PyFepRestr: Plugin to PyMOL Molecular Graphics System for Calculating the Free Energy of Ligand‒Receptor Binding

Crystallography Reports - The calculations of the free energy of ligand binding with a receptor (most often, protein) are widely used in the rational design of new bioactive compounds. The gold...     

Mössbauer Spectroscopy of Magnetic Nanoparticles: A Historical Perspective and State of the Art

Crystallography Reports - Mössbauer spectroscopy is one of the main methods that are successfully applied to study the properties of magnetic nanoparticles (MNPs), because the small MNP size...     

Crystal and Molecular Structure of 6,6′-Dimethoxy-gossypol:Acetic acid (1:1)

Abstract By crystallization from dilute solutions of acetic acid (2–4%) in diethyl ether, acetone, or methyl ethyl ketone, 6,6′-dimethoxy-gossypol forms a solvate with acetic acid in a one-to-one molar ratio. The compound crystallizes in the triclinic P space group and has unit cell dimensions of a = 7.5793(10) ?, b = 14.7211(19) ? and c = 14.740(2) ?, α = 106.260(3)°, β = 102.310(3)°, γ = 95.975(3)°, Z = 2. The structure was solved by direct methods and refined to an R1 value of 0.0394 on 4252 observed reflections. Enantiomeric pairs of dimethoxy-gossypol molecules form centrosymmetic dimers that are characterized by a pair of intermolecular hydrogen bonds and by hydrophobic stacking between pairs of naphthalene rings. The acetic acid molecule accepts a hydrogen bond from a gossypol hydroxyl group and donates to a hydrogen bond with one of the aldehyde groups of an adjacent gossypol molecule. Although there is less hydrogen bonding in this structure than in the gossypol:acetic acid (1:1) structure, the molecular packing of the two compounds is similar. Graphical abstract Crystal and molecular structure of 6,6′-dimethoxy-gossypol:acetic acid (1:1) Michael K. Dowd and Edwin D. Stevens The molecular structure of the acetic acid solvate of 6,6′-dimethoxy-gossypol is presented.      

Hydrogen-Bonded Molecular Ladders and Interlaced Networks in Complexes Built of V-Shaped Molecules 4,4′-Isopropylidenediphenol or 4,4′-Oxydibenzoic Acid with 4,4′-Bipyridine

Abstract  

The title compounds, C₁₀H₈N₂·C₁₅H₁₆O₂ (1) and C₁₀H₈N₂·C₁₄H₁₀O₅ (2), were synthesized by 4,4′-bipyridyl and two similar V-shaped molecules. The two complexes both crystallized in the same space group P2₁/n with the crystal cell parameters: a = 16.0536(3) ?, b = 6.42730(1) ?, c = 21.2717(4) ?, β = 102.330°, V = 2144.21(7) ?³, Z = 4 in compound 1 and a = 7.45020(10) ?, b = 10.0784(2) ?, c = 26.9430(5) ?, β = 92.1140(10)°, V = 2021.67(6) ?³, Z = 4 in compound 2. Compound 1 forms regular molecular chains containing alternative 4,4′-bipyridyl and 4,4′-isopropylidenediphenol units; the molecular components are linked by two types of O–H···N hydrogen bonds. Additionally, every two neighboring chains are connected to be a ladder structure by means of weak C–H···O interactions. In compound 2, 4,4′-bipyridyl and 4,4′-oxydibenzoic acid first construct one-dimensional architecture by strong O–H···N hydrogen bonds, which are similar with the interactions in compound 1. Secondly, two types of weak C–H···O contacts formed between 4,4′-bipyridyl and the acid link one-dimensional chains to be interlaced three-dimensional hydrogen-bonded networks.     

A review of: “Molecular Dynamics of Liquid Crystals”

Abstract

Editors: G.R. Luckhurst and C.A. Veracini NATO ASI Series C: Mathematical and Physical Sciences - Vol. 431 Proceedings of the NATO Advanced Study Institute on The Molecular Dynamics of Liquid Crystals. II Ciocco. Borga. Italy. 11 - 23 September 1989 ISBN 0-7923-2809-4     

Structural Investigation of Metal-Organic Cu(II) Coordination Frameworks Constructed from N-donor and α, ω-Dicarboxylate Ligands by One Pot Synthesis: Zigzag Strands,Layered Networks and Its Interaction with Lattice Water Molecules

Abstract  

Two metal organic frameworks involving α, ω-dicarboxylates and 2,2′-bpy, [Cu(2,2Bpy)(μ-adipate-H2)] _n ·2·H₂O 1 and [Cu₂ (2,2′-bpy)₂(μ-adipate-H)₂(μ-adipate-H2)]·3H₂O 2 have been synthesized by one pot reaction and structurally characterized. Pentacoordinated Cu(II) zigzag polymeric chain of 1 is composed of linking the adjacent Cu(2,2′-bpy)(H₂O) units through terminal craboxylate oxygens of two different adipate dianion in cis coordination pattern with the metal center. Both the Complexes were crystallized in triclinic system, P-1 space group with cell parameters a = 6.8948(5), b = 10.7098(7), c = 12.4332(8) ?; α = 82.1120(10), β = 80.4950(10), γ = 72.9560(10)°, V = 861.87(10) ?³ for 1, a = 9.5058(6), b = 9.9341(7), c = 12.6460(8) ?; α = 70.5080(10), β = 73.5740(10), γ = 75.0720(10)°, V = 1062.05(12) ?³ for 2 respectively. Extensive hydrogen bonding interaction is observed between the lattice water molecules and the coordination network. Compound 2 is a layered architecture, where the neutral framework is constructed by two different adipate anions (in monoanionic and dianionic form) coordinating to the metal center. Interestingly, three water molecules present in the lattice of compound 2 are involved in hydrogen bonding network among themselves, creating a centro-symmetric hexameric water cluster composed of a tetracyclic ring with dangling water molecules attached at alternate positions of the rectangle, which interact with the carboxylate oxygen, thereby extending the hydrogen bonded water network.     

Molecular and crystal structure of 4′-cyanobenzo-15-crown-5

The crystal structure of 4′-cyanobenzo-15-crown-5 is determined by X-ray diffraction. The crystallographic parameters of single crystals are as follows: a = 40.479(6) Å, b = 8.821(2) Å, c = 8.484(2) Å, β = 93.94(2)°, V = 3022.2 ų, Z = 8, d _calcd = 1.27 g/cm³, and space group C2/c. The structure is solved by the direct method and refined by the least-squares procedure to R = 0.068. The conformation of the macrocycle in 4′-cyano-B15C5 is described by the a-a-g ^? -a-a-g-g ^? -a-a-g-a-g-a-a-s sequence of torsion angles.     

4,4′-Di(N)Hexoxybenzalazine: Crystal and Molecular Structure and Phase Characterization of the Liquid Crystalline Compound

Abstract

The crystal and molecular structure of the mesogenic title compound (HBA) is described. Lattice parameters are: space group P1, a = 9.003(2) Å, b = 8.850(2) Å, c = 8.510(2) Å, α = 79.63(1)°, β = 65.04(1)°, γ = 87.41(1)° (at T = 299 K). The molecules contain a centre of symmetry and the phenyl rings are coplanar. In order to obtain better structural data for a comparison with its methoxy derivative (MBA) a redetermination of this structure was carried out using a new data set. The melting enthalpy of HBA is 45(2) kJmol^?1 (127.8(5)°C) its clearing enthalpy is 1.5(4) kJmol^?1 (153.2(5) °C). The fluctuation wave-length 2π/q_‖ of 27(2) Å in the nematic state can be compared with the molecular length of 31.63 Å.     

Molecular and crystal structures of mesomorphic aromatic esters: I. Structure of two isomers, p-butoxyphenyl p′-hexyloxybenzoate and p-hexyloxyphenyl p′-butoxybenzoate

Two isomers, p-butoxyphenyl p′-hexyloxybenzoate (1) and p-hexyloxyphenyl p′-butoxybenzoate (2), are studied by X-ray diffraction. Crystals 1 contain two crystallographically independent molecules, which differ in the conformation of one of their side chains. In both compounds, bond lengths and angles have standard values. The geometry of the central fragment Ph-Est-Ph is essentially the same in both isomers. One of the benzene rings is coplanar with the Est group, and the other ring, which is linked with this group through the oxygen atom, is almost perpendicular to the Est plane. In crystal 1, molecules are packed in such a fashion that, in any pair of neighboring molecules, the most closely spaced benzene rings are nearly perpendicular to each other, which corresponds to a weak C-H?π interaction. In the crystal packing of 2, neither perpendicular nor stacking motifs are observed. The supramolecular architecture of this compound is determined by directional specific interactions of the hydrogen bond type between the C-H benzene fragment and the ester oxygen atom of the neighboring molecule.     

Study of the Spin-Wave Dynamics of Amorphous Ferromagnets and Helimagnets with the Dzyaloshinskii‒Moriya Interaction

Crystallography Reports - The “inclined” dynamics method developed for studying spin waves in ferromagnets was proposed and implemented at the Leningrad Nuclear Physics Institute in...     

Crystal and Molecular Structure of the Nematogenic Compound 4′-Cyanophenyl-4-n-Pentoxybenzoate

The title compound with the formula C₅H₁₁O-C₆H₄-COO-C₆H₄-CN (CPPOB) crystallizes in the orthorhombic space group Pnam with a = 16.465 Å, b = 13.577 Å, c = 7. 621 Å and four molecules per unit cell. The structure has been solved by direct methods and refined to a final R value of 0.050. The CPPOB molecules have exact C_s symmetry as a consequence of their location on crystallographic mirror symmetry planes, the benzene ring to which the cyano group is attatched has a perpendicular orientation to the other ring in the plane. The molecules adopt a nearly optimal stretched form, neighbouring molecules make an angle of 35.2°. The results are discussed in relation to the mesomorphic behaviour of CPPOB.     

Molecular and crystal structure of bis-quinolizidine immonium salts,V: Δ11(16)-dehydrolupaninium perchlorate monohydrate

¹¹⁽¹⁶⁾-Dehydrolupaninium perchlorate monohydrate, [C₁₅H₂₃N₂O]⁺ClO₄·H₂O, was obtained from ¹²-dehydrolupanine, the product of mercuric acetate dehydrogenation of lupanine. It forms orthorhombic crystals, space groupp2₁2₁2₁,a=8.528(1),b=12.335(1),c=32.928(3) Å,V _c=3463.8 ų,Z=8,D _m=1.34,D _x=1.34 g cm^–3, (CuK)=20.7 cm^–1.F(OOO)=1472, mp=458 K; the finalR=0.086 for 2363 observed counter reflections. Two independent perchlorate anions and two independent cations are disordered. The conformations of the independent cations are similar: sofa (ringA), chair (ringB), intermediate between sofa and half-chair (ringC), and half-chair (ringD). The two lactam oxygens of the two independent cations are each hydrogen bonded to a different water molecule. From X-ray analysis and IR spectra in the condensed phase and¹³C-NMR measurements in DMSO-²H₆ and²H₂O it is evident that in the crystalline state as well as in solution, the immoniumlactam molecular structure is present in the compound studied.     

The Preparation and Properties of the α,ω-bis(4,4′-Cyanobiphenyloxy)Alkanes: Nematogenic Molecules with a Flexible Core

The first twelve members of the homologous series of α,ω-bis(4,4′-cyanobiphenyloxy) alkanes have been synthesised. The compounds are nematogenic, although the mesophases for the first and third members of the series are monotropic. Both the nematic-isotropic transition temperature and the entropy of transition exhibit a pronounced dependence on the length of the flexible core; this is analogous to that found for main chain thermotropic liquid crystal polymers.     

Electrical and sensory properties of zinc oxide – porous silicon nanosystems

Abstract

Zinc oxide nanostructures have been grown by electrochemical deposition on porous silicon–silicon substrate. The photoelectric and sensory properties of the obtained ZnO–porous silicon nanosystems were investigated in both DC and AC regimes. The obtained structures were characterized by photosensitivity in the 400–1100?nm wavelength range and by high sensitivity to moisture. Increase of relative humidity resulted in significant decrease of the electrical resistance and increase of the capacitance of the hybrid structures. To estimate the sensory properties of the ZnO–porous silicon nanostructures their adsorption sensitivity and dynamic characteristics were analyzed. Discovered features of the charge transport processes broaden the prospects of the semiconductor nanosystems application in gas sensors and photodetectors.     

Ground state structures of molecules “prepared” for phototautomerization: 2,2′-bipyridyl-3,3′-diol and 2,2′-bipyridyl-3-ol

The crystal structures of two molecules undergoing fast intramolecular excited state proton transfer (2,2-bipyridyl-3,3-diol, BP(OH)₂, and 2,2-bipyridyl-3-ol, BP(OH)) are reported and compared with the results ofab initio and molecular mechanics calculations. Strong intramolecular hydrogen bonding is observed in both cases. The pyridyl rings are coplanar in BP(OH)₂, whereas in BP(OH) they form an angle of 3.7°.Dedicated to Prof. R. Zahradnik on the occasion of his birthday.     

X-ray Crystal Structures of Silver Based Molecules Containing 5,5′-Dimethyl-2,2′-bipyridine and 2,2′-bipyridine

Abstract  

The reaction of AgBF₄ with 5,5′-dimethy-2,2′-bipyridine and 2,2′-bipyridine yields three previously unreported compounds. The molecular structures of these compounds were obtained by single-crystal X-ray diffraction. Crystallization of 1 occurs in the centrosymmetric triclinic space group P-1 (No. 2) with a = 13.0069(6), b = 13.5903(6), c = 13.9489(6); and α = 95.677(2), β = 98.995(2), γ = 101.716(2) and Z = 6. Crystallization of 2 occurs in the centrosymmetric monoclinic space group C2/c (No. 15) with a = 23.413(3), b = 11.2116(13), c = 13.0653(13) and β = 123.074(3), and Z = 4. Crystallization of 3 occurs in the centrosymmetric triclinic space group P-1 (No. 2) with a = 12.6843(12), b = 12.8834(13), c = 12.9887(13), and α = 96.172(5), β = 95.149(5), γ = 98.051(6) and Z = 2. Details of the synthesis and the structural characterization of the title compounds are presented and discussed.     

Syntheses and Photovoltaic Properties of Octyl Cyanoacetate Terminated Small Molecules Based on Benzo[1,2-b:4,5-b’]dithiophene for OPVs

There have been tremendous efforts to synthesize photoactive materials that are consisted of both donor and acceptor components together to increase the power conversion efficiency (PCE) of organic photovoltaic cells (OPVs). In order to improve the performance of the OPVs, in this study, we proposed new A-D-A (Acceptor-Donor-Acceptor) type small molecular donors based on the donor unit of benzo[1,2-b:4.5-b’]dithiophene (BDT) with an acceptor unit of alkyl cyanoacetate. We characterized prepared photoactive materials using ¹H NMR spectroscopy, DSC, CV (cyclic voltammetry), and UV/Vis spectroscopy. We also investigated the relationship between PCEs of OPVs and the active materials with variation of substituted methyl groups. The OPVs based on synthesized photoactive materials with different methyl substitutions showed different PCEs. Our results indicate that synthesized small molecular donor materials are promising donor materials for performance OPVs