Rutile Molecular Model and its EUC Determination by PM7

Rutile surface has been modeled in order to study its electronic properties as well as to determine its surface chemical reactivity. There have been constructed 10 different rutile structures, from a 6 atoms cluster (for the smallest) to a 356 atoms cluster (for the biggest). It was calculated for each cluster some physical parameters which are related to the electronic properties, such as work function, band gap, and density of states (DOS), in order to analyze the tendency of the cluster properties with the increase of atoms. From the data obtained, it was determined the Electronic Unit Cell (EUC), which refers to the modeled structure for what the electronic and reactivity properties of the system does no change, from clusters with different number of atoms. From the rutile EUC cluster it was determined its band gap with a value of 3.28 eV, which agreed with the experimental value of 3.0-3.1 eV. Furthermore, it was performed a reactivity surface study, which comprised the analysis of reactivity descriptors such as ionization potential, electronic affinity, total hardness, electronic chemical potential, electrophilicity and electronegativity. All theoretical calculations were performed using the semiempirical PM7 included in the 2012 version of MOPAC and the surfaces were modeled from crystallographic data.

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

Molecules ◽

10.3390/molecules25184043 ◽

2020 ◽

Vol 25 (18) ◽

pp. 4043 ◽

Cited By ~ 1

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.

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

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633617500766 ◽

2017 ◽

Vol 16 (08) ◽

pp. 1750076 ◽

Cited By ~ 1

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.

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

Journal of Quantum Chemistry ◽

10.1155/2014/850163 ◽

2014 ◽

Vol 2014 ◽

pp. 1-12 ◽

Cited By ~ 3

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.

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

Al-Nahrain Journal of Science ◽

10.22401/anjs.24.2.01 ◽

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.

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Understanding the Chemical Reactivity of Dihydroxyfumaric Acid and its Derivatives through Conceptual DFT

Revista de Chimie ◽

10.37358/rc.21.4.8465 ◽

2020 ◽

Vol 72 (4) ◽

pp. 162-174

Author(s):

Gheorghe Duca ◽

Natalia Bolocan

Keyword(s):

Active Sites ◽

Chemical Reactivity ◽

Conceptual Dft ◽

Total Hardness ◽

Hydroxyl Groups ◽

Reactivity Descriptors ◽

Local Reactivity ◽

Koopmans Theorem ◽

Chemical Reactivity Descriptors ◽

Homo And Lumo

The chemical reactivity descriptors have been calculated through Molecular Electron Density Theory encompassing Conceptual DFT. The validity of �Koopmans� theorem in DFT� (KID) has been assessed by a comparison between the global descriptors (electronegativity, total hardness, and global electrophilicity) calculated through vertical energy values and those arising from the HOMO and LUMO values. These results suggest that the KID procedure is valid and may be used, in conjunction with the B3LYP/3-611G(d, p) level of theory in further studies of related compounds in the aqueous medium. The active sites for nucleophilic and electrophilic attacks have been identified and verified using the local reactivity descriptors: the dual descriptor, the electrophilic and nucleophilic Parr functions, the local reactivity difference index Rk and MEP maps. Obtained results suggest that the antioxidant/antiradical power of investigated compounds may be explained by the highest ambiphilic activation of the oxygen atoms of the hydroxyl groups in the ene-diol moiety.

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

10.21203/rs.3.rs-1044760/v1 ◽

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.

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Electronic Structure of Silicide-Silicon Interfaces

MRS Proceedings ◽

10.1557/proc-10-21 ◽

1981 ◽

Vol 10 ◽

Author(s):

G. W. Rubloff ◽

P. S. Ho

Keyword(s):

Electronic Structure ◽

Transition Metal ◽

Band Gap ◽

Theoretical Calculations ◽

Chemical Reactivity ◽

Electronic States ◽

Composition Analysis ◽

Interfacial Region ◽

Silicide Formation ◽

Reaction Products

Over the past few years the electronic structure of transition metal-silicon and silicide-silicon interfaces (and of bulk silicide compounds) has been revealed for the first time, using surface spectroscopies (photoemission and Auger) and theoretical calculations. These investigations, which have included palladium, platinum, nickel, vanadium, chromium, molybdenum and tungsten, have elucidated the important role played by the chemical bond between the transition metal d and the Si 3p electrons. They have also shown the high chemical reactivity of the atomically clean transition metal-silicon interface, which leads to interfacial silicide formation at relatively low temperatures (i.e. markedly below those needed for bulk silicide formation on chemically cleaned silicon surfaces). As a result, silicide-like chemical bonding dominates the interface electronic structure of such contacts under a wide variety of conditions. Detailed comparisons of interface spectra (observed at low metal coverages) with those of the bulk silicide reaction products give strong evidence for additional electronic states of relatively high density (about 0.1 states per interface atom) which lie in or near the silicon band gap region. These states are believed to be true interface states associated with localized bonding configurations unique to the atoms at the interface, and they could explain the silicon-rich silicide composition of a thin (about 3–5 Å) interfacial region which has been observed by Auger composition analysis and suggested by chemical shifts in core and valence electron densities of states. Finally, metal atom diffusion into the silicon substrate has been observed in ion channeling studies and suggested from surface spectroscopy results; these impurity atoms should produce defect states localized near the interface and lying within the silicon band gap, although these electronic states have not yet been directly observed. As a whole these results present a fairly detailed picture of the electronic structure and chemistry of the silicide-silicon interface.However, correlations with the interface electrical properties are needed to ascertain which electronic features and chemical mechanisms in fact determine the Schottky barrier height of the contact.

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Reactivity and Stability of Metalloporphyrin Complex Formation: DFT and Experimental Study

Molecules ◽

10.3390/molecules25184221 ◽

2020 ◽

Vol 25 (18) ◽

pp. 4221 ◽

Cited By ~ 1

Author(s):

Rimadani Pratiwi ◽

Slamet Ibrahim ◽

Daryono H. Tjahjono

Keyword(s):

Lower Energy ◽

Chemical Potential ◽

Chemical Reactivity ◽

Binding Constants ◽

Stable Complex ◽

Chemical Hardness ◽

Reactivity Descriptors ◽

Chemical Reactivity Descriptors ◽

Electronic Chemical Potential ◽

Electronic Chemical

The interaction of three cationic porphyrins—meso-tetrakis (N-methylpyridinium-4-yl) porphyrin (TMPyP), meso-tetrakis (1,3-dimethylimidazolium-2-yl) porphyrin (TDMImP), and meso-tetrakis (1,2-dimethylpyrazolium-4-yl) porphyrin (TDMPzP)—with five heavy metals was studied computationally, and binding constants were calculated based on data obtained by an experimental method and compared. The reactivity and stability of their complexes formed with lead, cadmium, mercury, tin, and arsenic ions were observed in DFT global chemical reactivity descriptors: the electronic chemical potential (µ), chemical hardness (η), and electrophilicity (ω). The results show that M-TDMPzP has higher chemical hardness and lower electrophilicity compared to M-TMPyP and M-TDMImP, indicating the reaction of TDMPzP with metals will form a more stable complex. Specifically, Cd-TDMPzP complexes can stabilize the system, with a lower energy and electronic chemical potential, higher chemical hardness, smaller electrophilicity, and higher binding constant value compared to Pb-TDMPzP and Hg-TDMPzP. This result suggests that the interaction of the Cd2+ ion with TDMPzP will produce a stable complex.

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A Quantitative Structure-Activity Relationship Study on the Antimalarial Activities of 4-Aminoquinoline, Febrifugine and Artemisinin Compounds

International Journal of Quantitative Structure-Property Relationships ◽

10.4018/ijqspr.2020010104 ◽

2020 ◽

Vol 5 (1) ◽

pp. 63-79

Author(s):

Yu Heng Ou ◽

Chia Ming Chang

Keyword(s):

Plasmodium Falciparum ◽

Chemical Potential ◽

Chemical Reactivity ◽

Electron Flow ◽

Quantitative Structure Activity Relationship ◽

Structure Activity Relationship ◽

Activity Relationship ◽

Quantitative Structure ◽

Reactivity Descriptors ◽

Structure Activity

Quantum chemical molecular descriptors representing different types of chemical reactivity were employed to investigate the antimalarial activities of 4-aminoquinoline, febrifugine, artemisinin and their derivatives. The quantitative structure-activity relationship results reveal that: (i) the antimalarial activities of 4-aminoquinoline compounds against the chloroquine-sensitive Plasmodium falciparum 3D7 strain are mainly affected by the electron flow and polarization interactions; (ii) The reactivity descriptors for the activities of febrifugine compounds against the chloroquine-resistant Plasmodium falciparum FCR-3 strain are the electron-acceptance chemical potential, the maximum nucleophilic and electrophilic local softness, the maximum positive charge of the hydrogen atom, etc.; (iii) The electron-donation chemical potential, the maximum negative charge, the inverse of the apolar surface area and the molar volume of artemisinin compounds are the most important descriptors for evaluating the activity against the chloroquine-resistant Plasmodium falciparum W-2 strain.

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Synthesis of Functionalized Thiophene Based Pyrazole Amides via Various Catalytic Approaches: Structural Features through Computational Applications and Nonlinear Optical Properties

Molecules ◽

10.3390/molecules27020360 ◽

2022 ◽

Vol 27 (2) ◽

pp. 360

Author(s):

Iram Kanwal ◽

Nasir Rasool ◽

Syeda Huda Mehdi Zaidi ◽

Zainul Amiruddin Zakaria ◽

Muhammad Bilal ◽

...

Keyword(s):

Chemical Potential ◽

Chemical Reactivity ◽

Structural Features ◽

Frontier Molecular Orbital ◽

Chemical Hardness ◽

Reactivity Descriptors ◽

Nmr Data ◽

Amide Derivatives ◽

Non Linear ◽

Linear Optical

In the present study, pyrazole-thiophene-based amide derivatives were synthesized by different methodologies. Here, 5-Bromothiophene carboxylic acid (2) was reacted with substituted, unsubstituted, and protected pyrazole to synthesize the amide. It was observed that unsubstituted amide (5-bromo-N-(5-methyl-1H-pyrazol-3-yl)thiophene-2-carboxamide (7) was obtained at a good yield of about 68 percent. The unsubstituted amide (7) was arylated through Pd (0)-catalyzed Suzuki–Miyaura cross-coupling, in the presence of tripotassium phosphate (K3PO4) as a base, and with 1,4-dioxane as a solvent. Moderate to good yields (66–81%) of newly synthesized derivatives were obtained. The geometry of the synthesized compounds (9a–9h) and other physical properties, like non-linear optical (NLO) properties, nuclear magnetic resonance (NMR), and other chemical reactivity descriptors, including the chemical hardness, electronic chemical potential, ionization potential, electron affinity, and electrophilicity index have also been calculated for the synthesized compounds. In this study, DFT calculations have been used to investigate the electronic structure of the synthesized compounds and to compute their NMR data. It was also observed that the computed NMR data manifested significant agreement with the experimental NMR results. Furthermore, compound (9f) exhibits a better non-linear optical response compared to all other compounds in the series. Based on frontier molecular orbital (FMO) analysis and the reactivity descriptors, compounds (9c) and (9h) were predicted to be the most chemically reactive, while (9d) was estimated to be the most stable among the examined series of compounds.

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