produced, which can be tautomerized to the CH and NH tautomers via the intramolecular-proton transfer. Herein, employing density functional theory and handling the solvent effects with the PCM model, the structural parameters, energy behavior, and also tautomerization mechanism of the tautomers are investigated. Based on the DFT results and the obtained-AIM parameters, the CH tautomer is considered to be the most stable one. Also, the CH tautomer is a kinetically and thermodynamically controlled product in tautomerization of the OH tautomer in a methanol solution.

The mechanism to generate azomethine ylide from formaldehyde and glycine is systematically investigated. The density functional theory at the B3LYP/6-311++G(d,p) level is employed for both geometry optimization and single point energy calculation. Our results indicate that two possible pathways can lead to the generation of the carbinolamine intermediate with a favorable step-wise pathway. However, as for the step to form azomethine ylide, a concerted elimination of water and carbon dioxide is preferred. This calculation result is totally different from the widely accepted revised Rizzi mechanism.

By applying a three-dimensional holographic vector of the atomic interaction field (3D-HoVAIF) to express the structure of three classical peptide drugs, quantitative structure activity relationship (QSAR) models are built by the multiple linear regression. The accuracy of the proposed model is illustrated using (cross-validation) and r ² (test set validation). Moreover, the r _m² metrics is used to further refine the predictive ability of the developed QSAR models. The results show that 3D-HoVAIF, due to the high predictive ability, offers a useful alternative to the costly and time-consuming experiments determining the bioactivity of peptide drugs.

In this work, the molecular geometry of heptachlor is investigated using ab initio HF, DFT, LDA, and GGA methods. The natural bond orbital (NBO) analysis is performed at the B3LYP/6-311++G(d,p) level of theory. The first order hyperpolarizability b_total, the mean polarizability Da, the anisotropy of the polarizability Da, and the dipole moment m, are calculated by B3LYP/6-311++G(d,p) and HF/6-311++G(d,p) methods. The first order hyperpolarizability (b_total) is calculated based on the finite field approach. UV spectral parameters along with HOMO, LUMO energies for heptachlor are determined in vacuum and the solvent phase using HF, DFT, and TD-DFT/B3LYP methods implemented with the 6-311++G(d,p) basis set. Atomic charges and electron density of heptachlor in vacuum and ethanol are calculated using DFT/B3LYP and TD-DFT/B3LYP methods and the 6-311++G(d,p) basis set. In addition, after the frontier molecular orbitals (FMOs), the molecular electrostatic potential (MEP), the electrostatic potential (ESP), the electron density (ED), and the solvent accessible surface of heptachlor are visualized as a results of the B3LYP/6-311++G(d,p) calculation. Densities of states (DOS), the external electric field (EF) effect on the HOMO-LUMO gap, and the dipole moment are investigated by LDA and GGA methods.

DFT calculations are employed to investigate the effects of the addition of a photoisomerizable stilbene unit to Aida's molecular scissors on relative energies, dipole moments, and kinetic stability according to HOMO-LUMO energy gaps and amplitude of the open-close motion of blade moieties. The most obvious finding emerging from this study is the coming into existence of a new pair of molecular scissors operated by two photoswitchable units. Based on photoisomerization of azobenzene and stilbene units, four conformations appear for these new molecular scissors: cis-cis, cis-trans, trans-cis, and trans-trans. The HOMO-LUMO energy gaps promise that all isomers are kinetically stable. The other important finding is that in these new molecular scissors the dihedral angle between the two blade moieties can be controlled and measured through the open-close motion and the blade parts can adopt two middle states in addition to open-close forms.

This paper reports the optimized geometrical parameters of the stationary point for 2,3-bis(furan-2-yl)pyrazino[2,3-f][1,10]phenanthroline. The calculations are performed using the density functional theory (DFT) method at the B3LYP/ LanL2DZ level. Bond lengths and bond angles are determined for the compound and the amount of bond hybridization is calculated according to the natural bond orbital theory (NBO). The energy of frontier orbitals (HOMO and LUMO) are computed. In addition, the calculated data are accurately compared with the experimental results. This comparison shows that our theoretical data are in reasonable agreement with the experimental values.

A time dependent quantum-mechanical QM study is performed on the Cl + CH₄ → HCl + CH₃ reaction, using a pseudotriatomic ab initio based surface. Probabilities present some clear peaks versus t, which we assign to transition state resonances where the light H atom oscillates between heavy Cl and CH₃ groups. For ground-state reactants, the reactivity is of quantum origin. The reaction occurs through an abstraction mechanism, following both direct and an indirect mechanisms. The calculations show the participation of a short-lived collision complex in the microscopic reaction mechanism. This theoretical result and other oscillating properties found here could, however, be related to the existence of resonance for the production of HCl, as suggested by experimentalists.

The torsional potentials, molecular structures, conformational stability, and vibrational wavenumbers for the rotational isomers of 2-formylfuran and 3-formylfuran are computed using the density functional theory (B3LYP) method with the 6-31+G* basis set. All structures are fully optimized and the optimized geometries, rotational constants, dipole moments, and energies are presented. From the computations, both 2-formylfuran and 3-formylfuran are predicted to exist predominantly in trans conformation with a cis-trans rotational barrier of 11.19 kcal/mol and 8.10 kcal/mol, respectively. The vibrational wavenumbers and the corresponding vibrational assignments of the molecules in the C_s symmetry are examined and the infrared spectra of the molecules are simulated using the wavenumbers and the corresponding intensities obtained from the computations. The effect of solvents on the conformational stability of all the molecules in nine different solvents (heptane, chloroform, tetrahydrofuran, dichloroethane, acetone, ethanol, methanol, dimethylsulfoxide, and water) is investigated. The integral equation formalism in the polarizable continuum model (IEF-PCM) is used for all solution phase computations.

The structure, spectroscopic, thermodynamic, and electronic properties of zoledronic acid (ZL,1-hydroxy-2-(1H-imidazol-1-yl)ethane-1,1-diyldiphosphonic acid), typical third-generation nitrogen-containing bisphosphonates (N-BPs), have been investigated systematically. Six conformations are taken into account, including three unprotonated and three protonated structures. They are optimized by four different density functional theory (DFT) methods combined with four different basis sets to evaluate their performance in predicting the structural and spectral features of ZL. Thermodynamic properties are calculated based on the harmonic vibrational analysis, including the standard heat capacity (C_p,m⁰), entropy (S_m⁰), and enthalpy (H_m⁰). The ¹H and ¹³C NMR chemical shifts are calculated using the GIAO method and compared with the experimental data. Molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) analyses are also performed to study the electronic characteristics of the title compound.

The study of the host-guest association of Morin hydrate (MO) with b-cyclodextrin (b-CD) and C-hexylpyrogllol[4]arene (C-HPA) is reported in this paper. The iInclusion complexation of MO is studied by ultraviolet-visible, steady-state fluorescence, time-resolved fluorescence, ¹H nuclear magnetic resonance (NMR), and two dimentional rotating-frame nuclear overhauser effect correlation (2D ROESY) spectroscopic techniques. The stoichiometry and the binding constant for the MO-b-CD complex are derived from the linearity of the Benesi-Hildebrand equation. The binding constant for the MO-C-HPA complex is calculated from the nonlinear curve fitting of fluorescence intensities. The effects of the acid strength on the absorption and fluorescence spectra of MO are studied in the absence and the presence of b-CD/C-HPA host molecules. The pK_a values of the ground and the excited states are reported.

The unassigned configurations of a toxic metabolite to mammals extracted from Neosartorya fischeri (fischerin) in C19, C20, C21, and C22 are assigned as R, R, R, and S, respectively. In this assignment, the extensive ab initio calculations followed by chemical shift computations are performed. Computed chemical shifts are correlated to experimental ones in order to find the correct configuration shown here.

The titled molecule 4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]-N-methylthiazol-2-amine (C₁₇H₂₂N₂S) is synthesized and characterized by ¹H NMR, ¹³C NMR, IR, and X-ray single crystal determination. The compound crystallizes in the monoclinic space group <i>P</i> 2₁/ c with <i>a</i> = 6.3972(4) Å, <i>b</i> = 9.4988(6) Å, <i>c</i> = 26.016(2) Å and β = 93.496(7)°. In addition to the molecular geometry from the X-ray determination, vibrational frequencies and gauge, including the atomic orbital (GIAO), ¹H and ¹³C NMR chemical shift values of the titled compound in the ground state are calculated using the density functional (B3LYP) method with 6-31G( d ), 6-31++G(<i>d,p</i>) and 6-311+G(2<i>d,p</i>) basis sets. The calculated results show that the optimized geometries can well reproduce the crystal structure. Moreover, the theoretical vibrational frequencies and chemical shift values show good agreement with the experimental values. The predicted nonlinear optical properties of the titled compound are greater than those of urea. DFT calculations of the molecular electrostatic potentials and frontier molecular orbitals of the titled compound are carried out at the B3LYP/6-31G(<i>d</i>) level of theory.

A pyridine-diimine compound <i>N,N'</i>-[pyridine-2,6-diyldi( E )methylylidene]bis(4-chloroaniline) is synthesised by a Schiff base condensation of 2,6-diformylpyridine with 4-chloroaniline in methanol and characterised by spectroscopic and analytical techniques. The molecular structure of the compound is determined by the single crystal X-ray diffraction study. The compound crystallizes in the monoclinic crystal system, I 2/ c space group with unit cell parameters a = 7.0843(12) Å, b = 6.1909(11) Å, c = 36.262(6) Å, β = 91.576(3)°, <i>V</i> = 1589.8(5) ų and <i>Z</i> = 4. There is an intermolecular hydrogen bonding in the molecule resulting in a 1D hydrogen bonding chain and these hydrogen bonding chains are linked by Cl…HC(aromatic) interactions forming a 2D network. Crystal packing of the compound is determined by Cl…HC and p-p interactions. In the fluorescence emission spectra in CH₃CN, DMF, DMSO and EtOH, the compound shows only one emission maximum.

The molecular structure of 2-methyl-5-nitro-5-bromo-1,3,2-dioxaborinane and its complex with pyridine is determined by single crystal X-ray diffraction. The structure of the synthesized compounds in the solution is also confirmed by the NMR spectroscopy data, and the conformational preference of their molecules is confirmed by the calculations using hybrid density functional theory.

The X-ray crystallographic analysis of 1,7-difluoro-1,1,3,5,7,7-hexanitro-3,5-diazaheptane has been carried out. We have also determined its sensitivity to mechanical actions and a set of calculated and experimental data on explosion characteristics.

We report here the synthesis of the Z-3N(2-ethoxyphenyl)-2-N¢(2-ethoxyphenyl)-imino-thiazolidin-4-one compound. The crystal structure is determined by X-ray diffraction. The compound crystallizes in the monoclinic system with the space group P 2₁/ n and cell parameters: a = 9.4094(10) Å, b = 9.3066(10) Å, c = 20.960(2) Å, b = 99.0375(10)°, V = 1812.7(3) ų and Z = 4. The structure is refined to final R = 0.05 for 2083 observed reflections. The molecule in the crystal exhibits the intermolecular hydrogen bonds of C-H…O, C-H…N, and C-H…S types. Ab initio calculations are also performed at Hartree-Fock (HF) and density functional theory (DFT) levels. The full HF and DFT geometry optimization is carried out using the 6-31G( d , p ) basis set. The observed molecular structure is compared with that calculated by both HF and DFT methods. The optimized geometry of the titled compound is found to be consistent with the structure determined by X-ray diffraction.

Sterically hindered meso -tetramethyl- meso -tetraarylcalix[4]pyrroles 1-4 where aryl is p -fluorophenyl 1, p- chlorophenyl 2, and p -methylphenyl 3, 4 (configurational isomers) are synthesized and purified by the recrystallization technique. They are characterized by IR, ¹H and ¹³C NMR, and mass spectroscopy. Configurational isomers aabb (3) and aaaa (4) of meso -tetramethyl- meso -tetramethylphenylcalix[4]pyrroles are assigned by the ¹H NMR studies and confirmed by the X-ray diffraction analysis. The single crystal X-ray diffraction analysis reveals that the ethanol adduct of 1, the acetone adduct of 2 and 3 adopt the 1,2-conformation while the acetone-water adduct of 1 and the acetone adduct of 4 adopt partial cone and cone conformations respectively. The conformational diversity is due to non-covalent interactions among the encapsulated guest, pyrrolic NH protons, and meso- substituents. Anion binding studies (F^-, Cl^-, CH₃COO^-, _{) are carried out through ¹H NMR titrations; the binding constants are evaluated using the EQNMR program, displaying that they are more selective towards fluoride rather than other anions with the 1:1 stoichiometry. The configuration of compounds drastically influences the ion-recognition processes.}

The synthesis of two 1,2,4-benzothiadiazine derivatives, namely, 6-bromo-4 H -spiro[1,2,4-benzothiadiazine-3,1¢-cyclobutane] 1,1-dioxide (1) and 6-bromo-1¢-ethyl-4 H -spiro[1,2,4-benzothiadiazine-3,4¢-piperidine] 1,1-dioxide (2) is described in the present work. The synthesized compounds were studied by IR, ¹H and ¹³C NMR, and single crystal X-ray diffraction to determine their molecular and crystal structure. In both structures the conformation of the 1,2,4-thiadiazinane ring is a twisted chair and is stabilized by the intramolecular interaction of the C-H…O type. Compound 1 crystallizes in the monoclinic crystal system and space group C 2/ c with the unit cell parameters a = 15.8690(17) Å, b = 12.1453(16) Å, c = 12.0152(15) Å, b = 99.686(7)°, Z = 8 and V = 2282.7(5) ų. Compound 2 crystallizes in the monoclinic crystal system and space group P 2₁/c with the unit cell parameters a = 14.5748(6) Å, b = 9.3340(5) Å, c = 12.4283(6) Å, b = 112.757(2)°, Z = 4 and V = 1559.14(13) ų. In the crystal structures different packing motifs are implemented with the formation of supramolecular assemblies of different types due to classical hydrogen bonds such as N-H…O and intermolecular interactions of N-H…Br, N-H…N, C-H…O types and p…p stacking.

A new chalcone derivative 1-phenyl-3-(4-bis(2-chloroethyl)aminophenyl)-2-propen-1-one with the molecular formula C₁₉H₁₉Cl₂NO is synthesized by the Claisen-Schmidt condensation reaction. A transparent yellow single crystal was obtained by the slow evaporation solution growth technique using ethanol at room temperature. The compound crystallizes in the triclinic crystal system, P -1 space group, Z = 4, calculated density = 1.332 mg/m³, V = 1736.00(8) ų with unit cell parameters a = 7.8899(2) Å, b = 14.1924(4) Å, c = 15.7879(4) Å, a = 83.1280(10)°, b = 81.929(2)°, g =86.4820°. The second harmonic generation efficiency is found to be 1.5 times higher than that of urea. Thermal stability of the crystal is found to be 250°C determined from the thermogravimetric analysis. The FT-IR spectroscopy is used to identify the functional groups of the synthesized compound. The optical behavior of the grown crystal is examined by the UV-visible spectral analysis, which shows that the absorbance is almost negligible in the wavelength range 400-1300 nm.

Novel bis-NO-acyclic Schiff base compounds are synthesized by the condensation of 3-methoxy-4-(2-(4-formyl-2-ethoxyphenoxy)ethoxy)benzaldehyde with 2-aminophenol (L¹) or 4-aminophenol (L²). The titled compounds with the monoclinic space group C 2/ c are characterized by elemental analyses and single crystal X-ray diffraction.

We report the synthesis and characterization of two new macrocyclic Schiff base compounds: a 15-membered (1) and 16-membered (2) one. Their synthesis involves a Schiff base condensation of 2,2-dimethylpropanediamine and two dialdehydes: 5,5¢-dimethoxy-2,2¢-(ethane-1,2-diyldioxy)dibenzaldehyde and 5,5¢-dimethoxy-2,2¢-(propane-1,3-diyldioxy)dibenzaldehyde. The compounds are characterized by elemental analysis (CHN), FT-IR, ¹H and ¹³C-NMR spectroscopy, and single crystal X-ray diffraction. Compound 1 crystallizes in the monoclinic space group Cc with a = 11.0668(5) Å, b = 11.7962(5) Å, c = 17.1980(9) Å, b = 103.611(5)°, V = 2182.08(18) ų, Z = 4, R ( F ² > 2s( F ²)) = 0.048 and wR ( F ²) == 0.150, while compound 2 crystallizes in the monoclinic space group C 2/ c with a = 38.4782(15) Å, b = 5.6309(2) Å, c = 20.4029(7) Å, b = 102.524(4)°, V = 4315.4(3) ų, Z = 8, R ( F ² > 2s( F ²)) = 0.051 and wR ( F ²) = 0.130.

By single crystal X-ray diffraction the features of the molecular and crystal structures of 2-morpholino-5-trifluoromethyl-1,3,4-thiadiazole are determined. This is the main substance of the certified reference material of trifluoromethylmorpholinothiadiazole for the quantitative elemental analysis of fluoroorganic compounds.

By the interaction of methyl 1-bromocyclobutanecarboxylate with zinc and ethyl 6-bromo-2-oxo-2Н-chromene-3-carboxylate, ethyl E-6-bromo-4-[1-(methoxycarbonyl)cyclobutyl]-2-oxochromene-3-carboxylate is obtained whose structure is determined by X-ray crystallography.

A series of fluoro- and hydroxy-substituted thiocarboxyhydrazones, 2-(3-fluorobenzylidene)-N-methylhydrazinecarbothioamide (1), 2-(2,3-difluorobenzylidene)-N-methylhydrazinecarbothioamide (2), and 2-(2-hydroxybenzylidene)-N-methylhydrazinecarbothioamide (3), are synthesized and characterized by elemental analysis, IR and UV-vis spectra, and single crystal X-ray diffraction. Structures of the three compounds are similar, but with a slight modification due to fluoro substituting groups. The crystal structures of the compounds are stabilized by hydrogen bonds and π⋯π interactions. The antimicrobial activity of the compounds shows that they are effective against some bacteria.

Two bromo-substituted Schiff bases 5-bromo-2-methoxy-4-( p -tolyliminomethyl)phenol (1) and 2-bromo-6-[(6-methylpyridin-2-ylimino)methyl]phenol (2) are prepared and characterized by elemental analysis, ¹H and ¹³C NMR, and single crystal X-ray diffraction. Compound 1 crystallizes in the triclinic space group _{with unit cell dimensions a = 6.228(1) Å, b = 10.929(2) Å, c = 21.312(2) Å, α = 104.230(2)°, β = 91.780(2)°, γ = 90.890(2)°, V = 1405.0(4) ų, Z = 4, R 1 = 0.0359, and wR 2 = 0.0830. Compound 2 crystallizes in the monoclinic space group P 21/ c with unit cell dimensions a = 8.180(2) Å, b = 12.011(3) Å, c = 12.843(3) Å, β = 106.263(2)°, V = 1211.4(4) ų, Z = 4, R 1 = 0.0364, and wR 2 = 0.0889. X-ray diffraction indicates that the Schiff base molecules of the compounds display trans configuration with respect to the C=N double bonds. The crystal structures of the compounds are stabilized by hydrogen bonds and weak π⋯π interactions.}

The single crystal X-ray analysis of 3-amino-1{[bis(benzylsulfanyl)methylidene]amino}urea shows that the compound crystallizes in the triclinic system with the space group P -1 and Z = 4. The asymmetric unit contains two independent molecules of 3-amino-1{[bis(benzylsulfanyl)methylidene]amino}urea. Both bis(benzylsulfanyl)methylidene groups are in a trans configuration with respect to the C16/O1/N3/N4 and C32/O2/N7/N8 fragments, respectively. The tautomeric transition energies of the three tautomeric forms are calculated at the generalized gradient approximation (GGA) level by the BLYP/DND method to estimate the kinetic and thermodynamic barriers. The keto form has a lower energy than the other two forms. Relatively lower values of kinetic barriers (about 58 kcal/mol for the transition between ( a ) and ( b ) forms) are found.

The title compound C₂₉H₂₈N₈O₄, 1,1¢-(propane-1,3-diyl)bis(5-benzyl-7-methyl-1H-pyrazolo[3,4-d]××pyrimidine-4,6(5H,7H)-dione) is characterized by single crystal X-ray diffraction. It crystallizes in the centrosymmetric space group P _{, with two molecules in the unit cell. There is one formula unit in the asymmetric unit with a folded conformation due to arene interaction and an unusually large angle of 124° in the propylene linker. The crystal structure is stabilized due to the presence of π-π and C-H…O interactions.}

8-(1-((5-Cyclopentenylpyridin-3-yl)methyl)piperidin-4-yl)-3,4-dihydroquinolin-2(1H)-one (1) and 8-(1-(3-cyclopentenylbenzyl)piperidin-4-yl)-3,4-dihydroquinolin-2(1H)-one (2) are synthesized and obtained in the crystalline state for X-ray diffraction studies. In the asymmetric unit of compound 1, there are two independent molecules (A and B) having similar conformations. In the crystals of compounds 1 and 2, individual molecules are linked by pairs of N-H⋯O hydrogen bonds forming A-A and B-B inversion dimers with _{(8) ring motifs. The dimers are stabilized by N-O hydrogen bonds and are linked via C-H⋯O short contact interactions, forming a three-dimensional and two-dimensional networks in 1 and 2 respectively. The network in 2 is further stabilized by a number of C-H⋯p interactions. Compounds 1 and 2 have a dual dopamine D2 and serotonin 5-HT1A receptor profile.}

The trans -[ReO₂(3,5-lut)₄]I₃ complex (trans-dioxotetra(3,5-lutidine)rhenium(V) triiodide) is obtained by the reaction of ReI₃ with 3,5-lutidine (3,5-lut) in acetonitrile. The structure is triclinic, space group PT, a = 8.5224(9) Å, b = 8.9607(9) Å, c = 12.6271(12) Å, α = 76.987(3)°, β = 73.932(3)°, γ = 65.500(3)°, V = 836.44(15) ų, Z = 1, d _calc = 2.040 g/cm³. Re atoms have an octahedral coordination environment formed by N atoms of 3,5-lutidine molecules and О atoms in the trans-position.