scholarly journals Density Functional Theory Analysis of Poly Glycolic Acid with Metal Ions (Na+, K+) Interaction

2019 ◽  
Vol 9 (1S3) ◽  
pp. 366-369
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Density Functional ◽  
Glycolic Acid ◽  
Carbonyl Oxygen ◽  
Chemical Hardness ◽  
Binding Affinities ◽  
Functional Theory ◽  
Fukui Functions ◽  
The Stability

The complexation between Poly glycolic acid (PGA) and alkali metal ions (Na+ , K+ ) have been studied using B3LYP/6-311++G** method. The binding site of metal ion interaction on PGA is carbonyl oxygen. Both metal ions form bidendate complexation with PGA. Further, it can be noted that the PGA with K+ complex is more stable than the PGA with Na+ complex. The binding affinities (ΔH), basicity (ΔG) and the complexation entropies (ΔS) of all the studied systems are calculated. The interaction energy is maximum in PGA-Na+ than the PGA-K + complex. This is due to more charge transfer taking place between PGA and Na. The stability of the complex is studied by the chemical hardness value. The condensed Fukui functions are calculated and are used to predict the favourable reactive site

Electronic structures, spectroscopic properties, and reaction activities of porphyrins with alkali metal ions: density functional theory approach to the central metal effects

2012 ◽  
Vol 16 (07n08) ◽  
pp. 927-934 ◽  
Author(s):  
Luyang Zhao ◽  
Dongdong Qi ◽  
Lijuan Zhang ◽  
Ming Bai ◽  
Xue Cai
Keyword(s):  
Density Functional Theory ◽  
Alkali Metal ◽  
Metal Ions ◽  
Metal Ion ◽  
Density Functional ◽  
State Transitions ◽  
Theory Approach ◽  
Central Metal ◽  
Functional Theory ◽  
Molecular Stability

Density functional theory (DFT) calculation method was employed to investigate a series of nine alkali metal porphyrins (alk-Pors), namely HLiPor , HNaPor , HKPor , Li2Por , LiNaPor , LiKPor , Na2Por , NaKPor , and K2Por . These molecules show different configurations depending on different metal ions which locate over the central hole of the porphyrin ligand. Alk-Pors with larger-radius metal ion have smaller binding energy and thus is more difficult to keep stable. Further detailed molecular stability analysis was carried out by noncovalent interaction and electrostatic interaction via RDG and NBO charge distribution. UV-vis spectra of these nine compounds also show different spectral shapes depending on the central metals, and the dominant state transitions with high degeneracy are revealed to be influenced by high molecular symmetric order. Finally their difference in reactivity due to the electronegativity of central metals and the nature of porphyrin rings are predicted by electrostatic potential and Fukui functions.

scholarly journals The Inhibitory Effect of Some Natural Bioactive D-Glucopyranoside Derivatives against SARS-CoV-2 Main Protease (Mpro) and Spike Protease (Spro)

2021 ◽  
Vol 16 ◽  
pp. 1-18
Author(s):  
Ajoy Kumer ◽  
Unesco Chakma ◽  
Sarkar Mohammad Abe Kawsar
Keyword(s):  
Active Sites ◽  
Density Functional ◽  
Inhibitory Effect ◽  
Binding Affinities ◽  
Ligand Interaction ◽  
Functional Theory ◽  
Main Protease ◽  
Mean Square Fluctuation ◽  
Chemical Descriptors ◽  
The Stability

Outbreak of coronavirus seems to have exacerbated across the globe, but drugs have not been discovered till now. Due to having the antiviral activity of D-glucopyranoside derivatives, this study was designed to examine as the inhibitor by in sillico study against the main protease (Mpro) and Spike protease (Spro) of SARS-CoV-2. First, these derivatives were optimised by Density Functional Theory (DFT). The observation of this study was monitored by molecular docking tools calculating the binding affinities. Afterwards, the ligand interaction with protein was accounted for selecting the how to bind of active sites of the protein. Next, the root means square deviation (RMSD) and root mean square fluctuation (RMSF) were illustrated for determining the stability of the docked complex. Finally, AMDET properties were calculated as well as the Lipisinki rule. All of the derivates showed a binding affinity more than -6.0 kcal/mol while derivatives 2, 3, and 9 were the best-bonded scoring inhibitor against Mpro and Spro. In addition, the chemical descriptors were more supportive tools as an inhibitor, and the Lipisinki rule was satisfied for maximum molecules as a drug. Besides, D-glucopyranoside derivatives may be predicted that they are non-carcinogenic and low toxic for both aquatic and non-aquatic species.

THEORETICAL STUDIES ON THE CONFORMATION AND COORDINATION OF N-(1-PHENYL-3-METHYL-4-PROPENYLIDENE-5-PYRAZOLONE)-SALICYLIDENE

2013 ◽  
Vol 12 (05) ◽  
pp. 1350036
Author(s):  
ANJIE LIU ◽  
YINLING YANG ◽  
DIANZENG JIA ◽  
DONGLING WU ◽  
LANG LIU ◽  
...  
Keyword(s):  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Dft Calculation ◽  
Chemical Potential ◽  
Chemical Hardness ◽  
Theoretical Studies ◽  
Electrophilic Attack ◽  
Functional Theory ◽  
Global Indices ◽  
The Stability

Density functional theory (DFT) calculation has been carried out to investigate the isomers of N -(1-phenyl-3-methyl-4-propenylidene-5-pyrazolone)-salicylidene. Chemical potential, chemical hardness and global electrophilicity, which are considered as global indices, have been calculated to assess the stability and reactivity of the tautomers. The condensed Fukui function is calculated for predicting the most probable sites for electrophilic attack. Molecular electrostatic potential is calculated to predict the regions for electrophilic attack.

scholarly journals Chemical-Reactivity Properties, Drug Likeness, and Bioactivity Scores of Seragamides A–F Anticancer Marine Peptides: Conceptual Density Functional Theory Viewpoint

Computation ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 52 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Drug Repurposing ◽  
Chemical Hardness ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Fukui Functions ◽  
Reactivity Descriptors

A methodology based on concepts that arose from Density Functional Theory (CDFT) was chosen for the calculation of global and local reactivity descriptors of the Seragamide family of marine anticancer peptides. Determination of active sites for the molecules was achieved by resorting to some descriptors within Molecular Electron Density Theory (MEDT) such as Fukui functions. The pKas of the six studied peptides were established using a proposed relationship between this property and calculated chemical hardness. The drug likenesses and bioactivity properties of the peptides considered in this study were obtained by resorting to a homology model by comparison with the bioactivity of related molecules in their interaction with different receptors. With the object of analyzing the concept of drug repurposing, a study of potential AGE-inhibition abilities of Seragamides peptides was pursued by comparison with well-known drugs that are already available as pharmaceuticals.

Thermodynamic Stability of Hexagonal and Rhombohedral Bn at Cvd Conditions from Van der Waals Corrected First Principles Calculations

2019 ◽  
Author(s):  
Henrik Pedersen ◽  
Björn Alling ◽  
Hans Högberg ◽  
Annop Ektarawong
Keyword(s):  
Thin Films ◽  
Thermodynamic Stability ◽  
First Principles ◽  
Thermal Equilibrium ◽  
Density Functional ◽  
Van Der Waals ◽  
Chemical Vapor ◽  
First Principles Calculations ◽  
Functional Theory ◽  
The Stability

Thin films of boron nitride (BN), particularly the sp<sup>2</sup>-hybridized polytypes hexagonal BN (h-BN) and rhombohedral BN (r-BN) are interesting for several electronic applications given band gaps in the UV. They are typically deposited close to thermal equilibrium by chemical vapor deposition (CVD) at temperatures and pressures in the regions 1400-1800 K and 1000-10000 Pa, respectively. In this letter, we use van der Waals corrected density functional theory and thermodynamic stability calculations to determine the stability of r-BN and compare it to that of h-BN as well as to cubic BN and wurtzitic BN. We find that r-BN is the stable sp<sup>2</sup>-hybridized phase at CVD conditions, while h-BN is metastable. Thus, our calculations suggest that thin films of h-BN must be deposited far from thermal equilibrium.

Site preference and atomic ordering in the ternary Rh5Ga2As: first-principles calculations

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Nilanjan Roy ◽  
Sucharita Giri ◽  
Harshit ◽  
Partha P. Jana
Keyword(s):  
Total Energy ◽  
First Principles ◽  
Density Functional ◽  
Structure Type ◽  
Site Preference ◽  
X Ray Diffraction ◽  
Atomic Ordering ◽  
Functional Theory ◽  
The Stability ◽  
Bonding Characteristics

Abstract The site preference and atomic ordering of the ternary Rh5Ga2As have been investigated using first-principles density functional theory (DFT). An interesting atomic ordering of two neighboring elements Ga and As reported in the structure of Rh5Ga2As by X-ray diffraction data only is confirmed by first-principles total-energy calculations. The previously reported experimental model with Ga/As ordering is indeed the most stable in the structure of Rh5Ga2As. The calculation detected that there is an obvious trend concerning the influence of the heteroatomic Rh–Ga/As contacts on the calculated total energy. Interestingly, the orderly distribution of As and Ga that is found in the binary GaAs (Zinc-blende structure type), retained to ternary Rh5Ga2As. The density of states (DOS) and Crystal Orbital Hamiltonian Population (COHP) are calculated to enlighten the stability and bonding characteristics in the structure of Rh5Ga2As. The bonding analysis also confirms that Rh–Ga/As short contacts are the major driving force towards the overall stability of the compound.

scholarly journals Influence of Copper(I) Halides on the Reactivity of Aliphatic Carbodiimides

2020 ◽  
Vol 3 (1) ◽  
pp. 20
Author(s):  
Valentina Ferraro ◽  
Marco Bortoluzzi
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
General Formula ◽  
Electron Density ◽  
Density Functional ◽  
Functional Theory ◽  
Fukui Functions ◽  
Bond Lengths ◽  
Linear Complexes ◽  
Nitrogen Bond

The influence of copper(I) halides CuX (X = Cl, Br, I) on the electronic structure of N,N′-diisopropylcarbodiimide (DICDI) and N,N′-dicyclohexylcarbodiimide (DCC) was investigated by means of computational DFT (density functional theory) methods. The coordination of the considered carbodiimides occurs by one of the nitrogen atoms, with the formation of linear complexes having a general formula of [CuX(carbodiimide)]. Besides varying the carbon–nitrogen bond lengths, the thermodynamically favourable interaction with Cu(I) reduces the electron density on the carbodiimides and alters the energies of the (NCN)-centred, unoccupied orbitals. A small dependence of these effects on the choice of the halide was observable. The computed Fukui functions suggested negligible interaction of Cu(I) with incoming nucleophiles, and the reactivity of carbodiimides was altered by coordination mainly because of the increased electrophilicity of the {NCN} fragments.

scholarly journals H2O coordination in macropa complexes of f elements (Ac, La, Lu): feasibility of the 11th coordination site

2021 ◽  
Author(s):  
Attila Kovács ◽  
Zoltán Varga
Keyword(s):  
Aqueous Solution ◽  
Metal Ion ◽  
Density Functional ◽  
Molecular Level ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Coordination Site ◽  
Additional Ligand ◽  
Ligand Coordination ◽  
Bonding Properties

AbstractThe feasibility of an additional ligand coordination at the 11th coordination site of actinium, lanthanum, and lutetium ions in 10-fold coordinated macropa complexes has been studied by means of density functional theory calculations. The study covered the two main macropa conformers, Δ(δλδ)(δλδ) and Δ(λδλ)(λδλ), favoured by larger (Ac3+, La3+) and smaller (Lu3+) ions, respectively. At the molecular level, the coordination of H2O is the most favourable to the largest Ac3+ while only slightly less to La3+. Protonation of the picoline arms enhances the coordination by shifting the metal ion closer to the open site of the ligand. The choice of macropa conformer has only a slight influence on the strength and bonding properties of the H2O coordination. Aqueous solution environment decreases considerably the energy gain of H2O coordination at the 11th coordination site.

scholarly journals Weak Interactions in Cocrystals of Isoniazid with Glycolic and Mandelic Acids

Crystals ◽  
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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