scholarly journals Classical QSAR and Docking Simulation of 4-Pyridone Derivatives for Their Antimalarial Activity

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3166 ◽  
Author(s):  
Máryury Flores-Sumoza ◽  
Jackson Alcázar ◽  
Edgar Márquez ◽  
José Mora ◽  
Jesús Lezama ◽  
...  
Keyword(s):  
Density Functional ◽  
Cross Validation ◽  
Antimalarial Activity ◽  
Minimum Energy ◽  
Docking Simulation ◽  
Statistical Parameters ◽  
Functional Theory ◽  
Leave One Out ◽  
Small Chemical ◽  
Linear Regressions

In this work, the minimum energy structures of 22 4-pyridone derivatives have been optimized at Density Functional Theory level, and several quantum molecular, including electronic and thermodynamic descriptors, were computed for these substrates in order to obtain a statistical and meaningful QSAR equation. In this sense, by using multiple linear regressions, five mathematical models have been obtained. The best model with only four descriptors (r2 = 0.86, Q2 = 0.92, S.E.P = 0.38) was validated by the leave-one-out cross-validation method. The antimalarial activity can be explained by the combination of the four mentioned descriptors e.g., electronic potential, dipolar momentum, partition coefficient and molar refractivity. The statistical parameters of this model suggest that it is robust enough to predict the antimalarial activity of new possible compounds; consequently, three small chemical modifications into the structural core of these compounds were performed specifically on the most active compound of the series (compound 13). These three new suggested compounds were leveled as 13A, 13B and 13C, and the predicted biological antimalarial activity is 0.02 µM, 0.03 µM, and 0.07 µM, respectively. In order to complement these results focused on the possible action mechanism of the substrates, a docking simulation was included for these new structures as well as for the compound 13 and the docking scores (binding affinity) obtained for the interaction of these substrates with the cytochrome bc1, were −7.5, −7.2, −6.9 and −7.5 kcal/mol for 13A, 13B, 13C and compound 13, respectively, which suggests that these compounds are good candidates for its biological application in this illness.

scholarly journals In-silico Design of Aryl and Aralkyl Amine-Based Triazolopyrimidine Derivatives with Enhanced Activity Against Resistant Plasmodium falciparum

2020 ◽  
Author(s):  
Zakari Ya’u Ibrahim ◽  
Adamu Uzairu ◽  
Gideon Shallangwa ◽  
Stephen Abechi
Keyword(s):  
In Silico ◽  
Density Functional ◽  
Antimalarial Activity ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Randomization Test ◽  
Basis Set ◽  
Coefficient Of Determination ◽  
Statistical Parameters ◽  
Leave One Out

Abstract A blend of genetic algorithm with multiple linear regression (GA-MLR) method was utilized in generating a quantitative structure–activity relationship (QSAR) model on the antimalarial activity of aryl and aralkyl amine-based triazolopyrimidine derivatives. The structures of derivatives were optimized using density functional theory (DFT) DFT/B3LYP/6–31 + G* basis set to generate their molecular descriptors, where two (2) predictive models were developed with the aid of these descriptors. The model with an excellent statistical parameters; high coefficient of determination (R2) = 0.8884, cross-validated R2 (Q2cv) = 0.8317 and highest external validated R2 (R2pred) = 0.7019 was selected as the best model. The model generated was validated through internal (leave-one-out (LOO) cross-validation), external test set, and Y-randomization test. These parameters are indicators of robustness, excellent prediction, and validity of the selected model. The most relevant descriptor to the antimalarial activity in the model was found to be GATS6p (Geary autocorrelation—lag 6/weighted by polarizabilities), in the model due to its highest mean effect. The descriptor (GATS6p) was significant in the in-silico design of sixteen (16) derivatives of aryl and aralkyl amine-based triazolopyrimidine adopting compound DSM191 with the highest activity (pEC50 = 7.1805) as the design template. The design compound D8 was found to be the most active compound due to its superior hypothetical activity (pEC50 = 8.9545).

scholarly journals A NOVEL FRACTAL GEOMETRY DOPING FOR GRAPHENE NANORIBBON AND THE OPTIMIZATION OF CRYSTAL: A DENSITY FUNCTIONAL THEORY (DFT) STUDY

2020 ◽  
Vol 17 (35) ◽  
pp. 1148-1158
Author(s):  
Mohammed L. JABBAR ◽  
Kadhum J. AL-SHEJAIRY
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Energy Gap ◽  
Minimum Energy ◽  
Graphene Nanoribbon ◽  
Chemical Doping ◽  
Functional Theory ◽  
Lower Reactivity ◽  
The Density Functional Theory ◽  
Semiconductor Behavior

Chemical doping is a promising route to engineering and controlling the electronic properties of the zigzag graphene nanoribbon (ZGNR). By using the first-principles of the density functional theory (DFT) calculations at the B3LYP/ 6-31G, which implemented in the Gaussian 09 software, various properties, such as the geometrical structure, DOS, HOMO, LUMO infrared spectra, and energy gap of the ZGNR, were investigated with various sites and concentrations of the phosphorus (P). It was observed that the ZGNR could be converted from linear to fractal dimension by using phosphorus (P) impurities. Also, the fractal binary tree of the ZGNR and P-ZGNR structures is a highlight. The results demonstrated that the energy gap has different values, which located at this range from 0.51eV to 1.158 eV for pristine ZGNR and P-ZGNR structures. This range of energy gap is variable according to the use of GNRs in any apparatus. Then, the P-ZGNR has semiconductor behavior. Moreover, there are no imaginary wavenumbers on the evaluated vibrational spectrum confirms that the model corresponds to minimum energy. Then, these results make P-ZGNR can be utilized in various applications due to this structure became more stable and lower reactivity.

Spin Alignment Studies on the Muon-Site Determination in La2CuO4

2020 ◽  
Vol 860 ◽  
pp. 154-159
Author(s):  
Muhammad Redo Ramadhan ◽  
Irwan Ramli ◽  
Dita Puspita Sari ◽  
Budhy Kurniawan ◽  
Azwar Manaf ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Potential Distribution ◽  
Density Functional ◽  
Dft Calculation ◽  
Minimum Energy ◽  
Point Dipole ◽  
Spin Alignment ◽  
Functional Theory ◽  
Muon Site ◽  
Insulating Gap

Here we report spin-alignment contributions to muon coordinate calculated utilizing density functional theory (DFT) calculation. We estimated four different antiferromagnetic (AF) spin alignments in La2CuO4. We observed small changes by adjusting spin configurations in DFT calculations. Cu-spin value of 0.61 µB is constant in all calculations. The insulating gap of 1.9 eV is unchanged in all configurations. Muon coordinate was defined as the most minimum energy in atomic potential distribution. By assuming that Cu-spin is a point dipole for each atom, internal fields for muon were calculated and compared to known experimental results.

Conformation and electronic structure of Carbidopa. A QM/MD study

2016 ◽  
Vol 15 (01) ◽  
pp. 1650002
Author(s):  
Ghader M. Sukker ◽  
Nuha Wazzan ◽  
Ashour Ahmed ◽  
Rifaat Hilal
Keyword(s):  
Density Functional ◽  
Minimum Energy ◽  
Geometry Optimization ◽  
Md Simulations ◽  
Energy Structure ◽  
Functional Theory ◽  
Conformational Preferences ◽  
The Density Functional Theory ◽  
Quantum Chemical Topology ◽  
Bonding Characteristics

Carbidopa (CD) is a drug used in combination with L-dopa (LD) in treatment of Parkinson’s disease (PD). CD is an inhibitor for enzyme decarboxylase, yet its mode of action is not entirely known although it is believed to involve enzyme shape recognition. The present work attempts to investigate the conformational preferences of CD. Tight geometry optimization at the density functional theory (DFT)/B3LYP/6-311[Formula: see text]G** level of theory has been carried out. The shallow nature of the potential energy surface (PES) and the presence of several local minima within a small energy range necessitate the launching of DFT-based molecular dynamics (MD) simulations. Two MD experiments were submitted for 35,000 points each. The complete trajectory in time domain of 10.5 ps is analyzed and discussed. The global minimum energy structure of CD is localized and identified by subsequent frequency calculations. The quantum theory of atom in molecules (QTAIMs) is used to extract and compare the quantum chemical topology features of the electron density distribution in CD and LD. Bonding characteristics are analyzed and discussed within the natural bond orbital (NBO) framework.

scholarly journals Investigation of the absorption of CO2 in ionic liquid

2016 ◽  
Vol 29 (1) ◽  
pp. 41-46
Author(s):  
Kalyan Dhar ◽  
Syed Fahim
Keyword(s):  
Ionic Liquid ◽  
Binding Sites ◽  
Density Functional ◽  
Room Temperature ◽  
Minimum Energy ◽  
Environmental Concerns ◽  
Co2 Absorption ◽  
Solvation Model ◽  
Functional Theory ◽  
The Density Functional Theory

Due to environmental concerns, current interest is the development of technologies that may be able to remove CO2 efficiently from exhaust gases and thus avoid its dispersion in the atmosphere. The density functional theory (DFT) calculations with the modern continuum solvation model (IEFPCM-SMD) was used to study the mechanism of CO2 absorption in room temperature ionic liquid such as, [EMIM][BF4] (1-ethyl-3- methylimidazolium tetrafluoroborate). We determine the minimum energy structures and to determine the possible binding sites for CO2 absorption process in [EMIM][BF4]; by comparing the relative minimum energy of [EMIM][BF4] in the presence and absence of CO2.Bangladesh J. Sci. Res. 29(1): 41-46, June-2016

scholarly journals Density functional theory study on the electronic properties and stability of silicene/silicane nanoribbons

2015 ◽  
Vol 3 (16) ◽  
pp. 3954-3959 ◽  
Author(s):  
Q. G. Jiang ◽  
J. F. Zhang ◽  
Z. M. Ao ◽  
Y. P. Wu
Keyword(s):  
Density Functional Theory ◽  
Electronic Properties ◽  
Density Functional ◽  
Minimum Energy ◽  
Density Functional Theory Study ◽  
Hydrogen Atoms ◽  
Energy Barriers ◽  
Functional Theory ◽  
Diffusion Of Hydrogen

The minimum energy barriers for the diffusion of hydrogen atoms at the zigzag and armchair interfaces of SSNRs are respectively 1.54 and 1.47 eV.

Study of Elastic Properies of Ti3Al Intermetallic Compound Using the Ab Initio Calculation

2014 ◽  
Vol 805 ◽  
pp. 690-693
Author(s):  
Carlos Alberto Soufen ◽  
Marcelo Capella de Campos ◽  
Carlos Alberto Fonzar Pintão ◽  
Momotaro Imaizumi
Keyword(s):  
Intermetallic Compound ◽  
Elastic Properties ◽  
Density Functional ◽  
Minimum Energy ◽  
Young Modulus ◽  
Lattice Parameter ◽  
Full Potential ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Equilibrium Lattice Parameter

The elastic properties of a Ti3Al intermetallic compound were studied using full potential (FP LAPW ) with the APW+lo method. The FP-LAPW is among the most accurate band structure calculations currently available and is based on the density functional theory with general gradient approximation for the exchange and correlation potential. This method provides the structural properties of the ground state as bulk modulus, equilibrium lattice parameter, and equilibrium minimum energy, and the elastic properties as shear modulus, young modulus, Zener coefficient (anisotropy), and Poisson coefficient. The calculated elastic properties are coherent with the elastic properties of the material.

Systematic Gauge-Including Atomic Orbital-Hybrid Density Functional Theory Linear Regressions for 13C NMR Chemical Shifts Calculation

2020 ◽  
Vol 12 (3) ◽  
pp. 364-370
Author(s):  
Sara Sâmitha Souza ◽  
Mariana Aparecida de Souza Martins ◽  
Antonio Maia de Jesus Chaves Neto ◽  
Gunar Vingre Da Silva Mota ◽  
Fabio Luiz Paranhos Costa
Keyword(s):  
Density Functional Theory ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Density Functional ◽  
Chemical Shifts ◽  
Atomic Orbital ◽  
Basis Set ◽  
Functional Theory ◽  
Linear Regressions ◽  
Nuclear Magnetic

Density-functional theory calculations of the magnetic shielding for nuclear magnetic resonance provide an important contribution to understand the experimental values obtained in laboratory for chemical shifts present in the samples. From of a comparative of the performance of ten hybrid functional within of the framework of the density-functional theory using 10 different hybrid functionals with 3-21G (B1), 6-31G(d) (B2) and 6-31+ G(d, p) (B3) basis set, with intuit of evaluating of performance of the 13 C nuclear magnetic resonance from a representative of the terpene class and a heterocyclic compound, (–)-loliolide ((7aR)-6-hydroxy-4,4,7a-trimethyl-6,7-dihydro-5H1-benzofuran-2-one). This molecule, satisfactorily, represents the main structure of this class, with conformational freedom, optical activity and a benzofuran nucleus. The ωB97X-D, MPW1K and HSEH1PBE functionals presented the best calculation performance. It is interesting to note that after the use of linear regressions all root mean square error values for ωB97X-D were lower than 3 ppm. These are 2.91 ppm (B1), 2.46 (B2) ppm and 2.62 ppm (B3). The information contained in this work can be used for the assignment of experimental nuclear magnetic resonance spectra and will motivate further studies involving the theoretical calculation of the chemical shift of 13C.

scholarly journals Density functional theory study of the Jahn-Teller effect in cobaltocene

2009 ◽  
Vol 81 (8) ◽  
pp. 1397-1411 ◽  
Author(s):  
Matija Zlatar ◽  
Carl-Wilhelm Schläpfer ◽  
Emmanuel Penka Fowe ◽  
Claude A. Daul
Keyword(s):  
Density Functional Theory ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Density Functional ◽  
Energy Surface ◽  
Minimum Energy ◽  
Normal Modes ◽  
Coupling Coefficients ◽  
Functional Theory ◽  
Jahn Teller

A detailed discussion of the potential energy surface of bis(cyclopentadienyl)cobalt(II), cobaltocene, is given. Vibronic coupling coefficients are calculated using density functional theory (DFT). Results are in good agreement with experimental findings. On the basis of our calculation there is no second-order Jahn–Teller (JT) effect as predicted by group theory. The JT distortion can be expressed as a linear combination of all totally symmetric normal modes of the low-symmetry, minimum-energy conformation. The out-of-plane ring deformation is the most important mode. The JT distortion is analyzed by seeking the path of minimal energy of the adiabatic potential energy surface.

scholarly journals Electrocatalytic hydrogen evolution on the noble metal-free MoS2/carbon nanotube heterostructure: a theoretical study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Farhad Keivanimehr ◽  
Sajjad Habibzadeh ◽  
Alireza Baghban ◽  
Amin Esmaeili ◽  
Ahmad Mohaddespour ◽  
...  
Keyword(s):  
Hydrogen Evolution ◽  
Noble Metal ◽  
Electrocatalytic Activity ◽  
Density Functional ◽  
Minimum Energy ◽  
Chemical Properties ◽  
Binding Energies ◽  
Functional Theory ◽  
Metal Free ◽  
Physico Chemical

AbstractMolybdenum disulfide (MoS2) is considered as a promising noble-metal-free electrocatalyst for the Hydrogen Evolution Reaction (HER). However, to effectively employ such material in the HER process, the corresponding electrocatalytic activity should be comparable or even higher than that of Pt-based materials. Thus, efforts in structural design of MoS2 electrocatalyst should be taken to enhance the respective physico-chemical properties, particularly, the electronic properties. Indeed, no report has yet appeared about the possibility of an HER electrocatalytic association between the MoS2 and carbon nanotubes (CNT). Hence, this paper investigates the synergistic electrocatalytic activity of MoS2/ CNT heterostructure for HER by Density Functional Theory simulations. The characteristics of the heterostructure, including density of states, binding energies, charge transfer, bandgap structure and minimum-energy path for the HER process were discussed. It was found that regardless of its configuration, CNT is bound to MoS2 with an atomic interlayer gap of 3.37 Å and binding energy of 0.467 eV per carbon atom, suggesting a weak interaction between CNT and MoS2. In addition, the energy barrier of HER process was calculated lower in MoS2/CNT, 0.024 eV, than in the MoS2 monolayer, 0.067 eV. Thus, the study elaborately predicts that the proposed heterostructure improves the intrinsic electrocatalytic activity of MoS2.

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