scholarly journals Therortical Studies and Investagting of Selected Potnet CDK2 Inhibitors as Anticancer Agents

2021 ◽  
Author(s):  
Mohammad J Abunuwar ◽  
Adnan A Dahadha
Keyword(s):  
Anticancer Agents ◽  
Density Functional ◽  
Chemical Potential ◽  
Chemical Reactivity ◽  
Three Dimensional ◽  
Data Bank ◽  
Basis Set ◽  
Chemical Hardness ◽  
Cyclin Dependent Kinase ◽  
Reactivity Descriptors

Abstract In this study eight selected of the most potent cyclin dependent kinase 2 inhibitors in which targeting adenosine triphosphate -pocket site theoretically investigated to support literature information of frontier molecular orbitals, molecular electrostatic maps, and global chemical reactivity descriptors such as chemical hardness, chemical softness, chemical potential, electronegativity and electrophilicity of cyclin dependent kinase 2 inhibitors. Calculation and three-dimensional plotting were achieved through Gaussian 09W and Gausview 6 software’s utilizing density functional theory quantum modeling applying both hybrids extended and not extended basis set. Crystal structure of CDK2 with inhibitors was obtained from protein data bank and visualized through PyMol Schrödinger software to assign polar and non-polar interactions of inhibitors with enzyme. A promising conclusion trend obtained in this research regarding to molecules that could have an inhibition activity toward the cyclin dependent kinase 2 enzymes. Our theoretical investigation emphasizes that, the anti-cancer activity has directly relationship with value of chemical hardness and chemical softness, where the most potent compounds was the pyrazolopyrimidine and imidazole pyrimidine and they have higher chemical hardness value and at the same time lower value of chemical softness compared with the rest of compounds.

scholarly journals Topological Model on the Inductive Effect in Alkyl Halides Using Local Quantum Similarity and Reactivity Descriptors in the Density Functional Theory

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Alejandro Morales-Bayuelo ◽  
Ricardo Vivas-Reyes
Keyword(s):  
Density Functional ◽  
Chemical Potential ◽  
Inductive Effect ◽  
Chemical Reactivity ◽  
Topological Analysis ◽  
Basis Set ◽  
Organic Chemical ◽  
Quantum Similarity ◽  
Local Exchange ◽  
Reactivity Descriptors

We present a topological analysis to the inductive effect through steric and electrostatic scales of quantitative convergence. Using the molecular similarity field based in the local guantum similarity (LQS) with the Topo-Geometrical Superposition Algorithm (TGSA) alignment method and the chemical reactivity in the density function theory (DFT) context, all calculations were carried out with Amsterdam Density Functional (ADF) code, using the gradient generalized approximation (GGA) and local exchange correlations PW91, in order to characterize the electronic effect by atomic size in the halogens group using a standard Slater-type-orbital basis set. In addition, in this study we introduced news molecular bonding relationships in the inductive effect and the nature of the polar character in the C–H bond taking into account the global and local reactivity descriptors such as chemical potential, hardness, electrophilicity, and Fukui functions, respectively. These descriptors are used to find new alternative considerations on the inductive effect, unlike to the binding energy and dipole moment performed in the traditional organic chemical.

Calculation of global and local reactivity descriptors of carbodiimides, a DFT study

2017 ◽  
Vol 16 (03) ◽  
pp. 1750019 ◽  
Author(s):  
Kathy Ramirez-Balderrama ◽  
Erasmo Orrantia-Borunda ◽  
Norma Flores-Holguin
Keyword(s):  
Electron Affinity ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Chemical Hardness ◽  
Geometrical Parameters ◽  
Reactivity Descriptors ◽  
Local Reactivity ◽  
Global And Local ◽  
Local Reactivity Descriptors

Carbodiimides have been widely used for different purposes, such as an intermediary to form peptides bonds and esters, which have generated industrial, organic and biological applications. Diisoproylcarbodiimide (DIC), (3-(dimethylamino) propyl)ethylcarbodiimide (EDC) and N,N′-dicyclohexylcarbodiimide (DCC) are the most common carbodiimides, however, there exist other carbodiimides that are not normally used. Twelve carbodiimides including the above mentioned were chosen to study their chemical reactivity as well as their nucleophilic and electrophilic attack sites. Geometry optimization in gas and solution phases was obtained using Density Functional Theory (DFT) through B3LYP with 6-31G(d) and 6-311[Formula: see text]G(d,p) level. Global and local reactivity descriptors were calculated and analyzed such as chemical hardness, ionization potential, electron affinity, Fukui functions, dual descriptor and hypersoftness. The results obtained for geometrical parameters do not have significant differences for gas and solution phase. The introduction of diffuse functions has great impact in electron affinity, modifying notably the values of reactivity descriptors, but didn’t show qualitative differences, since the results found for both basis set calculations show that Cyanamide or CD1 is the most stable and CD11 present greater reactivity of all studied molecules. Also, the hypersoftness results obtained with 6-31G(d) are in agreement with the general affirmation that carbodiimides are easily attacked by nucleophiles and electrophiles in the central carbon–nitrogen double bond.

Combined experimental and theoretical studies on 4-(2-hydroxy-3-morpholin-4-yl-propoxy)-chromen-2-one

2016 ◽  
Vol 15 (02) ◽  
pp. 1650017
Author(s):  
Priyanka ◽  
Sanjay Kumar Srivastava ◽  
Diksha Katiyar
Keyword(s):  
Density Functional ◽  
Chemical Potential ◽  
Chemical Shifts ◽  
Basis Set ◽  
Chemical Hardness ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Hartree Fock ◽  
Homo And Lumo ◽  
Experimental And Theoretical Studies

The FTIR, UV–Vis and NMR spectra of 4-(2-hydroxy-3-morpholin-4-yl-propoxy)-chromen-2-one (4-HMPC) have been recorded and analyzed. The optimized geometry and harmonic vibrational frequencies of 4-HMPC were obtained by the Hartree–Fock (HF) and density functional theory (DFT) using B3LYP functional with 6-311[Formula: see text]G basis set. The 1H and [Formula: see text]C NMR chemical shifts were calculated by the GIAO method in chloroform. The absorption spectra of 4-HMPC were computed in ethanol and water solutions using TD-B3LYP/6-311[Formula: see text]G(d,p) approach. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the molecule. The results obtained from the studies of HOMO and LUMO were used to calculate the conceptual-DFT-based global reactivity descriptors such as electronic chemical potential, electronegativity, chemical hardness, global softness and electrophilicity index of the compound.

scholarly journals DFT investigations on arylsulphonyl pyrazole derivatives as potential ligands of selected kinases

2020 ◽  
Vol 18 (1) ◽  
pp. 857-873
Author(s):  
Kornelia Czaja ◽  
Jacek Kujawski ◽  
Radosław Kujawski ◽  
Marek K. Bernard
Keyword(s):  
Free Energy ◽  
Molecular Orbital ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Chemical Hardness ◽  
Free Energy Of Solvation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Condensed Fukui Functions ◽  
Charge Partitioning

AbstractUsing the density functional theory (DFT) formalism, we have investigated the properties of some arylsulphonyl indazole derivatives that we studied previously for their biological activity and susceptibility to interactions of azoles. This study includes the following physicochemical properties of these derivatives: electronegativity and polarisability (Mulliken charges, adjusted charge partitioning, and iterative-adjusted charge partitioning approaches); free energy of solvation (solvation model based on density model and M062X functional); highest occupied molecular orbital (HOMO)–lowest occupied molecular orbital (LUMO) gap together with the corresponding condensed Fukui functions, time-dependent DFT along with the UV spectra simulations using B3LYP, CAM-B3LYP, MPW1PW91, and WB97XD functionals, as well as linear response polarisable continuum model; and estimation of global chemical reactivity descriptors, particularly the chemical hardness factor. The charges on pyrrolic and pyridinic nitrogen (the latter one in the quinolone ring of compound 8, as well as condensed Fukui functions) reveal a significant role of these atoms in potential interactions of azole ligand–protein binding pocket. The lowest negative value of free energy of solvation can be attributed to carbazole 6, whereas pyrazole 7 has the least negative value of this energy. Moreover, the HOMO–LUMO gap and chemical hardness show that carbazole 6 and indole 5 exist as soft molecules, while fused pyrazole 7 has hard character.

scholarly journals Synthesis, Characterization, Catalytic Activity, and DFT Calculations of Zn(II) Hydrazone Complexes

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4043 ◽  
Author(s):  
Temiloluwa T. Adejumo ◽  
Nikolaos V. Tzouras ◽  
Leandros P. Zorba ◽  
Dušanka Radanović ◽  
Andrej Pevec ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Molecular Orbital ◽  
Density Functional ◽  
Chemical Potential ◽  
Chemical Reactivity ◽  
Geometry Optimization ◽  
Coupling Reaction ◽  
Functional Theory ◽  
Reactivity Descriptors

Two new Zn(II) complexes with tridentate hydrazone-based ligands (condensation products of 2-acetylthiazole) were synthesized and characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy and single crystal X-ray diffraction methods. The complexes 1, 2 and recently synthesized [ZnL3(NCS)2] (L3 = (E)-N,N,N-trimethyl-2-oxo-2-(2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)ethan-1-aminium) complex 3 were tested as potential catalysts for the ketone-amine-alkyne (KA2) coupling reaction. The gas-phase geometry optimization of newly synthesized and characterized Zn(II) complexes has been computed at the density functional theory (DFT)/B3LYP/6–31G level of theory, while the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO and LUMO) energies were calculated within the time-dependent density functional theory (TD-DFT) at B3LYP/6-31G and B3LYP/6-311G(d,p) levels of theory. From the energies of frontier molecular orbitals (HOMO–LUMO), the reactivity descriptors, such as chemical potential (μ), hardness (η), softness (S), electronegativity (χ) and electrophilicity index (ω) have been calculated. The energetic behavior of the investigated compounds (1 and 2) has been examined in gas phase and solvent media using the polarizable continuum model. For comparison reasons, the same calculations have been performed for recently synthesized [ZnL3(NCS)2] complex 3. DFT results show that compound 1 has the smaller frontier orbital gap so, it is more polarizable and is associated with a higher chemical reactivity, low kinetic stability and is termed as soft molecule.

New molecular target insights about protein kinases of the Plasmodium falciparum. Using molecular docking and DFT-based reactivity descriptors

2017 ◽  
Vol 16 (08) ◽  
pp. 1750076 ◽  
Author(s):  
Alejandro Morales-Bayuelo
Keyword(s):  
Plasmodium Falciparum ◽  
Protein Kinases ◽  
Density Functional ◽  
Chemical Potential ◽  
Chemical Reactivity ◽  
Binding Pocket ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Chemical Reactivity Descriptors ◽  
Hinge Zone

Currently, there is increasing interest in the potential of malaria inhibitors in Plasmodium falciparum activity. In this work, is propose a possible alternative to classifying 154 antimalarials, with P. falciparum activity. These antimalarials were synthesized by the Chibale’s group ( http://www.kellychibaleresearch.uct.ac.za/ ), with the goal of finding new insights on the binding pocket of the protein kinase PfPK5, PfPK7, PfCDPK1, PfCDPK4, PfMAP1, and PfPK6 of the malaria parasite. However, there is only information about crystallography of PfPK5 and PfPK7. The protein kinases PfCDPK1, PfCDPK4, PfMAP1, and PfPK6 were modeled using molecular homology. The validation used shows that our homology models can be an alternative for the protein kinases from P. falciparum, unknown today. The antimalarials were classified by taking into account the interactions in the hinge zone. These ligands bind to the kinase through the formation of one of two hydrogen bonds, with the backbone residues of the hinge region connecting the kinase N- and C-terminal loops. These interactions were supported by a reactivity chemistry analysis, using global chemical reactivity descriptors such as chemical potential, hardness, softness, electrophilicity, and the Fukui functions as local reactivity descriptors, within the Density Functional Theory (DFT) context.

scholarly journals Chemical Reactivity Properties, Solubilities, and Bioactivity Scores of Some Pigments Derived from Carotenoids of Marine Origin through Conceptual DFT Descriptors

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Carotenoid Pigments ◽  
Density Functionals ◽  
Solvation Model ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Chemical Reactivity Descriptors

Five density functionals, CAM-B3LYP, LC-ωHPBE, MN12SX, N12SX, and ωB97XD, in connection with the Def2TZVP basis set were assessed together with the SMD solvation model for the calculation of the molecular properties, chemical reactivities, and solubilities of some pigments derived from astaxanthin, β-cryptoxanthin, fucoxanthin, myxol, siphonaxanthin, siphonein, and zeaxanthin marine carotenoids in the presence of different solvents (hexane, methanol, ethanol, and water). All the chemical reactivity descriptors for the systems were calculated via conceptual density functional theory (CDFT). Finally, the potential bioavailability and druggability as well as the bioactivity scores for the marine carotenoid pigments were predicted through different methodologies already reported in the literature, which have been previously validated during the study of other natural products obtained from marine sources.

scholarly journals Theoretical Investigation on Biological Activity of Imidazole Derivatives [Carbenzim, Mebendazole] by using (DFT) and (PM3) Methods

2021 ◽  
Vol 24 (2) ◽  
pp. 1-8
Author(s):  
Amar Tuma Musa ◽  
◽  
Khalida Abaid ◽  
Keyword(s):  
Density Functional ◽  
Chemical Potential ◽  
Theoretical Study ◽  
Chemical Reactivity ◽  
Biological Activities ◽  
Biological Properties ◽  
Benzimidazole Derivatives ◽  
Log P ◽  
P Value ◽  
Reactivity Descriptors

The theoretical study represents an essential preliminary stage for the start of any industry, as it gives a theoretical description of the properties of compounds (chemical, physical and biological properties)without conducting research to find out about this and the least cost. Through the theoretical study, we extract a clear picture of the chemical compounds before starting to manufacture them to know the extent of their impact on human health and their chemical and biological effectiveness. Using the Density Functional Theory (DFT/B3LYP) with base 6-311G,throughGaussian 09 program, the optimize geometry,(bond lengths, angles bond)and vibrational spectra was calculated of the benzimidazole derivatives [Carbenzim (CZM), Mebendazole (MBZ)].Through orbital charts of HOMO and LUMO to study electronic properties. The HOMO-LUMO gap was also evaluated for chemical reactivity and determination of global reactivity descriptors (Hardness (),Softness (S), Electrophilicity(), Chemical potential(),Electronegativity(χ))] that defines compunds effectiveness and the their biological activities. In addition, (QSAR) data has been used to develop relationships between biological activities and thermophysical properties of chemicals, through the Hyper Chem8.0programbyusingSemi-empirical(SE)method at the (PM3) level. The LOG P value was calculated, binding energy, Polarizability, hydration energy, surface area, and electrostatic potential energy difference of two level.

scholarly journals Catalytic effect of TMCmHm  compounds on the reaction rate of  " Hydrazin - Oxygen "fuel cell  "TM = Cr, Sc, Ti, V and m= 4 or 5" A DFT Study ​

2021 ◽  
Author(s):  
Zohreh Mohammadi Ahmad Mahmodi ◽  
Mehran Aghaie ◽  
Maziar Noei ◽  
Hossein Aghaie
Keyword(s):  
Fuel Cell ◽  
Molecular Orbital ◽  
Density Functional ◽  
Reaction Rate ◽  
Chemical Potential ◽  
Organometallic Compounds ◽  
Basis Set ◽  
Optimal Structure ◽  
Chemical Hardness ◽  
Oxygen Fuel

Abstract Platinum and similar metals are suitable catalysts in response to fuel cells, however, because of being costly, their use is limited. So in this study, the catalytic efficiency of some organometallic compounds with the general formula TMCmHm on the reaction rate of "Hydrazine- Oxygen "fuel cell was studied via density Functional Theory (DFT). To perform the respect calculations, the PW91 method and 6-31 G(d) basis set were used. Bonds’ length of O=O and N-N increased in response to their adsorption onto TMCmHm and theoretical study of N2H4-O2 fuel cell the partial transfer of negative charge from organometallic compounds to their π * orbitals. Bond length of O=O increased by 24% due to its adsorption on ScC5H5 and N-N on ScC5H5 increased by 11%. The optimal structure of each studied organometallic compound was plotted by performing natural bond orbital calculations (NBO). The energy of the highest occupied molecular orbital (EHOMO) and the lowest unoccupied molecular orbital (ELUMO) were calculated. Besides, , the gap energies (Eg), chemical hardness (ɳ), chemical potential (µ), and electrophilicity (ω) were calculated in each case. Then, the optimal structure of O2/TMCmHm and N2H4/ TMCmHm pairs was plotted; the adsorption energy of O2 and N2H4 on each of TMCmHm was evaluated. The kinetic adsorption of O2 and N2H4 on the Sc C5H5 compound was investigated by the 6-31 G * method. The potential energy of O2/TMCmHm and N2H4/ TMCmHm pairs in the initial and final position and the transient state were estimated, and the respect kinetic parameters were calculated.

Studies of intramolecular H-bond interactions and solvent effects in the conformers of glycolic acid — A quantum chemical study

2018 ◽  
Vol 17 (01) ◽  
pp. 1850009 ◽  
Author(s):  
Mahendiraprabu Ganesan ◽  
Nirmala Vedamanickam ◽  
Selvarengan Paranthaman
Keyword(s):  
Solvent Effects ◽  
Density Functional ◽  
Glycolic Acid ◽  
Chemical Potential ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Basis Set ◽  
Chemical Hardness ◽  
Geometrical Parameters ◽  
Water Media

In this work, density functional theory is applied to understand the conformational stability and solvent effects on glycolic acid conformers in different solvents. In addition, the role of intramolecular hydrogen bond (H-bond) interactions in the stability of conformers are investigated. The molecular geometries of selected conformers are optimized using B3LYP and PBE0 functionals with 6-311[Formula: see text]G(d,p) basis set. The effects of solvent on the geometrical parameters, relative stability, dipole moment, chemical hardness, chemical potential, etc. are studied for the conformers of glycolic acid. Our calculations show that the order of stability of the SSC and AAT conformers does not change in liquid phase. However, the energy of SSC and AAT conformers is very close to each other in water media. In water media, strong intramolecular H-bond interaction is present in AAT conformer which causes the energy of AAT conformer to be very close to that of SSC conformer. This may be due to the influence of water media.

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