Theoretical and experimental studies on the structure and isomerization of isocyano and cyano cyclopolyenes

Quantum-chemical calculations in terms of the density functional theory showed that cyclopolyenyl isocyanides RNC are considerably less stable than the corresponding cyanides and that they are capable of undergoing RNC → RCN isomerization according to both 1,2-shift mechanism (cyclopropenyl and cyclopentadienyl isocyanides; ΔE ^≠ = 35.0 and 37.5 kcal/mol, respectively) and previously unknown 2,5-sigmatropic shift mechanism (cycloheptatrienyl isocyanide, ΔE ^≠ = 26.4 kcal/mol). Migration of cyano group in the cyclopentadiene and cycloheptatriene systems follows the 1,5-sigmatropic shift pattern. The activation barrier to 1,5-shift of cyano group around the cycloheptatriene ring was estimated by dynamic NMR in deuterated nitrobenzene (ΔG _190°C ^≠ = 26.5 kcal/mol).     

Structure and fluxional behavior of pentamethoxycarbonylcyclopentadiene

Quantum-chemical calculations by the density functional theory method at the B3LYP/6- 311++G** level have shown that the fulvene form of pentamethoxycarbonylcyclopentadiene 1 in the gas phase is more favorable in energy than cyclopentadiene form 2 by ΔE_ZPE = 7.8 kcal/mol. The fluxional behavior of fulvene 1, detected by dynamic NMR can be explained by the mechanism of circular low-barrier 1,9-O,O'-H shifts accompanied by rotations of the hydroxymethoxymethylene substituent about the С=С bond with the activation barrier ΔE_ZPE= 23.5 (gas) and 20.9 (CH₂Cl₂) kcal/mol. This reaction path is 18.6 kcal/mol more favorable in energy than transition of fulvene 1 to cyclopentadiene 2 with subsequent 1,5- sigmatropic hydrogen shifts in the five-membered ring.     

Quantum-chemical simulation of structure and conformational flexibility of 5,7-di(<Emphasis Type="Italic">tert</Emphasis>-butyl)-2-(8-hydroxyquinolin-2-yl)-1,3-tropolone

Density functional theory [DFT B3LYP/6-311++G(d,p)] simulation has revealed stable tautomers and conformers of polydentate ligand system based on 5,7-di(tert-butyl)-2-(8-hydroxyquinolin-2-yl)-1,3-tropolone with different structures of the coordination nodes, capable of formation of metal chelates. It has been shown that the tautomeric NH- and OH- forms with exo and endo location of the hydroxy group in the quinoline fragments (close in energy, ΔE_ZPE = 0.2–2.4 kcal/mol) are stabilized by intramolecular hydrogen bonds. Energy barriers of the interconversion of these forms via rotation about the C–OH bond of the phenolic fragment are of ΔE_ZPE^≠ = 2.1–4.2 kcal/mol, whereas the barrier of rotation about the bond between the quinoline and tropolone fragments is higher (ΔE_ZPE^≠ = 18.2 and 19.6 kcal/mol).     

Kinetics of thermal reaction HOCl ⇄ H(<Superscript>2</Superscript><Emphasis Type="Italic">S</Emphasis>) + OCl(<Emphasis Type="Italic">X</Emphasis><Superscript>2</Superscript>Π<Subscript><Emphasis Type="Italic">i</Emphasis></Subscript>) in gas phase

The kinetics of gas reaction \(HOCl\underset{{k_r }}{\overset{{k_f }}{\longleftrightarrow}}H(^2 S) + OCl(X^2 \Pi _i )\) was analyzed by the MP4 method. In the temperature range of 100–373 K the rate constants k _f and k _r and equilibrium constant K were changed from 1.10 × 10^?220 to 1.17 × 10^?52 s^?1, from 2.89 × 10^?16 to 1.68 × 10^?5s^?1 and from 3.80 × 10^?205 to 6.96 × 10^?48 respectively. In the above temperature range, the activation energy of the forward reaction (E _f) is 105.05 kcal/mol. In the same temperature interval there are two kinetic domains for the reverse reaction with activation energies (E _r1 = 5.53 kcal/mol when T is 100–273 K and E _r2 = 14.50 kcal/mol when T is 273–373 K, respectively.     

Crystal structure and thermodynamic stability of an acetone solvate of bis(trifluoroacetylacetonato)copper(II)

A solvate [Cu(CF₃COCHCOCH₃)₂(CH₃COCH₃)] has been synthesized and characterized for the first time. According to X-ray structural data (diffractometer X8 APEX BRUKER, radiation MoK _α, T = 150 K), it crystallizes in the monoclinic crystal system, space group P2₁/c, a = 8.9940(4) Å, b = 22.3966(11) Å, c = 8.1884(3) Å, β = 92.705(2)°, V = 1647.59(12) ų, Z = 4, d _calc = 1.725 g/cm³, final R = 0.0272. The structure is molecular. In the equatorial plane the atom Cu(II) is surrounded with four oxygen atoms of two chelating ligands (CF₃COCHCOCH₃)^?; Cu-O distances 1.927–1.937 Å, O-Cu-O angles 86.18–93.30° and 170.18–175.67°. Square coordination of Cu is complemented to the square-pyramidal one by the oxygen atom of an acetone molecule behaving as an axial ligand; Cu-O_acetone 2.342 Å, O-Cu-O_acetone 89.66–100.11°. In the studied compound disorder of one of the chelate ligands implies the co-existance of the molecules in the cis- and trans-configuration in the crystal under ratio 54.6:45.4. In air the solvate rapidly degrades losing acetone, while in a sealed vessel melts around 313 K. Temperature dependence of equilibrium vapor pressure of acetone over the complex was measured with the static spoon gauge technique, thermodynamic characteristics of its dissociation process being derived: [Cu(CF₃COCHCOCH₃)₂(CH₃COCH₃)]_s = [Cu(CF₃COCHCOCH₃)₂]_s + CH₃COCH_3g, ΔH _av ⁰ = 49.6(3) kJ/mol, ΔS _av ⁰ = 152(1) J/(mol K), ΔG _av ⁰ = 4.30(2) kJ/mol.     

Sigmatropic hydrogen shifts in aryltetraphenylcyclopentadienes

Dynamic NMR has revealed intramolecular migrations of hydrogen atom over the periphery of the five-membered ring in 5-(p-tolyl)-1,2,3,4-tetraphenylcyclopentadiene in a deuteronitrobenzene solution with energy barrier ΔG ₁₈₀ ^≠ = 24.8 kcal/mol. Quantum-chemical DFT calculations B3LYP/6-311++G** have shown that such migrations in 1,2,3,4,5-pentaphenylcyclopentadiene in the gas phase occur in a chiral conformation of propeller type by the mechanism of 1,5-sigmatropic hydrogen shifts with retention of configuration through asymmetric transition state with energy barrier ΔE _ZPE ^≠ = 25.9 kcal/mol. Enantiomers P and M can readily interconvert into each other (ΔE _ZPE ^≠ = 3.9 kcal/mol) owing to synchronous flip rotations of the phenyl groups.     

<Emphasis Type="Italic">N</Emphasis>-allyl and <Emphasis Type="Italic">N</Emphasis>-propargyl trifluoromethanesulfonimides. Theoretical analysis

Tautomers of N-allyl- and N-propargyl-substituted trifluoromethanesulfonimides (CF₃SO₂)₂NR (R = CH₂CH=CH₂, Z/E-CH=CHMe, CH₂C≡CH, CH=CH=CH₂, C≡CCH₂) were calculated by the DFT (B3LYP, wB97XD, PBE1PBE), MP2, and CBS-QB3 methods. The results were compared with the theoretical data for the corresponding amines and amides NHRR¹ (R¹ = H, CF₃SO₂). It was shown that there is no conjugation between the nitrogen atom and C=C bond and that conjugation exists with the C≡C bond with electron density displacement toward the nitrogen atom. The calculations of anions derived from N-allyl- and N-propargyl-trifluoromethanesulfonimides revealed the possibility of their rearrangement with elimination of trifluoromethanesulfinate anion and formation of its H-complex with N-(prop-2-en-1-ylidene)trifluoromethanesulfonamide or N-(prop-2-yn-1-ylidene)trifluoromethanesulfonamide.     

<Emphasis Type="Italic">Ab initio</Emphasis> study of scandium fluoride molecules: ScF,ScF<Subscript>2</Subscript>, AND ScF<Subscript>3</Subscript>

Equilibrium geometric parameters, normal mode frequencies and intensities in IR spectra, atomization enthalpy, and relative energies of low-lying electronic states of scandium fluoride molecules (ScF, ScF₂, and ScF₃) are calculated by the coupled-cluster method (CCSD(T)) in triple-, quadruple, and quintuple-zeta basis sets with the subsequent extrapolation of the calculation results to the complete basis set limit. The ScF molecule is also studied by the CCSDT technique. The error in the approximate calculation of triple excitations in the CCSD(T) method does not exceed 0.002 Å for the equilibrium internuclear distance R _e, 4 cm^?1 for the vibrational frequency, and 0.2 kcal/mol for the dissociation energy of the molecule. In the ground electronic state \(\tilde X^2 \) A ₁(C _2ν ) of ScF₂ molecules, R _e(Sc-F) = 1.827 Å and α_e(F-Sc-F) = 124.2°; the energy barrier to bending (linearization) h = E _min(D _g8h ) ? E _min(C_2ν) = 1652 cm^?1. The relative energies of Ã²Δ _g and \(\tilde B^2 \)Π _g electronic states are 3522 cm^?1 and 14633 cm^?1 respectively. The bond distance in the ScF₃ molecule (\(\tilde X^1 \) A′₁, D _3h ) is refined: R _e(Sc-F) = 1.842 Å. The atomization enthalpies Δ_at H ₂₉₈ ⁰ of ScF _k molecules are 139.9 kcal/mol, 289.0 kcal/mol, and 444.8 kcal/mol for k = 1, 2, 3 respectively.     

A study of the polymerization of ethylene on Ti(III) monocyclopentadienyl compounds by the density functional theory method

Density functional theory was used to study model ethylene reactions with CpTi^IIIEt⁺A^? (A^? = CH₃B(C₆F₅) ₃ ^? , or B(C₆F₅) ₄ ^? ; A^? can be absent) compounds. The polymerization of ethylene on an isolated CpTiEt⁺ cation is hindered because of equilibrium between the CpTi(C₂H₄)Et⁺ primary complex and the primary product of CpTiBu⁺ insertion. At the same time, the polymerization of ethylene on CpTiEt⁺A^? ion pairs (A^? = CH₃B(C₆F₅) ₃ ^? or B(C₆F₅) ₄ ^? ) is thermodynamically allowed (ΔE from ?26.2 to ?25.6 kcal/mol and ΔG ₂₉₈ from ?10.9 to ?10.4 kcal/mol) and is not related to overcoming substantial energy barriers (ΔE ^# = 8.2?12.3 kcal/mol and ΔG ₂₉₈ ^≠ ) = 7.8?13.3 kcal/mol). The degree of polymerization can be low because of the effective occurrence of polymer chain termination by hydrogen transfer from the polymer chain to the monomer.     

<Emphasis Type="Italic">Ab initio</Emphasis> quantum-chemical study of vinylation of pyrrole and 2-phenylazopyrrole with acetylene in a KOH/DMSO system

Interaction between pyrrole and its 2-vinyl, 2-azo, and 2-phenylazo derivatives with acetylene in the gas phase and DMSO was studied using the MP2/6-311++G**//MP2/6-31G* ab initio approach and including the solvation effects within the framework of the continuum model. Possible reasons are considered for the hindered character of direct vinylation of azopyrroles with acetylene in superbasic media. The introduction of the azo group in the 2 position of the pyrrole ring leads to the increased stability of the pyrrole anion and increased acidity from pK _a = 22.1 for pyrrole and pK _a = 20.5 for vinylpyrrole to pK _a = 16.6 and 16.4 for 2-azopyrrole and 2-phenylazopyrrole, respectively. The binding energy between the pyrrole anion and the acetylene molecule decreases concurrently. The heat of formation of the pyrrole anion adducts with acetylene changes from ΔH = 4.8 kcal/mol for pyrrole to ΔH = 22.4 kcal/mol for 2-phenylazopyrrole. For all anion adducts under study, preferable isomers are Z isomers formed by the interaction of pyrrole anions with the cis-distorted acetylene molecule, but the formation of the E isomers corresponds to a lower activation barrier, which explains known Z stereoselectivity of the nucleophilic addition to monosubstituted acetylenes. When an azo group is introduced, the reaction becomes more endothermal, and the energy barriers to the formation of both Z and E isomers increase. Among other reasons for lowering of the activity of 2-arylazopyrroles during vinylation we consider possible reaction of acetylene addition at the most remote nitrogen atom of the azo group and participation of the anion center in cation chelation (K⁺ in the calculation).     

Crystal and molecular structure of <Emphasis Type="Italic">E</Emphasis>-3-(1,3-dimethylindol-2-yl)methylene-4-isopropylidenetetrahydrofuran-2,5-dione

The crystal and molecular structure of E-3-(1,3-dimethylindol-2-yl)methylene-4-isopropylidenetetrahydrofuran-2,5-dione, C₁₈H₁₇NO₃ (I), was investigated by XRD. The monoclinic structure of I (space group P2₁/c, a = 12.411(2) Å, b = 7.586(1) Å, c = 16.107(3) Å, β = 96.90(2)°, Z = 4) was solved by direct methods and refined by the full-matrix least squares in an anisotropic approximation to R = 0.044 for all 2842 independent reflections collected (CAD-4 automatic diffractometer, λCuK _α). The geometric parameters of sterically strained molecule I were determined with a high accuracy.     

Synthesis and crystal structure of 1-ethyl-3-(phenyl)-1,2,3-triazolium percholorate

The isolation of stable carbenes of the Arduengo (1a) and Wanzlick (2a) type has prompted us to look for stable nitrenium ions of the related structural type 1-ethyl-3-(phenyl)-1,2,3-triazolium perchlorate (6⁺). The title compound C₁₀H₁₄Cl N₃O₄ was isolated and structure was investigated by X-ray crystallography. It crystallizes in the monoclinic space group P2₁/c with cell parameters a=6.697(4) Å, b=9.724(9) Å, c=19.844(2) Å and Z=4. The final residual factor is R1=0.0471 for 1545 reflections with I>2σ(I). The structure exhibits intermolecular hydrogen bonds.     

Synthesis,characterization, molecular docking,analgesic, antiplatelet and anticoagulant effects of dibenzylidene ketone derivatives

In this study dibenzylidene ketone derivatives (2E,5E)-2-(4-methoxybenzylidene)-5-(4-nitrobenzylidene) cyclopentanone (AK-1a) and (1E,4E)-4-(4-nitrobenzylidene)-1-(4-nitrophenyl) oct-1-en-3-one (AK-2a) were newly synthesized, inspired from curcuminoids natural origin. Novel scheme was used for synthesis of AK-1a and AK-2a. The synthesized compounds were characterized by spectroscopic techniques. AK-1a and AK-2a showed high computational affinities (E-value >???9.0 kcal/mol) against cyclooxygenase-1, cyclooxygenase-2, proteinase-activated receptor 1 and vitamin K epoxide reductase. AK-1a and AK-2a showed moderate docking affinities (E-value >???8.0 kcal/mol) against mu receptor, kappa receptor, delta receptor, human capsaicin receptor, glycoprotein IIb/IIIa, prostacyclin receptor I₂, antithrombin-III, factor-II and factor-X. AK-1a and AK-2a showed lower affinities (E-value >???7.0 kcal/mol) against purinoceptor-3, glycoprotein-VI and purinergic receptor P₂Y₁₂. In analgesic activity, AK-1a and AK-2a decreased numbers of acetic acid-induced writhes (P?<?0.001 vs. saline group) in mice. AK-1a and AK-2a significantly prolonged the latency time of mice (P?<?0.05, P?<?0.01 and P?<?0.001 vs. saline group) in hotplate assay. AK-1a and AK-2a inhibited arachidonic acid and adenosine diphosphate induced platelet aggregation with IC₅₀ values of 65.2, 37.7, 750.4 and 422 µM respectively. At 30, 100, 300 and 1000 µM concentrations, AK-1a and AK-2a increased plasma recalcification time (P?<?0.001 and P?<?0.001 vs. saline group) respectively. At 100, 300 and 1000 µg/kg doses, AK-1a and AK-2a effectively prolonged bleeding time (P?<?0.001 and P?<?0.01 vs. saline group) respectively. Thus in-silico, in-vitro and in-vivo investigation of AK-1a and AK-2a reports their analgesic, antiplatelet and anticoagulant actions.     

Crystal and molecular structure of <Emphasis Type="Italic">tris</Emphasis>(<Emphasis Type="Italic">m</Emphasis>-chlorophenyl)phosphine selenide

The crystal and molecular structure of tris(m-chlorophenyl)phosphine selenide, C₁₈H₁₂Cl₃PSe (I), was investigated by X-ray diffraction (XRD) analysis. The trigonal rhombohedral structure of I (space group \(R\overline 3 c\), a = 14.110(2) Å, c = 32.360(4) Å, Z = 12) was solved by direct methods and refined by least squares in an anisotropic approximation (R = 0.029) for 1319 averaged measured reflections (CAD-4 automatic diffractometer, λCuK_α).     

Structure and Fluxional Behavior of Phenylmercury Derivatives of N,N'-Diarylform(benz)amidines

Activation barriers for fast 1,3-N,N' migrations of phenylmercury groups in the corresponding derivatives of N,N'-di(p-tolyl)form(benz)amidines have been calculated by density functional theory B3LYP/Gen, 6-311++G(d,p)/SDD to be ΔE _ZPE ^≠ = 4.5 and 3.0 kcal/mol. The results correspond to the data of dynamic NMR, which have shown the upper limit of activation barriers of these rearrangements (ΔG^≠) to be below 8 kcal/mol. The calculations have shown that the most stable is the E-syn form of N-phenylmercury-N,N'-di(p-tolyl)form(benz)amidines stabilized by supplementary intramolecular coordination of mercury atom with imine nitrogen atom of the amidine triad.     

Crystal structure of benzoic acid 4-nitrobenzylidenhydrazide

The crystal structure of benzoic acid 4-nitrobenzylidenhydrazide has been determined. Crystal data: crystal system — monoclinic, a = 7.101(9) Å, b = 25.48(3) Å, c = 7.730(11) Å; β = 112.43(9)°, space group P2₁/n, Z = 4, R = 0.038. The compound under investigation has a non-planar structure in general, and the substituents at azomethine N-C bond are in E-position. Root-mean-square planes of the six-memebered heterocycles make angles of 29.9° and 37.7° to fairly planar hydrazine fragment. In crystalline state the compound forms layers, the molecules within the layers being linked by C-H...O bonds. Neighboring layers are connected by hydrogen bonds between carbonyl oxygen atoms and amide hydrogens.     

Theoretical and experimental study of molecular structure and vibrational spectra of <Emphasis Type="Italic">N</Emphasis>-(2-pyridylmethyl)-2-pyrazinecarboxamide

N-(2-Pyridylmethyl)-2-pyrazinecarboxamide was prepared and its crystal structure was investigated by X-ray analysis. The compound crystallizes in the triclinic space group \(P{\bar 1}\) with a = 4.262(3), b = 12.117(9), c = 20.840(18) Å, α = 91.802(6), β = 89.834(7), γ = 91.845(6)°, V = 1075.2(16) ų, Z = 4, and D = 1.323?Mg/m³. The structure was solved by direct method and refined to R = 0.0699 and wR ₂ = 0.1268 by full matrix anisotropic least-squares method. Using the Hartree-Fock and density functional method (B3LYP) with 6-31G(d) basis set, the molecular geometry and vibrational frequencies of the title compound has been investigated and compared with experimental ones from experimental studies. The optimized bond lengths obtained by RHF method and bond angles obtained by B3LYP method show better agreement with the experimental values. The vibrations computed of the title compound by the RHF and DFT methods are in good agreement with the observed IR spectra data.     

Electron diffraction and quantum-chemical studies of the molecular structure of 2-methylbenzenesulfochloride

A combined electron diffraction and quantum-chemical (MP2/6-31G**) study of the molecular structure of 2-methylbenzenesulfochloride at 336(5) K was carried out. It was found that the gas phase contained only one conformer, C ₁. The following structural parameters were obtained: r _h1(C-H)_av = 1.095(8) Å, r _h1(C-C)_Ph = 1.402(4) Å, r _h1(C_Ph-C_meth) = 1.507(13) Å, r _h1(C_Ph-S) = 1.763(6) Å, r _h1(S=O) = 1.418(4) Å, r _h1(S-Cl) = 2.048(5) Å, ∠(H-C-H)_meth/av = 107.3(96)°, ∠(Cl-S-O)_av = 106.4(3)°, ∠C_Ph-S-Cl = 100.8(9), ∠O=S=O = 120.8(10)°. The C_C-C_S-S-Cl torsion angle that defines the position of the S-Cl bond relative to the plane of the benzene ring is 75.6(20)°. The B3LYP/6-311+G** calculated barriers of internal rotation of the methyl and sulfochloride groups are 1.2 kcal/mol and V ₀₁ = 10.2 (V ₀₂ = 4.1) kcal/mol, respectively.     

Characteristics of the hydrogen bond and the structure of Н-complexes of <Emphasis Type="Italic">p</Emphasis>-n-propyloxybenzoic acid and <Emphasis Type="Italic">p</Emphasis>-n-propyloxy-<Emphasis Type="Italic">p</Emphasis>′-cyanobiphenyl

The conformational properties of p-n-propyloxybenzoic acid and p-n-propyloxy-p′-cyanobiphenyl molecules, which can exhibit liquid crystalline properties in the formation of Н-complexes, are studied (DFT/B3LYP)/cc-pVTZ method). It is found that a molecule of p-n-propyloxybenzoic acid has 16 conformers that can be divided into four groups with respect to relative energies (0 kcal/mol, 1.6 kcal/mol, 6.5 kcal/mol, and 8.1 kcal/mol), and a molecule of p-n-propyloxy-p′-cyanobiphenyl has six conformers with relative energies of 0 kcal/mol (two conformers, φ(С_Ph–O–C–C)=180°) and 1.6 kcal/mol (four conformers, φ(С_Ph–O–C–C)=64.4°). In all conformers of the 3-AOCB molecule, phenyl rings are turned at 35° relative to each other. A conformation with the planar arrangement of two rings has a higher energy by 1.5 kcal/mol. Barriers to the internal rotation of different groups are determined and it is established that the structural nonrigidity of the molecules is mainly due to the possible rotation of the–C₂Н₅ moiety about the C–C bond. It is shown that with increasing temperature the vibrational amplitudes of the OC₃H₇ substituent, which enhance the probabilities of transitions between the conformers, become appreciably larger. It is found that p-n-propyloxybenzoic acid and p-n-propyloxy-p′-cyanobiphenyl can form Н-complexes with the medium hydrogen bond. Two types of the structural organization of Н-complexes are considered: linear and angular. The similarity of energies of Н-complexes with different structures (NBO analysis) can be the reason for the occurrence of two liquid crystalline subphases of p-n-propyloxybenzoic acid and p-n-propyloxy-p′-cyanobiphenyl system.