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 A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy

2021 ◽  
Author(s):  
Fernando Jiménez-Grávalos ◽  
Dimas Suárez
Keyword(s):  
Quantum Chemical ◽  
Electrostatic Interactions ◽  
Binding Energies ◽  
Electrostatic Energy ◽  
Total Binding Energy ◽  
Chemical Topology ◽  
Electrostatic Binding ◽  
Quantum Chemical Topology ◽  
Interacting Quantum Atoms ◽  
Definition Of

<div>Basing on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the non-covalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials.</div>

scholarly journals A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy

2021 ◽  
Author(s):  
Fernando Jiménez-Grávalos ◽  
Dimas Suárez
Keyword(s):  
Quantum Chemical ◽  
Electrostatic Interactions ◽  
Binding Energies ◽  
Electrostatic Energy ◽  
Total Binding Energy ◽  
Chemical Topology ◽  
Electrostatic Binding ◽  
Quantum Chemical Topology ◽  
Interacting Quantum Atoms ◽  
Definition Of

<div>Basing on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the non-covalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials.</div>

scholarly journals Particularly strong C–H⋯π interactions between benzene and all-cis 1,2,3,4,5,6-hexafluorocyclohexane

2015 ◽  
Vol 17 (44) ◽  
pp. 29475-29478 ◽  
Author(s):  
Rodrigo A. Cormanich ◽  
Neil S. Keddie ◽  
Roberto Rittner ◽  
David O'Hagan ◽  
Michael Bühl
Keyword(s):  
Ab Initio ◽  
Interaction Energy ◽  
Benzene Molecule ◽  
Π Interactions ◽  
High Level

According to high-level ab initio results (SCS-MP2/CBS), the interaction energy between all-cis 1,2,3,4,5,6-hexafluorocyclohexane and a benzene molecule is at least −6 kcal mol−1, remarkably large for C–H⋯π interactions between hydrocarbons.

CAN SEMIEMPIRICAL QUANTUM MODELS CALCULATE THE BINDING ENERGY OF HYDROGEN BONDING FOR BIOLOGICAL SYSTEMS?

2009 ◽  
Vol 08 (04) ◽  
pp. 691-711 ◽  
Author(s):  
FENG FENG ◽  
HUAN WANG ◽  
WEI-HAI FANG ◽  
JIAN-GUO YU
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Density Functional ◽  
Biological Systems ◽  
Binding Energies ◽  
Semiempirical Model ◽  
Hydrogen Bonded Systems ◽  
High Level ◽  
Hydrogen Bonded

A modified semiempirical model named RM1BH, which is based on RM1 parameterizations, is proposed to simulate varied biological hydrogen-bonded systems. The RM1BH is formulated by adding Gaussian functions to the core–core repulsion items in original RM1 formula to reproduce the binding energies of hydrogen bonding of experimental and high-level computational results. In the parameterizations of our new model, 35 base-pair dimers, 18 amino acid residue dimers, 14 dimers between a base and an amino acid residue, and 20 other multimers were included. The results performed with RM1BH were compared with experimental values and the benchmark density-functional (B3LYP/6-31G**/BSSE) and Möller–Plesset perturbation (MP2/6-31G**/BSSE) calculations on various biological hydrogen-bonded systems. It was demonstrated that RM1BH model outperforms the PM3 and RM1 models in the calculations of the binding energies of biological hydrogen-bonded systems by very close agreement with the values of both high-level calculations and experiments. These results provide insight into the ideas, methods, and views of semiempirical modifications to investigate the weak interactions of biological systems.

scholarly journals Crystal structure from X-ray powder diffraction data, DFT-D calculation, Hirshfeld surface analysis, and energy frameworks of (RS)-trichlormethiazide

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Robert A. Toro ◽  
Analio Dugarte-Dugarte ◽  
Jacco van de Streek ◽  
José Antonio Henao ◽  
José Miguel Delgado ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Electrostatic Interactions ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Π Interactions

The structure of racemic (RS)-trichlormethiazide [systematic name: (RS)-6-chloro-3-(dichloromethyl)-1,1-dioxo-3,4-dihydro-2H-1λ6,2,4-benzothiadiazine-7-sulfonamide], C8H8Cl3N3O4S2 (RS-TCMZ), a diuretic drug used in the treatment of oedema and hypertension, was determined from laboratory X-ray powder diffraction data using DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915.], refined by the Rietveld method with TOPAS-Academic [Coelho (2018). J. Appl. Cryst. 51, 210–218], and optimized using DFT-D calculations. The extended structure consists of head-to-tail dimers connected by π–π interactions which, in turn, are connected by C—Cl...π interactions. They form chains propagating along [101], further connected by N—H...O hydrogen bonds to produce layers parallel to the ac plane that stack along the b-axis direction, connected by additional N—H...O hydrogen bonds. The Hirshfeld surface analysis indicates a major contribution of H...O and H...Cl interactions (32.2 and 21.7%, respectively). Energy framework calculations confirm the major contribution of electrostatic interactions (E elec) to the total energy (E tot). A comparison with the structure of S-TCMZ is also presented.

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 Phase Behavior of Melts of Diblock-Copolymers with One Charged Block

Polymers ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1027 ◽  
Author(s):  
Alexey A. Gavrilov ◽  
Alexander V. Chertovich ◽  
Igor I. Potemkin
Keyword(s):  
Phase Diagram ◽  
Phase Behavior ◽  
Electrostatic Interactions ◽  
Diblock Copolymers ◽  
Volume Fraction ◽  
Microphase Separation ◽  
Dissipative Particle Dynamics ◽  
Homogeneous Structure ◽  
Electrostatic Energy ◽  
Ordered Structures

In this work, we investigated the phase behavior of melts of block-copolymers with one charged block by means of dissipative particle dynamics with explicit electrostatic interactions. We assumed that all the Flory–Huggins χ parameters were equal to 0. We showed that the charge- correlation attraction solely can cause microphase separation with a long-range order; a phase diagram was constructed by varying the volume fraction of the uncharged block and the electrostatic interaction parameter λ (dimensionless Bjerrum length). The obtained phase diagram was compared to the phase diagram of “equivalent” neutral diblock-copolymers with the non-zero χ-parameter between the beads of different blocks. The neutral copolymers were constructed by grafting the counterions to the corresponding co-ions of the charged block with further switching off the electrostatic interactions. Surprisingly, the differences between these phase diagrams are rather subtle; the same phases in the same order are observed, and the positions of the order-disorder transition ODT points are similar if the λ-parameter is considered as an “effective” χ-parameter. Next, we studied the position of the ODT for lamellar structure depending on the chain length N. It turned out that while for the uncharged diblock copolymer the product χcrN was almost independent of N, for the diblock copolymers with one charged block we observed a significant increase in λcrN upon increasing N. This can be attributed to the fact that the counterion entropy prevents the formation of ordered structures, and its influence is more pronounced for longer chains since they undergo the transition to ordered structures at smaller values of λ, when the electrostatic energy becomes comparable to kbT. This was supported by studying the ODT in diblock-copolymers with charged blocks and counterions cross-linked to the charged monomer units. The ODT for such systems was observed at significantly lower values of λ, with the difference being more pronounced at longer chain lengths N. The fact that the microphase separation is observed even at zero Flory–Huggins parameter can be used for the creation of “high-χ” copolymers: The incorporation of charged groups (for example, ionic liquids) can significantly increase the segregation strength. The diffusion of counterions in the obtained ordered structures was studied and compared to the case of a system with the same number of charged groups but a homogeneous structure; the diffusion coefficient along the lamellar plane was found to be higher than in any direction in the homogeneous structure.

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.

scholarly journals Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations

2008 ◽  
Vol 465 (2103) ◽  
pp. 669-683 ◽  
Author(s):  
Quintin Hill ◽  
Chris-Kriton Skylaris
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Cost ◽  
Density Functional Theory Calculations ◽  
Binding Energies ◽  
Molecular Structures ◽  
Dispersion Interactions ◽  
Biomolecular Systems ◽  
Functional Theory ◽  
High Level

While density functional theory (DFT) allows accurate quantum mechanical simulations from first principles in molecules and solids, commonly used exchange-correlation density functionals provide a very incomplete description of dispersion interactions. One way to include such interactions is to augment the DFT energy expression by damped London energy expressions. Several variants of this have been developed for this task, which we discuss and compare in this paper. We have implemented these schemes in the ONETEP program, which is capable of DFT calculations with computational cost that increases linearly with the number of atoms. We have optimized all the parameters involved in our implementation of the dispersion correction, with the aim of simulating biomolecular systems. Our tests show that in cases where dispersion interactions are important this approach produces binding energies and molecular structures of a quality comparable with high-level wavefunction-based approaches.

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.

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