Contributions of secondary alcohol–ketone O—H...O=C and furan–acetate Csp 2—H...OOC synthons to the supramolecular packings of two bioactive molecules

2021 ◽  
Vol 77 (6) ◽  
Author(s):  
Patrice Kenfack Tsobnang ◽  
Armelle Tsamo Tontsa ◽  
Yves Alain Mbiangué ◽  
Pamela Kemda Nangmo ◽  
Saurelle Kenfack Tiofack ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Crystal Packing ◽  
Secondary Alcohol ◽  
Bioactive Molecules ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Space Group ◽  
Structural Database ◽  
First Time ◽  
Twist Boat

The crystal structures of rubescin D (1, C26H30O5) and monadelphin A (2, C30H36O11), bioactive molecules of the vilasinin and gedunin classes of limonoids, respectively, are reported for the first time and the synthons affecting their crystal packings are analyzed on the basis of their occurrences in molecules in the Cambridge Structural Database that share the same moieties. Rubescin D, 1, crystallizes in the space group P21 and its molecular structure consists of three six-membered rings A, C and D having, respectively, envelope, twist-boat and half-chair conformations, and three five-membered rings with half-chair (B and E) and planar conformations (F). Many synthons found in the crystal packing of 1 are in agreement with expectations derived from molecules displaying the same moieties. However, the secondary alcohol–ketone O—H...O=C synthon, which has a low occurrence (2.9%), contributes much to the layered packing, while the furan–ketone Csp 2—H...O=C and secondary alcohol–epoxide O—H...OC2 synthons usually found in these compounds (occurrences of 20.6 and 17.6%, respectively) are missing. The packing of 1 is close to that of ceramicine B (3), but is completely different from that of TS3 (4), suggesting that the absence of the epoxide group in 3 would have favoured the furan–secondary alcohol Csp 2—H...OH synthon and that the missing hydroxy group in 4, a strong hydrogen-bond donor, would have favoured the involvement of water molecules in the crystal packing. The molecular structure of monadelphin A, 2, consists of four six-membered fused rings (A, B, C and D) and one five-membered ring (E); they have twist-boat (A and C), chair (B), screw-boat (D) and planar (E) conformations. The molecule crystallizes in the space group P212121 with the contribution of many synthons usually found in compounds having the same moieties. However, the secondary alcohol–acetate O—H...OOC and secondary alcohol–ketone O—H...O=C synthons (occurrences of 16.7% each in these compounds) are missing. The furan–acetate Csp 2—H...OOC synthon not observed in these compounds greatly contributes to the layered packing of 2. The layered packing is very close to those of 7-oxogedunin (5) and 6-dehydro-7-deacetoxy-7-oxogedunin (6), which both crystallize in the space group P21.

scholarly journals Towards an understanding of the propensity for crystalline hydrate formation by molecular compounds

IUCrJ ◽  
2016 ◽  
Vol 3 (6) ◽  
pp. 430-439 ◽  
Author(s):  
Alankriti Bajpai ◽  
Hayley S. Scott ◽  
Tony Pham ◽  
Kai-Jie Chen ◽  
Brian Space ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Crystal Packing ◽  
Hydrate Formation ◽  
Crystalline Hydrate ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Screening Experiments ◽  
Group Form ◽  
Structural Database ◽  
Molecular Compounds

Hydrates are technologically important and ubiquitous yet they remain a poorly understood and understudied class of molecular crystals. In this work, we attempt to rationalize propensity towards hydrate formation through crystallization studies of molecules that lack strong hydrogen-bond donor groups. A Cambridge Structural Database (CSD) survey indicates that the statistical occurrence of hydrates in 124 molecules that contain five- and six-memberedN-heterocyclic aromatic moieties is 18.5%. However, hydrate screening experiments on a library of 11N-heterocyclic aromatic compounds with at least two acceptor moieties and no competing hydrogen-bond donors or acceptors reveals that over 70% of this group form hydrates, suggesting that extrapolation from CSD statistics might, at least in some cases, be deceiving. Slurrying in water and exposure to humidity were found to be the most effective discovery methods. Electrostatic potential maps and/or analysis of the crystal packing in anhydrate structures was used to rationalize why certain molecules did not readily form hydrates.

scholarly journals Synthon robustness by C-F groups in halogen substituted N-benzylideneanilines

2014 ◽  
Vol 70 (a1) ◽  
pp. C1811-C1811
Author(s):  
Gurpreet Kaur ◽  
Angshuman Roy Choudhury
Keyword(s):  
Crystal Structure ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Topological Analysis ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor ◽  
The Impact ◽  
Organic Fluorine

The arrangement of the molecules in their crystal structure is controlled by the non-covalent intermolecular interactions other than the effectual space filling. The role of strong hydrogen bonds in guiding the crystal packing is well-known in the literature. But, how significant are the weak interactions in the field of crystal engineering, has yet not been fully understood. Our aim is to comprehend the nature and strength of the weak interactions involving fluorine in guiding the packing of small organic molecules in their respective crystal structure. The reason being the controversies, which are involved regarding the interactions offered by "organic fluorine"[1] and also due to the importance of these interactions in the pharmaceutical industry. Some of the research groups indicate the incapability of interactions offered by fluorine in the formation of supramolecular motifs, whereas other groups have indicated that substantial role is being played by fluorine in constructing the lattice through C-H···F, C-F···F and C-F···π interactions in the presence and absence of strong hydrogen bond donor and acceptor groups. To understand more about these interactions, we have chosen a model system of halogen substituted N-benzylideneanilines[2]. In this system, we have analysed the impact of fluorine mediated interactions on the crystal packing by having fluorine as a substituent on both the phenyl rings. Then the robustness of the synthons offered by organic fluorine has been anticipated in the same system, but with one of the substituent as chlorine or bromine in either of the phenyl ring. It has been observed that the replacement of the non-interacting fluorine by its heavier analogue has not altered the supramolecular motif, which was formed by the other fluorine. But the crystal packing has been found to be completely altered in the molecules where the interacting fluorine was replaced by its heavier analogue. Salient features of our computational studies, which include the calculation of the stabilization energies of the studied dimers using MP2 method and their topological analysis using AIM2000, to support the experimental observations will also be presented to highlight the sturdiness of the synthons formed by so called "organic fluorine".

scholarly journals (1S,5R,7R,30S)-14-Deoxyisogarcinol

2012 ◽  
Vol 68 (6) ◽  
pp. o1861-o1862 ◽  
Author(s):  
Ranjeet Kaur ◽  
Prema G. Vasudev ◽  
Sunil K. Chattopadhyay
Keyword(s):  
Title Compound ◽  
Large Scale ◽  
Crystal Packing ◽  
Optical Rotation ◽  
Database Analysis ◽  
Relative Configuration ◽  
Garcinia Indica ◽  
Compound C ◽  
Structural Database ◽  
First Time

The title compound, C38H50O5 {systematic name: 10-(3-hydroxybenzoyl)-2,2,7,7-tetramethyl-3,6,8-tris(3-methylbut-2-enyl)-3,4,4a,5,6,7-hexahydro-4a,8-methano-2H-cycloocta[b]pyran-9,11(8H)-dione}, is a polyisoprenylated benzophenone, isolated for the first time from the fruits of Garcinia indica during our investigation of bioactive compounds from this plant and their large-scale extraction. The relative configuration of the title compound was chosen based on comparison of its spectroscopic and optical rotation data with that of the isomorphous and isostructural compound isogarcinol, whose absolute configuration is known. The crystal packing features O—H...O hydrogen bonds. A Cambridge Structural Database analysis revealed that the crystal structure reported here is isomorphous and isostructural with that of isogarcinol.

scholarly journals Crystallographic study of self-organization in the solid state including quasi-aromatic pseudo-ring stacking interactions in 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea and 1-benzoyl-3-(2-hydroxypropyl)thiourea

2017 ◽  
Vol 73 (1) ◽  
pp. 52-56 ◽  
Author(s):  
Andrzej Okuniewski ◽  
Damian Rosiak ◽  
Jarosław Chojnacki ◽  
Barbara Becker
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Strong Hydrogen Bond ◽  
Compound I ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Formation ◽  
Oh Groups ◽  
Space Group ◽  
Donor And Acceptor ◽  
Phenyl Rings

1-Benzoylthioureas contain both carbonyl and thiocarbonyl functional groups and are of interest for their biological activity, metal coordination ability and involvement in hydrogen-bond formation. Two novel 1-benzoylthiourea derivatives, namely 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea, C16H16N2O3S, (I), and 1-benzoyl-3-(2-hydroxypropyl)thiourea, C11H14N2O2S, (II), have been synthesized and characterized. Compound (I) crystallizes in the space group P\overline{1}, while (II) crystallizes in the space group P21/c. In both structures, intramolecular N—H...O hydrogen bonding is present. The resulting six-membered pseudo-rings are quasi-aromatic and, in each case, interact with phenyl rings via stacking-type interactions. C—H...O, C—H...S and C—H...π interactions are also present. In (I), there is one molecule in the asymmetric unit. Pairs of molecules are connected via two intermolecular N—H...S hydrogen bonds, forming centrosymmetric dimers. In (II), there are two symmetry-independent molecules that differ mainly in the relative orientations of the phenyl rings with respect to the thiourea cores. Additional strong hydrogen-bond donor and acceptor –OH groups participate in the formation of intermolecular N—H...O and O—H...S hydrogen bonds that join molecules into chains extending in the [001] direction.

Hydrogen bond competition between chemical groups: new methodology and the Cambridge Structural Database

2005 ◽  
Vol 220 (4) ◽  
Author(s):  
Lourdes Infantes ◽  
W. D. Sam Motherwell
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Intramolecular Hydrogen Bonding ◽  
Cambridge Structural Database ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Interactions ◽  
Hydrogen Bond Networks ◽  
Structural Database ◽  
Chemical Groups

AbstractThe probabilities of formation of intermolecular hydrogen bond interactions between chemical groups have been studied using new methodology to extract information from the Cambridge Structural Database (CSD). Data for 41052 crystal structures containing at least one strong hydrogen bond donor have been analysed using the RPluto program, assigning 108 chemical group codes to atoms, and creating tables of hydrogen contacts for subsequent analysis using the Access relational database software. This has enabled the study of competition effects where there are specified limited numbers of chemical groups in a structure, which is often difficult with the standard CSD search program, ConQuest. There are sufficiently high numbers of certain combinations of groups to make significant observations of the preference of a given donor for choices of acceptor atoms. For example, COOH…COOH contacts are frequently disrupted by groups such as keto carbonyl, whereas CONH…CONH is very robust and is seldom disrupted. There are a surprising number of structures that do not present any intermolecular hydrogen bond interactions, often due to intramolecular hydrogen bonding taking preference. There is a tendency to use as many groups as possible to build intermolecular hydrogen bond networks. An estimate is made of the relative strengths of self-association interactions which are, in decreasing order, CONH, COOH, alcoholic OH and phenolic OH. The frequency of preferred contacts in some cases allows one to predict the most probable contacts for a given molecule with a specific combination and ratio of chemical groups.

Crystal Structure of N,N'-Diphenyl-guanidinium m-Chlorobenzeneseleninate

1991 ◽  
Vol 44 (12) ◽  
pp. 1761 ◽  
Author(s):  
L Antolini ◽  
A Marchetti ◽  
C Preti ◽  
M Tagliazucchi ◽  
L Tassi ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Crystal Lattice ◽  
Vibrational Spectra ◽  
Crystal And Molecular Structure ◽  
Crystal Packing ◽  
Monoclinic Space Group ◽  
Space Group

The synthesis, and crystal and molecular structure of N,N′- diphenylguanidinium m- chlorobenzeneseleninate (C19H18CIN3O2Se), Mr 434.78, are reported. The crystal lattice of the compound belongs to the monoclinic space group P21/c with a 7.277(1), b 12.793(2), c 20.013(4) Ǻ, β 94.733(12)°, V 1859.8 Ǻ3, Z 4, Dobs 1.53 (by flotation), Dcalc 1.555 g cm-3, λ(Mo Kα ) 0.71069 Ǻ, μ 21.0 cm-1, F(000) 880, T 293 K, R 0.057 and Rw 0.059 for 1745 unique observed reflections with I>2.0σ(I). The crystal packing consists of parallel layers of anions intercalated with cations interacting through electrostatic contacts. Vibrational spectra have been also recorded, and are discussed.

Cinnamamide pharmacophore for anticonvulsant activity: evidence from crystallographic studies

2018 ◽  
Vol 74 (7) ◽  
pp. 782-788 ◽  
Author(s):  
Ewa Żesławska ◽  
Wojciech Nitek ◽  
Henryk Marona ◽  
Agnieszka Gunia-Krzyżak
Keyword(s):  
Crystal Structures ◽  
Anticonvulsant Activity ◽  
Crystal Packing ◽  
Pharmacophore Model ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Intramolecular Hydrogen ◽  
First Time

A number of cinnamamide derivatives possess anticonvulsant activity due to the presence of a number of important pharmacophore elements in their structures. In order to study the correlations between anticonvulsant activity and molecular structure, the crystal structures of three new cinnamamide derivatives with proven anticonvulsant activity were determined by X-ray diffraction, namely (R,S)-(2E)-N-(2-hydroxybutyl)-3-phenylprop-2-enamide–water (3/1), C13H17NO2·0.33H2O, (1), (2E)-N-(1-hydroxy-2-methylpropan-2-yl)-3-phenylprop-2-enamide, C13H17NO2, (2), and (R,S)-(2E)-N-(1-hydroxy-3-methyl-butan-2-yl)-3-phenylprop-2-enamide, C14H19NO2, (3). Compound (1) crystallizes in the space group P\overline{1} with three molecules in the asymmetric unit, whereas compounds (2) and (3) crystallize in the space group P21/c with one and two molecules, respectively, in their asymmetric units. The carbonyl group of (2) is engaged in an intramolecular hydrogen bond with the hydroxy group. This type of interaction is observed for the first time in these kinds of derivatives. A disorder of the substituent at the N atom occurs in the crystal structures of (2) and (3). The crystal packing of all three structures is dominated by a network of O—H...O and N—H...O hydrogen bonds, and leads to the formation of chains and/or rings. Furthermore, the crystal structures are stabilized by numerous C—H...O contacts. We analyzed the molecular structures and intermolecular interactions in order to propose a pharmacophore model for cinnamamide derivatives.

scholarly journals Molekül- und Kristallstruktur von 1.1-Dimethylsilylentitanocendichlorid, (CH3)2Si(C5H4)2TiCl2 / Molecular and Crystal Structure of l,r-Dimethylsilylene Titanocene Dichloride, (CH3)2Si(C5H4)2TiCl2

1981 ◽  
Vol 36 (10) ◽  
pp. 1208-1210 ◽  
Author(s):  
Hartmut Köpf ◽  
Joachim Pickardt
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Structure Determination ◽  
Titanocene Dichloride ◽  
Molecular And Crystal Structure ◽  
Monoclinic Space Group ◽  
Crystal Data ◽  
Space Group ◽  
X Ray ◽  
Structural Dimensions

Abstract The molecular structure of the bridged [1]-titanocenophane 1,1'-dimethylsilylene titanocene dichloride, (CH3)2Si(C5H4)2TiCl2, has been investigated by an X-ray structure determination. Crystal data: monoclinic, space group C2/c, Z = 4, a = 1332.9(3), 6 = 988.7(3), c = 1068.9(3) pm, β = 113.43(2)°. The results are compared with the structural dimensions of similar compounds: 1,1'-methylene titanocene dichloride, CH2(C5H4)TiCl2, with the unbridged titanocene dichloride, (C5H5)2TiCl2 and the ethylene-bridged compound (CH2)2(C5H4)2TiCl2

scholarly journals Accurate prediction of terahertz spectra of molecular crystals of fentanyl and its analogs

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chun-Hung Wang ◽  
Anthony C. Terracciano ◽  
Artёm E. Masunov ◽  
Mengyu Xu ◽  
Subith S. Vasu
Keyword(s):  
Molecular Structure ◽  
Crystal Packing ◽  
Molecular Crystals ◽  
Normal Modes ◽  
Rapid Identification ◽  
Medical Attention ◽  
Dispersion Interactions ◽  
Pain Reliever ◽  
Fentanyl Analogs ◽  
High Bioavailability

AbstractFentanyl is a potent synthetic opioid pain reliever with a high bioavailability that can be used as prescription anesthetic. Rapid identification via non-contact methods of both known and emerging opioid substances in the fentanyl family help identify the substances and enable rapid medical attention. We apply PBEh-3c method to identify vibrational normal modes from 0.01 to 3 THz in solid fentanyl and its selected analogs. The molecular structure of each fentanyl analog and unique arrangement of H-bonds and dispersion interactions significantly change crystal packing and is subsequently reflected in the THz spectrum. Further, the study of THz spectra of a series of stereoisomers shows that small changes in molecular structure results in distinct crystal packing and significantly alters THz spectra as well. We discuss spectral features of synthetic opioids with higher potency than conventional fentanyl such as ohmefentanyl and sufentanil and discover the pattern of THz spectra of fentanyl analogs.

Crystal and Molecular Structure of the Copper(I)-thiolate-selenide Complex [Ph4P][Cu(SeS2CNC4H8)(S2CN2C4H8)] with an Unusual Se-S Bond

1999 ◽  
Vol 54 (10) ◽  
pp. 1313-1317 ◽  
Author(s):  
Qianfeng Zhang ◽  
Jinxi Chen ◽  
Maochun Hong ◽  
Xinquan Xin ◽  
Hoong-Kun Fun
Keyword(s):  
Molecular Structure ◽  
Bond Length ◽  
Crystal And Molecular Structure ◽  
Monoclinic Space Group ◽  
Space Group ◽  
A Cell

Reaction of a DMF solution of Cu(S2CNC4H8) with [Ph4P]2[WSe4] affords [Ph4P]2[WSe4- (CuS2CNC4H8)3] (1) and [Ph4P][Cu(SeS2CNC4H )(S2CN2C4H8)] (2) in which a Se atom from the decomposition of the WSe42- anion has reacted with the pyrrolidyldithiocarbamate (C4H8dtc) ligand anion to form the new ligand anion SeS2CNC4H8⊖. Complex 2 crystallizes with four formula units in the monoclinic space group P21/c in a cell of dimensions a = 10.5824(2), b = 18.7575(3), c = 18.3268(4) Å and ß = 109.0980(10)°. 6055 independent reflections above background were measured with a diffractometer and the structure was refined anisotropically to R =0.073. The anion contains a three-coordinated copper(I) atom. The C4H8dtc⊖ ligand is bonded to the Cu+ cation in a terminal fashion, while SeS2CNC4H8⊖ chelates the Cu+ cation. The Se-S bond length is 2.231 (4) Å.

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