Experimental and theoretical structural studies on 4-(2-phenylethyl)-5-(2-furyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione

The structural and conformational features of 4-(2-phenylethyl)-5-(2-furyl)-2, 4-dihydro-3H-1,2,4-triazole-3-thione (1a), which can be related to the biological activity, have been investigated by X-ray diffraction and molecular modeling techniques. Ab initio method (RHF/6-31G) and density functional theory (B3LYP/6-31G(D)) have been used to calculate structural parameters, conformations, and relative energy of two tautomeric specious (1a and 1b) of the title compound. The geometry and the conformation of the thione form, 1a, is well reproduced by the DFT (B3LYP/6-31G(D)) method as compared with X-ray structure in which this form is found. The thione form is also predicted to be 14.42 kcal/mol more stable than the thiol form in the gas-phase by the DFT method.     

A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods

Conformational energies of different conformers have been calculated for a series of molecules using various molecular mechanics and semiempirical methods. The quality of the force fields has also been tested by calculating barriers to rotation about carbon-carbon bonds. The molecular mechanics force fields used are MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX, ver. Jan 89. The semiempirical methods used are AM1 and PM3. Molecules with different functional groups, for which good experimental data exist, have been selected. The semiempirical methods generally calculate barriers to rotation which are lower than the experimentally determined. The conformational energies for hydrocarbons are reasonably well reproduced by all tested methods although MM2(85) gives the quantitatively best agreement with experiments. For compounds containing oxygen, nitrogen and halogens MM2(85) gives results which are in best agreement with the experimentally determined values.     

AM1 calculations of rotation around essential single bonds and preferred conformations in conjugated molecules

Equilibrium twist angles, rotational barriers around essential single bonds, and preferred conformations for over 60 conjugated organic molecules were calculated using the semiempirical AM1 (Austin model 1) method. Comparison with ab initio and experimental data shows that AM1 can be applied quite successfully to conformational problems of this type. Relatively large errors are, however, found for compounds in which lone pair–hydrogen and especially lone pair–lone pair interactions are decisive for their conformational behavior. AM1-calculated rotational barriers in conjugated molecules, however, are found to be much too low. Moreover, AM1 does not seem to even correctly reproduce the trend of rotational barriers within a series of structurally related compounds. E/Z energy differences obtained by AM1 are also frequently considerably too low. In contrast to rotational barriers, their trends and thus conformational preferences, however, are quite satisfactorily calculated by this method. Ionization potentials obtained by AM1 are too high by about 0.5 eV. However, trends are quite well predicted.     

Molecular structures and spectroscopic characterization of cobalt(III) and nickel(II) complexes of <Emphasis Type="Italic">N</Emphasis>-(2-hydroxyethyl)-2-(thiophene-2-ylmethylene)-hydrazinecarbothioamide

Two complexes of a thiosemicarbazone ligand, namely N-(2-hydroxyethyl)-2-(thiophene-2-ylmethylene)-hydrazinecarbothioamide (HL), have been synthesized. The complexes have been characterized by physico-chemical and spectroscopic methods. The crystal and molecular structures of [CoL₃]·2MeOH (1) and [NiL₂] (2) have been determined by X-ray diffraction studies. For both complexes, the metal is coordinated through the sulfur and azomethine nitrogen atoms of the thiosemicarbazone. The ligand exists in its thiolate tautomeric form, and the central Co(III) and Ni(II) atoms have distorted octahedral and square planar geometries, respectively, with five-membered chelate rings formed by the ligand. The lattice of 1 shows infinite oxygen donor/acceptor hydrogen bonds in the ab plane and weak interactions between rings along the c axis, respectively, giving a supramolecular network. The molecular units in 2 are linked together by hydrogen bonds between the hydroxyl oxygen and hydrazone N proton, giving rise to an infinite ribbon extended along the c-axis. These chains are connected by N3–H3···O1 interactions that form a sheet within the ac plane.     

Synthesis,characterization and dynamic stereochemistry of thermochromic tris(dithiocarbamato)vanadium(III) complexes stereochemistry of thermochromic tris(dithiocarbamato)vanadium(III) complexes

The vanadium(III) complexes, V(S₂CNMe₂)₃ (1) and V(S₂CN ⁱ Pr₂)₃ (2) were prepared and characterized by analysis, IR, electronic and ¹H NMR spectra. The complexes show reversible thermochromic behaviour. MM2 calculations were used to simulate the molecular structure of 1. For 2, variable temperature ¹H NMR revealed hindered rotation about C–N bonds. The rotational energy barrier (38?kJ?mol^?1) was obtained by molecular mechanics force-field calculations.     

Conformational analysis of mono- and di-C-substituted derivatives ofcloso-3,3-[η2,3-(2-methylenebicyclo[2.2.1]hepta-2,5-dien-2-yl)]-1-R-2-R1-3,1,2-dicarbollylrhodium (R and R1=h, Me, or PhCH2)-(2-methylenebicyclo[2.2.1]hepta-2,5-dien-2-yl)]-1-R-2-R1-3,1,2-dicarbollylrhodium (R and R1=h, Me, or PhCH2)

A model has been developed that allows one to carry out molecular mechanics calculations of metallacarborane complexes with various ligands with the use of the MM3 program package. Based on X-ray structural data on a number of rhodium complexes in which the rhodium atom is coordinated by the η^2,3-norbornadienyl and η⁵-dicarbollyl ligands, a parameter set was developed for the compounds of the above-mentioned series. The use of this model made it possible to study the effects of various factors on the structures of the molecules ofcloso-3,3-(η^2,3-methylenenorbornadienyl)-1-R-3, 1,2-dicarbollylrhodium (R=Alk or ArAlk).     

Derivatives of 3-Deoxy-3-(N-Hydroxyamino)-D-Ribose

Abstract

A series of 3-(N-arylmethyl-N-hydroxyamino)-l,2-O-cyclopentylidene-3-deoxy-5-O-toluoyl-α-D-riboses has been prepared. The blocking groups used were chosen to allow an easy nucleosidation of these compounds to spin labelled analogs of natural nucleosides. The conformational behavior of the N-arylmethyl-N-hydroxyamino group has been studied using ³/_CH NMR coupling data and molecular mechanics computations. Upon spontaneous oxidation, these hydroxylamines led to the corresponding aminoxyl free radicals which were submitted to EPR spectroscopy and quantum mechanical computations at a semiempirical level (PM3).     

Synthesis and characterization of binuclear manganese(IV,IV) and mononuclear cobalt(II) complexes based on 2-(2-hydroxyphenyl)-1H-benzimidazole

The bidentate benzimidazolic hpbm (1), [2-(2-hydroxyphenyl)-1H-benzimidazole], was obtained under mild conditions, and its corresponding metal complexes, di-µ-oxo dimanganese(IV,IV) [Mn₂O₂(hpbm)₄ · 2Py · 5H₂O] (2), and mononuclear complex [Co(hpbm)₂] (3), were prepared and characterized. The crystal structures of 2 and 3 have been established by X-ray diffraction. Complex 2 consists of two six-coordinate manganese(IV) coordinated to two hpbm ligands and bridged by two O^2? with a Mn–Mn distance of 2.777 Å. For 3, a Co(II) is coordinated to two deprotonated hpbm in a nearly tetrahedral environment. Hydrogen bonds play pivotal roles in constructing the dimensional structures of both the compounds.     

3-(5-Substituted 2-Methoxyphenyl)-4-Nitro-2-Phenyl-5-Thiophene-2-yl-Isoxazolidines - Synthesis and Conformational Studies

Abstract

The synthesis of a new set of 2,3,4,5-substituted isoxazolidines having a sulfur containing heterocyclic moiety has been described. The structural features of the compounds have been analyzed by ¹H and ¹³C NMR spectroscopy as well as by single crystal X-ray studies.

[Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements for the following free supplemental resource: .cif file.]     

Experimental, theoretical and biological activity study on 1-(4,5-dihydro-3-arylpyrazol-1-yl)-2-(1H-1,2,4-triazol-1-yl)-ethanone

Four compounds have been synthesized and characterized by¹H NMR spectroscopy and elemental analyses, among which 1-(4,5-dihydro-3-phenyl-pyrazol-1-yl)-2-(1H-1,2,4-triazol-1-yl)ethanone 3a was further confirmed by X-ray crystallographic analysis. The biological activities of these compounds were tested, with the result that they displayed moderate fungicidal activities. In addition, a MO calculations using density functional theory (DFT) at B3LYP/6-31G^* level have also been carried out, and the structure–activity relationships for these compounds are discussed.     

Synthesis and Characterization of New Schiff Bases 2-(2-(2-(Aryl)Methyleneamino)Phenylthio) Ethylthio)-N-((aryl)Methylene)Benzeneamine

A series of Schiff bases containing four to six coordination sites N₂S₂ X₂(X = O,N) 2-(2-(2-(aryl)methyleneamino)phenylthio)ethylthio)-N-((aryl)methylene)benzeneamine (2c–f) were prepared from the reaction of 1,2-di(2-aminophenylthio)ethane (1) with aromatic aldehydes. All compounds were characterized by means IR, mass, ¹H and ¹³C NMR spectroscopy, and elemental analysis, and in the case of 2b with a single crystal X-ray diffraction. The X-ray crystal structure of 2b showed that the resonance occurs between aromatic rings, through the C=N bonds of the molecule.

Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.     

Synthesis, crystal and molecular structures, and steroechemical nonrigidity ofN-(chlorodimethylgermylmethyl)-andN-(bromodimethylgermylmethyl)-N-[(S)-1-phenylethyl]acetamides andN-(chlorodimethylgermylmethyl)-4-phenyl-2-pyrrolidone

RacemicN-(chlorodimethylgermylmethyl)-4-phenyl-2-pyrrolidone and the first optically active amide derivatives containing the asymmetrical carbon atom and the five-coordinate germanium atom,viz.,N-(chlorodimethylgermylmethyl)- andN-(bromodimethylgermyl-methyl)-N-[(S)-1-phenylethyl] acetamides, were synthesized. Their structures were established by X-ray diffraction analysis. The geometric characteristics of the trigonal-bipyramidal valence environment about the germanium atoms are compared with those of analogous enantiomeric silicon compounds and the related five-coordinate germanium compounds. The barriers to permutational isomerization of the title compounds were determined by dynamic¹H NMR spectroscopy. It was found that these barriers are higher than those of the corresponding silicon analogs. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 137–144, January, 2000.     

Regiospecific synthesis and structural study of some trifluoromethyl substituted dibenzosemibullvalenes

Summary Preparation of the regiospecifically trifluoromethyl substituted dibenzosemibullvalenes3 and5 is described. An unequivocal proof of chirality of3 and5 was obtained by enrichment of their enantiomers using liquid chromatography on triacetyl- or tribenzoylcellulose. The stereostructure of compounds3 to5 was proved by their¹H-NMR spectra and confirmed by X-ray crystallographic analysis. The geometrical data from X-ray structural analyses showed that five-membered rings involved in the skeleton of3 and5 adopt flattened envelope conformations. These results indicate also a significant substituent-induced bond length asymmetry in the cyclopropane rings of3 and5.Presented at the XIIIth IUPAC Symposium on Photochemistry, University of Warwick, Coventry, England, 1990     

Synthesis, crystal and molecular structures, and steroechemical nonrigidity ofN-(chlorodimethylgermylmethyl)-andN-(bromodimethylgermylmethyl)-N-[(S)-1-phenylethyl]acetamides andN-(chlorodimethylgermylmethyl)-4-phenyl-2-pyrrolidone

RacemicN-(chlorodimethylgermylmethyl)-4-phenyl-2-pyrrolidone and the first optically active amide derivatives containing the asymmetrical carbon atom and the five-coordinate germanium atom,viz.,N-(chlorodimethylgermylmethyl)- andN-(bromodimethylgermyl-methyl)-N-[(S)-1-phenylethyl] acetamides, were synthesized. Their structures were established by X-ray diffraction analysis. The geometric characteristics of the trigonal-bipyramidal valence environment about the germanium atoms are compared with those of analogous enantiomeric silicon compounds and the related five-coordinate germanium compounds. The barriers to permutational isomerization of the title compounds were determined by dynamic¹H NMR spectroscopy. It was found that these barriers are higher than those of the corresponding silicon analogs. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 137–144, January, 2000.     

Ab initio and molecular mechanics (MM2 and MM3) calculations of positively charged conjugated nitrogen-containing compounds

Ab initio calculations have been carried out on s-trans-N-vinylmethyleneammonium, pyridinium, and related compounds to obtain rotational barriers, structures, and vibrational frequencies. The restricted Hartree-Fock (RHF) level of theory with 6-31G** basis set was used for these calculations. In addition, the MM2(91) and MM3(94) force fields have been parameterized to calculate these positively charged nitrogen-containing compounds. A bond order term was incorporated in the force field to reproduce accurately the rotational barriers of s-trans-N-vinylmethyleneammonium and related compounds. Molecular mechanics geometries and vibrational frequencies compare well with those calculated by ab initio methods. © 1996 by John Wiley & Sons, Inc.     

5-(3,4-dichlorophenyl)-3-{[4-(2-pyridyl)piperazine-1-yl]methyl}-1,3,4-oxadiazole-2(3H)-one: Synthesis, characterization, X-ray and DFT structures

5-(3,4-Dichlorophenyl)-3-{[4-(2-pyridyl)piperazine-1-yl)]methyl}-1,3,4-oxadiazole-2(3H)-one C₁₈H₁₇Cl₂N₅O₂ (3) is synthesized and characterized by IR, ¹H NMR, ¹³C NMR, elemental analyses, single-crystal X-ray diffraction, and the molecular structure is also optimized at the B3LYP/6-31G(d,p) level using density functional theory (DFT). All data obtained from the spectral studies support the structural properties of 3. The molecules are linked principally by C-H??O hydrogen bonds involving carbonyl atoms and carboxylate O atoms, forming R ₂ ² (16) and R ₄ ² (20) rings that link to give a one-dimensional network of molecules. An extensive two-dimensional network of C-H??O hydrogen bonds and ?С??? interactions are responsible for crystal stabilization.     

Barriers to Internal Rotation and Conformational Behaviour of the MESO and D,L Isomers of Pt(II) Complexes with Antitumour Activity

Abstract

The conformational behaviour of a series of ring substituted (ortho-Cl, F and meta or para OH) Pt(II) complexes of general formula [(1,2-hydroxyphenyl)ethylenediamine]PtL₂ [L ? Cl, 1] has been studied by molecular mechanics (MM) methods. Preferred orientations of the phenyl rings, which are important for the complexes′ biological activity, were obtained by calculations of rotational energies about C_sp3?C_ar bonds for all theoretically possible isomers and conformers, meso-λ (R,S/S,R-λ), meso-δ (R,S/S,R-δ), d,l-δ (S,S/R,R-λ) and d,l-λ (S,S/R, R-δ). The influence of the ring substituents and the conformation type on the positions of the energy minima and barriers to rotations about C_sp3?C_ar and C_ar-O(H) bonds were investigated in detail. Theoretical predictions were compared with the experimental results where appropriate.     

Computational structural determination and energy landscape analysis of the hepatic carcinogen 2-(acetylamino)fluorene

 2-(Acetylamino)fluorene (AAF), a potent mutagen and a prototypical example of the mutagenic aromatic amines, forms covalent adducts to DNA after metabolic activation in the liver. A benchmark study of AAF is presented using a number of the most widely used molecular mechanics and semiempirical computational methods and models. The results are compared to higher-level quantum calculations and to experimentally obtained crystal structures. Hydrogen bonding between AAF molecules in the crystal phase complicates the direct comparison of gas-phase theoretical calculations with experiment, so Hartree–Fock (HF) and Becke–Perdew (BP) density functional theory (DFT) calculations are used as benchmarks for the semiempirical and molecular mechanics results. Systematic conformer searches and dihedral energy landscapes were carried out for AAF using the SYBYL and MMFF94 molecular mechanics force fields; the AM1, PM3 and MNDO semiempirical quantum mechanics methods; HF using the 3-21G*and 6-31G* basis sets; and DFT using the nonlocal BP functional and double numerical polarization basis sets. MMFF94, AM1, HF and DFT calculations all predict the same planar structures, whereas SYBYL, MNDO and PM3 all predict various nonplanar geometries. The AM1 energy landscape is in substantial agreement with HF and DFT predictions; MMFF94 is qualitatively similar to HF and DFT; and the MNDO, PM3 and SYBYL results are qualitatively different from the HF and DFT results and from each other. These results are attributed to deficiencies in MNDO, PM3 and SYBYL. The MNDO, PM3 and SYBYL models may be unreliable for compounds in which an amide group is immediately adjacent to an aromatic ring. Received: 26 May 2002 / Accepted: 12 December 2002 / Published online: 14 February 2003     

2-取代硫醚-5-(3,4,5-三甲氧基苯基)-1,3,4-噻二唑类化合物的合成、结构与体外抗癌活性

以天然产物没食子酸为原料经醚化、酯化、酰肼化、成盐、闭环、硫醚化六步反应合成了6个2-取代硫醚-5-(3,4,5-三甲氧基苯基)-1,3,4-噻二唑类衍生物, 釆用铟催化下水相合成目标化合物8, 具有反应条件温和, 合成收率高的特点; 用IR, ¹H NMR, ¹³C NMR和元素分析对各化合物进行了表征及结构确证, 并用X射线单晶衍射法测定了化合物8a [2-(2-氯-5-吡啶甲基)硫醚-5-(3,4,5-三甲氧基苯基)-1,3,4-噻二唑]的晶体结构, 采用MTT法进行了新化合物抑制PC3和BGC-823癌细胞体外试验, 结果表明在5μmol•L^－1浓度下化合物8e对PC3的抑制活性为55.71%. 化合物8b对BGC-823细胞抑制活性为66.21%.     

3-O-乙酰基熊果酸3-乙酰基-2-[(未)取代苯基]-2,3-二氢-1,3, -噁二唑-5-甲酯的合成及其抗炎活性研究

熊果酸与氯乙酸乙酯反应制得熊果酸乙氧甲酰基甲酯(2), 2与水合肼反应得到熊果酸甲酰肼甲酯(3), 3与羰基化合物反应得到一系列酰腙4a～4g, 再将4a～4g与乙酸酐作用, 环合得到3-O-乙酰基熊果酸3-乙酰基-2-[(未)取代苯基]-2,3-二氢-1,3,4-噁二唑-5-甲酯(5a～5g). 15个新化合物均未见文献报道, 其结构经¹H NMR, IR, MS加以确证, 并进行了药理结果筛选. 结果表明, 部分化合物具有良好的抗炎活性. 其中, 化合物5a (40 mg•kg^－1), 5d (40 mg•kg^－1), 5g (40 mg•kg^－1)与熊果酸相比, 具有更强的疗效.