DFT Study of Efinaconazole, an Antifungal Drug and Its Molecular Docking against a Holoenzyme (pdb id: 3IDB)

Efinaconazole (ECZ) is an antifungal drug. Various non-covalent interactions between ECZ and a holoenzyme (protein id: 3idb) has been investigated through computational study. The structure of ECZ was optimized using density functional theory (DFT) applying B3LYP/6-311G+(d,p) method. HOMO, LUMO, chemical hardness and softness, several thermochemical parameters, electrostatic potential surface, vibrational spectrum, total energy, and maximum internal force and maximum internal displacement with respect to optimization step number have been determined. The optimized ECZ ligand was subjected to molecular docking against the protein 3idb in Autodock Vina program. The different non-covalent interactions in the ligand-protein complex were visualized in BIOVIA Discovery Studio Visualizer. Various surface plots such as hydrogen bonds, ionizability, SAS, hydrophobicity, aromatic and charge surfaces were excerpted. ECZ molecule forms three strong hydrogen bonds with amino acid residues of the holoenzyme. In addition to this, it is significantly capable to form several other bonds which strengthen the ligand-protein interaction. The result showed that the ECZ molecule posed considerable binding affinity against the macromolecule.

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Computational study on transfer of L-ascorbic acid by UlaA throughEscherichia colimembrane

Journal of Bioinformatics and Computational Biology ◽

10.1142/s021972001750007x ◽

2017 ◽

Vol 15 (03) ◽

pp. 1750007 ◽

Cited By ~ 2

Author(s):

Ehsan Faghih-Mirzaee ◽

Maryam Dehestani ◽

Leila Zeidabadinejad

Keyword(s):

Ascorbic Acid ◽

Molecular Docking ◽

Active Sites ◽

Density Functional ◽

Md Simulation ◽

Computational Study ◽

Radius Of Gyration ◽

Internal Cavity ◽

Chemical Hardness ◽

E Coli

In this study, the transfer of L-ascorbic acid by UlaA through Escherichia coli (E. coli) membrane was evaluated using density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulation methods. DFT calculations at the B3lyp/6[Formula: see text]311[Formula: see text]G(p,d) level were performed to investigate the interaction properties and molecular descriptors. The physical properties, such as chemical potential, chemical hardness, and chemical electrophilicity of all studied molecules, were investigated. Natural population analysis was employed to describe the state of charge transfer between interactions using the natural bond orbital (NBO). The atoms in molecules (AIM) theory was used to examine the properties of the bond critical points such as their electron densities and Laplacians. Molecular docking studies showed that L-ascorbic acid was bounded to the internal cavity of UlaA. It was found that there were some hydrogen bond interactions between L-ascorbic acid and active sites of UlaA. The results of the MD simulation showed that the root mean square deviation (RMSD) of UlaA and L-ascorbic acid bound-UlaA reached equilibrium after 3.7[Formula: see text]ns. An evaluation of the radius of gyration ([Formula: see text]) revealed that UlaA and L-ascorbic acid bound-UlaA were stabilized around 10,000[Formula: see text]ns. Finally, analysis of the RMS fluctuations suggested that the structure of the L-ascorbic acid binding site remained approximately rigid during simulation. All obtained results shed light on the special manner of L-ascorbic acid transfer through E. coli membrane, and confirmed the results of previous studies on this issue.

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Vapour Pressure Isotope Eﬀect on Evaporation from Pure Organic Phases - a PIMD Approach

10.26434/chemrxiv.12003186.v1 ◽

2020 ◽

Author(s):

Luis Vasquez ◽

Agnieszka Dybala-Defratyka

Keyword(s):

Path Integral ◽

Vapour Pressure ◽

Density Functional ◽

Isotope Effects ◽

Tight Binding ◽

Decomposition Analysis ◽

Energy Decomposition Analysis ◽

Special Importance ◽

Non Covalent Interactions ◽

Covalent Interactions

Very often in order to understand physical and chemical processes taking place among several phases fractionation of naturally abundant isotopes is monitored. Its measurement can be accompanied by theoretical determination to provide a more insightful interpretation of observed phenomena. Predictions are challenging due to the complexity of the effects involved in fractionation such as solvent effects and non-covalent interactions governing the behavior of the system which results in the necessity of using large models of those systems. This is sometimes a bottleneck and limits the theoretical description to only a few methods. In this work vapour pressure isotope effects on evaporation from various organic solvents (ethanol, bromobenzene, dibromomethane, and trichloromethane) in the pure phase are estimated by combining force field or self-consistent charge density-functional tight-binding (SCC-DFTB) atomistic simulations with path integral principle. Furthermore, the recently developed Suzuki-Chin path integral is tested. In general, isotope effects are predicted qualitatively for most of the cases, however, the distinction between position-specific isotope effects observed for ethanol was only reproduced by SCC-DFTB, which indicates the importance of using non-harmonic bond approximations. Energy decomposition analysis performed using the symmetry-adapted perturbation theory (SAPT) revealed sometimes quite substantial differences in interaction energy depending on whether the studied system was treated classically or quantum mechanically. Those observed differences might be the source of different magnitudes of isotope effects predicted using these two different levels of theory which is of special importance for the systems governed by non-covalent interactions.

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Weak Interactions in Cocrystals of Isoniazid with Glycolic and Mandelic Acids

Crystals ◽

10.3390/cryst11040328 ◽

2021 ◽

Vol 11 (4) ◽

pp. 328

Author(s):

Raquel Álvarez-Vidaurre ◽

Alfonso Castiñeiras ◽

Antonio Frontera ◽

Isabel García-Santos ◽

Diego M. Gil ◽

...

Keyword(s):

Density Functional ◽

Glycolic Acid ◽

Weak Interactions ◽

Three Dimensional ◽

Functional Theory ◽

Molecular Systems ◽

X Ray Crystallography ◽

Hydroxycarboxylic Acids ◽

Non Covalent Interactions ◽

Covalent Interactions

This work deals with the preparation of pyridine-3-carbohydrazide (isoniazid, inh) cocrystals with two α-hydroxycarboxylic acids. The interaction of glycolic acid (H2ga) or d,l-mandelic acid (H2ma) resulted in the formation of cocrystals or salts of composition (inh)·(H2ga) (1) and [Hinh]+[Hma]–·(H2ma) (2) when reacted with isoniazid. An N′-(propan-2-ylidene)isonicotinic hydrazide hemihydrate, (pinh)·1/2(H2O) (3), was also prepared by condensation of isoniazid with acetone in the presence of glycolic acid. These prepared compounds were well characterized by elemental analysis, and spectroscopic methods, and their three-dimensional molecular structure was determined by single crystal X-ray crystallography. Hydrogen bonds involving the carboxylic acid occur consistently with the pyridine ring N atom of the isoniazid and its derivatives. The remaining hydrogen-bonding sites on the isoniazid backbone vary based on the steric influences of the derivative group. These are contrasted in each of the molecular systems. Finally, Hirshfeld surface analysis and Density-functional theory (DFT) calculations (including NCIplot and QTAIM analyses) have been performed to further characterize and rationalize the non-covalent interactions.

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1,3,5-Triaza-7-Phosphaadamantane (PTA) as a 31P NMR Probe for Organometallic Transition Metal Complexes in Solution

Molecules ◽

10.3390/molecules26051390 ◽

2021 ◽

Vol 26 (5) ◽

pp. 1390 ◽

Cited By ~ 1

Author(s):

Ilya G. Shenderovich

Keyword(s):

Chemical Shift ◽

Transition Metal ◽

Metal Complexes ◽

Transition Metal Complexes ◽

Density Functional ◽

Molecular Structures ◽

Basis Sets ◽

Functional Theory ◽

Non Covalent Interactions ◽

Covalent Interactions

Due to the rigid structure of 1,3,5-triaza-7-phosphaadamantane (PTA), its 31P chemical shift solely depends on non-covalent interactions in which the molecule is involved. The maximum range of change caused by the most common of these, hydrogen bonding, is only 6 ppm, because the active site is one of the PTA nitrogen atoms. In contrast, when the PTA phosphorus atom is coordinated to a metal, the range of change exceeds 100 ppm. This feature can be used to support or reject specific structural models of organometallic transition metal complexes in solution by comparing the experimental and Density Functional Theory (DFT) calculated values of this 31P chemical shift. This approach has been tested on a variety of the metals of groups 8–12 and molecular structures. General recommendations for appropriate basis sets are reported.

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Atoms in Highly Symmetric Environments: H in Rhodium and Cobalt Cages, H in an Octahedral Hole in MgO, and Metal Atoms Ca-Zn in C20 Fullerenes

Symmetry ◽

10.3390/sym13071281 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1281

Author(s):

Zikri Altun ◽

Erdi Ata Bleda ◽

Carl Trindle

Keyword(s):

Density Functional Theory ◽

Quantum Theory ◽

Coordination Number ◽

Electronic Structures ◽

Density Functional ◽

Functional Theory ◽

Metal Atoms ◽

Tetragonal Pyramidal ◽

Non Covalent Interactions ◽

Covalent Interactions

An atom trapped in a crystal vacancy, a metal cage, or a fullerene might have many immediate neighbors. Then, the familiar concept of valency or even coordination number seems inadequate to describe the environment of that atom. This difficulty in terminology is illustrated here by four systems: H atoms in tetragonal-pyramidal rhodium cages, H atom in an octahedral cobalt cage, H atom in a MgO octahedral hole, and metal atoms in C20 fullerenes. Density functional theory defines structure and energetics for the systems. Interactions of the atom with its container are characterized by the quantum theory of atoms in molecules (QTAIM) and the theory of non-covalent interactions (NCI). We establish that H atoms in H2Rh13(CO)243− trianion cannot be considered pentavalent, H atom in HCo6(CO)151− anion cannot be considered hexavalent, and H atom in MgO cannot be considered hexavalent. Instead, one should consider the H atom to be set in an environmental field defined by its 5, 6, and 6 neighbors; with interactions described by QTAIM. This point is further illustrated by the electronic structures and QTAIM parameters of M@C20, M=Ca to Zn. The analysis describes the systematic deformation and restoration of the symmetric fullerene in that series.

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The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution

Physical Chemistry Chemical Physics ◽

10.1039/d1cp03106f ◽

2021 ◽

Author(s):

Sascha Jähnigen ◽

Daniel Sebastiani ◽

Rodolphe Vuilleumier

Keyword(s):

Lactic Acid ◽

Circular Dichroism ◽

Computational Study ◽

Bulk Water ◽

Vibrational Circular Dichroism ◽

Ab Initio Molecular Dynamics ◽

Non Covalent Interactions ◽

Circular Dichroïsm ◽

Covalent Interactions

We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss...

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Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate. A DFT and Molecular docking study

Heliyon ◽

10.1016/j.heliyon.2021.e08204 ◽

2021 ◽

pp. e08204

Author(s):

Mouna Medimagh ◽

Noureddine Issaoui ◽

Sofian Gatfaoui ◽

Silvia Antonia Brandán ◽

Omar Al-Dossary ◽

...

Keyword(s):

Molecular Docking ◽

Ir Spectrum ◽

Docking Study ◽

Molecular Docking Study ◽

Ft Ir ◽

Non Covalent Interactions ◽

Covalent Interactions

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New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.12.283 ◽

2016 ◽

Vol 12 ◽

pp. 2834-2848 ◽

Cited By ~ 33

Author(s):

Pavel Nagorny ◽

Zhankui Sun

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Recent Progress ◽

Halogen Bonds ◽

Hydrogen Bond Donor ◽

New Approaches ◽

Substrate Activation ◽

Non Covalent Interactions ◽

Covalent Interactions ◽

Hydrogen Bond Donors

Hydrogen bond donor catalysis represents a rapidly growing subfield of organocatalysis. While traditional hydrogen bond donors containing N–H and O–H moieties have been effectively used for electrophile activation, activation based on other types of non-covalent interactions is less common. This mini review highlights recent progress in developing and exploring new organic catalysts for electrophile activation through the formation of C–H hydrogen bonds and C–X halogen bonds.

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Computational Study of Adsorption Effects of Karanjin Drug Over Carbon Nanotube (C56H16) as Factor of Drug Delivery System — A Quantum Chemical Approach

NANO ◽

10.1142/s179329202150106x ◽

2021 ◽

pp. 2150106

Author(s):

Anoop Kumar Pandey ◽

Vijay Singh ◽

Apoorva Dwivedi

Keyword(s):

Drug Delivery ◽

Carbon Nanotube ◽

Gas Phase ◽

Drug Delivery System ◽

Delivery System ◽

Quantum Chemical ◽

Density Functional ◽

Computational Study ◽

Chemical Hardness ◽

Adsorption Effect

Karanjin, phytochemical from Pongamia pinnata is reported to be effective against HIV that causes AIDS in humans, however, the delivery of this therapeutic molecule still needs improvement. Hence, this study provides a better understanding of the nonbonded interaction between an anti-HIV drug karanjin and carbon nanotube (CNT) (C56H16). The electronic structure and interaction properties of the molecule karanjin over the surface of CNT were theoretically studied in the gas phase by DFT/B3LYP/6-31G ([Formula: see text]) level of theory for the first time. The UV–Vis spectra and transitions of the karanjin drug, CNT (C56H16) and complex CNT (C-56)/karanjin in gas phase have been calculated by time-dependent density functional theory (TDDFT) for the investigation of adsorption effect. To support our hypothesis, we have performed quantum chemical analysis for CNT (C56H16)/karanjin in water and DMSO solvent. In this process, this CNT (C-56)/karanjin complex enters into affected cell in liquid medium. After that, the drug delivery system CNT (C-56) unloads karanjin at the affected site. The binding character interactive species have been determined by NBO and AIM analysis. The frontier orbital HOMO–LUMO gap, chemical softness, chemical hardness have also been calculated to understand its complete chemical properties. The outcomes from our interaction of drug karanjin with CNT (C56H16) will be instrumental for better drug delivery potential in the upcoming future.

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Depicting the Non-Covalent Interaction of Whey Proteins with Galangin or Genistein Using the Multi-Spectroscopic Techniques and Molecular Docking

Foods ◽

10.3390/foods8090360 ◽

2019 ◽

Vol 8 (9) ◽

pp. 360 ◽

Cited By ~ 1

Author(s):

Chun-Min Ma ◽

Xin-Huai Zhao

Keyword(s):

Molecular Docking ◽

Hydrophobic Interaction ◽

Whey Proteins ◽

Sodium Dodecyl ◽

Binding Constants ◽

Spectroscopic Techniques ◽

Stereochemical Structure ◽

Non Covalent Interactions ◽

Β Lactoglobulin ◽

Covalent Interactions

The non-covalent interactions between a commercial whey protein isolate (WPI) and two bioactive polyphenols galangin and genistein were studied at pH 6.8 via the multi-spectroscopic assays and molecular docking. When forming these WPI-polyphenol complexes, whey proteins had changed secondary structures while hydrophobic interaction was the major driving force. Detergent sodium dodecyl sulfate destroyed the hydrophobic interaction and thus decreased apparent binding constants of the WPI-polyphenol interactions. Urea led to hydrogen-bonds breakage and protein unfolding, and therefore increased apparent binding constants. Based on the measured apparent thermodynamic parameters like ΔH, ΔS, ΔG, and donor-acceptor distance, galangin with more planar stereochemical structure and random B-ring rotation showed higher affinity for WPI than genistein with location isomerism and twisted stereochemical structure. The molecular docking results disclosed that β-lactoglobulin of higher average hydrophobicity had better affinity for the two polyphenols than α-lactalbumin of lower average hydrophobicity while β-lactoglobulin possessed very similar binding sites to the two polyphenols. It is concluded that polyphenols might have different non-covalent interactions with food proteins, depending on the crucial polyphenol structures and protein hydrophobicity.

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