scholarly journals 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 ◽  
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.

scholarly journals Armchair Boron Nitride nanotubes—heterocyclic molecules interactions: A computational description

2015 ◽  
Vol 13 (1) ◽  
Author(s):  
Ernesto Chigo Anota ◽  
Gregorio Hernández Cocoletzi ◽  
Andres Manuel Garay Tapia
Keyword(s):  
Density Functional Theory ◽  
Boron Nitride ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Boron Nitride Nanotubes ◽  
Functional Theory ◽  
Heterocyclic Molecules ◽  
Non Covalent Interactions ◽  
Covalent Interactions

AbstractAb-initio calculations using density functional theory (DFT) are used to investigate the non-covalent interactions between single wall armchair boron nitride nanotubes (BNNTs) with open ends and several heterocyclic molecules: thiophene (T; C

scholarly journals Strength and Nature of Host-Guest Interactions in Metal-Organic Frameworks from a Quantum-Chemical Perspective

2021 ◽  
Author(s):  
Michelle Enst ◽  
Ganna Gryn'ova
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical ◽  
Density Functional ◽  
Metal Organic Frameworks ◽  
Energy Decomposition ◽  
Functional Theory ◽  
Metal Organic ◽  
Non Covalent Interactions ◽  
Decomposition Schemes ◽  
Covalent Interactions

<div> <div> <div> <p>Metal-organic frameworks offer a convenient means for capturing, transporting, and releasing small molecules. Rational design of such systems requires an in-depth understanding of the underlying non-covalent interactions, and the ability to easily and rapidly pre-screen candidate architectures in silico. In this work, we devised a recipe for computing the strength and analysing the nature of the host-guest interactions in MOFs. Using experimentally characterised complexes of calcium-adipate framework with 4,4’-bipyridine and 1,2-bis(4-pyridyl)ethane guests as test systems, we have assessed a range of density functional theory methods, energy decomposition schemes, and non-covalent interactions indicators across realistic periodic and finite supramolecular cluster scales. We find that appropriately constructed clusters readily reproduce the key interactions occurring in periodic models at a fraction of the computational cost and with an added benefit of diverse density partitioning schemes. Host-guest interaction energies can be reliably computed with dispersion- corrected density functional theory methods; however, decoding their precise nature demands insights from energy decomposition schemes and quantum-chemical tools beyond local bonding indices (e.g., the quantum theory of atoms in molecules), such as the non-covalent interactions index and the density overlap regions indicator. </p> </div> </div> </div>

scholarly journals The influence of the grafted aryl groups on the solvation properties of the graphyne and graphdiyne - a MD study

2019 ◽  
Vol 17 (1) ◽  
pp. 703-710 ◽  
Author(s):  
Avni Berisha
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Density Functional Theory ◽  
Density Functional ◽  
Phenyl Group ◽  
Functional Theory ◽  
Adsorption Sites ◽  
Water As Solvent ◽  
Non Covalent Interactions ◽  
Covalent Interactions

AbstractThe mechanism of the adsorption and grafting of diazonium cations onto the surface of graphyne and graphdiyne was investigated using Density Functional Theory (DFT). The adsorption energy (both in vacuum and water as solvent) of the phenyl diazonium cation was evaluated at three different positions of the graphyne and graphdiyne surface. Moreover, the lowest energy adsorption sites were used to calculate and plot Non-covalent Interactions (NCI). The Bond Dissociation Energy (BDE) results (up to 66 kcal/mol) for the scission of the phenyl group support the remarkable stability of the grafted layer. As both of these materials are non-dispersible in aqueous solution, in this work through the use of Molecular Mechanics (MM) and Molecular Dynamics (MD) we explored also the effect of the grafted substituted aryl groups derived from aryldiazonium salts onto the solvation properties of these materials.

Organometallic pyrene-containing porphyrins: Synthesis, characterization, and non-covalent interactions with C60 fullerenes

2016 ◽  
Vol 20 (08n11) ◽  
pp. 1098-1113 ◽  
Author(s):  
Yang Li ◽  
Hannah M. Rhoda ◽  
Anthony M. Wertish ◽  
Victor N. Nemykin
Keyword(s):  
Excited States ◽  
Electronic Structures ◽  
Density Functional ◽  
Functional Theory ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
C60 Fullerenes

A reaction between 5,10,15,20-tetra(4-hydroxyphenyl)porphyrin and 1-bromopyrene resulted in the formation of 5,10,15,20-tetra[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (1), while cross-condensation between 4-(4-(pyrenyl-1)butoxy)benzaldehyde, ferrocenecaboxaldehyde, and pyrrole resulted in the formation of 5-ferrocenyl-10,15,20-tri[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (2), 5,10-diferrocenyl-15,20-di[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (3), and 5,15-diferrocenyl-10,20-di[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (4). All pyrene-containing porphyrins were characterized by 1H NMR, UV-vis, MCD, and high-resolution ESI methods, while their electronic structures and the nature of the excited states were elucidated using density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. The molecular structure of 1 and its fluorescence quenching upon the addition of C[Formula: see text] fullerene was also investigated using X-ray crystallography and steady-state fluorescence approaches.

scholarly journals Strength and Nature of Host-Guest Interactions in Metal-Organic Frameworks from a Quantum-Chemical Perspective

2021 ◽  
Author(s):  
Michelle Enst ◽  
Ganna Gryn'ova
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical ◽  
Density Functional ◽  
Metal Organic Frameworks ◽  
Energy Decomposition ◽  
Functional Theory ◽  
Metal Organic ◽  
Non Covalent Interactions ◽  
Decomposition Schemes ◽  
Covalent Interactions

<div> <div> <div> <p>Metal-organic frameworks offer a convenient means for capturing, transporting, and releasing small molecules. Rational design of such systems requires an in-depth understanding of the underlying non-covalent interactions, and the ability to easily and rapidly pre-screen candidate architectures in silico. In this work, we devised a recipe for computing the strength and analysing the nature of the host-guest interactions in MOFs. Using experimentally characterised complexes of calcium-adipate framework with 4,4’-bipyridine and 1,2-bis(4-pyridyl)ethane guests as test systems, we have assessed a range of density functional theory methods, energy decomposition schemes, and non-covalent interactions indicators across realistic periodic and finite supramolecular cluster scales. We find that appropriately constructed clusters readily reproduce the key interactions occurring in periodic models at a fraction of the computational cost and with an added benefit of diverse density partitioning schemes. Host-guest interaction energies can be reliably computed with dispersion- corrected density functional theory methods; however, decoding their precise nature demands insights from energy decomposition schemes and quantum-chemical tools beyond local bonding indices (e.g., the quantum theory of atoms in molecules), such as the non-covalent interactions index and the density overlap regions indicator. </p> </div> </div> </div>

scholarly journals From Oligo(Phenyleneethynylene) Monomers to Supramolecular Helices: The Role of Intermolecular Interactions in Aggregation

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3530
Author(s):  
Berta Fernández ◽  
Zulema Fernández ◽  
Emilio Quiñoá ◽  
Félix Freire
Keyword(s):  
Density Functional Theory ◽  
Self Assembly ◽  
Density Functional ◽  
Point Of View ◽  
Basis Set ◽  
Theoretical Point ◽  
Functional Theory ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Supramolecular helices that arise from the self-assembly of small organic molecules via non-covalent interactions play an important role in the structure and properties of the corresponding materials. Here we study the supramolecular helical aggregation of oligo(phenyleneethynylene) monomers from a theoretical point of view, always guiding the studies with experimentally available data. In this way, by systematically increasing the number of monomer units, optimized n-mer geometries are obtained along with the corresponding absorption and circular dichroism spectra. For the geometry optimizations we use density functional theory together with the B3LYP-D3 functional and the 6–31G** basis set. For obtaining the spectra we resort to time-dependent density functional theory using the CAM-B3LYP functional and the 3–21G basis set. These combinations of density functional and basis set were selected after systematic convergence studies. The theoretical results are analyzed and compared to the experimentally available spectra, observing a good agreement.

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