What are preferred water–aromatic interactions in proteins and crystal structures of small molecules?

2014 ◽  
Vol 16 (43) ◽  
pp. 23549-23553 ◽  
Author(s):  
Goran V. Janjić ◽  
Saša N. Malkov ◽  
Miodrag V. Živković ◽  
Snežana D. Zarić
Keyword(s):  
Small Molecules ◽  
Crystal Structures ◽  
Water Molecules ◽  
Aromatic Rings ◽  
Aromatic Interactions

The distribution of water molecules around aromatic rings in proteins and crystal structures shows the largest number of the weakest interactions.

scholarly journals π-Stacking Stopper-Macrocycle Stabilized Dynamically Interlocked [2]Rotaxanes

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4704
Author(s):  
Sing-Ming Chan ◽  
Fung-Kit Tang ◽  
Ching-Yau Lam ◽  
Chak-Shing Kwan ◽  
Sam C. K. Hau ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Thermodynamic Stability ◽  
Combinatorial Library ◽  
Aromatic Rings ◽  
Interlocked Molecules ◽  
X Ray ◽  
Π Stacking ◽  
Dynamic Combinatorial Library

The synthesis of mechanically interlocked molecules is valuable due to their unique topologies. With π-stacking intercomponent interaction, e.g., phenanthroline and anthracene, novel [2]rotaxanes have been synthesized by dynamic imine clipping reaction. Their X-ray crystal structures indicate the π-stackings between the anthracene moiety (stopper) on the thread and the (hetero)aromatic rings at the macrocycle of the rotaxanes. Moreover, the length of glycol chains affects the extra π-stacking intercomponent interactions between the phenyl groups and the dimethoxy phenyl groups on the thread. Dynamic combinatorial library has shown at best 84% distribution of anthracene-threaded phenanthroline-based rotaxane, coinciding with the crystallography in that the additional π-stacking intercomponent interactions could increase the thermodynamic stability and selectivity of the rotaxanes.

Studies in aryltin chemistry. Part 6. Crystal and molecular structures of tetra(p-methylsulphonylphenyl)tin(IV) and tetra(p-methylsulphinylphenyl)tin(IV) monohydrate

1990 ◽  
Vol 68 (8) ◽  
pp. 1277-1282 ◽  
Author(s):  
Ivor Wharf ◽  
Michel G. Simard ◽  
Henry Lamparski
Keyword(s):  
Least Squares ◽  
Crystal Structures ◽  
Direct Method ◽  
Molecular Structures ◽  
Water Molecules ◽  
Monoclinic Space Group ◽  
Molecular Symmetry ◽  
Asymmetric Unit ◽  
Full Matrix ◽  
Space Group

Tetrakis(p-methylsulphonylphenyl)tin(IV) and tetrakis(p-methylsulphinylphenyl)tin(IV) n-hydrate have been prepared and their spectra (ir 1350–400 cm−1; nmr, 1H, 13C, 119Sn) and X-ray crystal structures are reported. The first compound is monoclinic, space group C2/c, Z = 4, with a = 21.589(6), b = 6.207(3), c = 22.861(11) Å, β = 93.80(3)° (22 °C); the structure was solved by the direct method and refined by full-matrix least squares calculations to R = 0.043 for 2755 observed reflections. It has 2 molecular symmetry with the methyl group and one oxygen atom completely disordered in both CH3S(O2) groups in the asymmetric unit. The second compound is tetragonal, space group P42/n, Z = 2, with a = b = 15.408(6), c = 6.379(2) Å (−100 °C); the structure was solved by the Patterson method and refined by full-matrix least squares calculations to R = 0.060 for 1209 observed reflections. It has [Formula: see text] molecular symmetry with the whole asymmetric unit disordered. Water molecules occupy positions on parallel 42 axes but molecular packing requirements prevent all sites having 100% occupancy giving n ~ 1 for the hydrate. Keywords: Tetra-aryltins, crystal structures, sulphone, sulphoxide, hydrogen-bonding.

scholarly journals Kristallstrukturen zweier Kupfer(II)-Cyclam-Komplexe: [{CuCl(C10N4H24)}2][CdCl4] und [Cu(C10N4H24)][CdCl3(H2O)2]Cl / Crystal Structures of Two Copper(II) Cyclam Complexes: [{CuCl(C10N4H24 )}2][CdCl4] and [Cu(C10N4H24)][CdCl3 (H2O)2]Cl

1995 ◽  
Vol 50 (5) ◽  
pp. 828-832 ◽  
Author(s):  
Joachim Pickardt ◽  
Isabella Hoffmeister
Keyword(s):  
Crystal Structures ◽  
Copper Atom ◽  
Water Molecules ◽  
Cadmium Atom ◽  
Bridging Ligands ◽  
Chlorine Atoms ◽  
Space Group ◽  
Distorted Octahedra ◽  
Cyclam Complexes

Abstract Crystals of both complexes were obtained by evaporation of the ethanol solvent. The crystals of [{CuCl(C10N4H24)}2][CdCl4] are tetragonal, space group I4̄2d, Z = 4, a = b = 1784.1(11), c = 1101.1(8) pm. Each copper atom is bonded to one cyclam ligand and two chlorine atoms which are acting as bridging ligands and connect the copper atoms to chains of distorted octahedra. Distorted tetrahedra of CdCl4 are situated in cavities between these chains. The crystals of [Cu(C10N4H24)][CdCl3(H2O)2]Cl are monoclinic (b), space group C2/c, Z = 4, a = 1581.9(8), b = 1323.3(7), c = 924.0(5) pm, β = 94.31(5)°. Cadmium is coordinated to four chlorine atoms and two water molecules, while all of the chlorine atoms act as bridging ligands connecting every cadmium atom to two adjacent cadmium atoms and to two copper atoms which lie in plane with the N atoms.

Crystal structures of tricalcium citrates

2018 ◽  
Vol 33 (2) ◽  
pp. 98-107 ◽  
Author(s):  
James A. Kaduk
Keyword(s):  
Crystal Structures ◽  
Density Functional ◽  
Three Dimensional ◽  
Water Molecules ◽  
Calcium Citrate ◽  
Powder Diffraction Data ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Calcium Supplements ◽  
Dimensional Network

The crystal structures of calcium citrate hexahydrate, calcium citrate tetrahydrate, and anhydrous calcium citrate have been solved using laboratory and synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Both the hexahydrate and tetrahydrate structures are characterized by layers of edge-sharing Ca coordination polyhedra, including triply chelated Ca. An additional isolated Ca is coordinated by water molecules, and two uncoordinated water molecules occur in the hexahydrate structure. The previously reported polymorph of the tetrahydrate contains the same layers, but only two H2O coordinated to the isolated Ca and two uncoordinated water molecules. Anhydrous calcium citrate has a three-dimensional network structure of Ca coordination polyhedra. The new polymorph of calcium citrate tetrahydrate is the major crystalline phase in several commercial calcium supplements.

Crystal structures of nickel(II) and copper(Il)-Schiff-bases complexes with tetramic and tetronic acid subunits

1994 ◽  
Vol 209 (12) ◽  
Author(s):  
G. Reck ◽  
B. Schulz ◽  
A. Zschunke ◽  
O. Tietze ◽  
J. Haferkorn
Keyword(s):  
Complex Formation ◽  
Water Molecule ◽  
Crystal Structures ◽  
Schiff Bases ◽  
Water Molecules ◽  
Ligand Molecule ◽  
Tetragonal Pyramid ◽  
Space Group ◽  
Tetronic Acid ◽  
Oxygen Ligand

AbstractN,N′-ethylene-bis-(tetronic-acid-3-formiminato)-copper(II)/K1 crystallizes in space groupN,N′-ethylene-bis-(tetronic-acid-3-formiminato)-nikkel(II)/K2 crystallizes in space groupN,N′-ethylene-bis-(1,5,5-trimethyltetramic-acid-3-formiminato)-copper(II)/K3 crystallizes in space groupIn K1 and K3 copper is coordinated by two nitrogen and two oxygen atoms of the ligand molecule as well as by one water molecule on top of a tetragonal pyramid. In K2 two water molecules are included in the complex formation. These and two nitrogen as well as two oxygen ligand atoms form a nearly regular octahedron.

Extrem asymmetrisch gebundene Wassermoleküle-Kristallstrukturen von Sr(OH)Cl · 4 H2O, Sr(OH)Br · 4 H2O und Ba(OH)I·4 H2O / Extremely Asymmetrically Bound Water Molecules-Crystal Structures of Sr(OH)Cl · 4 H2O, Sr(OH)Br · 4 H2O, and Ba(OH)I·4 H2O

1991 ◽  
Vol 46 (10) ◽  
pp. 1279-1286 ◽  
Author(s):  
Thomas Kellersohn ◽  
Konrad Beckenkamp ◽  
Heinz Dieter Lutz
Keyword(s):  
Crystal Structures ◽  
Bound Water ◽  
Structure Type ◽  
Water Molecules ◽  
Halide Ions ◽  
Weak Hydrogen Bond ◽  
Scanning Calorimetry ◽  
Unknown Structure ◽  
Stretching Vibrations ◽  
Strong Distortion

The crystal structures of isotypic Sr(OH)Cl ·4 H2O, Sr(OH)Br·4 H2O, and Ba(OH)I·4 H2O are reported. The title compounds crystallize in a hitherto unknown structure type, space group PĪ, Z = 2. The final R values obtained are 0.0261, 0.069, and 0.062, respectively. The coordination of the metal ions is monocapped square antiprismatic with 7 H2O, 1 OH- and 1 halide ion. The halide ions separate metal/water/hydroxide layers. Each of the four crystallographically different water molecules serves as donor for one very strong and one very weak hydrogen bond and, hence, is extremely asymmetrically bound. Owing to this strong distortion, the largest one known so far, the OH stretching vibrations of the H2O molecules are intramolecularly decoupled as shown from vibrational spectra. The enthalpies of dehydration obtained from differential scanning calorimetry are reported.

Structural and spectroscopic studies of transition metal nitrite complexes. V. Crystal structures and spectra of trans-Tetrakis(pyridine)dinitritonickel(II)-pyridine (1/2), trans-Tetrakis(4-methylpyridine)dinitritonickel(II) and trans-Tetrakis(pyrazole)-dinitritonickel(II)

1981 ◽  
Vol 34 (10) ◽  
pp. 2095 ◽  
Author(s):  
AJ Finney ◽  
MA Hitchman ◽  
CL Raston ◽  
GL Rowbottom ◽  
BW Skelton ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Transition Metal ◽  
Crystal Structures ◽  
Electronic Spectra ◽  
Spectroscopic Studies ◽  
Molecular Structures ◽  
Aromatic Rings ◽  
Paddle Wheel ◽  
Crystal And Molecular Structures ◽  
Infrared Frequencies

The crystal and molecular structures of the compounds [Ni(py)4(ONO)2],2py, [Ni(γmpy),(ONO)2] and [Ni(prz)4(ONO)2] are reported.�All three are trans nitrito complexes, the pyridine (py) compound containing two pyridine molecules of solvation. The aromatic rings in the first two complexes adopt 'paddle wheel' conformations with pitch angles varying between 40 and 70�. The nitrite ions are positioned so as to minimize repulsive interactions with the amines, and it seems likely that these groups bond through oxygen rather than nitrogen because this allows a lesser degree of interligand steric interference. The amine rings in [Ni(prz)4(ONO)2] are orthogonal to the plane containing the nickel and coordinated pyrazole nitrogen atoms; the nitrito groups are disordered between two inequivalent positions, each of which involves hydrogen bonding with the pyrazole NH groups. The nitrite infrared frequencies are similar to those observed for other nickel(II) nitrito complexes except that the antisymmetric NO stretching mode of one of the groups in the pyrazole complex is much lower in energy than expected, being in the range normally associated with a nitrogen-bonded or chelated nitrite group. It is suggested that this deviation may be caused by the hydrogen bonding in the complex. The electronic spectra of the compounds yield 10Dq values of 9100 and 8500 cm-1 for the nitrite ligands in [Ni(py)4(ONO)2] and Ni(prz)4(ONO)2], respectively, placing the nitrito group towards the weaker end of the spectro-chemical series.

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