Browse
Submit Data
Databases
API
Help

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DFT Study of Molecular and Electronic Structure of Y, La and Lu Complexes with Porphyrazine and Tetrakis(1,2,5-thiadiazole)porphyrazine.

ABSTRACT: Electronic and geometric structures of Y, La and Lu complexes with porphyrazine (Pz) and tetrakis(1,2,5-thiadiazole)porphyrazine (TTDPz) were investigated by density functional theory (DFT) calculations and compared. The nature of the bonds between metal atoms and nitrogen atoms has been described using the analysis of the electron density distribution in the frame of Bader's quantum theory of atoms in molecule (QTAIM). Simulation and interpretation of electronic spectra were performed with use of time-dependent density functional theory (TDDFT) calculations. Description of calculated IR spectra was carried out based on the analysis of the distribution of the potential energy of normal vibrations by natural vibrational coordinates.

SUBMITTER: Zhabanov YA

PROVIDER: S-EPMC7795284 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

DFT Study of Molecular and Electronic Structure of Y, La and Lu Complexes with Porphyrazine and Tetrakis(1,2,5-thiadiazole)porphyrazine.

Zhabanov Yuriy A YA Ryzhov Igor V IV Kuzmin Ilya A IA Eroshin Alexey V AV Stuzhin Pavel A PA

Molecules (Basel, Switzerland) 20201229 1

Electronic and geometric structures of Y, La and Lu complexes with porphyrazine (Pz) and tetrakis(1,2,5-thiadiazole)porphyrazine (TTDPz) were investigated by density functional theory (DFT) calculations and compared. The nature of the bonds between metal atoms and nitrogen atoms has been described using the analysis of the electron density distribution in the frame of Bader's quantum theory of atoms in molecule (QTAIM). Simulation and interpretation of electronic spectra were performed with use ...[more]

PMID: 33383750

Similar Datasets

DFT Study of Molecular and Electronic Structure of Ca(II) and Zn(II) Complexes with Porphyrazine and tetrakis(1,2,5-thiadiazole)porphyrazine.

Project description:Electronic and geometric structures of Ca(II) and Zn(II) complexes with porphyrazine (Pz) and tetrakis(1,2,5-thiadiazole)porphyrazine (TTDPz) were investigated by density functional theory (DFT) calculations and compared. The perimeter of the coordination cavity was found to be practically independent on the nature of a metal and a ligand. According to the results of the natural bond orbital (NBO) analysis and quantum theory of atoms in molecules (QTAIM) calculations, Ca-N bonds possess larger ionic contributions as compared to Zn-N. The model electronic absorption spectra obtained with the use of time-dependent density functional theory (TDDFT) calculations indicate a strong bathochromic shift (~70 nm) of the Q-band with a change of Pz ligand by TTDPz for both Ca and Zn complexes. Additionally, CaTTDPz was synthesized and its electronic absorption spectrum was recorded in pyridine and acetone.

| S-EPMC7215693 | biostudies-literature

Molecular Structure, Thermodynamic and Spectral Characteristics of Metal-Free and Nickel Complex of Tetrakis(1,2,5-thiadiazolo)porphyrazine.

Project description:The Knudsen effusion method with mass spectrometric control of the vapor composition was used to study the possibility of a congruent transition to the gas phase and to estimate the enthalpy of sublimation of metal-free tetrakis(1,2,5-thiadiazolo)porphyrazine and its nickel complex (H2TTDPz and NiTTDPz, respectively). The geometrical and electronic structure of H2TTDPz and NiTTDPz in ground and low-lying excited electronic states were determined by DFT calculations. The electronic structure of NiTTDPz was studied by the complete active space (CASSCF) method, following accounting dynamic correlation by multiconfigurational quasi-degenerate second-order perturbation theory (MCQDPT2). A geometrical structure of D2h and D4h symmetry was obtained for H2TTDPz and NiTTDPz, respectively. According to data obtained by the MCQDPT2 method, the nickel complex possesses the ground state 1A1g, and the wave function of the ground state has the form of a single determinant. Electronic absorption and vibrational (IR and resonance Raman) spectra of H2TTDPz and NiTTDPz were studied experimentally and simulated theoretically.

| S-EPMC8156015 | biostudies-literature

Heteroligand Iron(V) Complexes Containing Porphyrazine, trans-Di[benzo]porphyrazine or Tetra[benzo]porphyrazine, Oxo and Fluoro Ligands: DFT Quantum-Chemical Study.

Project description:By using quantum chemical calculation data obtained by the DFT method with the B3PW91/TZVP and OPBE/TZVP levels, the possibility of the existence of three Fe(V) complexes, each of which contains in the inner coordination sphere porphyrazine/trans-di[benzo]porphyrazine/tetra[benzo]porphyrazine (phthalocyanine), oxygen (O2-) and fluorine (F-) ions, was shown. Key geometric parameters of the molecular structure of these heteroligand complexes are given; it is noted that FeN4 chelate nodes, and all metal-chelate and non-chelate cycles in each of these compounds, are practically planar with the deviation from coplanarity, as a rule, by no more than 0.5°. Furthermore, the bond angles between two nitrogen atoms and an Fe atom are equal to 90°, or less than this by no more than 0.1°, while the bond angles between donor atoms N, Fe, and O or F, in most cases, albeit insignificantly, differ from this value. Nevertheless, the bond angles formed by Fe, O and F atoms are exactly 180°. It is shown that good agreement occurs between the structural data obtained using the above two versions of the DFT method. NBO analysis data for these complexes are presented; it is noted that, according to both DFT methods used, the ground state of the each of three complexes under consideration may be a spin quartet or spin doublet. Additionally, standard thermodynamic parameters of formation (standard enthalpy ∆fH0, entropy S0 and Gibbs's energy ∆fG0) for the macrocyclic compounds under consideration are calculated.

| S-EPMC10094394 | biostudies-literature

Influence of azacycle donor moieties on the photovoltaic properties of benzo[c][1,2,5]thiadiazole based organic systems: a DFT study.

Project description:Fullerene free organic chromophores are widely utilized to improve the efficacy of photovoltaic materials. Herein, we designed D-π-A-π-D form chromophores (TAZD1-TAZD5) via end-capped redistribution of donor moieties by keeping the same π-bridge and central acceptor unit for organic solar cells (OSCs). To analyze the photovoltaic characteristics of these derivatives, DFT estimations were accomplished at B3LYP/6-311 G (d,p) functional. Different investigations like frontier molecular orbital (FMO), absorption spectra (UV-Vis), density of states (DOS), binding energy (Eb), open circuit voltage (Voc), and transition density matrix (TDMs) were performed to examine the optical, photophysical and electronic characteristics of afore-mentioned chromophores. A suitable band gap (∆E = 2.723-2.659 eV) with larger bathochromic shift (λmax = 554.218-543.261 nm in acetonitrile) was seen in TAZD1-TAZD5. An effective charge transference from donor to acceptor via spacer was observed by FMO analysis which further supported by DOS and TDM. Further, lower binding energy values also supported the higher exciton dissociation and greater CT in TAZD1-TAZD5. Among all the designed chromophores, TAZD5 exhibited the narrowest Egap (2.659 eV) and maximum red-shifted absorption in solvent as well as gas phase i.e. 554.218 nm and 533.219 nm, respectively which perhaps as a result of the phenothiazine-based donor group (MPT). In a nutshell, all the tailored chromophores can be considered as efficient compounds for promising OSCs with a good Voc response, interestingly, TAZD5 is found to be excellent chromophores as compared to all these designed compounds.

| S-EPMC10480204 | biostudies-literature

Optimization of 1,2,5-thiadiazole carbamates as potent and selective ABHD6 inhibitors.

Project description:At present, inhibitors of ?/?-hydrolase domain?6 (ABHD6) are viewed as a promising approach to treat inflammation and metabolic disorders. This article describes the development of 1,2,5-thiadiazole carbamates as ABHD6 inhibitors. Altogether, 34 compounds were synthesized, and their inhibitory activity was tested using lysates of HEK293 cells transiently expressing human ABHD6 (hABHD6). Among the compound series, 4-morpholino-1,2,5-thiadiazol-3-yl cyclooctyl(methyl)carbamate (JZP-430) potently and irreversibly inhibited hABHD6 (IC50 =44 nM) and showed ?230-fold selectivity over fatty acid amide hydrolase (FAAH) and lysosomal acid lipase (LAL), the main off-targets of related compounds. Additionally, activity-based protein profiling indicated that JZP-430 displays good selectivity among the serine hydrolases of the mouse brain membrane proteome. JZP-430 has been identified as a highly selective, irreversible inhibitor of hABHD6, which may provide a novel approach in the treatment of obesity and type?II diabetes.

| S-EPMC4471478 | biostudies-literature

Gas-Phase Structures of Potassium Tetrakis(hexafluoro- acetylacetonato) Lanthanide(III) Complexes [KLn(C5 HF6 O2 )4 ] (Ln=La, Gd, Lu).

Project description:The molecular structures of potassium tetrakis(hexafluoroacetylacetonato)lanthanide(III) complexes [KLn(hfa)4 ] (Ln=La, Gd, Lu; hfa=C5 HF6 O2 ,) were studied by synchronous gas-phase electron diffraction/mass spectrometry (GED/MS) supported by quantum-chemical (DFT/PBE0) calculations. The compounds sublime congruently and the vapors contain a single molecular species: the heterobinuclear complex [KLn(hfa)4 ]. All molecules are of C1 symmetry with the lanthanide atom in the center of an LnO8 coordination polyhedron, while the potassium atom is coordinated by three ligands with formation of three K-O and three K-F bonds. One hfa ligand is not bonded to the potassium atom. Topological analysis of the electron-density distributions confirmed the existence of ionic-type K-O and K-F bonding. The structures of the free [KLn(hfa)4 ] molecules are compared with those of the related compounds [KDy(hfa)4 ] and [KEr(hfa)4 ] in their crystalline state. The complex nature of the chemical bonding is discussed on the basis of electron-density topology analyses.

| S-EPMC7839460 | biostudies-literature

DFT Quantum-Chemical Modeling Molecular Structures of Cobalt Macrocyclic Complexes with Porphyrazine or Its Benzo-Derivatives and Two Oxygen Acido Ligands.

Project description:Based on the results of a quantum chemical calculation using the DFT method with the OPBE/TZVP and B3PW91/TZVP levels, the possibility of the existence of three cobalt heteroligand complexes containing in the inner coordination sphere porphyrazine, di[benzo]- and tetra[benzo]porphyrazine, and two oxygen (O2-) ions with probable oxidation state VI of Co, which is unknown for this element at the present time, was shown. Data on the structural parameters are presented. It was shown that CoN4 chelate nodes as well as all metal-chelate and non-chelate cycles in each of these complexes, were strictly planar. Besides, the bond angles formed by two donor nitrogen atoms and a Co atom were close or equal to 90°, while the bond angles formed by donor atoms N, Co, and O, in most cases, albeit insignificantly, differed from this value. Good agreement between the calculated data obtained using the above two versions of the DFT method was found. Standard thermodynamic parameters of formation (standard enthalpy ?H0f, 298, entropy S0f, 298 and Gibbs's energy ?G0f, 298) for the indicated complexes were presented too.

| S-EPMC7730303 | biostudies-literature

A comparison between observed and DFT calculations on structure of 5-(4-chlorophenyl)-2-amino-1,3,4-thiadiazole.

Project description:The crystal and molecular structure of 5-(4-chlorophenyl)-2-amino-1,3,4-thiadiazole 3 was reported, which was characterized by various spectroscopic techniques (FT-IR, NMR and HRMS) and single-crystal X-ray diffraction. The crystal structure 3 (C8H6ClN3S) crystallized in the orthorhombic space group Pna21 and the unit cell consisted of 8 asymmetric molecules. The unit cell parameters were a?=?11.2027(2) Å, b?=?7.6705(2) Å, c?=?21.2166(6) Å, ??=???=???=?90°, V?=?1823.15(8) Å3, Z?=?8. In addition, the structural geometry (bond lengths, bond angles, and torsion angles), the electronic properties of mono and dimeric forms of compound 3 were calculated by using the density functional theory (DFT) method at B3LYP level 6-31+ G(d,p), 6-31++ G(d,p) and 6-311+ G(d,p) basis sets in ground state. A good correlation was found (R2?=?0.998) between the observed and theoretical vibrational frequencies. Frontier molecular orbitals (HOMO and LUMO) and Molecular Electrostatic Potential map of the compound was produced by using the optimized structures. The NBO analysis was suggested that the molecular system contains N-H…N hydrogen bonding, strong conjugative interactions and the molecule become more polarized owing to the movement of ?-electron cloud from donor to acceptor. The calculated structural and geometrical results were in good rational agreement with the experimental X-ray crystal structure data of 1,3,4-thiadiazol-2-amine, 3. The compound 3 exhibited n??* UV absorption peak of UV cutoff edge, and great magnitude of the first-order hyperpolarizability was observed. The obtained results suggest that compound 3 could have potential application as NLO material. Therefore, this study provides valuable insight experimentally and theoretically, for designing new chemical entities to meet the demands of specific applications.

| S-EPMC6917775 | biostudies-literature

Novel benzo-bis(1,2,5-thiadiazole) fluorophores for in vivo NIR-II imaging of cancer.

Project description:Optical imaging of diseases represents a highly dynamic and multidisciplinary research area, and second near-infrared window (NIR-II, 1000-1700 nm) imaging is at the forefront of the research on optical imaging techniques. Small-molecule based NIR-II (1000-1700 nm) dyes are highly promising candidates for in vivo molecular imaging because of their high biocompatibility, fast excretion, and high clinical translation ability. However, research reports on small-molecule based NIR-II dyes and probes are rare. Herein, we designed a series of fluorescent compounds (Q1, Q2, Q3, and Q4) and investigated the relationships between their structures and absorption/fluorescence properties. Q4 (maximum emission at 1100 nm) stood out as the dye with the best physical properties and thus was selected as a scaffold for the facile construction of two types of water-soluble and biocompatible NIR-II probes (Q4NPs and SCH1100). Highly specific gastrin-releasing peptide receptor (GRPR) targeted NIR-II imaging of prostate cancer in living mice was achieved using the small-molecule probe SCH1100, which represents the first small peptide based NIR-II probe for targeted cancer imaging. The attractive imaging properties of Q4-based NIR-II probes open up many opportunities for molecular imaging and clinical translation in the unique NIR-II window.

| S-EPMC6024204 | biostudies-literature

DFT Study on the Electronic Properties, Spectroscopic Profile, and Biological Activity of 2-Amino-5-trifluoromethyl-1,3,4-thiadiazole with Anticancer Properties.

Project description:Extensive investigation on the molecular and electronic structure of 2-amino-5-trifluoromethyl-1,3,4-thiadiazole in the ground state and in the first excited state has been performed. The energy barrier corresponding to the conversion between imino and amino tautomers has been calculated, which indicates the existence of amino tautomer in solid state for the title compound. The FT-Raman and FT-IR spectra were recorded and compared with theoretical vibrational wavenumbers, and a good coherence has been observed. The MESP map, dipole moment, polarizability, and hyperpolarizability have been calculated to comprehend the properties of the title molecule. High polarizability value estimation of the title compound may enhance its bioactivity. Natural bonding orbital analysis has been done on monomer and dimer to investigate the charge delocalization and strength of hydrogen bonding, respectively. Strong hydrogen bonding interaction energies of 17.09/17.49 kcal mol-1 have been calculated at the B3LYP/M06-2X functional. The UV-vis spectrum was recorded and related to the theoretical spectrum. The title compound was biologically examined for anticancer activity by studying the cytotoxic performance against two human cancer cell lines (A549 and HeLa) along with the molecular docking simulation. Both molecular docking and cytotoxic performance against cancer cell lines show positive outcomes, and the title compound appears to be a promising anticancer agent.

| S-EPMC7689922 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data