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.

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.

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.

A DFT Analysis of the Molecular Structures and Vibrational Spectra of Diphenylsulfone and 4,4'-Sulfonyldianiline (Dapsone)

2011 ◽  
Vol 66 (1) ◽  
pp. 69-76 ◽  
Author(s):  
Wolfgang Förner ◽  
Hassan M. Badawi
Keyword(s):  
Vibrational Spectra ◽  
Density Functional ◽  
Parent Compound ◽  
Harmonic Approximation ◽  
Molecular Structures ◽  
Spectral Lines ◽  
Basis Set ◽  
Minor Role ◽  
Parent Molecule ◽  
Chemical Difference

We have performed density functional calculations with the B3LYP functional and a 6-311G** basis set to obtain the vibrational spectra in harmonic approximation of the anti-leprosy drug Dapsone and the parent compound diphenylsulfone. Although the chemical difference between the two molecules is not that pronounced (Dapsone has amino groups in the para positions in the phenyl rings), Dapsone is an active drug, while to our knowledge diphenylsulfone shows no medical activity. We compared the theoretical results to experimental vibrational spectra found in the literature. With the help of the program GAUSSVIEW we were able to assign the experimentally found spectral lines to specific atomic motions. The remarkable difference between the two molecules, regarding their structural behavior, is that the drug Dapsone has a more flexible structure of the phenyl ring than the parent molecule has. This might contribute to a greater ability of the drug to fit into receptor sites in a cell membrane although one has to be well aware that this plays most propably only a minor role in the drug activity of Dapsone

Synthesis, XRD analysis and electronic structure of InGaTe2 chain semiconductor

2020 ◽  
pp. 2150029
Author(s):  
E. M. Gojayev ◽  
S. S. Osmanova ◽  
S. I. Safarova ◽  
D. M. Gafarova
Keyword(s):  
Band Structure ◽  
Density Functional ◽  
Plane Waves ◽  
Density Functional Method ◽  
Xrd Analysis ◽  
Unit Cell ◽  
Lattice Parameters ◽  
Tetragonal Symmetry ◽  
Diagonal Form ◽  
Surface Microrelief

In this work, we developed a technology for growing a single crystal of a ternary compound, using the Atomic Force Microscope (AFM), we studied the surface microrelief in 2D and 3D modes, using X-ray diffraction (XRD) analysis, determined the parameters of the unit cell of this phase and revealed that it crystallizes in tetragonal symmetry with lattice parameters [Formula: see text] Å and [Formula: see text] Å, space group I4/mcm. Using the density functional method, using the ABINIT software package, using the Troiller–Martins pseudopotentials in the basis of plane waves, the band structure was calculated, the origin of the valence and conduction bands was determined. It was revealed that this phase is a direct-gap semiconductor with a bandgap of 0.56 eV. The parameters of the InGaTe2 unit cell were calculated by the pseudopotential and linearized attached plane wave (LAPW) methods, the theoretical and experimental values of the lattice parameters are in good agreement. Based on the band structure, the effective masses of electrons and holes are determined. It is shown that the tensors of the inverse effective mass for both extreme have a diagonal form.

scholarly journals Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

2010 ◽  
Vol 66 (5) ◽  
pp. 544-558 ◽  
Author(s):  
Jacco van de Streek ◽  
Marcus A. Neumann
Keyword(s):  
Density Functional Theory ◽  
Crystal Structures ◽  
Density Functional ◽  
Unit Cell ◽  
Organic Crystal ◽  
Large Temperature ◽  
Unit Cell Parameters ◽  
Functional Theory ◽  
Cell Parameters ◽  
Experimental Crystal

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

An improved structural model for cellulose II

2013 ◽  
Vol 28 (3) ◽  
pp. 194-199 ◽  
Author(s):  
James A. Kaduk ◽  
Thomas N. Blanton
Keyword(s):  
Density Functional ◽  
Structural Model ◽  
Rietveld Method ◽  
Geometry Optimization ◽  
Precise Determination ◽  
Unit Cell ◽  
Cellulose Ii ◽  
Unit Cell Parameters ◽  
Cell Parameters

A sample of cellulose II, prepared by deacetylation of cellulose acetate, has permitted more precise determination of the unit-cell parameters by the Rietveld method. Cellulose II is monoclinic, with space group P21c-axis unique (or P1121) (No. 4) and refined unit-cell parameters a = 8.076(13), b = 9.144(10), c = 10.386(20) Å, γ = 117.00(8)°, and V = 683.5(18) Å3. A density functional geometry optimization using these fixed unit-cell parameters has resulted in an improved structural model for cellulose II. A powder pattern calculated from this new model has been submitted to the ICDD for inclusion in future releases of the Powder Diffraction File.

Charge transfer complexes between 2-, 3- and 4-aminopyridines and some π-acceptors in the gas phase and in chloroform: DFT calculations

2016 ◽  
Vol 15 (04) ◽  
pp. 1650029 ◽  
Author(s):  
Nuha Ahmed Wazzan
Keyword(s):  
Charge Transfer ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Molecular Structures ◽  
Basis Set ◽  
Charge Transfer Complexes ◽  
Good Correspondence ◽  
Electronic Distribution ◽  
Picryl Chloride

This work reports density functional theory (DFT) calculations on the molecular structures, electronic distribution, and UV-Vis and IR spectroscopy analysis of charge transfer complexes between aminopyridines (APYs), namely 2-APY, 3-APY and 4-APY, as electron-donors and some [Formula: see text]-electron-acceptors, namely chloranil (CHL), tetracyanoethylene (TCNE) and picryl chloride (PC), formed in the gas phase at the B3LYP/6-31[Formula: see text]G(d,p) method/basis set, and in chloroform at the same method/basis set using PCM as solvation model. Good correspondence was generally obtained between the calculated parameters and the experimental ones.

scholarly journals Crystals of the Arp2/3 complex in two new space groups with structural information about actin-related protein 2 and potential WASP binding sites

2015 ◽  
Vol 71 (9) ◽  
pp. 1161-1168 ◽  
Author(s):  
Christopher T. Jurgenson ◽  
Thomas D. Pollard
Keyword(s):  
Binding Site ◽  
Structural Information ◽  
Unit Cell ◽  
Molecular Structures ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Space Groups ◽  
Cell Parameters ◽  
New Space

Co-crystals of the bovine Arp2/3 complex with the CA motif from N-WASP in two new space groups were analyzed by X-ray diffraction. The crystals in the orthorhombic space groupP212121contained one complex per asymmetric unit, with unit-cell parametersa= 105.48,b= 156.71,c= 177.84 Å, and diffracted to 3.9 Å resolution. The crystals in the tetragonal space groupP41contained two complexes per asymmetric unit, with unit-cell parametersa=b= 149.93,c = 265.91 Å, and diffracted to 5.0 Å resolution. The electron-density maps of both new crystal forms had densities for small segments of subdomains 1 and 2 of Arp2. Both maps had density at the binding site on Arp3 for the C-terminal EWE tripeptide from N-WASP and a binding site proposed for the C motif of N-WASP in the barbed-end groove of Arp2. The map from the tetragonal crystal form had density near the barbed end of Arp3 that may correspond to the C helix of N-WASP. The noise levels and the low resolution of the maps made the assignment of specific molecular structures for any of these CA peptides impossible.

scholarly journals Study of Structural and Electronic Behavior of BeH2 as Hydrogen Storage Compound: An Ab Initio Approach

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Vikas Nayak ◽  
Suman Banger ◽  
U. P. Verma
Keyword(s):  
Hydrogen Storage ◽  
Electronic Properties ◽  
Density Functional ◽  
Correlation Energy ◽  
Electronic Band Structure ◽  
Unit Cell ◽  
Generalized Gradient ◽  
Hydrogen Atoms ◽  
Electronic Band ◽  
Cell Parameters

The quantum mechanical calculations based on density functional theory (DFT) have been performed to study ground state structural and electronic properties of BeH2 and along with doping of two (BeH2 + 2H) and four (BeH2 + 4H) hydrogen atoms. The generalized gradient approximation (GGA) has been employed for the exchange correlation energy. The most stable space group of BeH2 is Ibam. Its optimized equilibrium unit cell volume, bulk modulus and its first-order pressure derivative, and electronic properties have been obtained. Our predicted unit cell parameters for BeH2  a=9.2463 Å, b=4.2352 Å, and c=7.8464 Å are in very good agreement with the earlier reported experimental and theoretical results. The electronic band structure of BeH2 shows its behavior as an insulator. The stability of BeH2 along with doped hydrogen atoms increases, while the energy band gap decreases with the increase in number of doped hydrogen atoms. On these bases, we predict that BeH2 is a promising material for hydrogen storage.

Experimental FTIR and theoretical investigation of the molecular structure and vibrational spectra of acetanilide using DFT and dispersion correction to DFT

2019 ◽  
Vol 18 (02) ◽  
pp. 1950009 ◽  
Author(s):  
Yunusa Umar ◽  
Nedal Abu-Thabit ◽  
Paul Jerabek ◽  
Ponnadurai Ramasami
Keyword(s):  
Vibrational Spectra ◽  
Density Functional ◽  
Decomposition Analysis ◽  
Density Functional Theory Method ◽  
Molecular Structures ◽  
Basis Set ◽  
Potential Energy Distribution ◽  
Energy Decomposition Analysis ◽  
Dispersion Correction ◽  
Vibrational Assignments

The FTIR spectrum of acetanilide (ACN) is recorded and analyzed. The optimized molecular structures, harmonic vibrational wavenumbers and corresponding vibrational assignments of the ACN are computationally examined by using the B3LYP density functional theory method together with the standard 6-311[Formula: see text]G([Formula: see text],[Formula: see text]) basis set. From the calculations, the ACN is predicted to exist predominantly in trans configuration with the relative energy, rotational barrier, and population of 2.8[Formula: see text]kcal/mol, 14.8[Formula: see text]kcal/mol, and 99.5%, respectively. The optimized structure shows that the amide group (CO–NH) of trans-ACN adopts a planar peptide-like conformation. The effect of the incorporation of dispersion correction to the B3LYP on the calculated equilibrium structure and vibrational spectra of ACN is investigated. The highest occupied and the lowest unoccupied molecular orbitals, IR intensities and molecular electrostatic potential results are reported. In addition, reliable vibrational assignments have been made on the basis of Potential Energy Distribution (PED) using VEDA4 program. Simulated IR spectrum are compared with the experimental FTIR and FT-Raman spectra. Energy decomposition analysis (EDA) revealed that Pauli repulsion is responsible for the increased stability of the trans over the cis isomer.

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