scholarly journals Organomagnesium Crown Ethers and Their Binding Affinities with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ Ions - a Theoretical Study

2021 ◽  
Author(s):  
Krishnan Thirumoorthy ◽  
Uday Kumar Padidela ◽  
Pothiappan Vairaprakash ◽  
Venkatesan Thimmakondu
Keyword(s):  
Metal Ions ◽  
Crown Ethers ◽  
Density Functional ◽  
Building Blocks ◽  
Binding Energies ◽  
Binding Affinities ◽  
Free Energies ◽  
Delta G ◽  
Cluster Methods ◽  
First Time

Novel organomagnesium crown ether molecules have been computationally characterized for the first time using density functional theory (DFT). Monomer units of MgC6 have been used as building blocks. The potential energy surface of the parent elemental composition, MgC6H2, has been extensively explored using both DFT and coupled-cluster methods. It is concluded that the seven-membered ring isomer, 1-magnesacyclohept-4-en-2,6-diyne, is the thermodynamically most stable molecule at all levels. Thus, the latter has been used as the building block for organomagnesium crown ethers. Both alkali (Li+, Na+, and K+) and alkaline-earth (Be2+, Mg2+, and Ca2+) metal ions selective complexes have been theoretically identified. Binding energies (Delta E at 0 K) and thermally corrected Gibbs free energies (Delta G at 298.15 K) have<br>been computed for these metal ions with MgC6-9-crown-3 and MgC6-12-crown-4 to gauge their binding affinities.Novel organomagnesium crown ether molecules have been computationally characterized for the first time using density functional theory (DFT). Monomer units of MgC6 have been used as building blocks. The potential energy surface of the parent elemental composition, MgC6H2, has been extensively explored using both DFT and coupled-cluster methods. It is concluded that the seven-membered ring isomer, 1-magnesacyclohept-4-en-2,6-diyne, is the thermodynamically most stable molecule at all levels. Thus, the latter has been used as the building block for organomagnesium crown ethers. Both alkali (Li+, Na+, and K+) and alkaline-earth (Be2+, Mg2+, and Ca2+) metal ions selective complexes have been theoretically identified. Binding energies (Delta E at 0 K) and thermally corrected Gibbs free energies (Delta G at 298.15 K) have been computed for these metal ions with MgC6-9-crown-3 and MgC6-12-crown-4 to gauge their binding affinities.

scholarly journals Organomagnesium Crown Ethers and Their Binding Affinities with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ Ions - a Theoretical Study

2021 ◽  
Author(s):  
Krishnan Thirumoorthy ◽  
Uday Kumar Padidela ◽  
Pothiappan Vairaprakash ◽  
Venkatesan Thimmakondu
Keyword(s):  
Metal Ions ◽  
Crown Ethers ◽  
Density Functional ◽  
Building Blocks ◽  
Binding Energies ◽  
Binding Affinities ◽  
Free Energies ◽  
Delta G ◽  
Cluster Methods ◽  
First Time

Novel organomagnesium crown ether molecules have been computationally characterized for the first time using density functional theory (DFT). Monomer units of MgC6 have been used as building blocks. The potential energy surface of the parent elemental composition, MgC6H2, has been extensively explored using both DFT and coupled-cluster methods. It is concluded that the seven-membered ring isomer, 1-magnesacyclohept-4-en-2,6-diyne, is the thermodynamically most stable molecule at all levels. Thus, the latter has been used as the building block for organomagnesium crown ethers. Both alkali (Li+, Na+, and K+) and alkaline-earth (Be2+, Mg2+, and Ca2+) metal ions selective complexes have been theoretically identified. Binding energies (Delta E at 0 K) and thermally corrected Gibbs free energies (Delta G at 298.15 K) have<br>been computed for these metal ions with MgC6-9-crown-3 and MgC6-12-crown-4 to gauge their binding affinities.Novel organomagnesium crown ether molecules have been computationally characterized for the first time using density functional theory (DFT). Monomer units of MgC6 have been used as building blocks. The potential energy surface of the parent elemental composition, MgC6H2, has been extensively explored using both DFT and coupled-cluster methods. It is concluded that the seven-membered ring isomer, 1-magnesacyclohept-4-en-2,6-diyne, is the thermodynamically most stable molecule at all levels. Thus, the latter has been used as the building block for organomagnesium crown ethers. Both alkali (Li+, Na+, and K+) and alkaline-earth (Be2+, Mg2+, and Ca2+) metal ions selective complexes have been theoretically identified. Binding energies (Delta E at 0 K) and thermally corrected Gibbs free energies (Delta G at 298.15 K) have been computed for these metal ions with MgC6-9-crown-3 and MgC6-12-crown-4 to gauge their binding affinities.

scholarly journals Flat Crown Ethers with Planar Tetracoordinate Carbon Atoms

2020 ◽  
Author(s):  
Venkatesan Thimmakondu ◽  
Krishnan Thirumoorthy
Keyword(s):  
Carbon Atom ◽  
Crown Ether ◽  
Crown Ethers ◽  
In Silico ◽  
Alkaline Earth ◽  
Experimental Studies ◽  
Building Blocks ◽  
Binding Energies ◽  
High Symmetry ◽  
Structural Rigidity

Novel flat crown ether molecules have been characterized in silico using DFT hybrid and hybrid-meta functionals. Monomer units of Si2C3 with a planar tetracoordinate carbon atom have been used as building blocks. Alkali (Li+, Na+, K+, Rb+, and Cs+) and alkaline-earth (Ca2+, Sr2+, and Ba2+) metals, and uranyl (UO2+ 2 ) ion selective complexes have also been theoretically identified. The high symmetry and higher structural rigidity of the host molecules may likely to impart higher selectivity in chelation. Theoretical binding energies have been computed and experimental studies are invited.

scholarly journals Computational Study of the Stereoselectivity Profiles of the Diels-Alder Cycloaddition Reactions of Cyclopentadiene and Butadiene with Cyclopropenes

2020 ◽  
Author(s):  
Veejendra Yadav
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Theoretical Models ◽  
Diels Alder ◽  
Cycloaddition Reactions ◽  
Free Energies ◽  
Differential Activation ◽  
Activation Free Energy ◽  
The Difference ◽  
First Time

The <i>endo</i> and <i>exo</i> stereoselectivities of the Diels-Alder (DA) cycloaddition reactions of 3,3-disubstituted cyclopropenes with butadiene and cyclopentadiene, the latter for the first time, were investigated by means of density functional and quantum chemical calculations for a comparison. To establish distinction between the selectivites, activation free energies were systematically estimated in the gas phase and also in solvents. The differential activation free energies clearly predict exclusive <i>endo</i> configuration of the products formed from the reaction of the unsubstituted cyclopropene with butadiene and cyclopentadiene. However, the results were found to be markedly different for the substituted cyclopropenes from available experimental selectivities. It was also discovered that butadiene and cyclopentadiene are markedly different in their respective stereospecific product yields, nevertheless the difference between the two was only a methylene group. The failure of the differential activation free energy approach to predict the experimental stereoselectivities of the DA reactions of several perhalocyclopropenes with cyclopentadiene is probably due to yet insufficient development of the various theoretical models dealing with the <i>endo</i> and <i>exo</i> DA preferences.

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

scholarly journals Structural and Magnetic Studies on Nickel(II) and Cobalt(II) Complexes with Polychlorinated Diphenyl(4-pyridyl)methyl Radical Ligands

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5596
Author(s):  
Ryota Matsuoka ◽  
Tatsuhiro Yoshimoto ◽  
Yasutaka Kitagawa ◽  
Tetsuro Kusamoto
Keyword(s):  
Metal Ions ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Magnetic Interactions ◽  
Organic Radical ◽  
Methyl Radical ◽  
Magnetic Studies ◽  
Orthogonal Relationship ◽  
Magnetic Metal

New magnetic metal complexes with organic radical ligands, [M(hfac)2(PyBTM)2] (M = NiII, CoII; hfac = hexafluoroacetylacetonato, PyBTM = (3,5-dichloro-4-pyridyl)bis(2,4,6-trichlorophenyl)methyl radical), were prepared and their crystal structures, magnetic properties, and electronic structures were investigated. Metal ions in [M(hfac)2(PyBTM)2] constructed distorted octahedral coordination geometry, where the two PyBTM molecules ligated in the trans configuration. Magnetic investigation using a SQUID magnetometer revealed that χT increased with decreasing temperature from 300 K in the two complexes, indicating an efficient intramolecular ferromagnetic exchange interaction taking place between the spins on PyBTM and M with J/kB of 21.8 K and 11.8 K for [NiII(hfac)2(PyBTM)2] and [CoII(hfac)2(PyBTM)2]. The intramolecular ferromagnetic couplings in the two complexes could be explained by density functional theory calculations, and would be attributed to a nearly orthogonal relationship between the spin orbitals on PyBTM and the metal ions. These results demonstrate that pyridyl-containing triarylmethyl radicals are key building blocks for magnetic molecular materials with controllable/predictable magnetic interactions.

scholarly journals Accuracy and Reproducibility of Host-Guest Interactions in Zeolites

2020 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Binding Affinities ◽  
Computationally Efficient ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Dynamics Simulations

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, no benchmark examining these calculation strategies has been reported. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. We show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and together with the reported results, provide robust, reproducible, and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

scholarly journals Size-dependent trends in the hydrogen evolution activity and electronic structure of MoS2 nanotubes

2021 ◽  
Author(s):  
Charlie Ruffman ◽  
James Thomas Alan Gilmour ◽  
Anna L. Garden
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Hydrogen Evolution ◽  
Density Functional ◽  
Hydrogen Adsorption ◽  
Density Functional Theory Calculations ◽  
Free Energies ◽  
Functional Theory ◽  
Size Dependent ◽  
First Time

The thermodynamics of hydrogen evolution on MoS2 nanotubes is studied for the first time using periodic density functional theory calculations to obtain hydrogen adsorption free energies (ΔGH ads) on pristine...

scholarly journals A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA.

2000 ◽  
Vol 47 (1) ◽  
pp. 1-9 ◽  
Author(s):  
W R Rudnicki ◽  
M Kurzepa ◽  
T Szczepanik ◽  
W Priebe ◽  
B Lesyng
Keyword(s):  
Free Energy ◽  
Theoretical Model ◽  
Density Functional ◽  
Binding Free Energy ◽  
Binding Energies ◽  
Free Energies ◽  
Anthracycline Antibiotics ◽  
Free Energy Of Binding ◽  
Derivatives Of ◽  
Binding Free Energies

A theoretical model for predicting the free energy of binding between anthracycline antibiotics and DNA was developed using the electron density functional (DFT) and molecular mechanics (MM) methods. Partial DFT-ESP charges were used in calculating the MM binding energies for complexes formed between anthracycline antibiotics and oligodeoxynucleotides. These energies were then compared with experimental binding free energies. The good correlation between the experimental and theoretical energies allowed us to propose a model for predicting the binding free energy for derivatives of anthracycline antibiotics and for quickly screening new anthracycline derivatives.

Can Antimalarial Phytochemicals be a Possible Cure for COVID-19? Molecular Docking Studies of Some Phytochemicals to SARS-CoV-2 3C-like Protease

2021 ◽  
Vol 21 ◽  
Author(s):  
Anamul Hasan ◽  
Khoshnur Jannat ◽  
Tohmina Afroze Bondhon ◽  
Rownak Jahan ◽  
Md Shahadat Hossan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
Binding Energies ◽  
Binding Affinities ◽  
Drug Candidates ◽  
Lead Compounds ◽  
High Binding ◽  
Main Protease ◽  
Acridone Alkaloid ◽  
First Time

Objective: To evaluate the efficacy of reported anti-malarial phytochemicals as lead compounds for possible drug development against COVID-19. Methods: An in silico approach was used in this study to determine through molecular docking the binding affinities and site of binding of these phytochemicals to the 3C-like protease of COVID-19 which is considered as the main protease of the virus. Results: A number of anti-malarial phytochemicals like apigenin-7-O-glucoside, decurvisine, luteolin-7-O-glucoside, sargabolide J, and shizukaols A, B, F, and G showed predicted high binding energies with G values of -8.0 kcal/mol or higher. Shizukaols F and B demonstrated the best binding energies of -9.5 and -9.8, respectively. The acridone alkaloid 5-hydroxynoracronycine also gave a predicted high binding energy of -7.9 kcal/mol. Conclusion: This is for the first time that decursivine and several shizukaols were reported as potential anti-viral agents. These compounds merit further studies to determine whether they can be effective drug candidates against COVID-19.

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