Small Molecules, Non-Covalent Interactions, and Confinement

Abstract This review gives an overview of current trends in the investigation of confined molecules such as higher alcohols, ethylene glycol and polyethylene glycol as guest molecules in neat and functionalized mesoporous silica materials. All these molecules have both hydrophobic and hydrophilic parts. They are characteristic role-models for the investigation of confined surfactants. Their properties are studied by a combination of solid-state NMR and relaxometry with other physicochemical techniques and molecular dynamics techniques. It is shown that this combination delivers unique insights into the structure, arrangement, dynamical properties and the guest-host interactions inside the confinement.

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Self-assembly mode and supramolecular framework of cyclopentanocucurbit[6]uril and aromatic amines

Current Organic Chemistry ◽

10.2174/1385272825666211117153451 ◽

2021 ◽

Vol 25 ◽

Author(s):

Jun Zheng ◽

Yan Mei Jin ◽

Xi Nan Yang ◽

Lin Zhang ◽

Dao Fa Jiang ◽

...

Keyword(s):

Self Assembly ◽

Functional Materials ◽

Supramolecular Interactions ◽

X Ray Diffraction ◽

Guest Molecules ◽

Characterization Methods ◽

Potential Applications ◽

Non Covalent Interactions ◽

Multi Level ◽

Covalent Interactions

: Single-crystal X-ray diffraction analysis, nuclear magnetic resonance (NMR), and other characterization methods are used to characterize the complexes formed by cyclopentano-cucurbit[6]uril (abbreviated as CyP6Q[6]) as a host interacting with p-aminobenzenesulfonamide (G1), 4,4'-diaminobiphenyl (G2), and (E)-4,4'-diamino-1,2-diphenylethene (G3) as guests, respectively. The experimental results show that these three aromatic amine molecules have the same interaction mode with CyP6Q[6], interacting with its negatively electric potential portals. The supramolecular interactions include non-covalent interactions of hydrogen bonding and ion-dipole between host and guest molecules. CdCl2 acts as a structureinducing agent to form self-assemblies of multi-dimensional and multi-level supramolecular frameworks that may have potential applications in various functional materials.

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Recognition and Sensing of Chiral Organic Molecules by Chiral Porphyrinoids: A Review

Chemosensors ◽

10.3390/chemosensors9080204 ◽

2021 ◽

Vol 9 (8) ◽

pp. 204

Author(s):

Gabriele Travagliante ◽

Massimiliano Gaeta ◽

Roberto Purrello ◽

Alessandro D’Urso

Keyword(s):

Scientific Community ◽

Chiral Recognition ◽

Organic Molecules ◽

Chiral Discrimination ◽

Spectroscopic Techniques ◽

Chiral Molecules ◽

Relevant Research ◽

Non Covalent Interactions ◽

Organic Guests ◽

Covalent Interactions

Porphyrinoids are extremely attractive for their electronic, optical, and coordination properties as well as for their versatile substitution at meso/β-positions. All these features allow porphyrinoids to behave as chiroptical hosts for chiral recognition by means of non-covalent interactions towards chiral guests. Over the years, chiral discrimination of chiral molecules such as amino acids, alcohols, amines, hydroxy-carboxylic acids, etc. has aroused the interest of the scientific community. Hence, this review aims to report on the progress to date by illustrating some relevant research regarding the chiral recognition of a multitude of chiral organic guests through several chiral mono- and bis-porphyrins via different spectroscopic techniques.

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Physico-chemical and spectroscopic investigation of flavonoid dispersed C n TAB micelles

Royal Society Open Science ◽

10.1098/rsos.210758 ◽

2022 ◽

Vol 9 (1) ◽

Author(s):

Dileep Kumar ◽

K. M. Sachin ◽

Naveen Kumari ◽

Ajaya Bhattarai

Keyword(s):

Chemical Properties ◽

Isentropic Compressibility ◽

Solvent System ◽

Hexadecyltrimethylammonium Bromide ◽

Tetradecyltrimethylammonium Bromide ◽

Surfactant Micelles ◽

Surface Excess Concentration ◽

Physico Chemical ◽

Non Covalent Interactions ◽

Covalent Interactions

In this study, kaempferol (0.2 m/mmol kg −1 ) dispersed cationic surfactant micelles were prepared as a function of alkyltrimethylammonium bromide (C n TAB) hydrophobicity (C = 12 to C = 16). The dispersion study of kaempferol in different C n TAB, i.e. dodecyltrimethylammonium bromide (C = 12), tetradecyltrimethylammonium bromide (C = 14) and hexadecyltrimethylammonium bromide (C = 16), was conducted with the physico-chemical properties of density, sound velocity, viscosity, surface tension, isentropic compressibility, acoustic impedance, surface excess concentration and area occupied per molecule and thermodynamic parameters Gibbs free energy, enthalpy and activation energy measured at 298.15 K. These properties were measured with varying concentration of C n TAB from 0.0260 to 0.0305 mol kg −1 in a 10% (w/w) aqueous dimethyl sulfoxide solvent system. The variations in these measured properties have been used to infer the kaempferol dispersion stability via hydrophobic–hydrophilic, hydrophilic–hydrophilic, van der Waals, hydrogen bonding and other non-covalent interactions.

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Non-Covalent Interactions Atlas Benchmark Data Sets 3: Repulsive Contacts

10.26434/chemrxiv.13414931.v1 ◽

2020 ◽

Author(s):

Kristian Kříž ◽

Martin Nováček ◽

Jan Řezáč

Keyword(s):

Organic Molecules ◽

Energy Surface ◽

Molecular Complexes ◽

Data Sets ◽

Interaction Energies ◽

Data Set ◽

Benchmark Data ◽

Mechanical Methods ◽

Non Covalent Interactions ◽

Covalent Interactions

The new R739×5 data set from the Non-Covalent Interactions Atlas series (www.nciatlas.org) focuses on repulsive contacts in molecular complexes, covering organic molecules, sulfur, phosphorus, halogens and noble gases. Information on the repulsive parts of the potential energy surface is crucial for the development of robust empirically parametrized computational methods. We use the new data set of highly accurate CCSD(T)/CBS interaction energies to test existing DFT and semiempirical quantum-mechanical methods. On the example of the PM6 method, we analyze the source of the error and its relation to the difficulties in the description of conformational energies, and we also devise an immediately applicable correction that fixes the most serious uncorrected issues previously encountered in practical calculations.

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Steric “attraction”: not by dispersion alone

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.14.125 ◽

2018 ◽

Vol 14 ◽

pp. 1482-1490 ◽

Cited By ~ 9

Author(s):

Ganna Gryn’ova ◽

Clémence Corminboeuf

Keyword(s):

Structure Prediction ◽

Electrostatic Interactions ◽

Short Range ◽

Organic Molecules ◽

Crystal Structure Prediction ◽

Range Effect ◽

Electrostatic Stabilization ◽

Non Covalent Interactions ◽

London Dispersion ◽

Covalent Interactions

Non-covalent interactions between neutral, sterically hindered organic molecules generally involve a strong stabilizing contribution from dispersion forces that in many systems turns the ‘steric repulsion’ into a ‘steric attraction’. In addition to London dispersion, such systems benefit from electrostatic stabilization, which arises from a short-range effect of charge penetration and gets bigger with increasing steric bulk. In the present work, we quantify this contribution for a diverse set of molecular cores, ranging from unsubstituted benzene and cyclohexane to their derivatives carrying tert-butyl, phenyl, cyclohexyl and adamantyl substituents. While the importance of electrostatic interactions in the dimers of sp2-rich (e.g., π-conjugated) cores is well appreciated, less polarizable assemblies of sp3-rich systems with multiple short-range CH···HC contacts between the bulky cyclohexyl and adamantyl moieties are also significantly influenced by electrostatics. Charge penetration is drastically larger in absolute terms for the sp2-rich cores, but still has a non-negligible effect on the sp3-rich dimers, investigated herein, both in terms of their energetics and equilibrium interaction distances. These results emphasize the importance of this electrostatic effect, which has so far been less recognized in aliphatic systems compared to London dispersion, and are therefore likely to have implications for the development of force fields and methods for crystal structure prediction.

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Non-Covalent Interactions Atlas Benchmark Data Sets 2: Hydrogen Bonding in an Extended Chemical Space

10.26434/chemrxiv.12587537.v1 ◽

2020 ◽

Author(s):

Jan Řezáč

Keyword(s):

Hydrogen Bonding ◽

Organic Molecules ◽

Chemical Space ◽

Data Sets ◽

Data Set ◽

Benchmark Data ◽

Non Covalent Interactions ◽

Dissociation Curves ◽

New Generation ◽

Covalent Interactions

The Non-Covalent Interactions Atlas (www.nciatlas.org) aims to provide a new generation of benchmark data sets for non-covalent interactions. The HB300SPX data set presented here extends the coverage of hydrogen bonds to phosphorus, sulfur and halogens up to iodine. It is again complemented by a set of dissociation curves, HB300SPX×10. The new data make it possible to analyze the transferability of the parametrization of e.g. dispersion corrections for DFT from simple organic molecules to a broader chemical space. The HB300SPX×10 has also been used for the extension of the parametrization of hydrogen-bonding corrections in the semiempirical PM6-D3H4X and DFTB3-D3H5 methods to additional elements.<br>

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Luminescent Lanthanide-Macrocycle Supramolecular Assembly

Chemical Communications ◽

10.1039/d1cc04672a ◽

2021 ◽

Author(s):

Wei-Lei Zhou ◽

Yong Chen ◽

Wenjing Lin ◽

Yu Liu

Keyword(s):

Crown Ether ◽

Supramolecular Assembly ◽

Macrocyclic Compounds ◽

Guest Molecules ◽

Non Covalent Interactions ◽

Covalent Interactions

a series of macrocyclic compounds, including crown ether, cyclodextrin, cucurbituril and pillararene, bound with various specific organic/inorganic/biological guest molecules and ions through various non-covalent interactions, can not only make a...

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Robust Supramolecular Nano-Tunnels Built from Molecular Bricks

10.26434/chemrxiv.12646919.v1 ◽

2020 ◽

Author(s):

Peifa Wei ◽

Zheng Zheng ◽

Junyi Gong ◽

Jun Zhang ◽

Herman H.-Y. Sung ◽

...

Keyword(s):

Single Crystal ◽

Organic Molecules ◽

Co2 Adsorption ◽

Linear Molecule ◽

Self Healing ◽

Pi Stacking ◽

New Methods ◽

Hydrogen Bonding Interactions ◽

Non Covalent Interactions ◽

Covalent Interactions

Chemists are always seeking new methods to construct porous lattice frameworks using simple motifs as the impetus. Different from the extensively reported frameworks which were stabilized by extended bonding, porous crystals of discrete organic molecules is an emerging area of porous materials with dynamic and flexible conformation, consisting exclusively of non-covalent interactions. Herein we report geometrically simple linear molecule that assemble into a supramolecular nano-tunnel through synergy of anionic trident and multiple intermolecular pi-pi stacking interactions. The nano-tunnel crystal exhibit exceptional chemical stability in concentrated HCl and NaOH aqueous solutions, which is rarely been seen in supramolecular organic frameworks and often related to designed extensive hydrogen bonding interactions. Upon thermal treatment, the formed nano-tunnel crystals go through multistage single-crystal-to-single-crystal phase transformations accompanied by thermosalient effect. Aggregation-induced emission joins with the adaptive pores render the crystals with responsive fluorescent change from blue to yellow and visible self-healing porosity transformation upon being stimulated. Furthermore, the desolvated pores exhibit highly selective CO2 adsorption at ambient temperature. <br>

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Non-Covalent Interactions Atlas Benchmark Data Sets 3: Repulsive Contacts

10.26434/chemrxiv.13414931 ◽

2020 ◽

Author(s):

Kristian Kříž ◽

Martin Nováček ◽

Jan Řezáč

Keyword(s):

Organic Molecules ◽

Energy Surface ◽

Molecular Complexes ◽

Data Sets ◽

Interaction Energies ◽

Data Set ◽

Benchmark Data ◽

Mechanical Methods ◽

Non Covalent Interactions ◽

Covalent Interactions

The new R739×5 data set from the Non-Covalent Interactions Atlas series (www.nciatlas.org) focuses on repulsive contacts in molecular complexes, covering organic molecules, sulfur, phosphorus, halogens and noble gases. Information on the repulsive parts of the potential energy surface is crucial for the development of robust empirically parametrized computational methods. We use the new data set of highly accurate CCSD(T)/CBS interaction energies to test existing DFT and semiempirical quantum-mechanical methods. On the example of the PM6 method, we analyze the source of the error and its relation to the difficulties in the description of conformational energies, and we also devise an immediately applicable correction that fixes the most serious uncorrected issues previously encountered in practical calculations.

Download Full-text