Non-covalent interactions of Cysteine onto C60, C59Si, and C59Ge: A DFT study

Density Functional ◽

Physical Adsorption ◽

Amino Acid Molecule ◽

The Density Functional Theory ◽

Structure Of Nanomaterials ◽

Silicon And Germanium ◽

D Model ◽

Abstract The study of intermolecular interactions is of great importance. This study attempted to quantitatively examine the interactions between Cysteine (C3H7NO2S) and fullerene nanocages, C60, in a vacuum. As the frequent introduction of elements as impurities into the structure of nanomaterials can increase the intensity of intermolecular interactions, nanocages doped with silicon and germanium have also been studied as adsorbents C59Si and C59Ge. Quantum mechanical studies of such systems are possible in the density functional theory (DFT) framework. For this purpose, various functionals, such as B3LYP-D3, ωB97XD, and M062X, have been used. One of the most suitable basis functionals for the systems studied in this research is 6-311G (d), which has been used in both optimization calculations and calculations related to wave function analyses. The main part of this work is the study of various analyses that reveal the nature of the intermolecular interactions between the two components introduced above. The results of conceptual DFT, natural bond orbital, non-covalent interactions, and quantum theory of atoms in molecules were consistent and favored physical adsorption in all systems. Germanium had more adsorption energy than other dopants. The HOMO–LUMO energy gaps were as follows: C60: 5.996, C59Si: 5.309, and C59Ge: 5.188 eV at B3LYP-D3/6-311G (d) model chemistry. The adsorption sensitivity increased when an amino acid molecule interacted with doped C60, and this capability could be used to design a nanocarrier to detect Cysteine amino acids.

Intermolecular Interactions Between Serine and C60, C59Si, and C59Ge: A DFT Study

10.21203/rs.3.rs-770749/v1 ◽

2021 ◽

Author(s):

Mohsen Doust Mohammadi ◽

Hewa Y. Abdullah

Keyword(s):

Amino Acid ◽

Density Functional ◽

Physical Adsorption ◽

Amino Acid Molecule ◽

Functional Theory ◽

The Density Functional Theory ◽

Structure Of Nanomaterials ◽

Silicon And Germanium ◽

D Model

Abstract The study of intermolecular interactions is of great importance. This study attempted to quantitatively examine the interactions between Serine (C3H7NO3) and fullerene nanocages, C60, in vacuum. As the frequent introduction of elements as impurities into the structure of nanomaterials can increase the intensity of intermolecular interactions, nanocages doped with silicon and germanium have also been studied as adsorbents, C59Si and C59Ge. Quantum mechanical studies of such systems are possible in the density functional theory (DFT) framework. For this purpose, various functionals, such as B3LYP-D3, ωB97XD, and M062X, have been used. One of the most suitable basis functionals for the systems studied in this research is 6-311G (d), which has been used in both optimization calculations and calculations related to wave function analyses. The main part of this work is the study of various analyses that reveal the nature of the intermolecular interactions between the two components introduced above. The results of conceptual DFT, natural bond orbital, non-covalent interactions, and quantum theory of atoms in molecules were consistent and in favor of physical adsorption in all systems. Germanium had more adsorption energy than other dopants. The HOMO–LUMO energy gaps were as follows: C60: 5.996, C59Si: 5.309, and C59Ge: 5.188 eV at B3LYP-D3/6-311G (d) model chemistry. The sensitivity of the adsorption increased when an amino acid molecule interacted with doped C60, and this capability could be used to design nanocarrier to detect Serine amino acid.

Halogen Bonding in New Dichloride-Cobalt(II) Complex with Iodo Substituted Chalcone Ligands

Crystals ◽

10.3390/cryst10050354 ◽

2020 ◽

Vol 10 (5) ◽

pp. 354 ◽

Cited By ~ 1

Author(s):

Lukáš Masaryk ◽

Ján Moncol ◽

Radovan Herchel ◽

Ivan Nemec

Keyword(s):

Density Functional ◽

Halogen Bond ◽

Halogen Bonding ◽

Noncovalent Interaction ◽

X Ray Diffraction ◽

Functional Theory ◽

X Ray ◽

The Density Functional Theory ◽

The synthesis and properties of new chalcone ligand 4I-L ((2E)-1-[4-(1H-imidazol-1-yl)phenyl]-3-(4-iodophenyl)prop-2-en-1-one) and tetracoordinate Co(II) complex [Co(4I-L)2Cl2], (1a), are reported in this article. Upon recrystallization of 1a, the single crystals of [Co(4I-L)4Cl2]·2DMF·3Et2O (1b) were obtained and crystal structure was determined using X-ray diffraction. The non-covalent interactions in 1b were thoroughly analyzed and special attention was dedicated to interactions formed by the peripheral iodine substituents. The density functional theory (DFT), atoms in molecule (AIM) and noncovalent interaction (NCI) methods and electronic localization function (ELF) calculations were used to investigate halogen bond formed between the iodine functional groups and co-crystallized molecules of diethyl ether.

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 ◽

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.

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 ◽

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.

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 ◽

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.

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 ◽

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.

Quantitative analysis of weak non-covalent interactions in (Z)-3-(4-halophenyl)-2-(pyridin-2/3/4-yl)acrylonitriles

CrystEngComm ◽

10.1039/c7ce02096a ◽

2018 ◽

Vol 20 (19) ◽

pp. 2681-2697 ◽

Cited By ~ 19

Author(s):

Perumal Venkatesan ◽

Margarita Cerón ◽

Subbiah Thamotharan ◽

Fernando Robles ◽

M. Judith Percino

Keyword(s):

Quantitative Analysis ◽

Theoretical Investigation ◽

A detailed experimental and theoretical investigation on the intermolecular interactions in (Z)-3-(4-halophenyl)-2-(pyridin-2/3/4-yl)acrylonitriles is reported and different π staking motifs observed in these structures.

An Ultimate Investigation on the Adsorption of Amantadine on Pristine and Decorated Fullerenes C59X (X=Si, Ge, B, Al, Ga, N, P, and As): A DFT, NBO, and QTAIM Study

Journal of Computational Biophysics and Chemistry ◽

10.1142/s2737416521500022 ◽

2020 ◽

pp. 1-17

Author(s):

Mohsen Doust Mohammadi ◽

Idris H. Salih ◽

Hewa Y. Abdullah

Keyword(s):

Electronic Properties ◽

Density Functional ◽

Physical Adsorption ◽

Single Point ◽

Basis Set ◽

Total Density ◽

Electron Configuration ◽

Doped Fullerenes ◽

Donor Acceptor

In this investigation, the feasibility of detecting the amantadine (AMD) molecule onto the outer surface of pristine fullerene (C[Formula: see text]), as well as C[Formula: see text]X ([Formula: see text], Ge, B, Al, Ga, N, P, and As) decorated structures, was carefully evaluated. For achieving this goal, a density functional theory level of study using the HSEH1PBE functional together with a 6-311G(d) basis set has been used. Subsequently, the B3LYP-D3, wB97XD and M062X functionals with a 6-311G(d) basis set were also employed to consider the single point energies. Natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) were implemented using the B3LYP-D3/6-311G(d) method and the results were compatible with the electronic properties. In this regard, the total density of states (TDOSs), the Wiberg bond index (WBI), natural charge, natural electron configuration, donor–acceptor NBO interactions, and the second-order perturbation energies are performed to explore the nature of the intermolecular interactions. All of the energy calculations and population analyses denote that by adsorbing of the AMD molecule onto the surface of the considered nanostructures, the intermolecular interactions are of the type of strong physical adsorption. Among the doped fullerenes, Ge-doped structure has very high adsorption energy compared to other elements. Generally, it was revealed that the sensitivity of the adsorption will be increased when the AMD molecule interacts with the decorated fullerenes and decrease the HOMO–LUMO band gap; therefore, the change of electronic properties can be used to design suitable nanocarrier.

Performance of dispersion-corrected density functional theory for thermochemistry and non-covalent interactions

Journal of Cheminformatics ◽

10.1186/1758-2946-4-s1-p56 ◽

2012 ◽

Vol 4 (S1) ◽

Cited By ~ 2

Author(s):

Waldemar Hujo ◽

Stefan Grimme

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Functional Theory ◽

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

Open Chemistry ◽

10.1515/chem-2015-0088 ◽

2015 ◽

Vol 13 (1) ◽

Cited By ~ 6

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 ◽

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