scholarly journals Synthesis and structure of a complex of copper(I) with L-cysteine and chloride ions containing Cu12S6 nanoclusters

2021 ◽  
Vol 77 (4) ◽  
pp. 324-330
Author(s):  
Amir Gizatullin ◽  
Jonathan Becker ◽  
Daut Islamov ◽  
Nikita Serov ◽  
Siegfried Schindler ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Copper Ion ◽  
Chloride Ion ◽  
Chloride Ions ◽  
Chloride Complex ◽  
Water Molecules ◽  
Amino Groups ◽  
Acta Cryst ◽  
Fourier Transform Methods ◽  
Solvent Molecules

The title hydrated copper(I)–L-cysteine–chloride complex has a polymeric structure of composition {[Cu16(CysH2)6Cl16]·xH2O} n [CysH2 = HO2CCH(NH3 +)CH2S− or C3H7NO2S], namely, poly[[tetra-μ3-chlorido-deca-μ2-chlorido-dichloridohexakis(μ4-L-cysteinato)hexadecacopper] polyhydrate]. The copper atoms are linked by thiolate groups to form Cu12S6 nanoclusters that take the form of a tetrakis cuboctahedron, made up of a Cu12 cubo-octahedral subunit that is augmented by six sulfur atoms that are located symmetrically atop of each of the Cu4 square units of the Cu12 cubo-octahedron. The six S atoms thus form an octahedral subunit themselves. The exterior of the Cu12S6 sphere is decorated by chloride ions and trichlorocuprate units. Three chloride ions are coordinated in an irregular fashion to trigonal Cu3 subunits of the nanocluster, and four trigonal CuCl3 units are bonded via each of their chloride ions to a copper ion on the Cu12S6 sphere. The trigonal CuCl3 units are linked via Cu2Cl2 bridges covalently connected to equivalent units in neighboring nanoclusters. Four such connections are arranged in a tetrahedral fashion, thus creating an infinite diamond-like net of Cu12S6Cl4(CuCl3)4 nanoclusters. The network thus formed results in large channels occupied by solvent molecules that are mostly too ill-defined to model. The content of the voids, believed to be water molecules, was accounted for via reverse Fourier-transform methods using the SQUEEZE algorithm [Spek (2015). Acta Cryst. C71, 9–18]. The protonated amino groups of the cysteine ligands are directed away from the sphere, forming N—H...Cl hydrogen bonds with chloride-ion acceptors of their cluster. The protonated carboxy groups point outwards and presumably form O—H...O hydrogen bonds with the unresolved water molecules of the solvent channels. Disorder is observed in one of the two crystallographically unique [Cu16(CysH2)6Cl16] segments for three of the six cysteine anions.

scholarly journals Crystal structures of 6-nitroquinazolin-4(3H)-one, 6-aminoquinazolin-4(3H)-one and 4-aminoquinazoline hemihydrochloride dihydrate

2021 ◽  
Vol 77 (10) ◽  
pp. 989-993
Author(s):  
Kambarali Turgunov ◽  
Mirjalol Ziyadullaev ◽  
Farkhod Khoshimov ◽  
Rikhsiboy Karimov ◽  
Burkhon Elmuradov
Keyword(s):  
Three Dimensional ◽  
Chloride Ion ◽  
Chloride Ions ◽  
Chloride Anion ◽  
Water Molecules ◽  
Asymmetric Unit ◽  
Amino Groups ◽  
X Ray ◽  
Dimensional Network ◽  
Hydrogen Bonded

The title compounds, 6-nitroquinazolin-4(3H)-one (C8H5N3O3; I), 6-aminoquinazolin-4(3H)-one (C8H7N3O; II) and 4-aminoquinazolin-1-ium chloride–4-aminoquinazoline–water (1/1/2), (C8H8N3 +·Cl−·C8H7N3·2H2O; III) were synthesized and their structures were determined by single-crystal X-ray analysis. In the crystals of I and II, the quinazoline molecules form hydrogen-bonded dimers via N—H...O interactions. The dimers are connected by weak intermolecular C—H...N and C—H...O hydrogen bonds, forming a layered structure in the case of I. In the crystal of II, N—H...N and C—H...O interactions link the dimers into a three-dimensional network structure. The asymmetric unit of III consists of two quinazoline molecules, one of which is protonated, a chloride ion, and two water molecules. The chloride anion and the water molecules form hydrogen-bonded chains consisting of fused five-membered rings. The protonated and unprotonated quinazolin molecules are linked to the chloride ions and water molecules of the chain by their amino groups.

scholarly journals Different packing motifs in the crystal structures of three molecular salts containing the 2-amino-5-carboxyanilinium cation: C7H9N2O2 +·Cl−, C7H9N2O2 +·Br− and C7H9N2O2 +·NO3 −·H2O

2020 ◽  
Vol 76 (4) ◽  
pp. 527-533 ◽  
Author(s):  
Edson T. Mukombiwa ◽  
William T A Harrison
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Three Dimensional ◽  
Chloride Ion ◽  
Chloride Ions ◽  
Organic Cations ◽  
Water Molecules ◽  
Dimensional Network ◽  
Molecular Salts

The syntheses and crystal structures of three molecular salts of protonated 3,4-diaminobenzoic acid, viz. 2-amino-5-carboxyanilinium chloride, C7H9N2O2 +·Cl−, (I), 2-amino-5-carboxyanilinium bromide, C7H9N2O2 +·Br−, (II), and 2-amino-5-carboxyanilinium nitrate monohydrate, C7H9N2O2 +·NO3 −·H2O, (III), are described. The cation is protonated at the meta-N atom (with respect to the carboxy group) in each case. In the crystal of (I), carboxylic acid inversion dimers linked by pairwise O—H...O hydrogen bonds are seen and each N—H group forms a hydrogen bond to a chloride ion to result in (100) undulating layers of chloride ions bridged by the inversion dimers into a three-dimensional network. The extended structure of (II) features O—H...Br, N—H...Br and N—H...O hydrogen bonds: the last of these generates C(7) chains of cations. Overall, the packing in (II) features undulating (100) sheets of bromide ions alternating with the organic cations. Intermolecular interactions in the crystal of (III) include O—H...O, O—H...(O,O), N—H...O, N—H...N and O—H...N links. The cations are linked into (001) sheets, and the nitrate ions and water molecules form undulating chains. Taken together, alternating (001) slabs of organic cations plus anions/water molecules result. Hirshfeld surfaces and fingerprint plots were generated to give further insight into the intermolecular interactions in these structures. The crystal used for the data collection of (II) was twinned by rotation about [100] in reciprocal space in a 0.4896 (15):0.5104 (15) ratio.

Hydrogen-bonding patterns in bis[2,4,6-triazaniumylcyclohexane-1,3,5-tris(olate)-κ3O,O′,O′′]germanium(IV) tetrachloride hexahydrate

2016 ◽  
Vol 72 (1) ◽  
pp. 28-34
Author(s):  
Christian Neis ◽  
Bernd Morgenstern ◽  
Kaspar Hegetschweiler
Keyword(s):  
Hydrogen Bonding ◽  
Hydration Shell ◽  
Chloride Ions ◽  
Three Dimensions ◽  
Water Molecules ◽  
Amino Groups ◽  
Compound C ◽  
Hydrated Salt ◽  
Phd Thesis ◽  
Hydroxy Groups

A first preliminary report on the crystal structure of a hydrated salt formulated as [Ge(taci)2]Cl4·13H2O (taci is 1,3,5-triamino-1,3,5-trideoxy-cis-inositol) appeared more than 20 years ago [Ghisletta (1994). PhD thesis, ETH Zürich. Switzerland]. At that time it was not possible to discriminate unambiguously between the positions of some of the chloride ions and water O atoms, and disorder was thus postulated. In a new determination, a conclusive scheme of hydrogen bonding proves to be a particularly appealing aspect of the structure. Single crystals of the title compound, C12H30GeN6O64+·4Cl−·6H2O or [Ge(taci)2]2Cl8·12H2O, were grown from an aqueous solution by slow evaporation of the solvent. The two [Ge(taci)2]4+cations exhibit a double-adamantane-type structure with exclusive O-atom coordination and approximateD3dsymmetry. The taci ligands adopt a zwitterionic form with deprotonated hydroxy groups and protonated amino groups. Both cations are hydrogen bonded to six water molecules. The structure of the hydration shell of the two cations is, however, slightly different. The {[Ge(taci)2]·6H2O}4+aggregates are interlinked in all three dimensions by further hydrogen bonds of the types N—H...Cl...H—N, N—H...O(H)2...H—N, (Ge)O...H—O(H)...H—N, N—H...O(H)—H...Cl...H—N, (Ge)O...H—O—H...Cl...H—N, N—H...O(H)—H...Cl...H—(H)O...H—N, (Ge)O...H—O—H...Cl...H—(H)O...H—N and Ge(O)...H—O—H...Cl...H—O—H...O(Ge).

scholarly journals 2-[Hydroxy(2-methoxyphenyl)methyl]acrylonitrile

2012 ◽  
Vol 68 (8) ◽  
pp. o2467-o2467
Author(s):  
M. Bakthadoss ◽  
R. Selvakumar ◽  
R. Madhanraj ◽  
S. Murugavel
Keyword(s):  
Hydrogen Bonds ◽  
Diffraction Pattern ◽  
Benzene Ring ◽  
Dihedral Angle ◽  
Title Compound ◽  
Acta Cryst ◽  
Compound C ◽  
C And N ◽  
The Mean ◽  
Solvent Molecules

In the title compound, C11H11NO2, the mean planes formed by the benzene ring and the C and N atoms of the acryl group are almost orthogonal to each other, with a dihedral angle of 85.7 (1)°. During the structure analysis, it was observed that the unit cell contains large accessible voids, with a volume of 186.9 Å3, which may host disordered solvent molecules. This affects the diffraction pattern, mostly at low scattering angles. Density identified in these solvent-accessible areas was calculated and corrected for using the SQUEEZE routine inPLATON[Spek (2009),Acta Cryst.D65, 148–155]. Despite the presence of the hydroxy group in the molecule, no classical or nonclassical hydrogen bonds are observed in the structure. This may reflect the fact that the O—H group points towards the solvent-accessible void.

scholarly journals Solvent influence on intramolecular interactions and aromaticity in meta and para nitroanilines

2020 ◽  
Vol 31 (5) ◽  
pp. 1717-1728
Author(s):  
Krzysztof K. Zborowski ◽  
Halina Szatyłowicz ◽  
Tadeusz M. Krygowski
Keyword(s):  
Cluster Model ◽  
Density Functional ◽  
Intramolecular Interactions ◽  
Water Molecules ◽  
Amino Groups ◽  
Functional Theory ◽  
Hydration Effect ◽  
Solvent Influence ◽  
Solvation Models ◽  
Solvent Molecules

Abstract Theoretical density functional theory (B3LYP/6-31G**) was used to study the intra- and intermolecular interactions of nitrobenzene, aniline, and meta and para nitroaniline in various solvation models. The studied molecules were solvated by one or two water molecules in the presence of continuum solvation (the PCM model) or without it. Finally, the studied molecules were surrounded by a cluster of water molecules. For comparison, calculations were also made for separated molecules. Geometries, energies, hydrogen bonding between solutes and solvent molecules, atomic charges, and aromaticity were examined. The analysis was based on the Atoms in Molecules methodology and the Harmonic Oscillator Model of Aromaticity (HOMA) index. As a result, an extensive description of the solvation of nitro and amino groups and the effect of solvation on mutual interactions between these groups in meta and para nitroanilines is provided. It was found that in general, the PCM description of the hydration effect on the electronic structure of the studied systems (substituents) is consistent with the approach taking into account all individual interactions (cluster model).

On the differential hydration of various forms of glycine in diluted aqueous solutions: a Monte Carlo study

2012 ◽  
Vol 31 (2) ◽  
pp. 295
Author(s):  
Biljana Bujaroska ◽  
Kiro Stojanoski ◽  
Ljupco Pejov
Keyword(s):  
Monte Carlo ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Hydrogen Bonding Interaction ◽  
Liquid Environment ◽  
Zwitterionic Form ◽  
Solvent Water ◽  
Bonding Interaction ◽  
Solvent Molecules

Rigid-body Monte Carlo simulations were carried out to study the differential hydration of zwitterionic and neutral forms of glycine in water. To account for the solute polarization by the rather polar liquid environment, initial geometries were chosen as minima on the MP2/aug-cc-pVTZ potential energy surfaces of neutral and zwitterionic glycine continuously solvated by water, implementing the polarizable continuum model (PCM) within the integral equation formalism (IEFPCM). The dynamically changing hydrogen bonding network between the solute and solvent molecules was analyzed imposing distance, energy and angular distribution-based criteria. It was found that, on average, the zwitterionic form of glycine acts as an acceptor of 4.53 hydrogen bonds, while it plays the role of a proton donor in (on average) 2.73 hydrogen bonds with the solvent water molecules. In particular, we have found out that 2.73 solvent water molecules are involved in hydrogen bonding interaction with the ammonium group, acting as proton-acceptors. This is in excellent agreement with the recent experimental neutron diffraction studies, which have indicated that 3.0 water molecules reside in the vicinity of the NH3+ group of aqueous zwitterionic glycine. Neutral form of aqueous glycine, on the other hand, on average donates protons in 1.63 hydrogen bonds with the solvent water molecules, while at the same time it accepts 2.53 hydrogen bonds from the solvent molecules. The greater charge polarization in the zwitterionic form thus makes it much more exposed to hydrogen bonding interaction in polar medium such as water, which is certainly the main reason of the larger stability of this form of glycine in condensed media.

Redetermination of rifampicin pentahydrate revealing a zwitterionic form of the antibiotic

2012 ◽  
Vol 68 (5) ◽  
pp. o209-o212 ◽  
Author(s):  
Barbara Wicher ◽  
Krystian Pyta ◽  
Piotr Przybylski ◽  
Ewa Tykarska ◽  
Maria Gdaniec
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Amide Group ◽  
Water Molecules ◽  
Acta Cryst ◽  
Oh Groups ◽  
Zwitterionic Form ◽  
The Family

Rifampicin belongs to the family of naphthalenic ansamycin antibiotics. The first crystal structure of rifampicin in the form of the pentahydrate was reported in 1975 [Gadret, Goursolle, Leger & Colleter (1975).Acta Cryst.B31, 1454–1462] with the rifampicin molecule assumed to be neutral. Redetermination of this crystal structure now shows that one of the phenol –OH groups is deprotonated, with the proton transferred to a piperazine N atom, confirming earlier spectroscopic results that indicated a zwitterionic form for the molecule, namely (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-acetyloxy-6,9,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-8-[(E)-N-(4-methylpiperazin-4-ium-1-yl)formimidoyl]-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienimino)naphtho[2,1-b]furan-5-olate pentahydrate, C43H58N4O12·5H2O. The molecular structure of this antibiotic is stabilized by a system of four intramolecular O—H...O and N—H...N hydrogen bonds. Four of the symmetry-independent water molecules are arrangedviahydrogen bonds into helical chains extending along [100], whereas the fifth water molecule forms only one hydrogen bond, to the amide group O atom. The rifampicin molecules interactviaO—H...O hydrogen bonds, generating chains along [001]. Rifampicin pentahydrate is isostructural with recently reported rifampicin trihydrate methanol disolvate.

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 of 5-amino-5′-chloro-6-(4-chlorobenzoyl)-8-nitro-2,3-dihydro-1H-spiro[imidazo[1,2-a]pyridine-7,3′-indolin]-2′-one including an unknown solvent molecule

2014 ◽  
Vol 70 (9) ◽  
pp. o971-o972
Author(s):  
R. A. Nagalakshmi ◽  
J. Suresh ◽  
S. Sivakumar ◽  
R. Ranjith Kumar ◽  
P. L. Nilantha Lakshman
Keyword(s):  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Compound C ◽  
Benzoyl Group ◽  
Independent Molecules ◽  
Solvent Molecules ◽  
Intramolecular Hydrogen ◽  
Ring Motif

The asymmetric unit of the title compound, C21H15Cl2N5O4, contains two independent molecules (AandB) having similar conformations. The amine (NH2) group forms an intramolecular hydrogen bond with the benzoyl group, giving anS(6) ring motif in both molecules. The central six-membered rings adopt sofa conformations and the imidazole rings are planar (r.m.s deviations = 0.0150 and 0.0166 Å). The pyridine and imidazole rings are inclined to one another by 3.54 (1) and 3.03 (1)° in moleculesAandB, respectively. In the crystal, molecules are linked by N—H...O hydrogen bonds, forming chains along theaaxis which encloseR22(16) ring motifs. The rings are linked by weak N—H...O and C—H...O hydrogen bonds and C—H...π interactions forming sheets lying parallel to (001). A region of disordered electron density, most probably disordered solvent molecules, occupying voids ofca753 Å3for an electron count of 260, was treated using the SQUEEZE routine inPLATON[Spek (2009).Acta Cryst.D65, 148–155]. Their formula mass and unit-cell characteristics were not taken into account during refinement.

A single crystal X-ray study of a sulphate-bearing buttgenbachite, Cu36Cl7.8(NO3)1.3(SO4)0.35(OH)62.2.5.2H2O, and a re-examination of the crystal chemistry of the buttgenbachite-connellite series

2003 ◽  
Vol 67 (1) ◽  
pp. 47-60 ◽  
Author(s):  
D. E. Hibbs ◽  
P. Leverett ◽  
P. A. Williams
Keyword(s):  
Single Crystal ◽  
Democratic Republic ◽  
Democratic Republic Of Congo ◽  
Chloride Ion ◽  
Chloride Ions ◽  
Water Molecules ◽  
Data Set ◽  
X Ray ◽  
Positional Disorder ◽  
Anion Substitution

AbstractThe single-crystal X-ray structure of a sulphate-bearing buttgenbachite, Cu36Cl7.8(NO3)1.3(SO4)0.35(OH)62.2.5.2H2O, from Likasi, Democratic Republic of Congo, has been determined at 100 and 288 K. The basic framework of the structure is the same as has been previously reported for buttgenbachite, except for the identification of a hydrogen-bonded chloride ion (occupancy 0.6) at the origin instead of a Cu ion with partial occupancy. The nature of nitrate positional disorder along channels in the c direction and how this relates to the presence of other species such as chloride ions and water molecules and, most importantly, sulphate ions has been elucidated. One nitrate ion, with an occupancy of 0.18, lies at 2/3,l/3,l/4 and shares the site with a chloride ion (occupancy 0.30) and also a sulphate ion (occupancy 0.09); a second nitrate, with an occupancy of 0.24, lies at 2/3,1/3,0.084 and shares the site with a water molecule (occupancy 0.06). As a result, a formula of Cu36Cl7.8(NO3)1.3(SO4)0.35(OH)62.2.5.2H2O is obtained. Re-refinement of deposited data for a supposed connellite crystal from the Toughnut mine,Tombstone, Arizona gives a related, but different, pattern of anion substitution. No sulphate could be detected in the structure and it is evident that this structure refers to buttgenbachite. A nitrate nitrogen atom and a chloride ion are disordered at 2/3,l/3,l/4, the overall site being fully occupied. A chloride ion with ∼0.5 occupancy is sited at the origin and the formula Cu36Cl7.9(NO3)1.1(OH)63.4H2O is indicated. Re-refinement of a deposited data set for another buttgenbachite crystal from the Likasi mine reveals a partially occupied nitrate centred at 2/3,l/3, z and a partially occupied chloride at 2/3,l/3,l/4. Either 0.5Cl–, OH–, H2O or H3O+ is located at the origin. If the latter is the case, the stoichiometry for this buttgenbachite is Cu36Cl6.5(NO3)1.5(OH)64.5.5H2O. The present study has highlighted the fact that a range of compositions for buttgenbachite exists, depending on the pH and relative activities of chloride, nitrate and sulphate ions in solutions from which the mineral crystallizes.

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