Prediction of Partition Coefficients in SDS Micelles by DFT Calculations

A computational methodology using Density-Functional Theory (DFT) calculations was developed to determine the partition coefficient of a compound in a solution of Sodium Dodecyl Sulfate (SDS) micelles. Different sets of DFT calculations were used to predict the free energy of a set of 63 molecules in 15 different solvents with the purpose of identifying the solvents with similar physicochemical characteristics to the studied micelles. Experimental partition coefficients were obtained from Micellar Electrokinetic Chromatography (MEKC) measurements. The experimental partition coefficient of these molecules was compared with the predicted partition coefficient in heptane/water, cyclohexane/water, N-dodecane/water, pyridine/water, acetic acid/water, decan-1-ol/water, octanol/water, propan-2-ol/water, acetone/water, propan-1-ol/water, methanol/water, 1,2-ethane diol/water, dimethyl sulfoxide/water, formic acid/water, and diethyl sulphide/water systems. It is observed that the combination of pronan-1-ol/water solvent was the most appropriated to estimate the partition coefficient for SDS micelles. This approach allowed us to estimate the partition coefficient orders of magnitude faster than the classical molecular dynamics simulations. The DFT calculations were carried out with the well-known exchange correlation functional B3LYP and with the global hybrid functional M06-2X from the Minnesota functionals with 6-31++G ** basis set. The effect of solvation was considered by the continuum model based on density (SMD). The proposed workflow for the prediction rate of the participation coefficient unveiled the symmetric balance between the experimental data and the computational methods.

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In-silico Molecular Docking and ADME/Pharmacokinetic Prediction Studies of Some Novel Carboxamide Derivatives as Anti-tubercular Agents

Chemistry Africa ◽

10.1007/s42250-020-00162-3 ◽

2020 ◽

Vol 3 (4) ◽

pp. 989-1000

Author(s):

Mustapha Abdullahi ◽

Shola Elijah Adeniji

Keyword(s):

Molecular Docking ◽

Binding Affinity ◽

In Silico ◽

Density Functional ◽

Docking Simulation ◽

Basis Set ◽

Hybrid Functional ◽

Standard Drug

AbstractMolecular docking simulation of thirty-five (35) molecules of N-(2-phenoxy)ethyl imidazo[1,2-a]pyridine-3-carboxamide (IPA) with Mycobacterium tuberculosis target (DNA gyrase) was carried out so as to evaluate their theoretical binding affinities. The chemical structure of the molecules was accurately drawn using ChemDraw Ultra software, then optimized at density functional theory (DFT) using Becke’s three-parameter Lee–Yang–Parr hybrid functional (B3LYP/6-311**) basis set in a vacuum of Spartan 14 software. Subsequently, the docking operation was carried out using PyRx virtual screening software. Molecule 35 (M35) with the highest binding affinity of − 7.2 kcal/mol was selected as the lead molecule for structural modification which led to the development of four (4) newly hypothetical molecules D1, D2, D3 and D4. In addition, the D4 molecule with the highest binding affinity value of − 9.4 kcal/mol formed more H-bond interactions signifying better orientation of the ligand in the binding site compared to M35 and isoniazid standard drug. In-silico ADME and drug-likeness prediction of the molecules showed good pharmacokinetic properties having high gastrointestinal absorption, orally bioavailable, and less toxic. The outcome of the present research strengthens the relevance of these compounds as promising lead candidates for the treatment of multidrug-resistant tuberculosis which could help the medicinal chemists and pharmaceutical professionals in further designing and synthesis of more potent drug candidates. Moreover, the research also encouraged the in vivo and in vitro evaluation study for the proposed designed compounds to validate the computational findings.

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An Accurate and Efficient Method to Predict Y-NO Bond Homolysis Bond Dissociation Energies

Mathematical Problems in Engineering ◽

10.1155/2013/860357 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 4

Author(s):

Hong Zhi Li ◽

Lin Li ◽

Zi Yan Zhong ◽

Yi Han ◽

LiHong Hu ◽

...

Keyword(s):

Dft Calculations ◽

Density Functional ◽

Molecular Descriptors ◽

Basis Set ◽

Bond Dissociation Energies ◽

Data Set ◽

Test Set ◽

Bond Dissociation ◽

Dissociation Energies ◽

Bond Homolysis

The paper suggests a new method that combines the Kennard and Stone algorithm (Kenstone, KS), hierarchical clustering (HC), and ant colony optimization (ACO)-based extreme learning machine (ELM) (KS-HC/ACO-ELM) with the density functional theory (DFT) B3LYP/6-31G(d) method to improve the accuracy of DFT calculations for the Y-NO homolysis bond dissociation energies (BDE). In this method, Kenstone divides the whole data set into two parts, the training set and the test set; HC and ACO are used to perform the cluster analysis on molecular descriptors; correlation analysis is applied for selecting the most correlated molecular descriptors in the classes, and ELM is the nonlinear model for establishing the relationship between DFT calculations and homolysis BDE experimental values. The results show that the standard deviation of homolysis BDE in the molecular test set is reduced from 4.03 kcal mol−1calculated by the DFT B3LYP/6-31G(d) method to 0.30, 0.28, 0.29, and 0.32 kcal mol−1by the KS-ELM, KS-HC-ELM, and KS-ACO-ELM methods and the artificial neural network (ANN) combined with KS-HC, respectively. This method predicts accurate values with much higher efficiency when compared to the larger basis set DFT calculation and may also achieve similarly accurate calculation results for larger molecules.

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Analysis of vibratinal spectra of 8-hydroxyquinoline and its 5,7-dichloro, 5,7-dibromo, 5,7-diiodo and 5,7-dinitro derivatives based on density functional theory calculations

Open Chemistry ◽

10.2478/s11532-006-0061-x ◽

2007 ◽

Vol 5 (1) ◽

pp. 201-220 ◽

Cited By ~ 12

Author(s):

Khaled Bahgat ◽

Abdel Ragheb

Keyword(s):

Density Functional Theory ◽

Dft Calculations ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Basis Set ◽

Normal Coordinate ◽

Functional Theory ◽

The Density Functional Theory ◽

Vibrational Bands ◽

Good Agreement

AbstractThe geometry, frequency and intensity of the vibrational bands of 8-hydroxyquinoline and its 5,7-dichloro, 5,7-dibromo, 5,7-diiodo and 5,7-dinitro derivatives were obtained by the density functional theory (DFT) calculations with Becke3-Lee-Parr (B3LYP) functional and 6-31G* basis set. The effects of chloride, bromide, iodide and nitro substituent on the vibrational frequencies of 8-hydroxyquinoline have been investigated. The assignments have been proposed with aid of the results of normal coordinate analysis. The observed and calculated spectra are found to be in good agreement.

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Charge transfer complexes between 2-, 3- and 4-aminopyridines and some π-acceptors in the gas phase and in chloroform: DFT calculations

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633616500292 ◽

2016 ◽

Vol 15 (04) ◽

pp. 1650029 ◽

Cited By ~ 1

Author(s):

Nuha Ahmed Wazzan

Keyword(s):

Charge Transfer ◽

Dft Calculations ◽

Gas Phase ◽

Density Functional ◽

Molecular Structures ◽

Basis Set ◽

Charge Transfer Complexes ◽

Good Correspondence ◽

Electronic Distribution ◽

Picryl Chloride

This work reports density functional theory (DFT) calculations on the molecular structures, electronic distribution, and UV-Vis and IR spectroscopy analysis of charge transfer complexes between aminopyridines (APYs), namely 2-APY, 3-APY and 4-APY, as electron-donors and some [Formula: see text]-electron-acceptors, namely chloranil (CHL), tetracyanoethylene (TCNE) and picryl chloride (PC), formed in the gas phase at the B3LYP/6-31[Formula: see text]G(d,p) method/basis set, and in chloroform at the same method/basis set using PCM as solvation model. Good correspondence was generally obtained between the calculated parameters and the experimental ones.

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THEORETICAL INVESTIGATION OF THE EFFECT OF CONJUATION OF THIOPHENE RINGS ON THE CHARGE TRANSPORT OF THIENOCORONENE DERIVATIVES

Química Nova ◽

10.21577/0100-4042.20170820 ◽

2021 ◽

Author(s):

Ziran Chen ◽

Yujin Zhang ◽

Zhanrong He ◽

Yuan Li ◽

Meihao Xi ◽

...

Keyword(s):

Charge Carrier ◽

Charge Transport ◽

Carrier Mobility ◽

Density Functional ◽

Thiophene Ring ◽

Energy Charge ◽

Charge Carrier Mobility ◽

Basis Set ◽

Basis Sets ◽

Hybrid Functional

Based on density functional theory, quantum chemical calculations of the charge-transport rates were performed for five disc-shaped coronene derivatives with varying numbers of fused thiophene rings, using different basis sets 6-31+G(d) and 6-311++G(d,p), hybrid functionals (B3LYP, M06-2X, CAM-B3LYP, WB97XD, M08-HX), and a dispersion-corrected hybrid functional (M06-2X+D3). Our results indicate that increasing the basis set and adding diffusion and polarisation functions had little effect on the molecular reorganisation energy, charge-transport matrix element t, and charge carrier mobility μ. The charge carrier mobility calculated using B3LYP were relatively large, whereas the results calculated using CAM-B3LYP and WB97XD were similar. Among the five coronene derivatives, molecule b with one thiophene ring could be candidates for a n-type organic semiconductor, and molecule c with two thiophene rings can be designed as a p-type semiconductor.

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First theoretical probe for alkynyl bridged thiophene modified coumarin nonlinear optical materials with D-π-A and A-π-D-π-A structures

Journal of Nonlinear Optical Physics & Materials ◽

10.1142/s0218863522500084 ◽

2022 ◽

Author(s):

Shanggeng Li ◽

Fanghua Zhu ◽

Yawen Zhou ◽

Jiaming Hu ◽

Jing Li ◽

...

Keyword(s):

Density Functional ◽

Nonlinear Optical ◽

Molecular Design ◽

Energy Levels ◽

Basis Set ◽

Hybrid Functional ◽

Functional Theory ◽

Text Structures ◽

Polar Moment ◽

Vis Spectroscopy

First-principles exploration is very important to molecular design. In this study, geometric structure, intramolecular charge transfer (ICT), energy levels, polar moment, and ultraviolet–visible (UV–Vis) spectroscopy of eight novel and different alkynyl bridged thiophene modified coumarin nonlinear optical molecules with [Formula: see text]-[Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text]-[Formula: see text]-[Formula: see text]-[Formula: see text] structures had been studied by density-functional theory (DFT) calculations within B3LYP hybrid functional using 6-31 [Formula: see text], [Formula: see text] Gaussian type molecular-orbital basis set. This has guiding significance for the design of nonlinear optical molecules and the development of coumarin-based photoelectric molecules.

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Effect of phenolic radicals on the geometry and electronic structure of DNA base pairs: computational study

International Journal of Modern Physics C ◽

10.1142/s0129183116501199 ◽

2016 ◽

Vol 27 (10) ◽

pp. 1650119 ◽

Cited By ~ 3

Author(s):

Mohammad Zarei ◽

Abdolvahab Seif ◽

Khaled Azizi ◽

Mohanna Zarei ◽

Jamil Bahrami

Keyword(s):

Hydrogen Bond ◽

Dft Calculations ◽

Base Pair ◽

Density Functional ◽

Base Pairs ◽

Water Solvent ◽

Dna Base ◽

Dna Base Pairs ◽

Phenoxy Radicals ◽

Dna Base Pair

In this paper, we show the reaction of a hydroxyl, phenyl and phenoxy radicals with DNA base pairs by the density functional theory (DFT) calculations. The influence of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. The results showed that hydroxyl, phenyl and phenoxy radicals increase the length of the nearest hydrogen bond of adjacent DNA base pair which is accompanied by decrease in the length of furthest hydrogen bond of DNA base pair. Also, hydroxyl, phenyl and phenoxy radicals influenced the dihedral angle between DNA base pairs. According to the results, hydrogen bond lengths between AT and GC base pairs in water solvent are longer than vacuum. All of presented radicals influenced the structure and geometry of AT and GC base pairs, but phenoxy radical showed more influence on geometry and electronic properties of DNA base pairs compared with the phenyl and hydroxyl radicals.

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Influence of H, H2, O and O2 on Armchair SiGe Nanotubes: A Theoretical Study

Journal of Nanoscience and Nanotechnology ◽

10.1166/jnn.2016.12342 ◽

2016 ◽

Vol 16 (4) ◽

pp. 3447-3456

Author(s):

Prabath Wanaguru ◽

Asok K Ray ◽

Qiming Zhang

Keyword(s):

Molecular Orbital ◽

Density Functional ◽

Energy Gap ◽

Defect Density ◽

Basis Set ◽

Hybrid Functional ◽

Lumo Energy ◽

Adsorption Sites ◽

The Difference ◽

Controlled Adsorption

A systematic, hybrid density functional theory study of interaction between SiGe nanotubes (SiGeNTs) and X (X = H, O, H2 and O2) have been performed using the hybrid functional B3LYP and an all electron 3-21G* basis set implemented in GAUSSIAN 09 suite of software. All possible internal and external adsorption sites were considered, and it was found that H prefers to move onto top of an atom site while O prefers to incorporate into NT wall by breaking the bonds. Adsorption energies for H is ∼2.0 eV and for O it is ∼5.0 eV. Controlled adsorption of atomic H and several molecular O give rises to defect density states in the frontier orbital region. H rich adsorptions predict the difference between highest occupied molecular orbital (HOMO) energy and the lowest unoccupied molecular orbital (LUMO) energy increase while O rich adsorptions predict the decrease in HOMO-LUMO energy gap. O and O2 adsorptions predict definite ionic bonding character while H atomic adsorptions predict covalent bonding. H2 is very neutral towards the adsorption into SiGeNTs and clearly shows the physisorption adsorption. Considering the all adsorptions, the adsorptions happened within the Si vicinity of the SiGeNT shows the most stable and preferred adsorption region.

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Influence of water on the surface of graphene

EPJ Web of Conferences ◽

10.1051/epjconf/201817406002 ◽

2018 ◽

Vol 174 ◽

pp. 06002

Author(s):

Yunus Kaya ◽

Yalçin Kalkan ◽

Rob Veenhof

Keyword(s):

Density Functional Theory ◽

Water Molecule ◽

Density Functional ◽

Theoretical Models ◽

Surface Conductivity ◽

Basis Set ◽

Hybrid Functional ◽

Functional Theory ◽

The Density Functional Theory ◽

Influence Of Water

We have studied how water modifies the surface of graphene and in particular how the surface conductivity of graphene is affected. According to the literature, two types of interactions should be distinguished: physical, where a water molecule remains intact and is located at some distance from the mesh, and chemical, where a water molecule is imbricated in the graphene bond structure. We have developed theoretical models for both types of interactions using the density functional theory (DFT) with the B3LYP hybrid functional combined with the 6-31G(d) basis set. Our calculations show that the surface conductivity of graphene is reduced in the presence of water.

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Study on Pyrrole 4-Pyrazoline Derivatives: Experimental and Quantum Chemical Approaches

Australian Journal of Chemistry ◽

10.1071/ch15208 ◽

2016 ◽

Vol 69 (6) ◽

pp. 672 ◽

Cited By ~ 2

Author(s):

R. N. Singh ◽

Poonam Rawat ◽

Vikas Baboo

Keyword(s):

Dft Calculations ◽

13C Nmr ◽

Quantum Chemical ◽

Density Functional ◽

Electronic Absorption Spectra ◽

Quantum Chemical Study ◽

Basis Set ◽

Dft Methods ◽

Pyrrole Derivatives ◽

1H And 13C Nmr

As part of a study on pyrrole derivatives we report here a combined experimental and quantum chemical study of pyrrole 4-pyrazoline biheterocyclic derivatives. The structure of the synthesised compounds have been studied using experimental IR, UV, 1H and 13C NMR spectroscopic analyses along with density functional theory (DFT) calculations using the B3LYP functional with 6–311+G (d,p) basis set. The global, local reactivity, and thermodynamic parameters support the analysis. All the experimental vibrational bands have been discussed and assigned to normal modes on the basis of our calculations. In addition, the computed 1H and 13C NMR data, obtained by DFT calculations, are found to be in good agreement with the experimental data and serve as valuable tools in identifying the products. The vibrational analysis shows red shifts in vN–H and vC=O stretching vibrations as a result of dimer formation. The theoretical electronic absorption spectra have been calculated by using time dependent-DFT methods. The static first hyperpolarizability (β0) values for the synthesized pyrrole–pyrazoline derivatives 4A–D are calculated as 16.97 × 10–30, 47.64 × 10–30, 65.40 × 10–30, 65.39 × 10–30 esu, respectively, and increase from 4A to 4C as a result of the addition of an –NO2 acceptor in 4B and two –NO2 group acceptors in 4C. However, an additional –Cl group in 4D on the phenyl ring attached to the pyrazoline moiety does not result in a clear change from 4C. The calculated static and dynamic hyperpolarizability results show that the investigated molecules might be used as non-linear optical materials.

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