scholarly journals Reliable Comparison of Pnicogen, Chalcogen, and Halogen Bonds in Complexes of 6-OXF2-Fulvene (X = As, Sb, Se, Te, Be, I) With Three Electron Donors

2020 ◽  
Vol 8 ◽  
Author(s):  
Na Liu ◽  
Qingzhong Li ◽  
Sean A. C. McDowell
Keyword(s):  
Interaction Energy ◽  
Electrostatic Interaction ◽  
Halogen Bond ◽  
Electron Donors ◽  
Stable Complex ◽  
Interaction Energies ◽  
Halogen Bonds ◽  
Nitrogen Base ◽  
Pnicogen Bond ◽  
Polarization Contribution

The pnicogen, chalcogen, and halogen bonds between 6-OXF2-fulvene (X = As, Sb, Se, Te, Br, and I) and three nitrogen-containing bases (FCN, HCN, and NH3) are compared. For each nitrogen base, the halogen bond is strongest, followed by the pnicogen bond, and the chalcogen bond is weakest. For each type of bond, the binding increases in the FCN < HCN < NH3 pattern. Both FCN and HCN engage in a bond with comparable strengths and the interaction energies of most bonds are < −6 kcal/mol. However, the strongest base NH3 forms a much more stable complex, particularly for the halogen bond with the interaction energy going up to −18 kcal/mol. For the same type of interaction, its strength increases as the mass of the central X atom increases. These bonds are different in strength, but all of them are dominated by the electrostatic interaction, with the polarization contribution important for the stronger interaction. The presence of these bonds changes the geometries of 6-OXF2-fulvene, particularly for the halogen bond formed by NH3, where the F-X-F arrangement is almost vertical to the fulvene ring.

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 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.

A simple model for halogen bonds

2018 ◽  
Author(s):  
Robert A. Shaw ◽  
Grant Hill
Keyword(s):  
Simple Model ◽  
Statistical Model ◽  
Halogen Bond ◽  
Coupled Cluster ◽  
Interaction Energies ◽  
Halogen Bonds ◽  
Bond Interaction ◽  
Explicitly Correlated ◽  
Equilibrium Geometries

In this article we develop a simple statistical model for the prediction of halogen bond interaction energies at equilibrium geometries. The model is based on explicitly correlated coupled cluster results and produces root-mean-squared deviations of 0.14 and 0.28 kcal mol<sup>–1</sup> over separate fitting and validation sets, respectively. We also show how the model can be used to highlight cases where induction or dispersion significantly affect the underlying nature of the interaction.<br>

scholarly journals Halogen…π Interactions in the Complexes of Fluorenonophane With Haloforms

2021 ◽  
Author(s):  
Svitlana V. Shishkina ◽  
Viktoriya V. Dyakonenko ◽  
Oleg V. Shishkin ◽  
Volodimir P. Semynozhenko ◽  
Tatiana Yu. Bogashchenko ◽  
...  
Keyword(s):  
Halogen Atom ◽  
Halogen Bond ◽  
Bromine Atom ◽  
Quantum Chemical Study ◽  
Halogen Bonding ◽  
Chemical Study ◽  
Interaction Energies ◽  
Halogen Bonds ◽  
Guest Molecules ◽  
True Energy

Abstract The study of two complexes of fluorenonophane with CHCl3 and CHBr3 molecules has revealed that they differ mainly by the halogen bonds between host and guest molecules. The experimental and theoretical quantum chemical study has shown that the strength of a halogen bond depends on the nature of a halogen atom as well as its orientation to the π-system. The more positive electrostatic potential was revealed at the bromine atom indicating the stronger halogen bond with its participation that was confirmed by the interaction energies calculated for corresponding dimers and the evaluation of the true energy of a halogen bond. The orientation of the chlorine atom at the carbon aromatic atom instead of the center of the benzene ring leads to the shortest Hal…C distance that points out the stronger interaction according to the geometrical characteristics. The EDA analysis of the fluorenonophane complexes with CHCl3 and CHBr3 and their analogs with one halogen atom replaced by the hydrogen atom allows us to presume that the nature of halogen bonding is rather dispersive than electrostatic.

A simple model for halogen bonds

2018 ◽  
Author(s):  
Robert A. Shaw ◽  
Grant Hill
Keyword(s):  
Simple Model ◽  
Statistical Model ◽  
Halogen Bond ◽  
Coupled Cluster ◽  
Interaction Energies ◽  
Halogen Bonds ◽  
Bond Interaction ◽  
Explicitly Correlated ◽  
Equilibrium Geometries

In this article we develop a simple statistical model for the prediction of halogen bond interaction energies at equilibrium geometries. The model is based on explicitly correlated coupled cluster results and produces root-mean-squared deviations of 0.14 and 0.28 kcal mol<sup>–1</sup> over separate fitting and validation sets, respectively. We also show how the model can be used to highlight cases where induction or dispersion significantly affect the underlying nature of the interaction.<br>

scholarly journals Strength of the [Z–I···Hal]− and [Z–Hal···I]− Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 2083
Author(s):  
Maxim L. Kuznetsov
Keyword(s):  
Bond Length ◽  
Interaction Energy ◽  
Electron Density ◽  
Halogen Bond ◽  
Bond Critical Point ◽  
Halogen Bonds ◽  
Curvature Potential ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, Eint, using relationships between Eint and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between Eint and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z–I···Hal]– and [Z–Hal···I]– types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06–4.76 kcal/mol.

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.

Electrostatic interaction energies with overlap effects from a localized approach

2007 ◽  
Vol 445 (4-6) ◽  
pp. 315-320 ◽  
Author(s):  
Fazle Rob ◽  
Rafał Podeszwa ◽  
Krzysztof Szalewicz
Keyword(s):  
Electrostatic Interaction ◽  
Interaction Energies

Molecular tapes in the structure of isoguaninium chloride

2017 ◽  
Vol 74 (1) ◽  
pp. 108-112 ◽  
Author(s):  
Urszula Anna Budniak ◽  
Paulina Maria Dominiak
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Charge Density ◽  
Interaction Energy ◽  
Electrostatic Interaction ◽  
Electrostatic Interactions ◽  
The Other ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Structure

Isoguanine, an analogue of guanine, is of intrinsic interest as a noncanonical nucleobase. The crystal structure of isoguaninium chloride (systematic name: 6-amino-2-oxo-1H,7H-purin-3-ium chloride), C5H6N5O+·Cl−, has been determined by single-crystal X-ray diffraction. Structure analysis was supported by electrostatic interaction energy (E es) calculations based on charge density reconstructed with the UBDB databank. In the structure, two kinds of molecular tapes are observed, one parallel to (010) and the other parallel to (50\overline{4}). The tapes are formed by dimers of isoguaninium cations interacting with chloride anions. E es analysis indicates that cations in one kind of tape are oriented so as to minimize repulsive electrostatic interactions.

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