Some features of the crystal and molecular structure of N-(1,2,4-triazol-5-yl)benzamidine and its hydrochloride

The crystal and molecular structures of N-(1,2,4-triazol-5-yl)benzamidine (1) and its hydrochloride (2) were determined by x-ray crystallography. In compound 1 both independent molecules are Z isomers of the anidine substituted in the imino group and 5-substituted 1H-1,2,4-triazoles. In the crystal the molecules of compound 1 are linked into a stable dimer by intermolecular hydrogen bonds. An undissociated HCl molecule was unexpectedly found in the structure of compound 2, while the structure of the base corresponded to the Z isomer of the amidine substituted in the amino group and to 2H-1,2,4-triazole substituted at position 5. The structures of compounds 1 and 2 are stabilized by an intramolecular hydrogen bond. The HCl molecule participates in the formation of intermolecular hydrogen bonds in compound 2.N. D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, 117913 Moscow. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 6, pp. 1380–1386, June, 1992.     

Studies of intramolecular hydrogen bonds (IMHB): crystal and molecular structure of 2-(2′-hydroxy-phenyl)imidazoles

The molecular and crystal structure of 2-(2′-hydroxyphenyl)imidazole (2) and 1-methyl-2-(2′-hydroxyphenyl)imidazole (5) have been determined by X-ray analysis. Compound (2) presents a strong intramolecular hydrogen bond (IMHB) responsible for the planarity of the molecule. In both compounds the molecules form chains through N---H…O (compound 2) and O---H…N hydrogen bonds (compound 5) but giving rise to the same packing mode. Ab initio calculations (6–31G**) have been carried out on both compounds in order to study the effect of the IMHB on the structure.     

Synthesis and crystal structure of 9,10-dihydro-9,10-etheno-1,8-dichloro-11-diphenylphosphinyl-12-(diphenylphosphinylethynyl)anthracene

The title compound, 9,10-dihydro-9,10-etheno-1,8-dichloro-11-diphenylphosphinyl-12-(diphenylphosphinylethynyl)anthracene (1), has been synthesized and its crystal structure has been determined. The compound 1 crystallized into the triclinic space group P-1 with =74.837(4)°, β=88.156(4)°, γ=65.398(4)°, Z=2, D_c=1.352 gcm⁻³. In the crystal structure of 1a, one chloroform molecule was included by the compound 1 with a 1:1 ratio and the existence of non-classical intermolecular C–HO hydrogen bonds, intramolecular C–HCl and C–HO hydrogen bonds and π–π stacking were observed.     

Synthesis, Crystal Structure and Bioactivities of 1-（4-Chlorophenyl）-3- [ 5-（pyrid-4-yl）- 1,3,4-thiadiazol-2-yl] urea

The title compound 1-(4-chlorophenyl)-3-[5-(pyrid-4-yl)-1,3,4-thiadiazol-2-yl]urea (C14H10ClN5OS, Mr = 331.79) has been synthesized by the reaction of 2-amino-5-(pyrid-4-yl)- 1,3,4-thiadiazole with 4-chlorobenzoyl azide, and its crystal structure was determined by single-crystal X-ray diffraction. The crystal belongs to triclinic system, space group P with a = 5.8550(8), b = 7.5668(10), c = 16.416(2) , α = 78.364(2), β = 81.204(2), γ = 84.749(2)°, V = 702.58(16) 3, Z = 2, Dc = 1.568 g/cm3, μ = 0.429 mm-1, F(000) = 340, the final R = 0.0442 and wR = 0.1092 for 2001 observed reflections (I > 2σ(I)). X-ray diffraction analysis reveals that the title molecule is nearly planar. In the crystal structure, the molecules are linked by strong intermolecular N-H…N hydrogen bonds together with weak nonclassical intermolecular (C-H…Y, Y = N, O and Cl) hydrogen bonds and stacked through π-π interactions. The preliminary bioassay shows that the title compound exhibits good fungicidal activities against Rhizoctonia solani, Botrytis cinerea and Dothiorella gregaria.     

Synthesis and X-ray diffraction study of 5-(8-methoxy-2-methyl-6,7-methylenedioxy-1,2,3,4-tetrahydroisoquinolin-1-yl)-1,3-dimethylbarbituric acid

The reaction of cotarnine with 1,3-dimethylbarbituric acid afforded 5-(8-methoxy-2-methyl-6,7-methylenedioxy-1,2,3,4-tetrahydroisoquinolin-1-yl)-1,3-dimethylbarbituric acid. Its crystal structure was established by X-ray diffraction analysis and the structure in solution was studied by ¹H NMR spectroscopy. This compound has a zwitterionic structure. In the crystal, the molecules are linked in dimers by intermolecular hydrogen bonds, and in solutions, the dimers occur in equilibrium with the monomers.     

The crystal structure of 5-amino-6-chloro-4-nitro-2-(β-D-ribofuranosyl)-2H-pyridazin-3-one

The nucleoside, 5-amino-6-chloro-4-nitro-2-β-D-ribofuranosyl-2H-pyridazin-3-one ( 4 ), was synthesized as part of a study to prepare potential chemotherapeutic compounds. An X-ray crystal structure study of the compound was initiated in order to substantiate its formula and to examine its conformation and absolute configuration. The structure was determined using direct methods and refined to an R of 0.020 (R_w = 0.024). The compound has a glycosyl torsion angle of 71.2°. The structure contains three intermolecular hydrogen bonds and one intramolecular hydrogen bond.     

Crystal structure of inclusion compounds: The complexes of thecis-syn-cis and thecis-anti-cis isomers of dicyclohexano-18-crown-6 with 4-methylbenzenesulfamide

The crystal structure of two complexes of the isomerscis-syn-cis (isomer A) andcis-anti-cis (isomer B) of dicyclohexano-18-crown-6 with 4-methylbenzenesulfamide have been determined by X-ray single crystal diffraction methods. The two structures have been solved by direct methods and refined to agreement values of 0.067 and 0.038 for isomers A and B respectively. The first isomer forms an inclusion compound with a host/guest ratio of 1 : I; the second one of I:2. The amino groups of the guest molecules are connected by N-H...O hydrogen bonds with oxygen atoms of the polyether molecules. The methyl groups of 4-methylbenzenesulfamide do not form hydrogen bonds.[/p]The host-guest interactions in the molecular complexes, the reciprocal influence of the two molecules on their conformation and the intermolecular contacts between the molecules in the crystal are discussed.     

Synthesis and Crystal Structure of 3-（ 2- Hydroxybenzly ）-4-（ 4- Hydro xybenzylideneamino ）-（1H） - 1,2,4- Triazole-5-Thione and Its Antibacterial Activities

1 INTRODUCTION 2. 1 Physical measurements Azole derivatives, such as pyrazole, imidazole, All solvent and chemicals were commercial rea- triazole(including benzotriazole), tetrazole and indole, gents and used without further purification. Ele- have extensive biological activities. They have be- mental analyses were performed on a PE 1700 CHN come the central focus of studies for agricultural che- auto elemental analyzer. IR spectra were recorded on micals, medicines, plant growth regul…     

Synthesis and Crystal Structure of （S）-Ethyl-2-（2-methoxy-phenylsulfenamido）-3-（1H-indol-3-yl）propanoate

With an aim to discover novel AHAS inhibitors,the title compound (S)-ethyl-2(2-methoxy-phenylsulfenamido)-3-(1H-indol-3-yl)propanoate (C 21 H 22 N 2 O 4 S,M r=398.47) has been synthesized and its crystal structure was determined by single-crystal X-ray diffraction analysis.The crystal belongs to orthorhombic,space group P2 1 2 1 2 1 with a=8.078(2),b=12.824(4),c=18.788(6),V=1946.2(10) 3,Z=4,F(000)=840,D c=1.360 mg/m 3,μ=0.197 mm-1,the final R=0.0433 and wR=0.1035 for 3075 observed reflections with I > 2σ(Ⅰ).The absolute structure Flack parameter X of this compound is 0.00(8).A total of 14375 reflections were collected,of which 3431 were independent (R int=0.0437).X-ray analysis reveals that the crystal structure involves two intermolecular N-H···O and one N-H···S intermolecular hydrogen bonds with the neighboring molecules.The crystal structure was compared with our previously reported (S)-methyl 2-(4-R-phenylsulfonamido)-3-(1H-indol-3-yl)propanoate (R=H(1) and Cl(2)),which provided some useful information of these compounds.     

Synthesis and Crystal Structure of a New Quinazolinone Compound 2,3-Dihydro-2-（2-hydroxyphenyl）-3-phenyl-quinazolin-4（1H）-one

A new quinazolinone compound 2,3-dihydro-2-(2-hydroxyphenyl)-3-phenylquinazolin-4(IH)-one 3 ([C2oH16O2N2]-C2H5OH, Mr = 362.42) and compound 2-(2-hydroxybenzylidene-amino)-N-phenyl-benzamide 2 (C2oH16O2N2, Mr = 316.34) were prepared from a precursor of 2-amino-N-phenyl-benzamide 1 (C13H12ON2, Mr = 212.25). Compound 3 was characterized by single-crystal X-ray diffraction analysis. The crystal belongs to orthorhombic,space group Pbca with a = 1.2889(11), b = 1.6170(14), c = 1.7729(15) nm, V= 3.695(6) nm^3, Z= 8, F(000) = 1536, Mr = 362.42, Dc = 1.303 g/cm^3, μ(MoKa) = 0.087 mm^-1, R = 0.0447 and wR= 0.0879. The crystal structure analysis indicates that the title compound has a two-dimensional network structure formed by hydrogen bonds and electrostatic interactions.     

A New Route to Z-5-Fluoro-2-methyl-1- （p-methylsulfinylbenzylidene）-3-indenylacetic Acid and Its X-ray Diffraction Analysis

The title compound(Sulindac)was prepared from the corresponding sulfinyl compound p-methylsulfinylbenzylbromide by four-step reaction.The sole product(Z)-5-fuoror-2-methyl-1-(p-methylsulfinylbenzylidene)-3-indenylacetic acid(Sulindac)was obtained and the E isomer of it was not found.X-ray single crystal diffraction analysisshowed that the strong intermolecular hydrogen bonding and weak intermolecular hydrogen bonding coexisted inSulindac.     

2-乙氨基-6H-5-(1-苯基-3-甲基/苯基-5-吡唑啉酮-4-基)-1,3,4-噻二嗪的合成和晶体结构

利用1-苯基-3-甲基/苯基-4-氯乙酰基-吡唑啉酮-5(PMCP/DPCP)与4-乙基氨基硫脲(ETSC)发生缩合反应,生成了2个新的双杂环化合物2-乙氨基-6H-5-(1-苯基-3-甲基/苯基-5-吡唑啉酮-4-基)-1,3,4-噻二嗪(PMCP-ETSC/DPCP-ETSC),并对其进行元素分析、红外光谱、核磁共振表征和晶体结构分析.PMCP-ETSC晶体属于单斜晶系,Pm空间群,晶胞参数:a=0.7947(1)nm,b=0.8348(1)nm,c=1.1990(2)nm,β=106.07(1)°,V=0.77269(2)nm3,Z=2,Dc=1.356g/cm3,μ=0.219mm-1,F(000)=332,R=0.0298,wR=0.0704.该化合物通过分子间氢键形成沿c轴无限延伸的一维链状结构.DPCP-ETSC晶体属于正交晶系,Pna21空间群,晶胞参数:a=1.1478(2)nm,b=1.3545(2)nm,c=1.1994(2)nm,V=1.8646(4)nm3,Z=4,Dc=1.345g/cm3,μ=0.194mm-1,F(000)=792,R=0.0345,wR=0.0694,此化合物通过分子间氢键形成沿c轴成链状,沿ab平面成波浪状的超分子结构.     

Synthesis of newN-acylantipyrylureas and the crystal structure ofN-benzoyl-N′-[4-(2,3-dimethyl-1-phenylpyrazol-5-one)]urea

New derivatives of acylheterylureas were synthesized by reactions of acylisocyanates with 4-amino-2,3-dimethyl-l-phenylpyrazol-5-one. The structures of the compounds obtained have been established by IR and¹H NMR spectroscopy.N-Benzoyl-N′-[4-(1-phenyl-2,3-dimethylpyrazol-5-one)]urea has been studied by X-ray structural analysis. It was found that the molecule adopts ananti-syn conformation stabilized by an intermolecular hydrogen bond. In the crystal, molecules are linked in centrosymmetric dimers via intermolecular hydrogen bonds.     

Synthesis and crystal structure of 2-{5-[2-(2,6-dichlorophenylamino)benzyl]-4-p-tolyl-4H-1,2,4-triazol-3-ylthio}acetate

The compound 2-{5-[2-(2,6-dichlorophenylamino)benzyl]-4-p-tolyl-4H-1,2,4-triazol-3-ylthio}acetate has been prepared and characterized by IR, ¹H NMR, ¹³C NMR and mass spectra. The crystal and molecular structure were further confirmed using single crystal X-ray diffraction. The crystal structure has been found to be stabilized by intermolecular C–H···O interaction generating bifurcated hydrogen bonds whereas the C–H···N interactions generate chain of molecules. The intramolecular N–H···N hydrogen bond forms a ring with S(7) graph-set motif.     

Synthesis,Crystal Structure and Antifungal Activity of N-（Pyridine-2-methyl）-2-（4- chlorophenyl）-3-methylbutanamide

A novel compound N-（pyridine-2-methyl）-2-（4-chlorophenyl）-3-methylbutanamide, a racemic compound, has been synthesized with 2-（4-chlorophenyl）-3-methylbutyric acid and pyridin- 2-methylanamine as the raw materials, and its crystal structure （C17H19C1N2O, Mr = 302.79） was determined by single-crystal X-ray diffraction analysis. The crystal belongs to monoclinic, space group P21/n with a = 9.624（9）, b = 23.14（2）, c = 15.626（15）A, β = 106.199（14）°, V = 3342（5） A^3, Z = 8, Dc = 1.204 g/cm^3,μ = 0.23 mm^-1, F（000） = 1280, S = 1.032, R = 0.0681 and wR = 0.1508 for 6513 unique reflections （Rint = 0.0421） with 3375 observed ones. In the crystal structure, there are some intermolecular hydrogen bonds which stabilize the crystal structure. The preliminary bioassay shows that the title compound exhibits good antifungal activity against Botrytis cinerea, Gibberella zeae, Dothiorella gregaria and Colletotrichum gossypii.     

Synthesis and Crystal Structure of Trans-4-[(5-(2,4-Dichlorophenoxy)-3-methyl-1-phenyl-1H-pyrazol-4-yl)methyleneamino]-1,5-dimethyl-2-phenyl-1,2-dihydropyrazol-3-one

The title compound trans-4-[(5-(2,4-dichlorophenoxy)-3-methyl-1-phenyl-1H-pyra-zol-4-yl)methyleneamino]-1,5-dimethyl-2-phenyl-1,2-dihydropyrazol-3-one 3 (C28H23Cl2N5O2, Mr = 532.41) has been synthesized and its crystal structure was determined by single-crystal X-ray diffraction analysis. It crystallizes in triclinic, space group P1 with a = 8.9438(4), b = 11.6065(5), c = 14.2215(6) , α = 112.566(1), β = 92.324(2), γ = 102.91(1)o, V = 1315.65(10) 3, Z = 2, Dc = 1.344 g/cm3, μ(MoKα) = 0.282 mm-1, λ = 0.71073 , F(000) = 552, the final R = 0.0587 and wR = 0.1578 for 5071 observed reflections (I > 2σ(I)). X-ray analysis reveals that the product is a thermodynamically stable trans isomer. Intra-and intermolecular C(12)-H(12)···O(1) and C(28)-H(28)···O(1)#1 hydrogen bonds were observed in the title compound.     

Synthesis and Crystal Structure of 4-tert-Butyl-6-（4-chlorophenyl）-3,6- dihydro-2H-1,3-thiazin-2-iminium Chloride

The title compound, 4-tert-butyl-6-（4-chlorophenyl）-3,6-dihydro-2H-1,3-thiazin- 2-iminium chloride （C14H18C12N2S）, has been synthesized by the reaction of 1-（4-chlorophenyl）- 4,4-dimethylpent-1-en-3-one with thiourea, and its crystal structure was determined by single- crystal X-ray diffraction. The crystal belongs to the monoclinic system, space group P211c with a = 16.3064（11）, b = 9.4471（6）, c = 11.2626 （8）A, β = 108.400（1）°, Z = 4, V = 1646.28（19） A^3, Mr = 317.26, Dc = 1.280 g/cm^3, S = 1.078,μ = 0.510 mm^-1, F（000） = 664, the final R = 0.0514 and wR = 0.1412 for 3210 observed reflections （I 〉 2σ（I））. The thiazine ring system displays a twisted boat conformation, and three N-H,..Cl hydrogen bonds exist in the crystal. The combination of two N-H...Cl hydrogen bonds generate an R2^1 （6） ring.     

A Theoretical Study on the Photochromic Mechanism of 1-Phenyl-3-methyl-4-（6-hydro-4-amino-5-sulfo-2,3-pyrazine）-pyrazole-5-one

The photochromic mechanism of 1-phenyl-3-methyl-4-（6-hydro-4-amino-5-sulfo-2,3- pyrazine）-pyrazole-5-one has been investigated using the density functional theory（DFT）. The solvent effect is simulated using the polarizable continuum model（PCM） of the self-consistent reaction field theory. According to the crystal structure of the title compound, an intramolecular proton transfer mechanism from enol to keto form was proposed to interpret its photochromism. Bader＇s atom-in-molecule（AIM） theory is used to investigate the nature of hydrogen bonds and ring structures. Time-dependent density functional theory（TDDFT） calculation results show that the photochromic process from enol to keto form is reasonable. The conformation and molecular orbital analysis of enol and keto forms explain why only intramolecular proton transfer is possible. The results from analyzing the energy and dipole moments of enol form, transition state and keto form in the gas phase and in different solvents have been used to assess the stability of the title compound.     

Synthesis and Crystal Structure of (E)-2-(1-(2-Hydroxy-4-methoxyphenyl)ethylideneamino)-3-(4-hydroxyphenyl)methyl Propionate

(E)-2-(1-(2-Hydroxy-4-methoxyphenyl)ethylideneamino)-3-(4-hydroxyphenyl)methyl propionate (C22H27O6N, Mr = 401.45) has been synthesized by a condensation reaction of paeonol with tyrosin methyl ester hydrochloride, and its structure was determined by IR, NMR, HR MS and X-ray single-crystal diffraction. The crystal belongs to the monoclinic system, space group P21/c, with a = 11.91291(15), b = 9.49947(12), c = 19.8727(3) , β = 106.1104(15)°, V = 2160.60(5)3, Z = 4, Dc = 1.234 g/cm3, μ = 0.739 mm-1, F(000) = 856, R = 0.0466 and wR = 0.1461 for 3859 observed reflections with (Ⅰ> 2σ(Ⅰ)). In the crystal structure, the title compound is constructed by a centrosymmetric dimmer unit composed of a pair of π-π stacking enantiomers, and such units are linked by intermolecular O(5)-H(5)…O(1) and intramolecular N(1)-H(1)…O(1) hydrogen bonds.     

Synthesis of rac-(1R,4aR,9aR)-2-methyl-1,3,4,9a-tetrahydro-2H-1,4a-propanobenzofuro[2,3-c]pyridin-6-ol. An unusual double rearrangement leading to the ortho- and para-f oxide-bridged phenylmorphan isomers

In an attempt to obtain the para-f isomer, rac-(1R,4aR,9aR)-2-methyl-1,3,4,9a-tetrahydro-2H-1,4a-propanobenzofuro[2,3-c]pyridin-6-ol, via mesylation of an intermediate 9[small alpha]-hydroxyphenylmorphan, we obtained, instead, a rearranged chloro compound with a 5-membered nitrogen ring, 7-chloro-3a-(2,5-dimethoxyphenyl)-1-methyl-octahydroindole. This indole underwent a second rearrangement to give us the desired para-f isomer. The structures of the intermediate indole and the final product were unequivocally established by X-ray crystallography. A resynthesis of the known rac-(1R,4aR,9aR)-2-methyl-1,3,4,9a-tetrahydro-2H-1,4a-propanobenzofuro[2,3-c]pyridin-8-ol, the ortho-f isomer, was achieved using the reaction conditions for the para-f isomer, as well as under Mitsunobu reaction conditions where, unusually, the oxide-bridge ring in the 5-phenylmorphan was closed to obtain the desired product. The synthesis of the para-f isomer adds an additional compound to those oxide-bridged phenylmorphans that were initially visualized and synthesized; the establishment of the structure and configuration of 8 of the theoretically possible 12 racemates has now been achieved. The X-ray crystallographic structure analysis of the para-f isomer provides essential data that will be needed to establish the configuration of a ligand necessary to interact with an opioid receptor.