scholarly journals Crystallographic and DFT Studies on Pyrrolo[1,2-c]imidazole Scaffolds

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Manikandan Jayaraman ◽  
Rajarathinam Balakrishnan ◽  
Kannan Muthu ◽  
Manivel Panneerselvam ◽  
Vasuki Gnanasambandam ◽  
...  
Keyword(s):  
Density Functional ◽  
Crystal Packing ◽  
Stable State ◽  
Chair Conformation ◽  
Unit Cell ◽  
Basis Set ◽  
Monoclinic Space Group ◽  
Cell Parameters ◽  
B3lyp Method ◽  
The Stability

The crystal structures of the compounds C15H14N4O2 (1) and C16H16N4O4 (2) are reported and analyzed by single crystal X-ray diffraction technique. Compounds (1) and (2) crystallized in monoclinic space group P21/c and Cc with four molecules in the unit cell, respectively. The unit cell parameters for compound (1) are a = 11.4501(15) Å, b = 9.7869(11) Å, c = 12.3653(15) Å, β = 90.997(11)°, and Volume = 1385.5(3) Å3 and for compound (2) are a = 13.865(2) Å, b = 6.9538(8) Å, c = 16.841(2) Å, β = 98.602(11)°, and Volume = 1605.4(4) Å3. In both compounds (1) and (2), the pyrrolidine ring adopts half-chair conformation. Moreover, both inter- and intramolecular N–H⋯O hydrogen bonds stabilize the crystal structure and play a crucial role in crystal packing. This intermolecular interaction alone constructs C11 chain motif in both compounds. It is also supported by weak intermolecular π-π interaction which is essential for the stability of the crystal packing. Further, the Density Functional Theory (B3LYP) method with standard 6-31G basis set was used in the calculation and calculated geometrical parameter is correlated with the corresponding experimental data. The obtained HOMO and LUMO energies are in negative values indicating that the compounds are in stable state.

scholarly journals Intermolecular Interactions in Molecular Organic Crystals upon Relaxation of Lattice Parameters

Crystals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 665 ◽  
Author(s):  
Matthias Stein ◽  
Madalen Heimsaat
Keyword(s):  
Structure Prediction ◽  
Density Functional ◽  
Unit Cell ◽  
Lattice Parameters ◽  
Molecular Structures ◽  
Basis Set ◽  
Experimental Unit ◽  
Organic Crystals ◽  
Cell Parameters ◽  
Lattice Energies

Crystal structure prediction is based on the assumption that the most thermodynamically stable structure will crystallize first. The existence of other structures such as polymorphs or from counterenantiomers requires an accurate calculation of the electronic energy. Using atom-centered Gaussian basis functions in periodic Density Functional Theory (DFT) calculations in Turbomole, the performance of two dispersion-corrected functionals, PBE-D3 and B97-D, is assessed for molecular organic crystals of the X23 benchmark set. B97-D shows a MAE (mean absolute error) of 4 kJ/mol, compared to 9 kJ/mol for PBE-D3. A strategy for the convergence of lattice energies towards the basis set limit is outlined. A simultaneous minimization of molecular structures and lattice parameters shows that both methods are able to reproduce experimental unit cell parameters to within 4–5%. Calculated lattice energies, however, deviate slightly more from the experiment, i.e., by 0.4 kJ/mol after unit cell optimization for PBE-D3 and 0.5 kJ/mol for B97-D. The accuracy of the calculated lattice energies compared to the experimental values demonstrates the ability of current DFT methods to assist in the quest for possible polymorphs and enantioselective crystallization processes.

The Theoretical Research of Constitutive Property, Reactivity and FTIR of Chitosan

2010 ◽  
Vol 658 ◽  
pp. 177-180
Author(s):  
Juan Qin Xue ◽  
Dan Dan Wen ◽  
Li Hua Yu ◽  
Yu Jie Wang ◽  
Jun Zhu
Keyword(s):  
Molecular Orbital ◽  
Active Sites ◽  
Density Functional ◽  
Basis Set ◽  
Theoretical Research ◽  
Rotational Isomers ◽  
B3lyp Method ◽  
Stability Order ◽  
The Stability ◽  
Experimental Values

The structural optimization and the frequency for chitosan monomer, chitobiose and chitotriose with the quantum chemistry abinitio HF and the density functional B3LYP method by choosing 6-311 + G (d, p) as the basis set were calculated and studied. For its three rotational isomers, gauche-trans (gt), gauche - gauche (gg), and trans-gauche (tg), the calculations comparatively were performed respectively. The charge distribution and frontier molecular orbit were analyzed by using the method of natural bond orbital (NBO). The calculated IR spectrum was compared with the experimental data. The results showed that the three rotational isomers gt, gg, and tg can stably existed in chitosan with the stability order gg﹥gt﹥tg. Its highest occupied molecular orbital (HOMO) was provided primarily by nitrogen atom and its lowest unoccupied molecular orbital (LUMO) was provided mainly by the oxygen atom; Its reaction active sites were concentrated in -NH2 and –OH. The calculated infrared spectra were in good agreement with the experimental values.

Expression, purification and crystallization of the catalytic subunit of protein kinase CK2 from Zea mays

1998 ◽  
Vol 54 (1) ◽  
pp. 143-145 ◽  
Author(s):  
Barbara Guerra ◽  
Karsten Niefind ◽  
Lorenzo A. Pinna ◽  
Dietmar Schomburg ◽  
Olaf-Georg Issinger
Keyword(s):  
Protein Kinase ◽  
Protein Kinase Ck2 ◽  
Crystal Packing ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Rays ◽  
Α Subunit ◽  
Cell Parameters ◽  
Packing Parameter ◽  
Kinase Ck2

The catalytic (α) subunit of protein kinase CK2 (CK2α) was originally cloned and overexpressed in the Escherichia coli strain pT7-7/BL21(DE3). The protein has been purified to homogeneity and crystallized. The crystals belong to the monoclinic space group C2, they have unit-cell parameters a = 142.6, b = 61.3, c = 45.6 Å, β = 103.3° and diffract X-rays to at least 2.0 Å resolution. The calculated crystal packing parameter is Vm = 2.47 Å3 Da−1 suggesting that one CK2α molecule is contained in the asymmetric unit and that the solvent content of the unit cell is 50%.

scholarly journals Synthesis, Crystal Structure, and DFT Study of Ethyl 1-(2-(Hydroxyimino)-2-phenylethyl)-3-phenyl-1H-pyrazole-5-carboxylate

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Jin-Hui Zhou ◽  
Liang-Wen Zheng ◽  
Mao-Cai Yan ◽  
Mao-Jian Shi ◽  
Jing Liu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Crystal Packing ◽  
Pyrazole Ring ◽  
Basis Set ◽  
Monoclinic Space Group ◽  
Hybrid Functional ◽  
Cell Parameters ◽  
Total Energies ◽  
Calculated Equilibrium

The crystal structure of ethyl 1-(2-(hydroxyimino)-2-phenylethyl)-3-phenyl-1H-pyrazole-5-carboxylate has been determined by X-ray single crystal diffraction. The crystal of the title compound is the monoclinic space group P2/c with unit cell parameters of a=8.634(2) Å, b=9.616(2) Å, c=22.190(3) Å, β=99.2652°, V=1818.3(4) Å3, and Z=4. The dihedral angles formed by the planes of the central pyrazole ring and the adjacent benzene rings are 73.60(7)° and 3.55(7)°, respectively. The combination of the weak intermolecular C-H⋯O and N-H⋯O hydrogen-bonding interactions stabilizes the crystal packing. The geometries of its Z and E isomers and the corresponding transition state (TS), as well as the dimer of its Z isomer, are optimized using the B3LYP hybrid functional coupled with def-TZVP triple-zeta polarized basis set. The bond angles and bond lengths of the optimized structure of Z dimer are very consistent with those of its single crystal parameters. Double-hybrid functional PWPB95-D3 in combination with very highly accurate basis set def2-QZVP is employed to evaluate accurate energy of each isomer and TS. The calculated equilibrium constant between Z and E isomers corresponds to the [Z]/[E] ratio of 4.29. Mulliken atomic charges and electrostatic potential (ESP) on molecular van der Waals (vdW) surface are calculated in order to study and predict the intermolecular interactions. The molecular total energies and frontier orbital analysis are also discussed.

scholarly journals Synthesis and Crystal Structure of 1-(4-Nitrobenzyl)-3-allyl-1H-benzo[d]imidazol-2(3H)-one

2013 ◽  
Vol 2013 ◽  
pp. 1-8
Author(s):  
Dounia Belaziz ◽  
Santiago V. Luis ◽  
Youssef Kandri Rodi ◽  
Inés Martí ◽  
Vicente Martí-Centelles
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Van Der Waals Interactions ◽  
Monoclinic Space Group ◽  
Synthesis And Crystal Structure ◽  
Cell Parameters ◽  
Computational Calculations ◽  
The Stability

A functionalized benzimidazole, 1-(4-nitrobenzyl)-3-allyl-1H-benzo[d]imidazol-2(3H)-one, has been synthesized, and the crystal structure was determined and analyzed. This compound crystallizes in the monoclinic, space group P21/n (number 14)cwith cell parameters,a=7.12148(8) Å,b=16.12035(17) Å,c=13.04169(17) Å,β=93.3043(11),V=1494.71(3) Å3, andDcalc= 1.375 g/mm3. The solid state geometry is stabilized by intermolecularπ–πinteractions along with the van der Waals interactions which contribute to the stability of the crystal packing. Computational calculations have been used to properly understand the main intermolecular interactions present in the crystal.

Quantum Mechanical Investigation of Geometrical Structure and Dynamic Behavior of h-BNNT (9,9-5) and h-AlNNT (9,9-5)Single-Walled Nanotubes: NBO Analysis

2019 ◽  
Vol 16 (9) ◽  
pp. 705-717
Author(s):  
Mehrnoosh Khaleghian ◽  
Fatemeh Azarakhshi
Keyword(s):  
Carbon Nanotubes ◽  
Density Functional ◽  
Structural Parameters ◽  
Energy Levels ◽  
Nbo Analysis ◽  
Electronic Energy ◽  
Boron Nitride Nanotubes ◽  
Basis Set ◽  
B3lyp Method ◽  
Mechanical Investigation

In the present research, B45H36N45 Born Nitride (9,9) nanotube (BNNT) and Al45H36N45 Aluminum nitride (9,9) nanotube (AlNNT) have been studied, both having the same length of 5 angstroms. The main reason for choosing boron nitride nanotubes is their interesting properties compared with carbon nanotubes. For example, resistance to oxidation at high temperatures, chemical and thermal stability higher rather than carbon nanotubes and conductivity in these nanotubes, unlike carbon nanotubes, does not depend on the type of nanotube chirality. The method used in this study is the density functional theory (DFT) at Becke3, Lee-Yang-Parr (B3LYP) method and 6-31G* basis set for all the calculations. At first, the samples were simulated and then the optimized structure was obtained using Gaussian 09 software. The structural parameters of each nanotube were determined in 5 layers. Frequency calculations in order to extract the thermodynamic parameters and natural bond orbital (NBO) calculations have been performed to evaluate the electron density and electrostatic environment of different layers, energy levels and related parameters, such as ionization energy and electronic energy, bond gap energy and the share of hybrid orbitals of different layers.

AlN Nanotubes: A DFT Study of Al-27 and N-14 Electric Field Gradient Tensors

2007 ◽  
Vol 62 (12) ◽  
pp. 711-715 ◽  
Author(s):  
Ahmad Seif ◽  
Mahmoud Mirzaei ◽  
Mehran Aghaie ◽  
Asadollah Boshra
Keyword(s):  
Electric Field ◽  
Electric Field Gradient ◽  
Field Gradient ◽  
Density Functional ◽  
Quadrupole Coupling Constant ◽  
Basis Set ◽  
Basis Sets ◽  
B3lyp Method ◽  
Package Program ◽  
Nqr Parameters

Density functional theory (DFT) calculations were performed to calculate the electric field gradient (EFG) tensors at the sites of aliminium (27Al) and nitrogen (14N) nuclei in an 1 nm of length (6,0) single-walled aliminium nitride nanotube (AlNNT) in three forms of the tubes, i. e. hydrogencapped, aliminium-terminated and nitrogen-terminated as representatives of zigzag AlNNTs. At first, each form was optimized at the level of the Becke3,Lee-Yang-Parr (B3LYP) method, 6-311G∗∗ basis set. After, the EFG tensors were calculated at the level of the B3LYP method, 6-311++G∗∗ and individual gauge for localized orbitals (IGLO-II and IGLO-III) types of basis sets in each of the three optimized forms and were converted to experimentally measurable nuclear quadrupole resonance (NQR) parameters, i. e. quadrupole coupling constant (qcc) and asymmetry parameter (ηQ). The evaluated NQR parameters revealed that the considered model of AlNNT can be divided into four equivalent layers with similar electrostatic properties.With the exception of Al-1, all of the three other Al layers have almost the same properties, however, N layers show significant differences in the magnitudes of the NQR parameters in the length of the nanotube. Furthermore, the evaluated NQR parameters of Al-1 in the Al-terminated form and N-1 in the N-terminated form revealed the different roles of Al (base agent) and of N (acid agent) in AlNNT. All the calculations were carried out using the GAUSSIAN 98 package program.

scholarly journals One-Dimensional Organic–Inorganic Material (C6H9N2)2BiCl5: From Synthesis to Structural, Spectroscopic, and Electronic Characterizations

2021 ◽  
Vol 22 (4) ◽  
pp. 2030
Author(s):  
Hela Ferjani ◽  
Hammouda Chebbi ◽  
Mohammed Fettouhi
Keyword(s):  
Hydrogen Bonding ◽  
Density Functional ◽  
Crystal Packing ◽  
Diffuse Reflectance Spectrum ◽  
Enrichment Ratio ◽  
One Dimensional ◽  
Organic Part ◽  
Fukui Indices ◽  
The Stability ◽  
The One

The new organic–inorganic compound (C6H9N2)2BiCl5 (I) has been grown by the solvent evaporation method. The one-dimensional (1D) structure of the allylimidazolium chlorobismuthate (I) has been determined by single crystal X-ray diffraction. It crystallizes in the centrosymmetric space group C2/c and consists of 1-allylimidazolium cations and (1D) chains of the anion BiCl52−, built up of corner-sharing [BiCl63−] octahedra which are interconnected by means of hydrogen bonding contacts N/C–H⋯Cl. The intermolecular interactions were quantified using Hirshfeld surface analysis and the enrichment ratio established that the most important role in the stability of the crystal structure was provided by hydrogen bonding and H···H interactions. The highest value of E was calculated for the contact N⋯C (6.87) followed by C⋯C (2.85) and Bi⋯Cl (2.43). These contacts were favored and made the main contribution to the crystal packing. The vibrational modes were identified and assigned by infrared and Raman spectroscopy. The optical band gap (Eg = 3.26 eV) was calculated from the diffuse reflectance spectrum and showed that we can consider the material as a semiconductor. The density functional theory (DFT) has been used to determine the calculated gap, which was about 3.73 eV, and to explain the electronic structure of the title compound, its optical properties, and the stability of the organic part by the calculation of HOMO and LUMO energy and the Fukui indices.

Pb-Sb zrudnění z Antimonitové žíly, důl Rudolf, Bohutín (Česká republika)

2021 ◽  
Vol 29 (2) ◽  
pp. 275-280
Author(s):  
Pavel Škácha ◽  
Jiří Sejkora
Keyword(s):  
Czech Republic ◽  
Chemical Composition ◽  
Empirical Formula ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Ore District ◽  
Archive Material

The Pb-Sb mineralization with dominant stibnite and plagionite and associated semseyite and zinkenite was found in an archive material collected at the Antimonitová vein, Bohutín, Březové Hory ore district (Czech Republic). Plagionite forms subhedral aggregates up to 1 mm in size. The unit-cell parameters of plagionite for monoclinic space group C2/c refined from the X-ray powder data are: a 13.4890(17), b 11.8670(14), c 19.997(2) Å, β 107.199(8)° and V 3057.9(6) Å3. Its chemical composition (average of 26 analyses, based on 30 apfu) corresponds to the empirical formula Pb5.02Sb8.15S16.82. Associated zinkenite is forming subhedral crystals up to 1 mm in size. Its empirical formula can be expressed as (Cu0.25Ag0.02Fe0.01)Σ0.28Pb9.22Sb22.19S41.31 (average of 26 analyses, based on 73 apfu). Semseyite aggregates have the empirical formula (Pb8.72Fe0.14)8.86Sb8.42S20.73 (average of 11 analyses, based on 38 apfu).

Systematic ab initio study of the compressibility of silicate garnets

2001 ◽  
Vol 57 (2) ◽  
pp. 163-177 ◽  
Author(s):  
V. Milman ◽  
E. V. Akhmatskaya ◽  
R. H. Nobes ◽  
B. Winkler ◽  
C. J. Pickard ◽  
...  
Keyword(s):  
Experimental Data ◽  
Density Functional ◽  
Structural Parameters ◽  
Applied Pressure ◽  
Basis Set ◽  
Ionic Radii ◽  
Cell Parameters ◽  
The Density Functional Theory ◽  
Dodecahedral Site ◽  
Compression Mechanism

The structural properties of the silicate garnets andradite, Ca3Fe2Si3O12, uvarovite, Ca3Cr2Si3O12, knorringite, Mg3Cr2Si3O12, goldmanite, Ca3V2Si3O12, blythite, Mn^{2+}_3Mn^{3+}_2Si3O12, skiagite, Fe^{2+}_3Fe^{3+}_2Si3O12, calderite, Mn^{2+}_3Fe^{3+}_2Si3O12, and khoharite, Mg3Fe^{3+}_2Si3O12, have been investigated with a quantum-mechanical model as a function of applied pressure. The study has been performed with the density functional theory code CASTEP, which uses pseudopotentials and a plane-wave basis set. All structural parameters have been optimized. The calculated static geometries (cell parameters, internal coordinates of atoms and bond lengths), bulk moduli and their pressure derivatives are in good agreement with the experimental data available. Predictions are made for those cases where no experimental data have been reported. The data clearly indicate that the elastic properties of all silicate garnets are dominated by the compressibility of the dodecahedral site. The compression mechanism is found to be based on a bending of the angle between the centers of the SiO4 tetrahedra and the adjacent octahedra, as in the aluminosilicate garnets. An analysis of the relationship between ionic radii of the cations and the compressibility of silicate garnets is presented.

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