Beta-alanine-hydrochloride (2:1) crystal: structure, 13C NMR and vibrational properties,protonation character

The crystal structure of beta-alanine-hydrochloride (2:1) complex (2A-HCl) has been determined by X-ray diffraction method at 298 and 100 K as monoclinic, space group C2/c, Z=4. The crystal comprises chloride anions and protonated beta-alanine dimers: two beta-alanine zwitterions are joined by strong, symmetric (Ci) hydrogen bond with the O...O distance of 2.473 A at room temperature. Powder FT-IR and FT-Raman as well as solid state 13C NMR spectra provide insights into the solid structure of this complex, character of its hydrogen bonds and the beta-alanine protonation.     

Sarcosine-maleic acid (1:1) crystal: structure, 13C NMR and vibrational properties,protonation character

The crystal structure of sarcosine-maleic acid (1:1) complex has been determined by X-ray diffraction method at 293 K as monoclinic, space group C2/c, Z=8. The crystal unit consists of semi-maleate and sarcosinium ions with two strong hydrogen bonds: the intramolecular one in the maleic part of the complex and the intermolecular one between sarcosinium and semi-maleate carboxylic groups. Phase transitions in this crystal are excluded. Its structure is in accordance with FT-IR, FT-Raman and 13C NMR study. Properties of the titled crystal and a family of similar amino acid-maleic acid systems are compared and discussed. Special attention is paid for relations between different structural and spectroscopic parameters as well as for character of hydrogen bonds formed in these crystalline complexes.     

Pseudorotaxane structure of a fullerene derivative--cyclodextrin 1:2 complex

X-Ray crystallography revealed that the C(60) derivative·γ-cyclodextrin (γ-CDx) complex has a pseudorotaxane structure and the structure of the crystal clarified the importance of multi-point hydrogen bonds between two γ-CDxs for stabilising the 3·γ-CDx complex.     

Crystal Structure of Human CD47 in Complex with Engineered SIRPα.D1(N80A)

Background: Targeting the CD47/SIRPα signaling pathway represents a novel approach to enhance anti-tumor immunity. However, the crystal structure of the CD47/SIRPα has not been fully studied. This study aims to analyze the structure interface of the complex of CD47 and IMM01, a novel recombinant SIRPα-Fc fusion protein. Methods: IMM01-Fab/CD47 complex was crystalized, and diffraction images were collected. The complex structure was determined by molecular replacement using the program PHASER with the CD47-SIRPαv2 structure (PDB code 2JJT) as a search model. The model was manually built using the COOT program and refined using TLS parameters in REFMAC from the CCP4 program suite. Results: Crystallization and structure determination analysis of the interface of IMM01/CD47 structure demonstrated CD47 surface buried by IMM01. Comparison with the literature structure (PDB ID 2JJT) showed that the interactions of IMM01/CD47 structure are the same. All the hydrogen bonds that appear in the literature structure are also present in the IMM01/CD47 structure. These common hydrogen bonds are stable under different crystal packing styles, suggesting that these hydrogen bonds are important for protein binding. In the structure of human CD47 in complex with human SIRPα, except SER66, the amino acids that form hydrogen bonds are all conserved. Furthermore, comparing with the structure of PDB ID 2JJT, the salt bridge interaction from IMM01/CD47 structure are very similar, except the salt bridge bond between LYS53 in IMM01 and GLU106 in CD47, which only occurs between the B and D chains. However, as the side chain conformation of LYS53 in chain A is slightly different, the salt bridge bond is absent between the A and C chains. At this site between chain A and chain C, there are a salt bridge bond between LYS53 (A) and GLU104 (C) and a salt bridge bond between HIS56 (A) and GLU106 (C) instead. According to the sequence alignment results of SIRPα, SIRPβ and SIRPγ in the literature of PDB ID 2JJT, except ASP100, the amino acids that form common salt bridge bonds are all conserved. Conclusion: Our data demonstrated crystal structure of the IMM01/CD47 complex and provides a structural basis for the structural binding interface and future clinical applications.     

A novel Zn(II) complex based on 1H-1,2,3-benzotriazol-1-ylacetic acid and 1H-1,2,3-benzotriazole ligands: Synthesis, crystal structure, and photoluminescent property

A novel complex formulated as [Zn(HBTA)₂(L)₂] · 2H₂O (I), where HL = 1H-1,2,3-benzotriazol-l-ylacetic acid, HBTA = 1H-1,2,3-benzotriazole, has been synthesized and structurally characterized by single crystal X-ray diffraction. Complex I shows a mononuclear structure, which is assembled into 1D chain via intermolecular π…π interactions and N-H…O hydrogen bonds. Different chains are linked by C-H…O hydrogen bonds into 2D layer. The photoluminescence property of the complex has been investigated.     

Organotin mefenamic complexes—preparations,spectroscopic studies and crystal structure of a triphenyltin ester of mefenamic acid: novel anti‐tuberculosis agents

The triphenyltin adduct of mefenamic acid, [SnPh₃L] ( 1 ), the monophenyltin complex [PhSnOL] _n ( 2 ), and the dibutyltin complex [SnBu₂L₂] (3), where HL is 2‐[bis(2,3‐dimethylphenyl)amino]benzoic acid (mefenamic acid), have been prepared and structurally characterized by means of vibrational, ¹H and ¹³C NMR spectroscopies. The crystal structure of 1 has been determined by X‐ray crystallography. X‐ray analysis revealed a pseudo‐pentacoordinated structure containing Ph₃Sn coordinated to the carboxylato group. The structural distortion is a displacement from the tetrahedron toward the trigonal bipyramid. Significant C? H–π interactions and intramolecular hydrogen bonds stabilize the structure 1. The polar imino hydrogen atom participates in intramolecular hydrogen bonds. Complex 1 is self‐assembled via C? H–π and stacking interactions. Vibrational and NMR data are discussed in terms of the crystal structure and the proposed structures for 1–3. Compounds 1 and 3 were tested for antimycobacterial activity against Mycobacterium tuberculosis H37Rv. Copyright © 2002 John Wiley & Sons, Ltd.     

A novel 1:2 cucurbit[8]uril inclusion complex with N-phenylpiperazine hydrochloride

A new 1:2 inclusion complex of cucurbit[8]uril (CB[8]) and protonated N-phenylpiperazine was synthesized and characterized by ¹H NMR and X-ray crystallography. The crystal structure showed that the phenyl rings of the two equivalents of guest encapsulated in the cavity of CB[8] are parallel to one another with a mean plane separation of 3.899 Å. In contrast, the piperazinyl phenyl ammonium moieties slightly protrude from the ureidyl carbonyl lined portals in order to accommodate the ion–dipole interaction between host and guest which provides a substantial driving force for the assembly. The oxygen atoms of the carbonyl groups form hydrogen bonds with the hydrogen atoms in both bridging methylene groups of CB[8] and water molecules. There are also hydrogen bonds formed among CB[8], water, and the protonated piperazinyl rings. These hydrogen bonds are formed between the ureidyl C=O groups and hydrogens in methylenes of piperazinyl rings; through hydrogen bonding N⁺–H···O(H)–H···O=C. The protonated piperazinyl rings connect the carbonyl groups with the bridging water molecules.     

Conformations and Self-association of Trifluoro-N-(3-formylcyclohept-2-en-1-yl)methanesulfonamide

The structure of trifluoro-N-(3-formylcyclohept-2-en-1-yl)methanesulfonamide and its self-association in solution have been studied by IR spectroscopy and quantum chemical methods [B3LYP/6-311G(d,p), AIM]; proton affinities of basic centers in its molecule have been evaluated. Trifluoro-N-(3-formylcyclohept-2-en-1-yl)methanesulfonamide in inert solvents forms cyclic dimers, whereas in crystal chain associates are more likely to be formed via hydrogen bonding between the NH and C=O groups of neighboring molecules. The carbonyl group in the title compound undergoes protonation only by the action of very strong trifluoromethanesulfonic acid. Weaker acids give rise to solvate H-complexes at the NH, C=O, and S=O groups. The topology of hydrogen bonds in dimers of different types has been analyzed in terms of the AIM theory.     

Crystal structures of dicarboxy-2,2'-bipyridyl complexes: the role of hydrogen bonding and stacking interactions

The crystal structures of three complexes of dicarboxy-2,2'-bipyridyl ligands, 5,5'-dicarboxy-2,2'-bipyridyl (1) and 4,4'-dicarboxy-2,2'-bipyridyl (2) are reported. [Rh(1H)3] shows two interpenetrating, homochiral rhombohedral networks linked by short carboxylate-carboxylic acid hydrogen bonds, in which each complex acts as a node for six hydrogen bonds. [Ru(1H2)(1H)2] forms only four such hydrogen bonds, leading to the formation of heterochiral chains held together by stacking between bipyridyls. [Co(2H)3] can in principle form six hydrogen bonds, but in practice forms only four in a layer structure where stacking interactions are important. This is attributed to differences in molecular shape.     

Crystal and molecular structure of 1:1 molecular complexes of triphenyl-N-(4-methylpyridyl-2)phosphinimine and triphenyl-N-(3-methylpyridyl-2)phosphinimine with perchloric acid

X-ray diffraction analysis has been used to determine the crystal structures of the 1:1-composition products of protonation by perchloric acid of isomeric triphenyl-N-(4-methylpyridyl-2)phosphinimine (1) and triphenyl-N-(3-methylpyridyl-2)phosphinimine (2). The structures were refined toR=0.048 andR=0.052, respectively, using 2274 (1) and 2647 (2) reflections. The protonation centers are located at the sites of N atoms of the pyridine ring (1) and the phosphinimino group (2). The distribution of the bond lengths in the cations suggests that a significant contribution is made by a phosphonic structure with positive charges localized on the P atoms. N-H...O hydrogen bonds, with lengths of 2.890(4) and 3.020(3) Å, connect cations and anions in both structures.A. N. Nesmeyanov Institute of Heteroorganic Compounds, Russian Academy of Sciences, 117813 Moscow. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 3, pp. 629–635, March, 1992.     

Synthesis of [L-Ala-1]RA-VII, [D-Ala-2]RA-VII,and [D-Ala-4]RA-VII by epimerization of RA-VII,an antitumor bicyclic hexapeptide from Rubia plants,through oxazoles

Three epimers of a natural cyclic hexapeptide RA-VII were prepared via formation of oxazoles from thioamides or thioimidates of RA-VII followed by hydrolysis. They are the epimers at l-Ala-1, d-Ala-2, and d-Ala-4, respectively. The one having l-Ala-1 adopted trans-cis-trans-trans-trans-trans (t-c-t-t-t-t) amide configurations in the crystal, a type-VI beta-turn for residues 1-4 stabilized by one intramolecular hydrogen bond between Ala-4 NH and l-Ala-1 C = O, and in CDCl(3) existed as a mixture of six conformers, of which the major conformer was very similar to that in the crystal, but quite different from that of RA-VII in solution. The second epimer, having d-Ala-2 had in the crystalline state t-t-t-t-c-t amide configurations, a gamma-turn at Tyr-3 stabilized by two intramolecular hydrogen bonds between d-Ala-2 NH and Ala-4 C = O and between Ala-4 NH and d-Ala-2 C = O, and existed in CDCl(3) as a single conformer, the structure of which was very similar to its crystal structure, and to the crystal structure of peptide 25 except for the backbone and the side chains at residues 1 and 2. The third epimer, having d-Ala-4 had t-c-t-t-c-t amide configurations in the crystal, a type-VI beta-turn for residues 1-4 as observed in the first epimer, and in CDCl(3) existed in three conformers, of which the major one was similar to that in the crystal but different from that of RA-VII in solution. The three epimers showed very weak cytotoxicity on P-388 leukemia cells, which may be because of their conformational differences from the active conformation of RA-VII.     

甘氨酸与间硝基苯甲酸加合物的合成及晶体结构

The title 1:1 adduct, has been prepared and a large single crystal with dimensions of 5 mm×50 mm×20 mm was obtained by slow-cooling method. It produces the green radiation at 532 nm under the irradiation of Nd~3+: YAG laser beam at 1064nm. The crystal structure of this potential non-linear optical material was determined by X-ray diffraction method. The crystal is orthorbombic, space group Pca2_1, with a=2.2701(5) nm, b=0.5852(2) nm, c=0.7815(2) nm, Z=4; final R is 0.054 for 702 observed reflections. The intermolecular hydrogen bonds are formed between the amino and carboxyl groups of glycines, which connect the glycine molecules to form two-dimensional network parallel to the (100) plane, while the intermolecular hydrogen bonds between the carboxyl group of glycine and the carboxyl group of m-nitrobenzoic acid let the latter link to above mentioned two-dimensional network.     

巯基乙酸锑(Ⅲ)配合物合成与晶体结构

以三氧化二锑和巯基乙酸在水溶液中反应合成了配合物HSb(SCH2COO)2,并通过元素分析、红外光谱、X射线粉末衍射进行了表征,利用单晶X射线四圆衍射法测定了晶体结构,结果表明该配合物晶体属于单斜晶系,C2/c空间群,晶胞参数为:a=1.40005(8)nm,b=1.19121(8)nm,c=1.23588(8)nm,β=126.822(1)°,V=1.6499(2)nm^3,Dc=2.439g·cm^-3,Z=8,R1=0.0250。并对X射线粉末衍射数据进行了指标化,其结果与单晶数据吻合。     

Synthesis and Crystal Structure of (2S,2'S,4'R)-2-(1-Hydroxy-1-ethylpropyl)-1-[(1'-p-tosyl-4'-hydroxypyrrolidin-2'-yl)methyl]pyrrolidine

1 INTRODUCTION In recent years, chiral β-amino alcohols have attracted much attention due to their special bio- logical functions and catalytic activities. Chiral β- amino alcohol moieties are usually found not only in natural products (e.g., cinchona alkaloids, ephe- drine, toxal, etc.) with special biological activities[1, 2], but also critical structural segments of some syn- thesized biologically active compounds, such as adrenergic agonists or antagolist[3, 4] and inhibitors for HI…     

Fluoride und Fluorosäuren. V. Kristallstruktur der 1:4-Phase im System Wasser-Fluorwasserstoff und eine neue Untersuchung einer der 1:2-Phasen

Fluorides and Fluoro Acids. V. Crystal Structure of the 1:4 Phase in the System Water-Hydrogen Fluoride and a New Investigation of One of the 1:2 Phases In the quasi binary system H₂O? HF the 1:2 phase of known crystal structure was recognized as the stable high-temperature phase. A more accurate redetermination of its structure (monoclinic, space group P2₁/c, Z = 4, a = 3.477, b = 6.024, c = 11.358 Å, β = 96.70° at ?100°C, R = 0.032 for 1356 observed MoKα data) confirmed the previous results of a layer structure formed by strong hydrogen bonds. H₃OF · HF appears besides H₃OHF₂ as a possible structural formula. — The crystal structure of the 1:4 phase of the system was also determined (triclinic, P1 , Z = 2, a = 5.574, b = 6.429, c = 6.874 Å, α = 115.79, β = 96.63, γ = 108.79° at ?113°C, R = 0.049 for 1942 observed MoKα data). By strong hydrogen bonds the atoms form rings, which are condensed to parallel ribbons. Possible structural formulae, based on the distribution of interatomic distances, are H₃OH₃F₄, H₃OH₂F₃ · HF and H₃OF · 3 HF. — Interatomic distances in the hydrogen bonds F? H…?F and O? H…?F of both structures and the known one of the 1:1 phase are discussed in comparison.     

咪唑配合物[Co(C3H4N2)6](PhCHCHCOO)2的合成及晶体结构

The complex [Co(Im)6](Cin)2 (Im=imidazole,Cin=cinnamate) was prepared by reaction of Co(PhCHCHCOO)2 with imidazole in ethanol. It has been determined by single crystal X-ray analyses. The crystals are triclinic, space group P, with a=9.7601(3),b=10.5935(3),c=11.3269(2)(A),α =69.948(1),β =71.027(1),γ =62.803(1)°, and Z=1. The crystal structure of the title complex consists of monomeric [Co(Im)6]2+ cations and cinnamate anions in which the cobalt(Ⅱ) ion assumes a centrosymmetric octahedral geometry with the CoN6 chromophore. In the solid state, the complex forms a three dimensional network through N-H… O hydrogen bonds, the intermolecular hydrogen bonds connect the [Co(Im)6]2+ cations and cinnamate anions.The cinnamate anions are nearly planar.     

分子动力学模拟研究质子化态在HIV-1 Protease-Indinavir复合物中的作用

I 型人体免疫缺陷病毒(HIV-1)蛋白酶中Asp25/Asp25'的质子化对于理论研究HIV-1 蛋白酶和抑制剂的作用机制
以及氨基酸变异对抗药性的影响有重要意义. 分别对Protease-Indinavir (PR-IDV)复合物的六种可能的质子化态进行了
5 ns 的分子动力学模拟, 分析了不同状态对动力学特征和结构的影响, 用molecular mechanics/Possion-Boltzman surface
area (MM-PBSA)方法计算了PR 和IDV 在各种状态下的结合自由能. 计算结果说明A 链Asp25 的OD2 的质子化是最
为可能的状态. 对PR-IDV 复合物中起到媒介作用的水分子与PR-IDV 复合物形成的氢键进行了分析, 分析结果说明不
同的质子化态对水分子在PR-IDV 复合物中所起的媒介作用没有影响, 这一结果与我们先前对PR-BEA369 复合物的研
究不同. 我们的研究结果为更高效的PR 抑制剂的设计以及PR 氨基酸变异对药物抗药性的研究提供了理论上的指导.     

Ring pucker in dihydroaromatic epoxides: The molecular structure ofr-1-hydroxy-t-2-methyl-t,t-3,4-epoxy-1,2,3,4-tetrahydronaphthalene

The crystal structure of the derivative of tetrahydronaphthalene with substituent epoxy, hydroxyl, and methyl groups in the more saturated ring (r-1-hydroxy-t-2-methyl-t,t-3,4-epoxy-1,2,3,4-tetrahydronaphthalene) has been determined. The hydroxyl and methyl groups are both found to beequatorial. The crystal structure is characterized by chains of molecules linked by O-H O hydrogen bonds involving the hydroxyl groups; these hydrogen bonds lie approximately parallel to theb axis. The conformations of the epoxide-bearing rings in various hydroxy epoxides are compared and shown to be similar.     

Synthesis and Crystal Structure of a Di-μ_2-phenolic Bridged Binuclear Manganese(Ⅲ) Schiff Base Complex

A new complex [Mn(L)(NCS)]2·0.5CH3CN (H2L = N,N'-bis(chlorosalicylidene)-1,2-diaminoethane) has been synthesized,and its structure (C70H51Cl8Mn4N13O8S4,Mr = 1833.84) was determined by single-crystal X-ray diffraction analysis. The crystal belongs to the monoclinic system,space group C2/c with a = 25.883(2),b = 12.3320(13),c = 13.5951(16) ,β = 112.906(2),V = 3997.2(7) 3,Z = 2,Dc = 1.524 g/cm3,μ(MoKα) = 1.050mm-1,F(000) = 1852,S = 1.098,the final R = 0.0630 and wR = 0.1847 for 2542 reflections with Ⅰ 2σ(Ⅰ). The centrosymmetric title complex contains a dimer in which two distorted octahedral Mn(Ⅲ) centers are bridged equatorially by phenolic oxygen of the Schiff base ligand. The units of the complex are linked via weak C-H···N hydrogen bonds,leading to the formation of 1D chains along the b axis. The weak π-π packing interactions and weak intermolecular C(3)-H(3)···N(3) hydrogen bonds stabilize the crystal structure.