scholarly journals Intramolecular Spodium Bonds in Zn(II) Complexes: Insights from Theory and Experiment

2020 ◽  
Vol 21 (19) ◽  
pp. 7091 ◽  
Author(s):  
Mainak Karmakar ◽  
Antonio Frontera ◽  
Shouvik Chattopadhyay ◽  
Tiddo J. Mooibroek ◽  
Antonio Bauzá
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Noncovalent Interactions ◽  
Noncovalent Interaction ◽  
Functional Theory ◽  
X Ray ◽  
Structure Database ◽  
Interaction Plot ◽  
Solid State Structures ◽  
Theory And Experiment

Two new dinuclear zinc(II) complexes, [Zn2(µ1,3-OAc)(L1)2]I·MeOH (1) and [Zn2(µ1,3-OAc)(L2)(NCS)] (2), (where HL1 = 2-(((3-(dimethylamino)propyl)amino)methyl)-6-methoxy-phenol and H2L2 = 2,2′-[(1-Methyl-1,2-ethanediyl)bis(iminomethylene)]bis[6-ethoxyphenol]) have been synthesized and characterized by elemental and spectral analysis. Their X-ray solid state structures have been determined, revealing the existence of intramolecular Zn···O spodium bonds in both complexes due to the presence of methoxy (1) or ethoxy (2) substituents adjacent to the coordinated phenolic O-atom. These noncovalent interactions have been studied using density functional theory (DFT) calculations, the quantum theory of “atoms-in-molecules” and the noncovalent interaction plot. Moreover, a search in the Cambridge structure database (CSD) has been conducted in order to investigate the prevalence of intramolecular spodium bonds in Zn complexes. To our knowledge this is the first investigation dealing with intramolecular spodium bonds.

scholarly journals On the Importance of Halogen Bonding Interactions in Two X-ray Structures Containing All Four (F, Cl, Br, I) Halogen Atoms

Crystals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1406
Author(s):  
Dmitriy F. Mertsalov ◽  
Rosa M. Gomila ◽  
Vladimir P. Zaytsev ◽  
Mikhail S. Grigoriev ◽  
Eugeniya V. Nikitina ◽  
...  
Keyword(s):  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Halogen Bonding ◽  
Noncovalent Interaction ◽  
Functional Theory ◽  
X Ray ◽  
Halogen Atoms ◽  
Interaction Plot

This manuscript reports the synthesis and X-ray characterization of two octahydro-1H-4,6-epoxycyclopenta[c]pyridin-1-one derivatives that contain the four most abundant halogen atoms (Ha) in the structure with the aim of studying the formation of Ha···Ha halogen bonding interactions. The anisotropy of electron density at the heavier halogen atoms provokes the formation of multiple Ha···Ha contacts in the solid state. That is, the heavier Ha-atoms exhibit a region of positive electrostatic potential (σ-hole) along the C–Ha bond and a belt of negative electrostatic potential (σ-lumps) around the atoms. The halogen bonding assemblies in both compounds were analyzed using density functional theory (DFT) calculations, molecular electrostatic potential (MEP) surfaces, the quantum theory of “atom-in-molecules” (QTAIM), the noncovalent interaction plot (NCIplot), and the electron localization function (ELF).

scholarly journals Sildenafil–Resorcinol Cocrystal: XRPD Structure and DFT Calculations

Crystals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1126
Author(s):  
Rafael Barbas ◽  
Vineet Kumar ◽  
Oriol Vallcorba ◽  
Rafel Prohens ◽  
Antonio Frontera
Keyword(s):  
Crystal Structure ◽  
Dft Calculations ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Noncovalent Interaction ◽  
Functional Theory ◽  
X Ray ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Interaction Plot

Herein, the X-ray powder diffraction (XRPD) crystal structure of a new Sildenafil cocrystal is reported, where resorcinol has been used as the coformer. The crystal structure has been solved by means of direct space methods used in combination with density functional theory (DFT) calculations. In the structure, the Sildenafil and resorcinol molecules form cooperative hydrogen bond (HB) and π-stacking interactions that have been analyzed using DFT calculations, the molecular electrostatic potential (MEP) surface, and noncovalent interaction plot (NCI plot). The formation of O–H⋯N H-bonds between resorcinol and Sildenafil increases the dipole moment and enhances the antiparallel π-stacking interaction.

Diphenylmethane and diphenyl ether — experimental conformations and torsional surfaces calculated with AM1, MNDO, PM3, and density functional theory (Becke3LYP)

1997 ◽  
Vol 75 (7) ◽  
pp. 1011-1022 ◽  
Author(s):  
Thomas Straßner
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Diphenyl Ether ◽  
Stationary Points ◽  
Semiempirical Methods ◽  
Functional Theory ◽  
X Ray ◽  
Diphenyl Ethers ◽  
Energy Surfaces ◽  
Solid State Structures

The complete energy surfaces of the torsion around the central C—O or C—CH2 bonds in diphenyl ether (DPE) and diphenylmethane (DPM) are calculated with semiempirical methods (AM1, MNDO, PM3) and density functional theory (Becke3LYP/3-21G). Stationary points are optimized at the Becke3LYP/6-31G(d) level of theory. The geometry of a very recently published X-ray structure of 4,4′-bis[N-(2,4,6-trimethyl)benzenesulfonamide]diphenylmethane (1), as well as the solid state structures of many other diphenyl ethers and diphenylmethanes, is found in the low-energy regions of the AM1 surfaces of the parent compounds. Keywords: Conformational analysis, diphenyl ether, diphenylmethane, quantum chemistry (AM1, MNDO, PM3), density functional theory (Becke3LYP).

scholarly journals Oxalic Acid, a Versatile Coformer for Multicomponent Forms with 9-Ethyladenine

Crystals ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 89
Author(s):  
Mónica Benito ◽  
Miquel Barceló-Oliver ◽  
Antonio Frontera ◽  
Elies Molins
Keyword(s):  
Oxalic Acid ◽  
Density Functional ◽  
Noncovalent Interaction ◽  
Supramolecular Interactions ◽  
Molar Ratio ◽  
Functional Theory ◽  
X Ray ◽  
Solution Crystallization ◽  
Interaction Plot ◽  
Salt Screening

Six new multicomponent solids of 9-ethyladenine and oxalic acid have been detected and characterized. The salt screening has been performed by mechanochemical and solvent crystallization processes. Single crystals of the anhydrous salts in 1:1 and 2:1 nucleobase:coformer molar ratio were obtained by solution crystallization and elucidated by single-crystal X-ray analysis. The supramolecular interactions observed in these solids have been studied using density functional theory (DFT) calculations and characterized by the quantum theory of “atoms in molecules” (QTAIM) and the noncovalent interaction plot (NCIPlot) index methods. The energies of the H-bonding networks observed in the solid state of the anhydrous salts in 1:1 and 2:1 nucleobase:coformer are reported, disclosing the strong nature of the charge assisted NH···O hydrogen bonds and also the relative importance of ancillary C–H··O H-bonds.

Highly Electron-Deficient Pyridinium-Nitrones for Rapid and Tunable Inverse-Electron-Demand Strain-Promoted Alkyne-Nitrone Cycloaddition to Bicyclo[6.1.0]nonyne

2019 ◽  
Author(s):  
Praveen Gunawardene ◽  
Wilson Luo ◽  
Alexander M. Polgar ◽  
John F. Corrigan ◽  
Mark Workentin
Keyword(s):  
Density Functional Theory ◽  
Reaction Kinetics ◽  
Density Functional ◽  
Functional Theory ◽  
X Ray ◽  
Inverse Electron Demand ◽  
X Ray Crystallography ◽  
Electron Demand

<div> <div> <p>Highly accelerated inverse-electron-demand strain-promoted alkyne-nitrone cycloaddition (IED SPANC) between a sta- ble cyclooctyne (bicyclo[6.1.0]nonyne (BCN)) and nitrones delocalized into a Cα-pyridinium functionality is reported, with the most electron-deficient “pyridinium-nitrone” displaying among the most rapid cycloadditions to BCN that is currently reported. Density functional theory (DFT) and X-ray crystallography are explored to rationalize the effects of N- and Cα-substituent modifications at the nitrone on IED SPANC reaction kinetics and the overall rapid reactivity of pyridinium-delocalized nitrones.</p> </div> </div>

scholarly journals Polymorphs of Rb3ScF6: X-ray and Neutron Diffraction, Solid-State NMR, and Density Functional Theory Calculations Study

2021 ◽  
Vol 60 (8) ◽  
pp. 6016-6026
Author(s):  
Aydar Rakhmatullin ◽  
Maxim S. Molokeev ◽  
Graham King ◽  
Ilya B. Polovov ◽  
Konstantin V. Maksimtsev ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Solid State ◽  
Neutron Diffraction ◽  
Solid State Nmr ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
X Ray

A DFT study of spherands containing five anisyl groups — Highly preorganized to bind the alkali metal

2006 ◽  
Vol 84 (8) ◽  
pp. 1045-1049 ◽  
Author(s):  
Shabaan AK Elroby ◽  
Kyu Hwan Lee ◽  
Seung Joo Cho ◽  
Alan Hinchliffe
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Ionic Radius ◽  
Binding Energies ◽  
Cavity Size ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Good Agreement

Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygens during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. We used standard B3LYP/6-31G** (5d) density functional theory (DFT) to investigate the complexation between spherands containing five anisyl groups, with CH2–O–CH2 (2) and CH2–S–CH2 (3) units in an 18-membered macrocyclic ring, and the cationic guests (Li+, Na+, and K+). Our geometric structure results for spherands 1, 2, and 3 are in good agreement with the previously reported X-ray diffraction data. The absolute values of the binding energy of all the spherands are inversely proportional to the ionic radius of the guests. The results, taken as a whole, show that replacement of one anisyl group by CH2–O–CH2 (2) and CH2–S–CH2 (3) makes the cavity bigger and less preorganized. In addition, both the binding and specificity decrease for small ions. The spherands 2 and 3 appear beautifully preorganized to bind all guests, so it is not surprising that their binding energies are close to the parent spherand 1. Interestingly, there is a clear linear relation between the radius of the cavity and the binding energy (R2 = 0.999).Key words: spherands, preorganization, density functional theory, binding energy, cavity size.

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