On generalized partition methods for interaction energies

2020 ◽  
Vol 22 (42) ◽  
pp. 24291-24298
Author(s):  
Stefano Racioppi ◽  
Angelo Sironi ◽  
Piero Macchi
Keyword(s):  
Interaction Energy ◽  
Supramolecular Chemistry ◽  
Chemical Bonding ◽  
Interaction Energies ◽  
Important Means ◽  
Generalized Partition

The breakdown of interaction energy has always been a very important means to understand chemical bonding and it has become a seamlessly useful tool for modern supramolecular chemistry.

scholarly journals Intermolecular Non-Covalent Carbon-Bonding Interactions with Methyl Groups: A CSD, PDB and DFT Study

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3370 ◽  
Author(s):  
Tiddo J. Mooibroek
Keyword(s):  
Hydrogen Bonding ◽  
Solid State ◽  
Dft Calculations ◽  
Interaction Energy ◽  
Weak Interaction ◽  
Systematic Evaluation ◽  
Methyl Groups ◽  
Interaction Energies ◽  
Hydrogen Bonding Interactions ◽  
Carbon Bonding

A systematic evaluation of the CSD and the PDB in conjunction with DFT calculations reveal that non-covalent Carbon-bonding interactions with X–CH3 can be weakly directional in the solid state (P ≤ 1.5) when X = N or O. This is comparable to very weak CH hydrogen bonding interactions and is in line with the weak interaction energies calculated (≤ –1.5 kcal·mol−1) of typical charge neutral adducts such as [Me3N-CH3···OH2] (2a). The interaction energy is enhanced to ≤–5 kcal·mol−1 when X is more electron withdrawing such as in [O2N-CH3··O=Cdme] (20b) and to ≤18 kcal·mol−1 in cationic species like [Me3O+-CH3···OH2]+ (8a).

Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methods

2020 ◽  
Vol 76 (6) ◽  
pp. 630-651
Author(s):  
Daniel Nguyen ◽  
Piero Macchi ◽  
Anatoliy Volkov
Keyword(s):  
Interaction Energy ◽  
Crystal Structures ◽  
Electron Density ◽  
Small Molecule ◽  
Electrostatic Interaction ◽  
Multipole Moment ◽  
Interaction Energies ◽  
Acta Cryst ◽  
Löwdin Α Function ◽  
Direct Summation

The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170–175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536; Nguyen & Volkov (2019). Acta Cryst. A75, 448–464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, L-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283–4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10−5 kJ mol−1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28–64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.

scholarly journals Van der Waals interactions between polymers with sequence-specific polarizabilities: Stiff polymers and Gaussian coils

2016 ◽  
Vol 31 (02n03) ◽  
pp. 1641035 ◽  
Author(s):  
Bing-Sui Lu ◽  
Ali Naji ◽  
Rudolf Podgornik
Keyword(s):  
Interaction Energy ◽  
Van Der Waals ◽  
Pairwise Interaction ◽  
Van Der Waals Interaction ◽  
Van Der Waals Interactions ◽  
Attractive Interaction ◽  
Gyration Radius ◽  
Interaction Energies ◽  
Anisotropic Interaction ◽  
Decay Behavior

We consider the van der Waals interaction between a pair of polymers with quenched heterogeneous sequences of local polarizabilities along their backbones, and study the effective pairwise interaction energy for both stiff polymers and flexible Gaussian coils. In particular, we focus on the cases where the pair of polarizability sequences are (i) distinct and (ii) identical. We find that the pairwise interaction energies of distinct and identical Gaussian coils are both isotropic and exhibit the same decay behavior for separations larger than their gyration radius, in contradistinction to the orientationally anisotropic interaction energies of distinct and identical stiff polymers. For both Gaussian coils and stiff polymers, the attractive interaction between identical polymers is enhanced if the polarizability sequence is more heterogeneous.

NONADDITIVE EFFECTS IN H2 AND HF TETRAMERS

2004 ◽  
Vol 03 (01) ◽  
pp. 15-22 ◽  
Author(s):  
JINSHAN LI ◽  
FUQIAN JING
Keyword(s):  
Binding Energy ◽  
Interaction Energy ◽  
Minimum Point ◽  
Total Binding Energy ◽  
Interaction Energies ◽  
Body Interaction ◽  
Total Binding ◽  
Intermolecular Distances ◽  
Nonadditive Effects ◽  
Negligible Contribution

Nonadditive three- and four-body interaction energies have been calculated for HF tetramer at the MP2/aug-cc-pVTZ level and for H 2 tetramer at the MP4(SDTQ)/aug-cc-pVTZ level using the so-called fifteen-point method. Calculated results show that with intermolecular distances decreasing from 3.0 to 1.7 Å the nonadditive three- and four-body interactions may be: (a) more and more attractive; (b) more and more repulsive; or (c) extremely weak. Strangely the minimum point of nonadditive three- and four-body interaction potentials has not been found up to now. For both H 2 and HF tetramers the nonadditive four-body interaction energy makes a negligible contribution to total binding energy when intermolecular distances are compressed from 3.0 to 1.7 Å.

scholarly journals New Ligands and New Insights for Vitamin D Receptor from Charge Density

2014 ◽  
Vol 70 (a1) ◽  
pp. C966-C966
Author(s):  
Maura Malińska ◽  
Andrzej Kutner ◽  
Krzysztof Woźniak
Keyword(s):  
Vitamin D ◽  
Hydrogen Bonds ◽  
Charge Density ◽  
Interaction Energy ◽  
Vitamin D Receptor ◽  
Electrostatic Interaction ◽  
Interaction Energies ◽  
Average Strength ◽  
Vitamin D Analogs ◽  
Wide Range

Vitamin D protective effects result from its role as a nuclear transcription factor that regulates cell growth, differentiation, and a wide range of cellular mechanisms crucial to the development and progression of cancer.[1] Many academic investigators and pharmaceutical companies try to develop calcitriol analogs that exhibit equal or even increased anti-proliferative activity while exhibiting a reduced tendency to cause hypercalcemia. Analysis of 24 Vitamin D analogs bearing similar molecular structures with a complex of a Vitamin D Receptor (VDR) enabled the design of new agonists (TB1, TB2, TB3 and TB4). Undertaken approach was to minimize the electrostatic interaction energies available after the reconstruction of charge density with the aid of the pseudoatom databank (UBDB[2]). Comprehensive studies revealed 29 residues crucial for agonist binding. Trp286, which is specific to VDR among the representatives of the Nuclear Receptor Family, plays the crucial role of positioning the ligand forming dispersive interactions, mostly C-H...π, with an average strength of -4 kcal mol-1. The ligand binding pocket is primarily composed of hydrophobic residues, however there are 6 hydrogen bonds characteristic for all the ligands. They electrostatic interaction energies strongly contribute to the total interaction energy, with an average strength of -8, -19, -11 and -12 kcal mol-1 for hydrogen bonds to Ser237, Arg274, Ser278 and Tyr143. The aliphatic chain of the Vitamin D analogs adopt an extended conformation and the 25-hydroxyl group is hydrogen bonded to His305 and His397 with electrostatic interaction energies of -13 and -11 kcal mol-1. The geometries of complexes of the proposed ligand with VDR were obtained by the docking procedure implemented in Autodock4.3[3]. New agonsits form all mentioned before interactions with VDR. The final results of electrostatic interaction energy for TB1 and TB2 are -153 and -120 kcal mol-1, and this results are the smallest among all studied Vitamin D analogs.

scholarly journals Halogen Interactions in Halogenated Oxindoles: Crystallographic and Computational Investigations of Intermolecular Interactions

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5487
Author(s):  
Rodrigo A. Lemos Silva ◽  
Demetrio A. da Silva Filho ◽  
Megan E. Moberg ◽  
Ted M. Pappenfus ◽  
Daron E. Janzen
Keyword(s):  
Interaction Energy ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Basis Set ◽  
Interaction Energies ◽  
Functional Theory ◽  
Basis Set Superposition Error ◽  
Reduced Density Gradient ◽  
Moller Plesset ◽  
Reduced Density

X-ray structural determinations and computational studies were used to investigate halogen interactions in two halogenated oxindoles. Comparative analyses of the interaction energy and the interaction properties were carried out for Br···Br, C-H···Br, C-H···O and N-H···O interactions. Employing Møller–Plesset second-order perturbation theory (MP2) and density functional theory (DFT), the basis set superposition error (BSSE) corrected interaction energy (Eint(BSSE)) was determined using a supramolecular approach. The Eint(BSSE) results were compared with interaction energies obtained by Quantum Theory of Atoms in Molecules (QTAIM)-based methods. Reduced Density Gradient (RDG), QTAIM and Natural bond orbital (NBO) calculations provided insight into possible pathways for the intermolecular interactions examined. Comparative analysis employing the electron density at the bond critical points (BCP) and molecular electrostatic potential (MEP) showed that the interaction energies and the relative orientations of the monomers in the dimers may in part be understood in light of charge redistribution in these two compounds.

scholarly journals Dataset of Noncovalent Intermolecular Interaction Energy Curves for 24 Small High-Spin Open-Shell Dimers

2021 ◽  
Author(s):  
Katarzyna Madajczyk ◽  
Piotr Zuchowski ◽  
Filip Brzęk ◽  
Łukasz Rajchel ◽  
Dariusz Kędziera ◽  
...  
Keyword(s):  
Interaction Energy ◽  
Intermolecular Interaction ◽  
High Spin ◽  
Open Shell ◽  
Basis Set ◽  
Interaction Energies ◽  
Intermolecular Interaction Energy ◽  
Complete Basis ◽  
Complete Basis Set ◽  
Basis Set Extrapolation

<div>We introduce a dataset of 24 interaction energy curves of open-shell noncovalent dimers, referred to as the O24x5 dataset. The dataset consists of high-spin dimers up to eleven atoms selected to assure diversity with respect to interactions types: dispersion, electrostatics and induction. The benchmark interaction energies are obtained at the restricted open-shell CCSD(T) level of theory with complete basis set extrapolation aug-cc-pVQZ--> aug-cc-pV5Z.</div>

scholarly journals Interaction Patterns for Staggered Assembly of Fibrils from Semiflexible Chains

Symmetry ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1926
Author(s):  
Arnoud Jongeling ◽  
Carsten Svaneborg ◽  
Renko de Vries
Keyword(s):  
Interaction Energy ◽  
Self Assembly ◽  
Compact Objects ◽  
The Self ◽  
Interaction Patterns ◽  
Interaction Energies ◽  
Colloidal Interactions ◽  
Dynamics Simulations ◽  
Positively Charged ◽  
Simple Interaction

The design of colloidal interactions to achieve target self-assembled structures has especially been done for compact objects such as spheres with isotropic interaction potentials, patchy spheres and other compact objects with patchy interactions. Inspired by the self-assembly of collagen-I fibrils and intermediate filaments, we here consider the design of interaction patterns on semiflexible chains that could drive their staggered assembly into regular (para)crystalline fibrils. We consider semiflexible chains composed of a finite number of types of interaction beads (uncharged hydrophilic, hydrophobic, positively charged and negatively charged) and optimize the sequence of these interaction beads with respect to the interaction energy of the semiflexible chains in a number of target-staggered crystalline packings. We find that structures with the lowest interaction energies, that form simple lattices, also have low values of L/D (where L is chain length and D is stagger). In the low interaction energy sequences, similar types of interaction beads cluster together to form stretches. Langevin Dynamics simulations confirm that semiflexible chains with optimal sequences self-assemble into the designed staggered (para)crystalline fibrils. We conclude that very simple interaction patterns should suffice to drive the assembly of long semiflexible chains into staggered (para)crystalline fibrils.

scholarly journals Analysis of Three-Phase Structure of Epoxy Resin/CNT/Graphene by Molecular Simulation

Polymers ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 1821
Author(s):  
Shun Naito ◽  
Jun Koyanagi ◽  
Takuji Komukai ◽  
Toshikazu Uno
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Carbon Fiber ◽  
Epoxy Resin ◽  
Interaction Energy ◽  
Phase Structure ◽  
Initial Position ◽  
Interaction Energies ◽  
Three Phase ◽  
Dynamics Models

In this study, the three-phase structure consisting of epoxy resin, carbon nanotubes (CNTs), and graphene, which is assumed to be the surface of carbon fiber, was simulated using molecular dynamics. Models in which the CNT number and initial position of CNT are varied were prepared in this study. Relaxation calculation for each three-phase model was implemented, and the movement of molecules was investigated. When CNTs are located between the graphene and epoxy at initial, how the epoxy approaches to graphene was discussed. Besides, interaction energies between CNT/graphene, CNT/epoxy, and graphene/epoxy were evaluated after relaxations. The value of the interaction energy between two individual molecules (epoxy resin and graphene, CNTs and graphene, epoxy resin and CNTs) among three-phase structure were obtained, respectively, and those mechanisms were discussed in this study.

Comparison of the selectivity of [M(12-Crown-4)]+ (M=Li+, Na+, K+) complexes for halide anions and some neutral molecules; a computational study

2015 ◽  
Vol 14 (08) ◽  
pp. 1550057 ◽  
Author(s):  
Faranak Dastineh ◽  
Sadegh Salehzadeh ◽  
Mehdi Bayat ◽  
Yazdan Maghsoud
Keyword(s):  
Interaction Energy ◽  
Gas Phase ◽  
High Selectivity ◽  
Theoretical Study ◽  
Computational Study ◽  
Decomposition Analysis ◽  
Interaction Energies ◽  
Halide Anions ◽  
Bonding Interaction ◽  
M 12

A theoretical study on the selectivity of a series of [M(12C4)][Formula: see text] (M = Li[Formula: see text], Na[Formula: see text], K[Formula: see text], 12C4 = 12-crown-4) complexes for F[Formula: see text], Cl[Formula: see text] and Br[Formula: see text] anions and a number of neutral molecules (CH3CN, CH3OH, NH3, H2O, py, and 12C4) is reported. At first, it was shown that in the gas phase among all studied halide anions and neutral molecules, halides have much more bonding interaction with all [M(12C4)][Formula: see text] cations. Calculated interaction energies of above anions and [M(12C4)][Formula: see text] cations decrease from F[Formula: see text] to Br[Formula: see text]. Also the interaction energy of halide anions with [M(12C4)][Formula: see text] complexes, decreases from [Li(12C4)][Formula: see text] to [K(12C4)][Formula: see text]. The electron decomposition analysis showed that the bond between [M(12C4)][Formula: see text] complexes and both the neutral and anion guests is mainly electrostatic in nature. Then the selectivity of [M(12C4)][Formula: see text] complexes for studied anions and neutral molecules are compared in methanol, acetone, acetonitrile, and nitromethane solutions. It was shown that both the desolvation process of reactants and the strength of host–guest interactions have significant effect on the selectivities. Thus the selectivity of [Li(12C4)][Formula: see text] cation for NH3and H2O neutral molecules in solution, in contrast to the gas phase, is higher than that for bromide anion. The results of calculations showed that all [M(12C4)][Formula: see text] complexes, specially [Li(12C4)][Formula: see text], have high selectivity for F[Formula: see text] over other halide anions and neutral molecules.

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