Relationship between cation–π and anion–π interactions: individual binding energies in the π–Mz+–π–X−–π system

2013 ◽  
Vol 112 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Ali Ebrahimi ◽  
Sayyed Mostafa Habibi Khorassani ◽  
Roya Behazin ◽  
Shiva Rezazadeh ◽  
Abolfazl Azizi ◽  
...  
Keyword(s):  
Binding Energies ◽  
Π Interactions

scholarly journals An accurate single descriptor for ion–π interactions

2020 ◽  
Vol 7 (6) ◽  
pp. 1036-1045 ◽  
Author(s):  
Zhangyun Liu ◽  
Zheng Chen ◽  
Jinyang Xi ◽  
Xin Xu
Keyword(s):  
Electrostatic Interactions ◽  
Quantitative Description ◽  
Physical Nature ◽  
Binding Energies ◽  
Electrostatic Energy ◽  
Π Interactions ◽  
Practical Strategy ◽  
Leading Term ◽  
Level Method ◽  
High Level

Abstract Non-covalent interactions between ions and π systems play an important role in molecular recognition, catalysis and biology. To guide the screen and design for artificial hosts, catalysts and drug delivery, understanding the physical nature of ion–π complexes via descriptors is indispensable. However, even with multiple descriptors that contain the leading term of electrostatic and polarized interactions, the quantitative description for the binding energies (BEs) of ion–π complexes is still lacking because of the intrinsic shortcomings of the commonly used descriptors. Here, we have shown that the impartment of orbital details into the electrostatic energy (coined as OEE) makes an excellent single descriptor for BEs of not only spherical, but also multiply-shaped, ion–π systems, highlighting the importance of an accurate description of the electrostatic interactions. Our results have further demonstrated that OEEs from a low-level method could be calibrated to BEs from a high-level method, offering a powerful practical strategy for an accurate prediction of a set of ion–π interactions.

scholarly journals The Importance of CH···X (X = O, π) Interaction of a New Mixed Ligand Cu(II) Coordination Polymer: Structure, Hirshfeld Surface and Theoretical Studies

Crystals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 455 ◽  
Author(s):  
Saikat Seth
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Noncovalent Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Mixed Ligand ◽  
Binding Energies ◽  
Zigzag Chain ◽  
X Ray ◽  
Π Interactions

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.

Intermolecular π/π and H/π interactions in dimers researched by different computational methods

2014 ◽  
Vol 13 (07) ◽  
pp. 1450057
Author(s):  
Cuihong Wang ◽  
Yue Jiang ◽  
Ruiqin Zhang ◽  
Zijing Lin
Keyword(s):  
High Efficiency ◽  
Dipole Moments ◽  
Binding Energies ◽  
Basis Set ◽  
Theoretical Research ◽  
Basis Sets ◽  
Π Interactions ◽  
Π Stacking ◽  
Structures And Properties ◽  
Satisfactory Precision

The analysis of π/π and H /π interactions in complexes are a challenging aspect of theoretical research. Due to the different approximations of different levels of theory, results tend to be inconsistent. We compared the reliabilities of HF, SVWN, M06L, PW91, BLYP, B3LYP, BHandHLYP, B97D, MP2, and DFTB-D approaches in researching π/π and H /π interactions by calculating the binding energies of five benzene-containing dimers. The effects of 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results were analyzed too. We found that the DFTB-D and B97D methods combined with the 6-311++G** basis set perform well for dimers that contain π/π and H /π interactions. With high efficiency and satisfactory precision, DFTB-D is helpful for the calculation of complexes containing π/π and H /π stacking. We further calculated the structures and properties of phenylalanine-containing dimers using the DFTB-D and B97D methods. The properties of low energy conformers such as rotational constants, dipole moments and molecular orbitals were also analyzed. These data should be helpful for research into systems that contain π/π and H /π stacking.

scholarly journals Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations

Molecules ◽  
2021 ◽  
Vol 26 (24) ◽  
pp. 7598
Author(s):  
Markus Koch ◽  
Marina Saphiannikova ◽  
Olga Guskova
Keyword(s):  
Hydrogen Bonds ◽  
Md Simulations ◽  
Binding Energies ◽  
Atomistic Simulations ◽  
Π Interactions ◽  
Different Types ◽  
Non Covalent Interactions ◽  
Experimental Works ◽  
Supramolecular Aggregates ◽  
Covalent Interactions

We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of π–π interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the π–π interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, π–π stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.

π–π INTERACTION IN BENZENE DIMER STUDIED USING DENSITY FUNCTIONAL THEORY AUGMENTED WITH AN EMPIRICAL DISPERSION TERM

2010 ◽  
Vol 09 (supp01) ◽  
pp. 109-123 ◽  
Author(s):  
CHAO FENG ◽  
CHENSHENG LIN ◽  
XIAOHONG ZHANG ◽  
RUIQIN ZHANG
Keyword(s):  
Density Functional Theory ◽  
Long Range ◽  
Density Functional ◽  
Theoretical Method ◽  
Binding Energies ◽  
Basis Sets ◽  
Functional Theory ◽  
Π Interactions ◽  
Benzene Dimer ◽  
Dispersion Term

The π–π interactions in various configurations of benzene dimers were studied using a density functional theoretical method augmented with an empirical dispersion term (acronym DFT-D) which is capable of describing long-range dispersive interaction. Compared with the previous CCSD(T) calculations, our approach using PBE functional and polarized triple-ζ quality basis sets provides reasonably accurate binding energies and equilibrium intermolecular geometries of the considered benzene dimer configurations, although the calculations are not counterpoisely corrected. It is expected that our approach can be utilized to evaluate the π–π interactions in large complex systems.

scholarly journals Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA–protein complexes

2021 ◽  
Author(s):  
Katie A Wilson ◽  
Ryan W Kung ◽  
Simmone D’souza ◽  
Stacey D Wetmore
Keyword(s):  
Amino Acids ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Noncovalent Interactions ◽  
Binding Energies ◽  
Amino Acid Side Chain ◽  
Π Interactions ◽  
Maximum Stability ◽  
Protein Components ◽  
Rna Protein Complexes

Abstract A set of >300 nonredundant high-resolution RNA–protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted π–π interaction) or ribose moiety (denoted sugar–π). The resulting dataset of >1500 RNA–protein π-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA–protein π-interaction, with π–π contacts making up 59% of the identified interactions. RNA–protein π–π and sugar–π contacts exhibit a range in the RNA and protein components involved, relative monomer orientations and quantum mechanically predicted binding energies. Interestingly, π–π and sugar–π interactions occur more frequently with RNA (4.8 contacts/structure) than DNA (2.6). Moreover, the maximum stability is greater for RNA–protein contacts than DNA–protein interactions. In addition to highlighting distinct differences between RNA and DNA–protein binding, this work has generated the largest dataset of RNA–protein π-interactions to date, thereby underscoring that RNA–protein π-contacts are ubiquitous in nature, and key to the stability and function of RNA–protein complexes.

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