Removing the C-terminal protecting group enlarges the crystal size: Z–(Gly–Aib)2–OH·H2O

2020 ◽  
Vol 76 (12) ◽  
pp. 1057-1061
Author(s):  
Renate Gessmann ◽  
Hans Brückner ◽  
Kyriacos Petratos
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Size ◽  
Crystal Packing ◽  
Strong Relationship ◽  
Symmetry Operation ◽  
Type I ◽  
Protecting Group ◽  
Intermolecular Hydrogen Bonds ◽  
Aminoisobutyric Acid ◽  
Intramolecular Hydrogen

The achiral tetrapeptide monohydrate N-(benzyloxycarbonyl)glycyl-α-aminoisobutyrylglycyl-α-aminoisobutyric acid monohydrate, Z–Gly–Aib–Gly–Aib–OH·H2O (Z is benzyloxycarbonyl, Aib is α-aminoisobutyric acid and Gly is glycine) or C20H28N4O7·H2O, exhibits two conformations related by the symmetry operation of an inversion centre. It adopts only one of two possible intramolecular hydrogen bonds in a type I (and I′) β-turn and forms a maximum of intermolecular hydrogen bonds partly mediated by water. The space group, the molecular structure and the crystal packing differ from two already described (Gly–Aib)2 peptides which vary only in the protecting groups. This structure confirms the high structural flexibility of Gly–Aib peptides and points to a strong relationship between intermolecular hydrogen bonding and crystal quality and size.

scholarly journals Tetrahydroberberine, a pharmacologically active naturally occurring alkaloid

2015 ◽  
Vol 71 (4) ◽  
pp. 262-265 ◽  
Author(s):  
Subramanya Pingali ◽  
James P. Donahue ◽  
Florastina Payton-Stewart
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Racemic Mixture ◽  
Inversion Center ◽  
Intermolecular Hydrogen Bonds ◽  
Naturally Occurring ◽  
Pharmacologically Active

Tetrahydroberberine (systematic name: 9,10-dimethoxy-5,8,13,13a-tetrahydro-6H-benzo[g][1,3]benzodioxolo[5,6-a]quinolizine), C20H21NO4, a widely distributed naturally occurring alkaloid, has been crystallized as a racemic mixture about an inversion center. A bent conformation of the molecule is observed, with an angle of 24.72 (5)° between the arene rings at the two ends of the reduced quinolizinium core. The intermolecular hydrogen bonds that play an apparent role in crystal packing are 1,3-benzodioxole –CH2...OCH3and –OCH3...OCH3interactions between neighboring molecules.

scholarly journals The Effects of the Solvents on the Macrocyclic Structures: From Rigid Pillararene to Flexible Crown Ether

2021 ◽  
Author(s):  
Shuangshuang Wang ◽  
Yanzhen Yin ◽  
Jian Gao ◽  
Xingtang Liang ◽  
Haixin Shi
Keyword(s):  
Hydrogen Bonds ◽  
Structural Design ◽  
Structural Features ◽  
Intermolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
Effect Of Solvents ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen ◽  
Macrocyclic Molecules ◽  
Polarity Of Solvents

The differences in the macrocyclic structures lead to different flexibilities, and yet the effect of solvents on the conformations is not clear so far. In this work, the conformations of four representational macrocyclic molecules (pillar[5]arene, p-tert-butyl calix[6]arene, benzylic amide macrocycle and dibenzo-18-crown-6) in three solvents with distinct polarity have been studied by all-atom molecular dynamics simulations. The structural features of the macrocycles in the solvents indicate that the conformations are related to the polarity of the solvents and the formation of hydrogen bonds. For the pillar[5]arene, the benzylic amide macrocycle and the dibenzo-18-crown-6, that cannot form intramolecular hydrogen bonds, the polarity of solvents is the major contributing factor in the conformations. The formation of intramolecular hydrogen bonds, in contrast, determinates the conformations of the calix[6]arene. Furthermore, the slight fluctuations of the structures will result in tremendous change of the intramolecular hydrogen bonds of the macrocycles and the intermolecular hydrogen bonds between the macrocycles and the solvents. The current theoretical studies that serve as a basis for the macrocyclic chemistry are valuable for the efficient structural design of the macrocyclic molecules.

scholarly journals Synthesis and crystal structures of a bis(3-hydroxy-cyclohex-2-en-1-one) and two hexahydroquinoline derivatives

2020 ◽  
Vol 76 (2) ◽  
pp. 125-131
Author(s):  
Scott A. Steiger ◽  
Chun Li ◽  
Christina Gates ◽  
Nicholas R. Natale
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Crystal Packing ◽  
Structural Features ◽  
Boat Conformation ◽  
Two Dimensional ◽  
Aryl Group ◽  
Dimensional Network ◽  
A Chain ◽  
Intramolecular Hydrogen

The title compound I, 2,2′-[(2-nitrophenyl)methylene]bis(3-hydroxy-5,5-dimethylcyclohex-2-enone), C23H27NO6, features a 1,3-ketone–enol conformation which is stabilized by two intramolecular hydrogen bonds. The most prominent intermolecular interactions in compound I are C—H...O hydrogen bonds, which link molecules into a two-dimensional network parallel to the (001) plane and a chain perpendicular to (1\overline{1}1). Both title compounds II, ethyl 4-(4-hydroxy-3,5-dimethoxyphenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C23H29NO6, and III, ethyl 4-(anthracen-9-yl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C29H29NO3, share the same structural features, such as a shallow boat conformation of the dihydropyridine group and an orthogonal aryl group attached to the dihydropyridine. Intermolecular N—H...O bonding is present in the crystal packing of both compound II and III.

Hydroxy Derivatives of Poststerone and Its Nontrivial 13(14→8)-Abeo-analogues: Synthesis, Crystal Packing, and Intermolecular Hydrogen Bonds

2021 ◽  
Vol 1227 ◽  
pp. 129509
Author(s):  
Rimma G. Savchenko ◽  
Ekaterina S. Mescheryakova ◽  
Kamil Sh. Bikmukhametov ◽  
Arthur R. Tulyabaev ◽  
Lyudmila V. Parfenova ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Intermolecular Hydrogen Bonds ◽  
Derivatives Of

The achiral tetrapeptideZ-Aib-Aib-Aib-Gly-OtBu

2014 ◽  
Vol 70 (11) ◽  
pp. 1046-1049 ◽  
Author(s):  
Renate Gessmann ◽  
Hans Brückner ◽  
Kyriacos Petratos
Keyword(s):  
Hydrogen Bonds ◽  
Butyl Ester ◽  
Relative Orientation ◽  
Asymmetric Unit ◽  
Intramolecular Hydrogen Bonds ◽  
Aminoisobutyric Acid ◽  
C Terminus ◽  
Intramolecular Hydrogen

The title achiral peptideN-benzyloxycarbonyl-α-aminoisobutyryl-α-aminoisobutyryl-α-aminoisobutyrylglycinetert-butyl ester orZ-Aib-Aib-Aib-Gly-OtBu (Aib is α-aminoisobutyric acid,Zis benzyloxycarbonyl, Gly is glycine and OtBu indicates thetert-butyl ester), C26H40N4O7, is partly hydrated (0.075H2O) and has two different conformations which together constitute the asymmetric unit. Both molecules form incipient 310-helices. They differ in the relative orientation of the N-terminal protection group and at the C-terminus. There are two 4→1 intramolecular hydrogen bonds.

N-(4-Methylbenzoyl)-N′-(4-methylphenyl)thiourea

2007 ◽  
Vol 63 (11) ◽  
pp. o4395-o4395
Author(s):  
S. Aminah A. Razis ◽  
M. Sukeri M. Yusof ◽  
A. Maisara Kadir ◽  
Bohari M. Yamin
Keyword(s):  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Intermolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
Compound C ◽  
Intramolecular Hydrogen

The title compound, C16H16N2OS, adopts a trans–cis configuration of the 4-methylbenzoyl and 4-methylphenyl groups, with respect to the thiono S atom across the thiourea C—N bonds. The dihedral angle between the two groups is 10.36 (8)°. The structure is stabilized by intermolecular hydrogen bonds which form dimers. There are also intramolecular hydrogen bonds.

scholarly journals Deprotonation of resorcinarenes and novel ammonium salt complexes

2014 ◽  
Vol 70 (a1) ◽  
pp. C678-C678
Author(s):  
Ngong Beyeh ◽  
Arto Valkonen ◽  
Fanfang Pan ◽  
Kari Rissanen
Keyword(s):  
Hydrogen Bonds ◽  
Binding Sites ◽  
Molecular Complexes ◽  
Ammonium Salts ◽  
Hydroxyl Groups ◽  
Binding Modes ◽  
Intermolecular Hydrogen Bonds ◽  
Guest Molecules ◽  
Cone Conformation ◽  
Intramolecular Hydrogen

The bowl shape cavity of resorcinarenes usually stabilized by four intramolecular hydrogen bonds offers an interesting array of binding modes such as C–H...π and cation...π interactions to recognize a variety of guests. The multiple hydroxyl groups can participate in a series of intermolecular hydrogen bonds with guest molecules. This unique cone conformation of resorcinarenes has led to the synthesis of many receptors with convergent arrangement of binding sites suitable for molecular recognition in many applications. Unfunctionalized resorcinarenes are known to easily form molecular complexes with guests of varying shapes and sizes. Amines are very common bases used in many catalytic processes. A good example is the use of amines as bases in the alkylation and acylation of resorcinarenes leading to cavitands, carcerands, hemicarcerands and velcrands. The use of amines in such reactions is to deprotonate the resorcinarene hydroxyl groups, hence facilitating the alkylation and acylation processes. The subsequently protonated ammonium cation then forms interesting supramolecular complexes with the anionic and dianionic resorcinarenes. Furthermore, secondary and tertiary ammonium salts possess hydrogen bond donating -NH2 and -NH respectively and these can further enhance their complexation through intermolecular hydrogen bonds. Here we present our recent examples of supramolecular assemblies resulting from the deprotonation of resorcinarenes by mono- and dibasic amines. Also, our latest supramolecular co-crystals between resorcinarenes as the receptors and a series of secondary and tertiary mono- and diammonium cations are illustrated.

Dicatharanthinium (2R,3R)-tartrate trihydrate

2006 ◽  
Vol 62 (4) ◽  
pp. o1414-o1416
Author(s):  
Sai-Feng Pei ◽  
Cui-Rong Sun ◽  
Mao-Lin Hu ◽  
Yuan-Jiang Pan
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Chair Conformation ◽  
Ring System ◽  
Indole Ring ◽  
Intermolecular Hydrogen Bonds ◽  
Water Solvent ◽  
Planar Conformation ◽  
Solvent Molecules ◽  
Tartrate Anion

The title salt, bis(methyl 3,4-didehydroibogamin-6-ium-18-carboxylate) (2R,3R)-tartrate trihydrate, 2C21H25N2O2 +·C4H4O6 2−·3H2O, contains two catharanthinium cations, a (2R,3R)-tartrate anion and three water solvent molecules. The cation contains an indole ring system with a planar conformation and a seven-membered nitrogen-containing ring with a distorted chair conformation. A network of O—H...O and N—H...O intermolecular hydrogen bonds stabilizes the crystal packing.

Heterocyclic Tautomerism. II. 4-Acylpyrazolones. X-Ray Crystal Structures of 4-Benzoyl-5-methyl-2-phenylpyrazol-3(2H)-one and 4-Acetoacetyl-3-methyl-1-phenylpyrazol-5-ol

1985 ◽  
Vol 38 (3) ◽  
pp. 401 ◽  
Author(s):  
MJ O'Connell ◽  
CG Ramsay ◽  
PJ Steel
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Room Temperature ◽  
Crystalline Form ◽  
Intermolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
X Ray ◽  
Intramolecular Hydrogen

The colourless crystalline form of the benzoylpyrazolone (2) has molecules with the NH structure (2c) stabilized by intermolecular hydrogen bonds. At room temperature crystals are monoclinic: P21/c, a 13.508(5), b 9.124(4), c 11.451(3)Ǻ, β 90.80(3)°, Z4; the structure was refined to R 0.059, Rw 0.048. The acetoacetylpyrazolone (3) has the OH structure (3c) with two intramolecular hydrogen bonds. At 193 K crystals are triclinic: Pī , a 7.142(2), b 13.704(8), c 14.699(7)Ǻ, α 117.36(3), β 96.87(3), γ 93.73(3)°, Z 4; the structure was refined to R 0.049, Rw 0.054.

scholarly journals Di-μ-chlorido-bis[chlorido(dimethylformamide-κN)(3,5-diphenyl-1H-pyrazole-κN2)copper(II)]

IUCrData ◽  
2018 ◽  
Vol 3 (8) ◽  
Author(s):  
Mercedes S. Naugle ◽  
Brittany T. Keller ◽  
Matthias Zeller ◽  
Curtis M. Zaleski
Keyword(s):  
Hydrogen Bonds ◽  
Pyrazole Ring ◽  
Chloride Anion ◽  
Monoclinic Space Group ◽  
Intermolecular Hydrogen Bonds ◽  
Coordination Environment ◽  
Pyramidal Geometry ◽  
Intramolecular Hydrogen ◽  
Square Pyramidal Geometry ◽  
Fourth Position

The title compound, [Cu2Cl4(C15H12N2)2(C3H7NO)2], Cu2(μ-Cl)2Cl2(3,5-diphenyl-1H-pyrazole)2(DMF)2, where DMF isN,N-dimethylformamide, crystallizes in the monoclinic space groupP21/n. The five-coordinate CuIIions have a distorted square-pyramidal geometry and are joinedviatwo μ-Cl anions. The coordination environment of each CuIIion is completed by a terminal chloride anion, a nitrogen-coordinated 3,5-diphenyl-1H-pyrazole molecule, and a DMF molecule. Two intramolecular hydrogen bonds exist in the molecule as the H atom of the protonated N atom of the 3,5-diphenyl-1H-pyrazole bonds to a terminal chloride anion of the adjacent CuIIcation. In addition, molecules are linked into a two-dimensional sheetviaweak C—H...Cl intermolecular hydrogen bonds. Each dimer hydrogen bonds to four neighboring molecules as the H atom of the C atom in the fourth position of the pyrazole ring bonds to a μ-Cl on a neighboring molecule.

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