scholarly journals Unraveling the Effects of Co-Crystallization on the UV/Vis Absorption Spectra of an N-Salicylideneaniline Derivative. A Computational RI-CC2 Investigation

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4512
Author(s):  
Jean Quertinmont ◽  
Tom Leyssens ◽  
Johan Wouters ◽  
Benoît Champagne
Keyword(s):  
Optical Properties ◽  
Crystal Field ◽  
Indirect Effects ◽  
Density Functional ◽  
Crystal Packing ◽  
Density Functional Theory Method ◽  
Oscillator Strengths ◽  
Excitation Energies ◽  
Keto Form ◽  
Cell Parameters

This work aims at unraveling the effects of co-crystallization on the optical properties of an N-salicylideneaniline-derived molecular switch transforming between an enol and a keto form. This is achieved by way of a two-step multi-scale method where (i) the molecular geometry and unit cell parameters are optimized using a periodic boundary conditions density functional theory method and (ii) the optical properties are computed for a selection of clusters embedded in an array of point-charges that reproduce the crystal field electronic potential. The optical properties (vertical excitation energies and oscillator strengths) are obtained at the RI-CC2/def2-TZVPD level of approximation. This method allows us to decompose the effects of co-crystallization into (i) indirect effects, the geometry changes of the chromophore due to crystal packing with the coformer, and (ii) direct ones, the polarization due to the interacting coformer and to the crystal field. For the former effects, variations of a crucial torsion angle lead to modification of the π-conjugation and therefore to the decrease or increase of the excitation energies. About the latter, they are antagonistic: (i) the coformer is not directly involved in the excitations but its polarization decreases the excitation energies while (ii) the crystal field has the opposite effect. For the co-crystals with succinic and fumaric acids, combining these direct and indirect effects leads to a hypsochromic shift of the first absorption band with respect to the reference crystal, in agreement with experimental data.

Geometry Optimization, UV/Vis, NBO, HOMO and LUMO, Excited State and Antioxidant Evaluation of Pyrimidine Derivatives

2020 ◽  
Vol 17 ◽  
Author(s):  
Siyamak Shahab ◽  
Masoome Sheikhi ◽  
Evgeni Kvasyuk ◽  
Aliaksei G. Sysa ◽  
Radwan Alnajjar ◽  
...  
Keyword(s):  
Density Functional ◽  
Antioxidant Properties ◽  
Geometry Optimization ◽  
Dft Method ◽  
Oscillator Strengths ◽  
Equilibrium Geometry ◽  
Pyrimidine Derivatives ◽  
Excitation Energies ◽  
Solvent Water ◽  
Homo And Lumo

: In this research, the four pyrimidine derivatives have been studied by using density functional theory (DFT/B3LYP/6-31G*) in solvent water for the first time. After quantum-chemical calculations, the title compounds have been synthesized. The electronic spectra of the new derivatives in a solvent water were performed by time-dependent DFT (TD-DFT) method. The equilibrium geometry, the HOMO and LUMO orbitals, MEP, excitation energies, natural charges, oscillator strengths for the molecules have also been calculated. NBO analysis has been calculated in order to elucidate the intramolecular, rehybridization and delocalization of electron density. These molecules have high antioxidant potential due to the planarity and formation of intramolecular hydrogen bonds. Antioxidant properties of the title compounds have been investigated and discussed.

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.

Effect of packing motifs on the energy ranking and electronic properties of putative crystal structures of tricyano-1,4-dithiino[c]-isothiazole

2016 ◽  
Vol 72 (4) ◽  
pp. 562-570 ◽  
Author(s):  
Farren Curtis ◽  
Xiaopeng Wang ◽  
Noa Marom
Keyword(s):  
Crystal Structure ◽  
Optical Properties ◽  
Structure Prediction ◽  
Density Functional ◽  
Crystal Packing ◽  
Crystal Structure Prediction ◽  
Dispersion Interactions ◽  
Blind Test ◽  
Electronic And Optical Properties ◽  
Inclusive Density

We present an analysis of putative structures of tricyano-1,4-dithiino[c]-isothiazole (TCS3), generated within the sixth crystal structure prediction blind test. Typical packing motifs are identified and characterized in terms of distinct patterns of close contacts and regions of electrostatic and dispersion interactions. We find that different dispersion-inclusive density functional theory (DFT) methods systematically favor specific packing motifs, which may affect the outcome of crystal structure prediction efforts. The effect of crystal packing on the electronic and optical properties of TCS3 is investigated using many-body perturbation theory within theGWapproximation and the Bethe–Salpeter equation (BSE). We find that a structure withPna21symmetry and a bilayer packing motif exhibits intermolecular bonding patterns reminiscent of π–π stacking and has markedly different electronic and optical properties than the experimentally observedP21/nstructure with a cyclic dimer motif, including a narrower band gap, enhanced band dispersion and broader optical absorption. ThePna21bilayer structure is close in energy to the observed structure and may be feasible to grow.

scholarly journals OS100: A Benchmark Set of 100 Digitized UV-Visible Spectra and Derived Experimental Oscillator Strengths

2021 ◽  
Author(s):  
Astrid Tarleton ◽  
Jorge Garcia-Alvarez ◽  
Anah Wynn ◽  
Cade Awbrey ◽  
Tomas Roberts ◽  
...  
Keyword(s):  
Density Functional ◽  
Oscillator Strengths ◽  
Learning Approaches ◽  
Excitation Energies ◽  
Absorption Bands ◽  
Visible Absorption ◽  
Plain Text ◽  
Solvent Model ◽  
Visible Spectra ◽  
Uv Visible

Excited-state quantum chemical calculations typically report excitation energies and oscillator strengths, ƒ, for each electronic transition. On the other hand, UV-visible spectrophotometric experiments report energy-dependent molar extinction/attenuation coefficients, ε(v), that determine the absorption band line shapes. ε(v) and ƒ are related, but this relation is complicated by various broadening and solvation effects. We fit and integrated experimental UV-visible spectra to obtain ƒexp values for absorption bands and estimated the uncertainty in the fitting. We derived 164 ƒexp values from 100 organic molecules ranging in size from 6-34 atoms. The corresponding computed oscillator strengths (ƒcomp) were obtained with time-dependent density functional theory and a polarizable continuum solvent model. By expressing experimental and computed absorption strengths using a common quantity, we directly compared ƒcomp and ƒexp. While ƒcomp and ƒexp are well correlated (linear regression R2=0. 921), ƒcomp in most cases significantly overestimates ƒexp (regression slope=1.34). The agreement between absolute ƒcomp and ƒexp values was substantially improved by accounting for a solvent refractive index factor, as suggested in some derivations in the literature. The 100 digitized UV-visible spectra are included as plain text files in the supporting information to aid in benchmarking computational or machine-learning approaches that aim to simulate realistic UV-visible absorption spectra.

DFT/MRCI calculations on the excited states of porphyrin, hydroporphyrins, tetrazaporphyrins and metalloporphyrins

2001 ◽  
Vol 05 (03) ◽  
pp. 225-232 ◽  
Author(s):  
ANDREAS B. J. PARUSEL ◽  
STEFAN GRIMME
Keyword(s):  
Excited States ◽  
Density Functional ◽  
Significant Contribution ◽  
Electronic Absorption Spectra ◽  
Blue Shift ◽  
Oscillator Strengths ◽  
Excitation Energies ◽  
Functional Theory ◽  
Intense Color ◽  
Higher Excited States

A combination of density functional theory and multi-reference configuration interaction methods (DFT/MRCI) has been applied to the calculation of electronic absorption spectra in a series of porphyrin-type molecules. The calculated excitation energies and oscillator strengths for free-base porphyrin ( PH 2) are in excellent agreement with experiment for both lower and higher excited states which are characterized by a significant contribution of double excitations (>20%). The 41 B 2 u , 41 B 3 u , and 51 B 2 u states are assigned to the L-band and the 71 B 3 u state to the M-band. The results for the hydroporphyrins chlorin ( CH 2) and bacteriochlorin ( BH 2) are in agreement with the experimentally observed increase in intensity for the Q-bands relative to PH 2. For BH 2 we predict a red shift of the Q x -band (0.2 eV) and a blue shift of the B-band (0.5–0.7 eV) in comparison to both PH 2 and CH 2. For porphyrazine ( PzH 2) and the commercial pigment phthalocyanine ( PcH 2) the calculated oscillator strengths of the Q- and B-bands are of comparable size explaining the intense color of PcH 2. For the metalloporphyrins with magnesium ( PMg ) and zinc ( PZn ), the x- and y-polarized components of the Q- and B-bands collapse, due to the higher D4 h symmetry of the molecules. The calculations reproduce the slight, experimentally observed increase in the oscillator strength of the Q-band and the decrease for the B-band. These effects are ascribed to the electropositive nature of the metals relative to hydrogen. Except for the Q-bands, which are adequately described by the 'four-orbital model,' it is essential to account for excitations outside the four frontier orbitals as well as double and triple excitations for accurate reproduction of experimental data. We compare our results both with experiment and, where available, recent first-principle SAC-CI, MRMP, and TDDFT calculations.

Molecular Docking, Topological Analysis and Vibrational Studies on N-(2-Bromoethyl) Succinimide: Antidepressant Agent

2020 ◽  
Vol 17 ◽  
Author(s):  
Aslı Eşme
Keyword(s):  
Molecular Docking ◽  
Density Functional ◽  
Topological Analysis ◽  
Biological Properties ◽  
Vibrational Frequencies ◽  
Oscillator Strengths ◽  
Potential Energy Distribution ◽  
Geometrical Parameters ◽  
Molecular Docking Study ◽  
Excitation Energies

Abstract:: N-(2-Bromoethyl) succinimide (N2BES) is a compound with antidepressant pharmacological properties. N-(2-Bromoethyl) succinimide was analyzed for its structural, electronic, vibrational, topological, and biological properties. The molecular geometrical parameters such as bond lengths (Å), bond angles (º), and dihedral angles (º) of N2BES and harmonic vibrational frequencies were investigated using the density functional theory calculations with the B3LYP/6-311++G(d,p) level of theory. Experimental vibrational frequencies of N2BES were recorded in the region 4000–400 cm-1 (FT-IR) and 4000–100 cm-1 (FT-Raman) and compared with the theoretical frequencies were made on the basis of potential energy distribution (PED) analysis. Frontier molecular orbitals (FMOs), global reactivity descriptors, density of states (DOS) prop-erties, molecular electrostatic potential (MEP), natural bond orbital (NBO) analysis, topological analysis of the reduced density gradient (RDG), localized orbital locator (LOL), bond critical points (BCP) for N2BES are investigated by theoret-ical calculations. The experimental UV-Vis measured within the 200-500 nm and calculated electronic transitions of ab-sorption wavelength (λ), excitation energies (E), oscillator strengths (f), and assignments in ethanol solvent. In addition, the molecular docking study of the title molecule predicts its binding orientation in the active site of the target serotonin 1A (5-HT1A) protein.

Crystal Structure, Optical Properties of Molecular Crystals 1, 3-propanediol Bis(4-aminobenzoate)

2014 ◽  
Vol 1052 ◽  
pp. 207-211
Author(s):  
Rui Ting Xue ◽  
Wei Song Sun ◽  
Si Rong Yu
Keyword(s):  
Crystal Structure ◽  
Optical Properties ◽  
Density Functional ◽  
Molecular Crystals ◽  
Density Functional Theory Method ◽  
Theory Method ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
The Density Functional Theory

The crystal structure of 1, 3-propanediol bis (4-aminobenzoate) has been determined by single crystal X-ray diffraction. The UV-vis spectra have been characterized experimentally. The nonlinear optical properties were investigated with the density functional theory method. The calculated first hyperpolarizability values are 7.69×10-30, 14.22×10-30 and 26.66×10-30 esu for the monomer, dimmer and trimer structure of the compound. The results show that the compound has high hyperpolarizability and the hyperpolarizability multipled along with the increasing number of the molecules.

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