scholarly journals Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions

Crystals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 668 ◽  
Author(s):  
Prashant Kumar ◽  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Intermolecular Interactions ◽  
Critical Points ◽  
Electrostatic Interactions ◽  
Point Of View ◽  
Ionic Crystals ◽  
Interaction Energies ◽  
Electron Densities ◽  
Charge Densities ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π…π stacking and many other kinds of non-covalent atom–atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449–469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (Ees) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to Ees. To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (EEML) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between EEML and Ees. However, strong relation between EEML and the charge penetration component of Ees is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom–atom approach to analyse non-covalent interactions do complement each other, even in ionic systems.

scholarly journals Interactions between large molecules pose a puzzle for reference quantum mechanical methods

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yasmine S. Al-Hamdani ◽  
Péter R. Nagy ◽  
Andrea Zen ◽  
Dennis Barton ◽  
Mihály Kállay ◽  
...  
Keyword(s):  
Experimental Information ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Small Organic Molecules ◽  
Large Molecules ◽  
Reference Information ◽  
Mechanical Methods ◽  
Non Covalent Interactions ◽  
Semi Empirical ◽  
Covalent Interactions

AbstractQuantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol−1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.

scholarly journals Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall

2018 ◽  
Author(s):  
Alister T. Boags ◽  
Firdaus Samsudin ◽  
Syma Khalid
Keyword(s):  
Cell Wall ◽  
Electrostatic Interactions ◽  
Cell Envelope ◽  
Binding Domain ◽  
Gram Negative Bacteria ◽  
Inner Membrane ◽  
E Coli ◽  
Non Covalent Interactions ◽  
Covalent Interactions

SUMMARYWe present a molecular modeling and simulation study of the of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. We show that non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. When OmpA is truncated to remove the peptidoglycan binding domain, TolR is able to pull the cell wall down towards the inner membrane. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria.

Quantitative analysis of weak non-covalent interactions in (Z)-3-(4-halophenyl)-2-(pyridin-2/3/4-yl)acrylonitriles

CrystEngComm ◽  
2018 ◽  
Vol 20 (19) ◽  
pp. 2681-2697 ◽  
Author(s):  
Perumal Venkatesan ◽  
Margarita Cerón ◽  
Subbiah Thamotharan ◽  
Fernando Robles ◽  
M. Judith Percino
Keyword(s):  
Quantitative Analysis ◽  
Intermolecular Interactions ◽  
Theoretical Investigation ◽  
Non Covalent Interactions ◽  
Covalent Interactions

A detailed experimental and theoretical investigation on the intermolecular interactions in (Z)-3-(4-halophenyl)-2-(pyridin-2/3/4-yl)acrylonitriles is reported and different π staking motifs observed in these structures.

Destabilization is as important as binding

1993 ◽  
Vol 345 (1674) ◽  
pp. 3-10 ◽  
Keyword(s):  
Binding Energy ◽  
Gibbs Energy ◽  
Active Site ◽  
Electrostatic Interactions ◽  
Large Fraction ◽  
Geometric Distortion ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Enzymes make use of non-covalent interactions with their substrates to bring about a large fraction of their catalytic activity. These interactions must destabilize, or increase the Gibbs energy, of the substrate in the active site in order that the transition state can be reached easily. This destabilization may be brought about by utilization of the intrinsic binding energy between the active site and the bound substrate by desolvation of charged groups, geometric distortion, electrostatic interactions and, especially, loss of entropy in the enzyme-substrate complex. These mechanisms are described by interaction energies and require utilization of the intrinsic binding energy that is realized from non-covalent interactions between the enzyme and substrate. Receptors and coupled vectorial processes, such as muscle contraction and active transport, utilize binding energy similarly to avoid large peaks and valleys along the Gibbs energy profile of the reaction under physiological conditions.

Performance of Becke’s half-and-half functional for non-covalent interactions: energetics, geometries and electron densities

2009 ◽  
Vol 15 (9) ◽  
pp. 1051-1060 ◽  
Author(s):  
Konstantinos Gkionis ◽  
J. Grant Hill ◽  
Steven P. Oldfield ◽  
James A. Platts
Keyword(s):  
Electron Densities ◽  
Non Covalent Interactions ◽  
Covalent Interactions

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

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.

scholarly journals Steric “attraction”: not by dispersion alone

2018 ◽  
Vol 14 ◽  
pp. 1482-1490 ◽  
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.

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

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.

Molecular Interactions within the Crystal Packing of Busulfan (DNA Cross-Linking Agent) by Hirshfeld Surface Analysis

2020 ◽  
Vol 10 (3) ◽  
pp. 199-205
Author(s):  
Datla Rajaniverma ◽  
Dasari J. Rao ◽  
Shaikh R. Begum ◽  
Vishnubolta Seetaramaiah ◽  
Yajjala Ramakrishna ◽  
...  
Keyword(s):  
Surface Analysis ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Crystallographic Structure ◽  
Surface Mapping ◽  
Fingerprint Plot ◽  
Theoretical Approaches ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Background: Non-Covalent Interactions (NCIs) play a vital role in the chemical process. Certain Experimental and theoretical approaches provide information about the stronger and weaker interactions. In the present work, we have implemented Hirshfeld charges based surface mapping to find the weaker interactions between the molecules of busulfan. Objective: The main objective of this work is to recognize the non-covalent interactions which are not simply drawn from the experimental and conventional theoretical approach. It aims to provide more insightful information into the crystallographic structure. Methods: In the present work, we have implemented a Hirshfeld surface mapping which incorporates periodic boundary conditions of the crystalline geometry. Each point of the isosurface is defined by two distances i.e. de, the distance from the point to the nearest atom outside to the surface and di, the distance to the nearest atom inside the surface. Also, for precise identification of intermolecular interactions, mapping by normalized contact distance dnorm is also considered. Fingerprint plot di vs de for various types of interactions were also provided. Results: The Hirshfeld surface and fingerprint plot show the very weak H···H interactions in addition to the O···H interactions. This enables the visualization of very weak interactions. Conclusion: This proposed work on Hirschfeld surface analysis accounts for the solidstate environment of the busulfan, crystallographic parameters and packing information. Hence, the interactions obtained for monomer and extended molecular framework in this work are more reliable to study the intermolecular interactions. The 2D finger print plots revealed the predominant O⋅⋅⋅H interactions within the crystal packing. In addition to O⋅⋅⋅H interactions, H⋅⋅⋅H interaction were also identified.

Sign in / Sign up

Export Citation Format

Share Document