scholarly journals A Preview of a Construction of a Crystal Lattice Based on Intermolecular Interactions

Crystals ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 159
Author(s):  
Vladimír Hejtmánek ◽  
Martin Dračínský ◽  
Jan Sýkora
Keyword(s):  
Intermolecular Interactions ◽  
Structural Model ◽  
Crystal Packing ◽  
General Procedure ◽  
3D Structure ◽  
One Dimension ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Repetitive Motif

A general procedure of crystal packing reconstruction using a certain number of intermolecular interactions is introduced and demonstrated on the crystal structure of l-histidine·HCl·H2O. Geometric restrictions based on intermolecular interactions are used for formation of a molecular pair as a basic repetitive motif of the crystal packing. The geometric restrictions were applied gradually within a supervised procedure, narrowing the scope of possible arrangement of two adjacent molecules. Subsequently, a pair of histidine molecules was used for construction of a molecular chain. The chain formed contained translation information on histidine molecules in one dimension, which coincided with one of the cell parameters. Furthermore, the periodicity in the second and third dimensions can be accomplished by chain assembly into sheets (2D), and sheets can be arranged into the final 3D structure. For this purpose, the rest of the available intermolecular interactions could be used to control the mutual assembly of molecular chains and sheets. Complete molecular packing would enable derivation of standard crystallographic parameters that can be used for verification of the structural model obtained. However, the procedure described for construction of the whole 3D structure from molecular chains was not attempted, and is only briefly outlined here. The procedure described can be employed especially when standard crystallographic parameters are not available and traditional methods based on X-ray diffraction fail.

Synthesis, growth, structure and characterization of molybdenum zinc thiourea complex crystals

2015 ◽  
Vol 71 (3) ◽  
pp. 285-292 ◽  
Author(s):  
M. Rajasekar ◽  
K. Muthu ◽  
A. Aditya Prasad ◽  
R. Agilandeshwari ◽  
SP Meenakshisundaram
Keyword(s):  
Single Crystal ◽  
Diffraction Analysis ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Second Harmonic ◽  
Morphological Changes ◽  
Strong Interactions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters

Single crystals of molybdenum-incorporated tris(thiourea)zinc(II) sulfate (MoZTS) are grown by the slow evaporation solution growth technique. Crystal composition as determined by single-crystal X-ray diffraction analysis reveals that it belongs to the orthorhombic system with space groupPca21and cell parametersa= 11.153 (2),b= 7.7691 (14),c= 15.408 (3) Å,V= 1335.14 (4) Å3andZ= 4. The surface morphological changes are studied by scanning electron microscopy. The vibrational patterns in FT–IR are used to identify the functional group and TGA/DTA (thermogravimetric analysis/differential thermal analysis) indicates the stability of the material. The structure and the crystallinity of the material were confirmed by powder X-ray diffraction analysis and the simulated X-ray diffraction (XRD) closely matches the experimental one with varied intensity patterns. The band gap energy is estimated using diffuse reflectance data by the application of the Kubelka–Munk algorithm. The relative second harmonic generation (SHG) efficiency measurements reveal that MoZTS has an efficiency comparable to that of tris(thiourea)zinc(II) sulfate (ZTS). Hirshfeld surfaces were derived using single-crystal X-ray diffraction data. Investigation of the intermolecular interactions and crystal packingviaHirshfeld surface analysis reveal that the close contacts are associated with strong interactions. Intermolecular interactions as revealed by the fingerprint plot and close packing could be the possible reasons for facile charge transfer leading to SHG activity.

Structural Model for Ferrihydrite

Clay Minerals ◽  
1993 ◽  
Vol 28 (2) ◽  
pp. 185-207 ◽  
Author(s):  
V. A. Drits ◽  
B. A. Sakharov ◽  
A. L. Salyn ◽  
A. Manceau
Keyword(s):  
Structural Model ◽  
Structural Difference ◽  
Coherent Scattering ◽  
Close Packing ◽  
X Ray Diffraction ◽  
Actual Structure ◽  
X Ray ◽  
Cell Parameters ◽  
Super Cell ◽  
Mean Dimension

AbstractThe structure of 6-line and 2-line ferrihydrite (Fh) has been reconsidered. X-ray diffraction (XRD) curves were first simulated for the different structural models so far proposed, and it is shown that neither of these corresponds to the actual structure of ferrihydrite. On the basis of agreement between experimental and simulated XRD curves it is shown that Fh is a mixture of three components: (i) Defect-free Fh consisting of anionic ABACA . . . close packing in which Fe atoms occupy only octahedral sites with 50% probability; the hexagonal unit-cell parameters are a = 2-96 Å and c = 9-40 Å, and the space group is P1c. (ii) Defective Fh in which Ac1Bc2A and Ab1Cb2A structural fragments occur with equal probability and alternate completely at random; Fe atoms within each of these fragments have identical ordered distribution with in the hexagonal super-cell with a = 5.26 Å. (iii) Ultradispersed hematite with mean dimension of coherent scattering domains (CSD) of 10-20 Å. The main structural difference between 6-line and 2-line Fh is the size of their CSD which is extremely small for the latter structure. Nearest Fe-Fe distances calculated for this new structural model are very close to those determined by EXAFS spectroscopy on the same samples.

The influence of the type of halogen substituent and its position on the molecular conformation, intermolecular interactions and crystal packing for a series of 1-benzoyl-3-(halogenophenyl)thioureas

2021 ◽  
Vol 77 (1) ◽  
pp. 11-19
Author(s):  
Damian Rosiak ◽  
Andrzej Okuniewski ◽  
Jarosław Chojnacki
Keyword(s):  
Intermolecular Interactions ◽  
Phenyl Ring ◽  
Benzoyl Chloride ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Theoretical Calculations ◽  
The Novel ◽  
X Ray Diffraction ◽  
X Ray ◽  
C Nmr

By the reaction of benzoyl chloride, potassium isothiocyanate and the appropriate halogenoaniline, i.e. 2/3/4-(bromo/iodo)aniline, we have obtained five new 1-benzoyl-3-(halogenophenyl)thioureas, namely, 1-benzoyl-3-(2-bromophenyl)thiourea and 1-benzoyl-3-(3-bromophenyl)thiourea, C14H11BrN2OS, and 1-benzoyl-3-(2-iodophenyl)thiourea, 1-benzoyl-3-(3-iodophenyl)thiourea and 1-benzoyl-3-(4-iodophenyl)thiourea, C14H11IN2OS. Structural and conformational features of the compounds have been analyzed using X-ray diffraction and theoretical calculations. The novel compounds were characterized by solid-state IR and 1H/13C NMR spectroscopy. The conformations and intermolecular interactions, such as hydrogen bonds, π–π and S(6)...π stacking, and X...O (X = I or Br), I...S and I...π, have been examined and rationalized, together with four analogous compounds described previously in the literature. The set of nine compounds was chosen to examine how a change of the halogen atom and its position on the phenyl ring affects the molecular and crystal structures.

scholarly journals A 1:1 energetic co-crystal formed between trinitrotoluene and 2,3-diaminotoluene

2018 ◽  
Vol 37 (1) ◽  
pp. 61 ◽  
Author(s):  
Nilgun Sen
Keyword(s):  
Single Crystal ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Main Mechanism ◽  
Oxygen Balance ◽  
X Ray Diffraction ◽  
X Ray ◽  
Fingerprint Plots ◽  
Hirshfeld Surfaces ◽  
Π Stacking

A 1:1 co-crystal of trinitrotoluene (TNT) and 2,3-diaminotoluene was prepared by solvent evapo- ration, and the structure of the co-crystal was determined by single-crystal and powder X-ray diffraction. The results indicate that the main mechanism of co-crystallization originates from the intermolecular hy- drogen bonding (amino-nitro) and π-π stacking. We also examined the Hirshfeld surfaces and associated fingerprint plots of the co-crystal and reveal that the structures are stabilized by H…H, O–H, O…O and C…C (π-π) intermolecular interactions. We analyzed the crystal packing and show its influence upon im- pact sensitivity. The results highlight that co-crystallization is an effective way to modify the sensitivity, oxygen balance and density of explosives. 

scholarly journals Molecular Structures Polymorphism the Role of F…F Interactions in Crystal Packing of Fluorinated Tosylates

Crystals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 242 ◽  
Author(s):  
Dmitry E. Arkhipov ◽  
Alexander V. Lyubeshkin ◽  
Alexander D. Volodin ◽  
Alexander A. Korlyukov
Keyword(s):  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
Total Contribution ◽  
X Ray ◽  
Weak Hydrogen Bonds ◽  
Intermolecular Bonding

The peculiarities of interatomic interactions formed by fluorine atoms were studied in four tosylate derivatives p-CH3C6H4OSO2CH2CF2CF3 and p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5, 7) using X-ray diffraction and quantum chemical calculations. Compounds p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5) were crystallized in several polymorph modifications. Analysis of intermolecular bonding was carried out using QTAIM approach and energy partitioning. All compounds are characterized by crystal packing of similar type and the contribution of intermolecular interactions formed by fluorine atoms to lattice energy is raised along with the increase of their amount. The energy of intra- and intermolecular F…F interactions is varied in range 0.5–13.0 kJ/mol. Total contribution of F…F interactions to lattice energy does not exceed 40%. Crystal structures of studied compounds are stabilized mainly by C-H…O and C-H…F weak hydrogen bonds. The analysis of intermolecular interactions and lattice energies in polymorphs of p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5) has shown that most stabilized are characterized by the least contribution of F…F interactions.

Study on a Novel Structure of C21H9Ba2SrN3O12

2013 ◽  
Vol 834-836 ◽  
pp. 494-499
Author(s):  
Hai Xing Liu ◽  
Qing Liu ◽  
Xiao Ping Zhang ◽  
Quan Hua Fan ◽  
Lin Tong Wang ◽  
...  
Keyword(s):  
Hydrothermal Reaction ◽  
Crystal Packing ◽  
Hydrogen Bonding Interaction ◽  
X Ray Diffraction ◽  
Monoclinic System ◽  
X Ray ◽  
Cell Parameters ◽  
Compound C ◽  
Novel Structure ◽  
Bonding Interaction

In the title compound, C21H9Ba2N3O12Sr, is prepared from a hydrothermal reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. The compound crystallize in Monoclinic, system with space group and cell parameters, C2/c, a=22.668 Å, b=10.937 Å, c=9.05 Å, α=γ=90°, β=90.582°, V=2243.6 Å3. The crystal packing is stabilized by O-H...O and O-H...N hydrogen bonding interaction.

scholarly journals Synthesis, crystal structure, polymorphism and microscopic luminescence properties of anthracene derivative compounds

2020 ◽  
Vol 76 (3) ◽  
pp. 427-435 ◽  
Author(s):  
Anna Moliterni ◽  
Davide Altamura ◽  
Rocco Lassandro ◽  
Vincent Olieric ◽  
Gianmarco Ferri ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Building Blocks ◽  
Luminescence Properties ◽  
Fluorescence Lifetime Imaging ◽  
Optical Investigation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Anthracene Derivative

Anthracene derivative compounds are currently investigated because of their unique physical properties (e.g. bright luminescence and emission tunability), which make them ideal candidates for advanced optoelectronic devices. Intermolecular interactions are the basis of the tunability of the optical and electronic properties of these compounds, whose prediction and exploitation benefit from knowledge of the crystal structure and the packing architecture. Polymorphism can occur due to the weak intermolecular interactions, requiring detailed structural analysis to clarify the origin of observed material property modifications. Here, two silylethyne-substituted anthracene compounds are characterized by single-crystal synchrotron X-ray diffraction, identifying a new polymorph in the process. Additionally, laser confocal microscopy and fluorescence lifetime imaging microscopy confirm the results obtained by the X-ray diffraction characterization, i.e. shifting the substituents towards the external benzene rings of the anthracene unit favours π–π interactions, impacting on both the morphology and the microscopic optical properties of the crystals. The compounds with more isolated anthracene units feature shorter lifetime and emission spectra, more similar to those of isolated molecules. The crystallographic study, supported by the optical investigation, sheds light on the influence of non-covalent interactions on the crystal packing and luminescence properties of anthracene derivatives, providing a further step towards their efficient use as building blocks in active components of light sources and photonic networks.

scholarly journals SYNTHESIS AND STRUCTURAL CHARACTERIZATION OF THE 1:1 PROTON TRANSFER SALT OF MALONIC ACID WITH P-CHLOROANILINE

2017 ◽  
Vol 14 (28) ◽  
pp. 66-71
Author(s):  
Gerson E. DELGADO ◽  
Lusbely BELANDRIA ◽  
Asiloé J. MORA ◽  
Julia BRUNO-COLMENÁREZ ◽  
Gustavo MARROQUÍN
Keyword(s):  
Hydrogen Bonds ◽  
Malonic Acid ◽  
Crystal Packing ◽  
Chemical Properties ◽  
Supramolecular Assembly ◽  
X Ray Diffraction ◽  
Monoclinic System ◽  
X Ray ◽  
Cell Parameters

The design of multicomponent crystals offers a means to modify the physicochemical properties of crystals without altering the chemical properties of a particular molecule. In this study, a multicomponent crystal, the salt of malonic acid with p-chloroaniline, was synthetized and structurally characterized. The title compound wasprepared by grinding in an agate mortar, and its structure was studied by powder and single-crystal X-ray diffraction. This compound crystallize in the monoclinic system with space group P21/c, Z = 4, and unit cell parameters a = 12.9776(7)Å, b = 9.2308(5)Å, c = 8.5170(5)Å, β = 93.474(3)°. The multicomponent compound, p-chloroanilinium semi-malonate, can be described as an ionic ensemble assisted by hydrogen bonds established between p-chloroanilinium cations and semi-malonate anions. The molecular structure and crystal packing are stabilized mainly by intermolecular O-H•••O and N-H•••O hydrogen bonds interactions. The molecules construct a supramolecular assembly with a two-dimensional hydrogen bonded network along the ca plane.

Halogen...halogen interactions in pressure-frozen ortho- and meta-dichlorobenzene isomers

2007 ◽  
Vol 63 (1) ◽  
pp. 124-131 ◽  
Author(s):  
Maciej Bujak ◽  
Kamil Dziubek ◽  
Andrzej Katrusiak
Keyword(s):  
Intermolecular Interactions ◽  
Room Temperature ◽  
Diamond Anvil Cell ◽  
Crystal Packing ◽  
Molecular Shape ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diamond Anvil ◽  
Steric Hindrances

Isomers 1,2-dichlorobenzene (o-DCB) and 1,3-dichlorobenzene (m-DCB) were high-pressure frozen in-situ in a Merrill–Bassett diamond–anvil cell and their structures determined at room temperature and at 0.18 (5) GPa for o-DCB, and 0.17 (5) GPa for m-DCB by single-crystal X-ray diffraction. The patterns of halogen...halogen intermolecular interactions in these structures can be considered to be the main cohesive forces responsible for the molecular arrangements in these crystals. The molecular packing of dichlorobenzene isomers, including three polymorphs of 1,4-dichlorobenzene (p-DCB), have been compared and relations between their molecular symmetry, packing arrangements, intermolecular interactions and melting points discussed. The topology of the crystal packing in dichlorobenzene isomers results from the interplay of the molecular shape, steric hindrances and intermolecular interactions. The non-planar arrangement of the dichlorobenzene molecules in the crystal structures can be justified by the distributions of the electrostatic potential on molecular surfaces, which determines electrostatic intermolecular interactions.

scholarly journals Crystallization and X-ray diffraction analysis of the HMG domain of the chondrogenesis master regulator Sox9 in complex with a ChIP-Seq-identified DNA element

2015 ◽  
Vol 71 (11) ◽  
pp. 1437-1441 ◽  
Author(s):  
Saravanan Vivekanandan ◽  
Balasubramanian Moovarkumudalvan ◽  
Julien Lescar ◽  
Prasanna R. Kolatkar
Keyword(s):  
Crystal Packing ◽  
Consensus Sequence ◽  
Potassium Phosphate ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Master Regulator ◽  
X Ray ◽  
Cell Parameters ◽  
Promoter Dna ◽  
Dna Complex

Sox9 is a fundamental sex-determining gene and the master regulator of chondrogenesis, and is involved in the development of various vital organs such as testes, kidney, heart and brain, and in skeletal development. Similar to other known Sox transcription factors, Sox9 recognizes and binds DNA with the consensus sequence C(T/A)TTG(T/A)(T/A) through the highly conserved HMG domain. Nonetheless, the molecular basis of the functional specificity of Sox9 in key developmental processes is still unclear. As an initial step towards a mechanistic understanding of Sox9 transcriptional regulation, the current work describes the details of the purification of the mouse Sox9 HMG domain (mSox9HMG), its crystallization in complex with a ChIP-Seq-identified FOXP2 promoter DNA element and the X-ray diffraction data analysis of this complex. The mSox9HMG–FOXP2 promoter DNA complex was crystallized by the hanging-drop vapour-diffusion method using 20% PEG 3350 in 200 mMsodium/potassium phosphate with 100 mMbis-tris propane at pH 8.5. The crystals diffracted to 2.7 Å resolution and the complex crystallized in the tetragonal space groupP41212, with unit-cell parametersa=b= 99.49,c= 45.89 Å. Crystal-packing parameters revealed that asymmetric unit contained one mSox9HMG–FOXP2 promoter DNA complex with an estimated solvent content of 64%.

Sign in / Sign up

Export Citation Format

Share Document