Crystal structure and packing energy calculations of (+)-6-aminopenicillanic acid

2013 ◽  
Vol 69 (11) ◽  
pp. 1238-1242 ◽  
Author(s):  
Sofiane Saouane ◽  
Gernot Buth ◽  
Francesca P. A. Fabbiani
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Lattice Energy ◽  
Interaction Energies ◽  
Energy Calculations ◽  
X Ray ◽  
Carboxylate Groups ◽  
Dimensional Network ◽  
Complementary Analysis

The X-ray single-crystal structure of (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid, commonly known as (+)-6-aminopenicillanic acid (C8H12N2O3S) and a precursor of a variety of semi-synthetic penicillins, has been determined from synchrotron data at 150 K. The structure represents an ordered zwitterion and the crystals are nonmerohedrally twinned. The crystal structure is composed of a three-dimensional network built by three charge-assisted hydrogen bonds between the ammonium and carboxylate groups. The complementary analysis of the crystal packing by thePIXELmethod brings to light the nature and ranking of the energetically most stabilizing intermolecular interaction energies. In accordance with the zwitterionic nature of the structure,PIXELlattice energy calculations confirm the predominance of the Coulombic term (−379.1 kJ mol−1) ahead of the polarization (−141.4 kJ mol−1), dispersion (−133.7 kJ mol−1) and repulsion (266.3 kJ mol−1) contributions.

Structural reinvestigation of the photoluminescent complex [NdCl2(H2O)6]Cl

2013 ◽  
Vol 69 (9) ◽  
pp. 1002-1005 ◽  
Author(s):  
Kuan-Ying Hsieh ◽  
El-Eulmi Bendeif ◽  
Sebastien Pillet ◽  
Abdelatif Doudouh ◽  
Dominik Schaniel ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Local Structure ◽  
Pair Distribution Function ◽  
Structural Model ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Crystalline Material ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dimensional Network

The structure of the photoluminescent compound hexaaquadichloridoneodymium(III) chloride has been redetermined from single-crystal X-ray diffraction data at 100 K, with the aim of providing an accurate structural model for the bulk crystalline material. The crystal structure may be described as a network of [NdCl2(H2O)6]+cations with distorted square-antiprism geometry around the NdIIIcentre. The NdIIIcation and the nonbonded Cl−anion are both located on twofold symmetry axes. The crystal packing consists of three different neodymium pairs linked by a three-dimensional network of O—H...Cl intermolecular interactions. The pair distribution function (PDF) calculated from the experimentally determined structure is used for the discussion of the local structure.

scholarly journals Crystal structure of (R)-5-[(R)-3-(4-chlorophenyl)-5-methyl-4,5-dihydroisoxazol-5-yl]-2-methylcyclohex-2-enone

2020 ◽  
Vol 76 (3) ◽  
pp. 400-403
Author(s):  
Ali Oubella ◽  
My Youssef Ait Itto ◽  
Aziz Auhmani ◽  
Abdelkhalek Riahi ◽  
Jean-Claude Daran ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Column Chromatography ◽  
Title Compound ◽  
Crystal Packing ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
H Nmr ◽  
Compound C ◽  
Dimensional Network

The title compound, C17H18ClNO2, was prepared and isolated as a pure diastereoisomer, using column chromatography followed by a succession of fractional crystallizations. Its exact structure was fully identified via 1H NMR and confirmed by X-ray diffraction. It is built up from a central five-membered dihydroisoxazole ring to which a p-chlorophenyl group and a cyclohex-2-enone ring are attached in the 3 and 5 positions. The cyclohex-2-one and isoxazoline rings each exhibit an envelope conformation. The crystal packing features C—H...O, C—H...N and C—H...π interactions, which generate a three-dimensional network.

Synthesis, structure and selective luminescence sensing for iron(III) ions of a three-dimensional zinc(II) (4,6)-connected coordination network

2019 ◽  
Vol 75 (2) ◽  
pp. 141-149 ◽  
Author(s):  
Feng Su ◽  
Cheng-Yong Zhou ◽  
Lin-Tao Wu ◽  
Xi Wu ◽  
Chun Han ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Electronic Configuration ◽  
Organic Ligands ◽  
Tetracarboxylic Acid ◽  
X Ray Diffraction ◽  
X Ray ◽  
Carboxylate Groups ◽  
Dimensional Network ◽  
Solvent Stability ◽  
Solvothermal Conditions

Coordination polymers constructed from conjugated organic ligands and metal ions with a d 10 electronic configuration exhibit intriguing properties for chemical sensing and photochemistry. A ZnII-based coordination polymer, namely poly[aqua(μ6-biphenyl-3,3′,5,5′-tetracarboxylato)(μ2-4,4′-bipyridine)dizinc(II)], [Zn2(C16H6O8)(C10H8N2)(H2O)2] n or [Zn2(m,m-bpta)(4,4′-bipy)(H2O)2] n , was synthesized from a mixture of biphenyl-3,3′,5,5′-tetracarboxylic acid [H4(m,m-bpta)], 4,4′-bipyridine (4,4′-bipy) and Zn(NO3)2·6H2O under solvothermal conditions. The title complex has been structurally characterized by IR spectroscopy, elemental analysis, single-crystal X-ray diffraction and powder X-ray diffraction analysis, and features a μ6-coordination mode. The ZnII ions adopt square-pyramidal geometries and are bridged by two syn–syn carboxylate groups to form [Zn2(COO)2] secondary buildding units (SBUs). The SBUs are crosslinked by (m,m-bpta)4− ligands to produce a two-dimensional grid-like layer that exhibits a stair-like structure along the a axis. Adjacent layers are linked by 4,4′-bipy ligands to form a three-dimensional network with a {44.610.8}{44.62} topology. In the solid state, the complex displays a strong photoluminescence and an excellent solvent stability. In addition, the luminescence sensing results indicate a highly selective and sensitive sensing for Fe3+ ions.

Crystal and Molecular Structure of 3-Iodo-2-propynyl-N-butylcarbamate

1997 ◽  
Vol 52 (2) ◽  
pp. 256-258 ◽  
Author(s):  
Evgeni V. Avtomonov ◽  
Rainer Grüning ◽  
Jörg Lorberth
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Title Compound ◽  
Crystal And Molecular Structure ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dimensional Network ◽  
Carbamate Group ◽  
Oxygen Atoms

Abstract The crystal structure of the title compound has been determined by X-ray diffraction methods. Due to the Lewis acidic character of the iodine substituent a “zig-zag” chain is formed via intermolecular interactions (2.933(4) A) between iodine and oxygen atoms of theocarbamate moiety. A three-dimensional network is formed through hydrogen-bridging (2.04 A) between NH-groups and the oxygen atoms of the neighbouring carbamate group of the next molecule.

Crystal structure of (Z)-cefprozil monohydrate, C18H19N3O5S(H2O)

2019 ◽  
Vol 34 (4) ◽  
pp. 379-388
Author(s):  
Zachary R. Butler ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Three Dimensional ◽  
Ion Pair ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
X Ray ◽  
Dimensional Network ◽  
Acid Proton

The crystal structure of cefprozil monohydrate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Cefprozil monohydrate crystallizes in space group P21 (#4) with a = 11.26513(6), b = 11.34004(5), c = 14.72649(11) Å, β = 90.1250(4)°, V = 1881.262(15) Å3, and Z = 4. Although a reasonable fit was obtained using an orthorhombic model, closer examination showed that many peaks were split and/or had shoulders, and thus the true symmetry was monoclinic. DFT calculations revealed that one carboxylic acid proton moved to an amino group. The structure thus contains one ion pair and one pair of neutral molecules. This protonation was confirmed by infrared spectroscopy. There is an extensive array of hydrogen bonds resulting in a three-dimensional network. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: quantitative inputs towards the energetics associated with crystal packing

2014 ◽  
Vol 70 (4) ◽  
pp. 681-696 ◽  
Author(s):  
Piyush Panini ◽  
K. N. Venugopala ◽  
Bharti Odhav ◽  
Deepak Chopra
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Biologically Active ◽  
Two Dimensional ◽  
Energy Calculations ◽  
X Ray ◽  
Fingerprint Plots

A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (AandB) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N—H]+...Cl−and [C—H]+...Cl−hydrogen bonds mainly stabilizes the crystal packing in both formsAandB, while in the case ofB·H2O [N—H]+...Owaterand Owater—H...Cl−hydrogen bonds along with [N—H]+...Cl−and [C—H]+...Cl−provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case ofA, form (I) (monoclinic) is more stable whereas forBit is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms ofAandBand its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. TheR/E(distance–energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organicR+and Cl−) or highly destabilizing Coulombic contacts. The difference in crystal packing and associated intermolecular interactions between polymorphs (in the case ofA) or the hydrates (in the case ofB) have been clearly elucidated by the analysis of Hirshfeld surfaces and two-dimensional fingerprint plots. The relative contributions of the various interactions to the Hirshfeld surface for the cationic (dihydropyrimidinium) part and anionic (chloride ion) part for the two forms ofAandBand its hydrate were observed to be different.

scholarly journals Crystal structure and Hirshfeld analysis of trans-bis(5-fluoroindoline-2,3-dione 3-oximato-κ2 O 2,N 3)-trans-bis(pyridine-κN)copper(II)

2018 ◽  
Vol 74 (4) ◽  
pp. 428-432
Author(s):  
Ana Paula Lopes de Melo ◽  
Leandro Bresolin ◽  
Bianca Barreto Martins ◽  
Vanessa Carratu Gervini ◽  
Adriano Bof de Oliveira
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Molar Ratio ◽  
Pyridine Ligands ◽  
Dimensional Network ◽  
Centroid Distance ◽  
Distorted Octahedral ◽  
Hirshfeld Analysis ◽  
Isatin Derivatives

The reaction in methanol of CuII acetate monohydrate with 5-fluoroisatin 3-oxime deprotonated with KOH in a 1:2 molar ratio and recrystallization from pyridine yielded the title compound, [Cu(C8H4FN2O2)2(C5H5N)2]. In the centrosymmetric complex, the anionic form of the isatin oxime acts as a κ2 N,O donor, building five-membered metallarings. The CuII cation is sixfold coordinated in a slightly distorted octahedral environment by two trans, equatorial, anionic isatin derivatives and two trans pyridine ligands in axial positions. The complexes are linked by hydrogen bonding into a three-dimensional network, which is also stabilized by π–π stacking interactions [centroid-to-centroid distance = 3.7352 (9) Å] and C—H...π contacts. The Hirshfeld surface analysis indicates that the major contributions for the crystal packing are H...H (31.80%), H...C (24.30%), H...O (15.20%) and H...F (10.80%). This work is the second report in the literature of a crystal structure of a coordination compound with isatin 3-oxime ligands (coordination chemistry).

Study on Novel Structure of Potassium Borate Hydrate: K(H4B5O10)·2(H2O)

2012 ◽  
Vol 531-532 ◽  
pp. 409-412
Author(s):  
Hai Xing Liu ◽  
Fang Fang Jian ◽  
Jing Wang ◽  
Guang Zeng ◽  
Hui Juan Yue ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Potassium Borate ◽  
Polyhydroxy Compounds ◽  
Novel Structure ◽  
Solution Reaction

Numerous stable complexes of boric acid with polyhydroxy compounds, including tartaric, salicylic, citric, malic, and other acids, are known. The structure of some compounds contains polyanion. In this paper, a novel potassium borate hydrate [K(H4B5O10) •2(H2O)] has been synthesized from a solution reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. Orthorhombic, Aba2. a = 11.0781(14) Å b = 11.1780(15) Å c = 9.0508(11) Å α=β=γ=90°. V= 1120.8(2) Å3. Z=4. Rgt = 0.0244, wRref = 0.0623. T= 298 K. The crystal packing is stabilized by O-H...O hydrogen bonds interaction and three dimensional framwork structure is formed. The work is originality and has a new crystallographic structure shape.

New Inclusion Compounds of Selenourea with Tetraethyl- and Tetra-n-propylammonium Halides

1997 ◽  
Vol 53 (2) ◽  
pp. 262-271 ◽  
Author(s):  
Q. Li ◽  
T. C. W. Mak
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Crystal Data ◽  
Tetraethylammonium Chloride ◽  
Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Network ◽  
Single Column

Air-sensitive selenourea inclusion complexes tetraethylammonium chloride–selenourea (1/2), (C2H5)4N+.C1−.2[(NH2)2CSe] (1), tetra-n-propyl-ammonium chloride–selenourea (1/3), (n-C3H7)4N+.C1−.3[(NH2)2CSe] (2), tetra-n-propylammonium bromide–selenourea (1/3), (n-C3H7)4N+.Br−.3[(NH2)2CSe] (3), and tetra-n-propylammonium iodide–selenourea (1/1), (n-C3H7)4N+.I−.(NH2)2CSe (4), have been prepared and characterized by X-ray crystallography. Crystal data, Mo Kα radiation: (1), space group P21/n, Z = 4, a = 8.768 (5), b = 11.036 (6), c = 19.79 (1) Å, β = 96.92 (1)°, R F = 0.055 for 1468 observed data; (2), space group Cc, Z = 4, a = 18.091 (4), b = 13.719 (3), c = 11.539 (2) Å, β = 111.93 (3)°, R F = 0.051 for 1187 observed data; (3), space group Cc, Z = 4, a = 18.309  (4), b = 13.807 (3), c = 11.577 (2) Å, β = 112.45 (3)°, R F = 0.049 for 1592 observed data; (4), space group P21/n, Z = 4, a = 8.976 (1), b = 14.455 (2), c = 15.377 (3) Å, β = 94.16(1)°, R F = 0.062 for 1984 observed data. In the crystal structure of (1) the parallel alternate arrangement of selenourea–chloride ribbons and selenourea chains generates a puckered layer and the cations are sandwiched between them. In the isomorphous complexes (2) and (3) wide selenourea–halide double ribbons are crosslinked by bridging selenourea molecules via N—H...Se and N—H...X hydrogen bonds [average N...Se = 3.521 (8) and 3.527 (7), N...Cl = 3.354 (8) and N...Br = 3.500 (7) Å in (2) and (3), respectively] to form a channel-like three-dimensional network and the cations are accommodated in a single column within each channel. In the crystal structure of (4) the selenourea molecules are joined in the shoulder-to-shoulder fashion via N—H...Se hydrogen bonds [N...Se = 3.529 (7) and 3.534 (7) Å] to generate a ribbon and each selenourea molecule also forms a pair of chelating N—H...I hydrogen bonds [N...I = 3.567 (7) and 3.652 (7) Å] to an adjacent iodide ion.

scholarly journals Synthesis, crystal structure and charge-distribution validation of a new alluaudite-type phosphate, Na2.22Mn0.87In1.68(PO4)3

2020 ◽  
Vol 76 (8) ◽  
pp. 1369-1372
Author(s):  
Abdessalem Badri ◽  
Inmaculada Alvarez-Serrano ◽  
María Luisa López ◽  
Mongi Ben Amara
Keyword(s):  
Crystal Structure ◽  
Single Crystals ◽  
Three Dimensional ◽  
Structure Type ◽  
X Ray Diffraction ◽  
Flux Method ◽  
X Ray ◽  
Coordination Numbers ◽  
Dimensional Network ◽  
Anionic Framework

Na2.22Mn0.87In1.68(PO4)3, sodium manganese indium tris(phosphate) (2.22/0.87/1.68), was obtained in the form of single crystals by a flux method and was structurally characterized by single-crystal X-ray diffraction. The compound belongs to the alluaudite structure type (space group C2/c) with general formula X(2)X(1)M(1)M(2)2(PO4)3. The X(2) and X(1) sites are partially occupied by sodium [occupancy 0.7676 (17) and 1/2] while the M(1) and M(2) sites are fully occupied within a mixed distribution of sodium/manganese(II) and manganese(II)/indium, respectively. The three-dimensional anionic framework is built up on the basis of M(2)2O10 dimers that share opposite edges with M(1)O6 octahedra, thus forming infinite chains extending parallel to [10\overline{1}]. The linkage between these chains is ensured by PO4 tetrahedra through common vertices. The three-dimensional network thus constructed delimits two types of hexagonal channels, resulting from the catenation of M(2)2O10 dimers, M(1)O6 octahedra and PO4 tetrahedra through edge- and corner-sharing. The channels are occupied by Na+ cations with coordination numbers of seven and eight.

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