scholarly journals Synthesis and absolute structure of (R)-2-(benzylselanyl)-1-phenylethanaminium hydrogen sulfate monohydrate: crystal structure and Hirshfeld surface analyses

2021 ◽  
Vol 77 (11) ◽  
Author(s):  
H. R. Rajegowda ◽  
P. A. Suchetan ◽  
R. J. Butcher ◽  
P. Raghavendra Kumar
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Shape Index ◽  
Hirshfeld Surface ◽  
Water Molecules ◽  
Hydrogen Sulfate ◽  
Hydrogen Atoms ◽  
Amine Nitrogen Atom ◽  
Amine Nitrogen

A hydrogen sulfate salt, C15H18NSe+·HSO4 −·H2O or [BnSeCH2CH(Ph)NH3 +](HSO4 −), of a chiral selenated amine (R)-2-(benzylselanyl)-1-phenylethanamine (BnSeCH2CH(Ph)NH2) has been synthesized and characterized by elemental analysis,1H and 13C{1H} NMR, FT–IR analysis, and single-crystal X-ray diffraction studies. The title salt crystallizes in the monohydrate form in the non-centrosymmetric monoclinic P21 space group. The cation is somewhat W shaped with the dihedral angle between the two aromatic rings being 60.9 (4)°. The carbon atom attached to the amine nitrogen atom is chiral and in the R configuration, and, the –C—C– bond of the –CH2—CH– fragment has a staggered conformation. In the crystal structure, two HSO4 − anions and two water molecules form an R 4 4(12) tetrameric type of assembly comprised of alternating HSO4 − anions and water molecules via discrete D(2) O—H...O hydrogen bonds. This tetrameric assembly aggregates along the b-axis direction as an infinite one-dimensional tape. Adjacent tapes are interconnected via discrete D(2) N—H...O hydrogen bonds between the three amino hydrogen atoms of the cation sandwiched between the two tapes and the three HSO4 − anions of the nearest asymmetric units, resulting in a complex two-dimensional sheet along the ab plane. The pendant arrangement of the cations is stabilized by C—H...π interactions between adjacent cations running as chains down the [010] axis. Secondary Se...O [3.1474 (4) Å] interactions are also observed in the crystal structure. A Hirshfeld surface analysis, including d norm, shape-index and fingerprint plots of the cation, anion and solvent molecule, was carried out to confirm the presence of various interactions in the crystal structure.

scholarly journals Tris(cis-2-hydroxycyclohexane-1,3,5-triaminium) hydrogen sulfate octachloride dihydrate

2012 ◽  
Vol 68 (6) ◽  
pp. o1899-o1900
Author(s):  
Christian Neis ◽  
Günter J. Merten ◽  
Kaspar Hegetschweiler
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Chloride Ions ◽  
Water Molecules ◽  
Hydrogen Sulfate ◽  
Sulfate Ion ◽  
Hydrogen Atoms ◽  
Threefold Axis ◽  
Sulfate Anion ◽  
Counter Ions

The 2-hydroxycyclohexane-1,3,5-triaminium (= H3 L 3+) cation of the title compound, 3C6H18N3O3+·8Cl−·HSO4 −·2H2O, exhibits a cyclohexane chair with three equatorial ammonium groups and one axial hydroxy group in an all-cis configuration. The hydrogen sulfate anion and two water molecules lie on or in proximity to a threefold axis and are disordered. The crystal structure features N—H...Cl and O—H...Cl hydrogen bonds. Three C 3-symmetric motifs can be identified in the structure: (i) Two chloride ions (on the C 3-axis) together with three H3 L 3+ cations constitute an [(H3 L)3Cl2]7+ cage. (ii) The lipophilic C6H6-sides of three H3 L 3+ cations, which are oriented directly towards the C 3-axis, generate a lipophilic void. The void is filled with the disordered water molecules and with the disordered part of the hydrogen sulfate ion. The hydrogen atoms of these disordered moieties were not located. (iii) Three H3 L 3+ cations together with one HSO4 − and three Cl− counter-ions form an [(HSO4)(H3 L)3Cl3]5+ cage. Looking along the C 3-axis, these three motifs are arranged in the order (cage 1)...(lipophilic void)...(cage 2). The crystal studied was found to be a racemic twin.

scholarly journals Spectral, Thermal, Crystal Structure, Hirshfeld Surface Analyses and Biological Activities of New Hydrazinium Dipicolinato Copper(II) Tetrahydrate

2019 ◽  
Vol 31 (8) ◽  
pp. 1755-1761
Author(s):  
K. Naresh ◽  
B.N. Sivasankar
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Water Clusters ◽  
Hirshfeld Surface ◽  
Water Molecules ◽  
X Ray ◽  
Biological Studies ◽  
Calf Thymus ◽  
Hydrazinium Cation

A new copper complex of pyridine-2,6-dicarboxylate containing hydrazinium cation, formulated as (N2H5)2[Cu(PDC)2]·4H2O (PDC = pyridine-2,6-dicarboxylate) has been synthesized from copper(II) nitrate, hydrazine hydrate and pyridine-2,6-dicarboxylic acid as a single crystal and characterized by elemental analysis and spectroscopic (IR and UV-visible), thermal (TG/DTG), single crystal X-ray diffraction and biological studies. A six-coordinate complex with a distorted octahedral geometry around Cu(II) ion is proposed and confirmed by X-ray single crystal method. The structure reveals that two pyridine-2,6-dicarboxylate species acting as tridentate ligands and hydrazinium cation present as a counter ion along with non-coordinated four water molecules. The structural units of copper(II) is mutually held by the hydrogen bonds and π···π and C–O···π interactions. The copper(II) complex is connected to one another via O–H···O hydrogen bonds, forming water clusters, which plays an important role in the stabilization of the crystal structure. In the water clusters, the water molecules are trapped by the cooperative association of coordination interactions as well as hydrogen bonds. Both cation and anion interactions and crystal from various types of intermolecular contacts and their importance were explored using Hirshfeld surface analysis. This indicates that O···H/H···O interactions are the superior interactions conforming excessive H-bond in the molecular structure. The interaction of copper(II) complex with calf thymus DNA (CT-DNA) was investigated by electronic absorption spectroscopic technique. The electronic evidence strongly shows that the compound interacts with calf thymus through intercalation with a binding constant of Kb = 5.7 × 104 M–1.

scholarly journals A cinnamaldehyde Schiff base ofS-(4-methylbenzyl) dithiocarbazate: crystal structure, Hirshfeld surface analysis and computational study

2017 ◽  
Vol 73 (4) ◽  
pp. 543-549 ◽  
Author(s):  
Enis Nadia Md Yusof ◽  
Mohamed I. M. Tahir ◽  
Thahira B. S. A. Ravoof ◽  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Mirror Symmetry ◽  
Computational Study ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Hydrogen Atoms ◽  
Benzyl Substituent

The title dithiocarbazate ester (I), C18H18N2S2[systematic name: (E)-4-methylbenzyl 2-[(E)-3-phenylallylidene]hydrazinecarbodithioate, comprises an almost planar central CN2S2residue [r.m.s. deviation = 0.0131 Å]. The methylene(tolyl-4) group forms a dihedral angle of 72.25 (4)° with the best plane through the remaining non-hydrogen atoms [r.m.s. deviation = 0.0586 Å] so the molecule approximates mirror symmetry with the 4-tolyl group bisected by the plane. The configuration about both double bonds in the N—N=C—C=C chain isE; the chain has an alltransconformation. In the crystal, eight-membered centrosymmetric thioamide synthons, {...HNCS}2, are formedviaN—H...S(thione) hydrogen bonds. Connections between the dimersviaC—H...π interactions lead to a three-dimensional architecture. A Hirshfeld surface analysis shows that (I) possesses an interaction profile similar to that of a closely related analogue with anS-bound benzyl substituent, (II). Computational chemistry indicates the dimeric species of (II) connectedviaN—H...S hydrogen bonds is about 0.94 kcal mol−1more stable than that in (I).

Crystal Structure of Adeninium Trichloromercurate(II),

1975 ◽  
Vol 53 (15) ◽  
pp. 2345-2350 ◽  
Author(s):  
Monique Authier-Martin ◽  
André L. Beauchamp
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Least Squares ◽  
Title Compound ◽  
Heavy Atom ◽  
Chloride Ions ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Space Group ◽  
Heavy Atom Method

The title compound belongs to space group P21/c with a = 23.99(1), b = 4.245(2), c = 25.98(1) Å, β = 117.58(7)°, and Z = 8. The structure was solved by the heavy-atom method and refined by block-diagonal least squares on 2589 independent observed reflections. All non-hydrogen atoms were refined anisotropically and some of the hydrogen atoms were located but their parameters were not refined. The final values of R and Rw were 0.042 and 0.047, respectively.The two nonequivalent mercury atoms have very similar environments. Two short Hg—Cl bonds (2.34–2.38 Å) at ∼ 165° define a quasi-molecular HgCl2 unit. Overall octahedral coordination is completed with two chloride ions at 2.76–2.84 Å and two chlorine atoms at 3.19–3.26 Å on neighboring HgCl2 quasi-molecules. HgCl6 octahedra share edges to form twofold ribbons in the b direction. This pattern of octahedra is identical with the onereported for β-NH4HgCl3. The cations are pairs of N(1)-protonated adenine molecules linked by two N(10)—H(10)… N(7) hydrogen bonds and stacked in the b direction. Water molecules act as acceptors in moderately strong hydrogen bonds with acidic protons H(1) and H(9) of adeninium ions. Other generally weaker hydrogen bonds exist between the various parts of the structure.

scholarly journals Crystal structure and Hirshfeld surface analysis of tris(2,2′-bipyridine)nickel(II) bis(1,1,3,3-tetracyano-2-ethoxypropenide) dihydrate

2019 ◽  
Vol 75 (6) ◽  
pp. 867-871
Author(s):  
Ignacio Chi-Duran ◽  
Zouaoui Setifi ◽  
Fatima Setifi ◽  
Christian Jelsch ◽  
Bernd Morgenstern ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Title Compound ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Racemic Mixture ◽  
Water Molecules ◽  
Monoclinic Space Group ◽  
Two Dimensional

The title compound, [Ni(C10H8N2)3](C9H5N4O)2·2H2O, crystallizes as a racemic mixture in the monoclinic space group C2/c. In the crystal, the 1,1,3,3-tetracyano-2-ethoxypropenide anions and the water molecules are linked by O—H...N hydrogen bonds, forming chains running along the [010] direction. The bpy ligands of the cation are linked to the chain via C—H...π(cation) interactions involving the CH3 group. The intermolecular interactions were investigated by Hirshfeld surface analysis and two-dimensional fingerprint plots.

Re-investigation of the crystal structure of whewellite [Ca(C2O4)·H2O] and the dehydration mechanism of caoxite [Ca(C2O4)·3H2O]

2005 ◽  
Vol 69 (1) ◽  
pp. 77-88 ◽  
Author(s):  
T. Echigo ◽  
M. Kimata ◽  
A. Kyono ◽  
M. Shimizu ◽  
T. Hatta
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Structure Refinement ◽  
Structural Features ◽  
Infrared Analysis ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Direct Transformation ◽  
Dehydration Mechanism ◽  
The Difference

AbstractThe crystal structure of whewellite [Ca(C2O4)·H2O] and the dehydration mechanism of caoxite [Ca(C2O4)·3H2O] have been studied by means of differential thermal analysis, X-ray diffraction (powder and single-crystal) analysis and infrared analysis. The first and second analyses confirmed the direct transformation of caoxite into whewellite without an intermediate weddellite [Ca(C2O4)·2H2O] stage. Infrared spectra obtained from caoxite, weddellite and whewellite emphasize the similarity of the O–H-stretching band and O–C–O-stretching band in whewellite and caoxite and the unique bands of weddellite. The structure refinement at low temperature (123 K) reveals that all the hydrogen atoms of whewellite form hydrogen bonds and the two water molecules prop up the crystal structure by the hydrogen bonds that cause a strong anisotropy of the displacement parameter.Comparing the structural features of whewellite with those of weddellite and caoxite suggests that caoxite and whewellite have a sheet structure consisting of Ca2+ ions and oxalate ions although weddellite does not. It is additionally confirmed that the sheets of caoxite are corrugated by hydrogen bonds but whewellite has flat sheets. The corrugated sheets of caoxite would be flattened by dehydration so the direct transformation of caoxite into whewellite would not occur via weddellite. Essential for this transformation is the dehydration of interlayered water molecules in caoxite leading to the building of the crystal structure of whewellite on its intralayered water molecules. The difference in conformation of water molecules between those two crystal structures may explain the more common occurrence of whewellite than of caoxite in nature.

scholarly journals Crystal structure and Hirshfeld surface analysis of (μ-2-{4-[(carboxylatomethyl)carbamoyl]benzamido}acetato-κ2 O:O′)bis[bis(1,10-phenanthroline-κ2 N,N′)copper(II)] dinitrate N,N′-(1,4-phenylenedicarbonyl)diglycine monosolvate octahydrate

2019 ◽  
Vol 75 (5) ◽  
pp. 667-674 ◽  
Author(s):  
Niels-Patrick Pook ◽  
Arnold Adam ◽  
Mimoza Gjikaj
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Complex Cation ◽  
Solvent Molecule ◽  
Lone Pair ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Water Molecules ◽  
Π Stacking ◽  
Phenanthroline Ligands

The centrosymmetric binuclear complex cation of the title compound, [Cu2(C12H10N2O6)(C12H8N2)4](NO3)2·C12H12N2O6·8H2O, is composed of a CuII atom with a distorted trigonal–bipyramidal coordination environment defined by four N atoms from two bidentate 1,10-phenanthroline ligands and one oxygen atom from one-half of the monodentate N,N′-(1,4-phenylenedicarbonyl)diglycinate anion. The asymmetric unit is completed by one-half of the N,N′-(1,4-phenylenedicarbonyl)diglycine solvent molecule, which is located on a centre of inversion, by one nitrate counter-anion and four water molecules. In the crystal, the cationic complexes are linked via intermolecular π–π stacking and through lone-pair...π interactions involving the N,N′-(1,4-phenylenedicarbonyl)diglycinate anion and the phenanthroline ligands. The N,N′-(1,4-phenylenedicarbonyl)diglycine solvent molecule is involved in classical and non-classical hydrogen-bonding interactions, as well as π–π stacking interactions. The centroid-to-centroid distances between aromatic entities are in the range 3.5402 (5)–4.3673 (4) Å. The crystal structure is stabilized by further C—H...O contacts as well as by O—H...O and N—H...O hydrogen bonds between water molecules, the nitrate anions, the N,N′-(1,4-phenylenedicarbonyl)diglycinate ligands, N,N′-(1,4-phenylenedicarbonyl)diglycine solvent molecules and phenanthroline ligands, giving rise to a supramolecular framework. A Hirshfeld surface analysis was carried out to quantify these interactions.

scholarly journals Crystal structure of bis(piperazin-1-ium-κN 4)bis(thiosulfato-κS)zinc(II) dihydrate

2018 ◽  
Vol 74 (2) ◽  
pp. 176-179
Author(s):  
Avijit Kumar Paul
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Water Molecules ◽  
Tetrahedral Coordination ◽  
Metal Centre ◽  
Hydrogen Atoms

In the title compound, [Zn(C4H11N2)2(S2O3)2]·2H2O, two thiosulfate ions coordinate to the zinc(II) atom through the terminal S atoms. The tetrahedral coordination around the ZnII ion is completed by ligating to two N atoms of two piperazinium ions. The remaining two N atoms of the piperazinium ions are diprotonated and do not coordinate to the metal centre. In the crystal, however, they are involved in N—H...Owater and N—H...Osulfato hydrogen bonds. Together, a series of N—H...O and O—H...O hydrogen bonds, involving the O atoms of the thiosulfate ions and the water molecules as acceptors and the hydrogen atoms of the piperazinium ions and the water molecules as donors, form a three-dimensional supramolecuar structure. Within this framework there are a number of intra- and intermolecular C—H...O and C—H...S contacts present.

scholarly journals Crystal structure of pantoprazole sodium sesquihydrate Form I, C16H14F2N3O4SNa(H2O)1.5

2020 ◽  
Vol 35 (1) ◽  
pp. 53-60
Author(s):  
Diana Gonzalez ◽  
Joseph T. Golab ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Powder Diffraction File ◽  
Trigonal Bipyramidal ◽  
Pyridine Nitrogen ◽  
Coordination Spheres

The crystal structure of pantoprazole sodium sesquihydrate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Pantoprazole sodium sesquihydrate crystallizes in space group Pbca (#61) with a = 33.4862(6), b = 17.29311(10), c = 13.55953(10) Å, V = 7852.06(14) Å3, and Z = 16. The crystal structure is characterized by layers parallel to the bc-plane. One layer contains the Na coordination spheres. The two independent sodium ions are trigonal bipyramidal and octahedral. The NaO3N2 and NaO4N2 coordination spheres share an edge to form pairs. The sodium bond valence sums are 1.17 and 1.15. The difluoromethyl groups are probably disordered. Two water molecules act as hydrogen bond donors to pyridine nitrogen atoms and sulfoxide oxygen atoms. The third water molecule participates in bifurcated hydrogen bonds, but one of its hydrogen atoms does not participate in hydrogen bonds. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1424.

scholarly journals Pyridine-4-carboxamidoxime N-oxide

IUCrData ◽  
2020 ◽  
Vol 5 (10) ◽  
Author(s):  
Clifford W. Padgett ◽  
Kirkland Sheriff ◽  
Will E. Lynch
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Nitrogen Atom ◽  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Metal Organic Frameworks ◽  
Amine Nitrogen Atom ◽  
Amine Nitrogen ◽  
Compound C ◽  
Metal Organic

Our work in the area of synthesis of metal–organic frameworks (MOFs) based on organic N-oxides led to the crystallization of pyridine-4-carboxamidoxime N-oxide. Herein we report the first crystal structure of the title compound, C6H7N3O2 [systematic name: (Z)-4-(N′-hydroxycarbamimidoyl)pyridine N-oxide]. The hydroxycarbamimidoyl group is essentially coplanar with the aromatic ring, r.m.s.d. = 0.112 Å. The compound crystallizes in hydrogen-bonding layers built from the formation of strong O—H...O hydrogen bonds between the oxime oxygen atom and the oxygen atom of the N-oxide, and the formation of N—H...O hydrogen bonds between one amine nitrogen atom and the N-oxide oxygen atom. These combined build R 3 4(24) ring motifs in the crystal. The crystal structure has no π–π interactions.

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