Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions

Kumar, Prashant; Cabaj, Małgorzata Katarzyna; Pazio, Aleksandra; Dominiak, Paulina M.

doi:10.1107/s2052252518006346

Cited by 12 publications

(30 citation statements)

References 142 publications

(117 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Topology analysis done in MoPro led to the same results as the one from XD2016. Bond paths (BPs) and bond critical points (BCPs) were found (see HB in Table 1) for almost all hydrogen bonds previously identified on the basis of geometry (see HB in Table 3 in [30]), regardless if they are formed between cations and anions or between two cations. The range of values of BCP properties are similar to the ones for neutral base pairs [59,60].…”

Section: Qtaim Analysismentioning

confidence: 97%

“…The following charge density models of cytosinum chloride (CC), adeninium chloride hemihydrate (ACH) and guaninium dichloride (GDC) crystals were taken from [30] and continued to be analysed in this paper: a) Experimental charge densities (Exp.) in the Stewart-Hansen-Coppens [31,32] multipole model (MM) representation with the Cl -1 ion scattering radial function and ion configuration; b) Charge densities reconstructed with University at Buffalo Databank (UBDB) in the Stewart-Hansen-Coppens multipole model representation parameterised on experimental geometries using the LSDB program [33] and the UBDB2011 version of the databank [34]; c) Theoretical electron densities computed directly from periodic wave functions obtained from periodic quantum mechanical geometry optimization (Theo.…”

Section: Crystal Charge Density Modelsmentioning

confidence: 99%

Section: Crystal Charge Density Modelsmentioning

confidence: 99%

“…The following interaction energies for isolated dimers with geometry as found in studied crystals were taken from [30] and continued to be analysed in this paper:…”

Section: Intermolecular Interaction Energies and Electrostatic Contrimentioning

confidence: 99%

“…Our aim is to qualitatively and quantitatively characterise these interactions in order to understand the interplay between the molecular and crystal architecture in ionic systems. In the first paper [30] of the series we provided detailed structural analysis of molecular motifs found in the studied crystals to give a basis for further charge Crystals 2019, 9,668 3 of 17 density and energy investigations. We discovered that molecules in the studied crystals are not fully ionized and some dimers of single protonated bases, namely cytosinium-cytosinium trans sugar/sugar edge pairs and adeninium-adeninium trans Hoogsteen/Hoogsteen edge pairs, exhibited attractive electrostatic interactions or unusually low repulsion despite identical molecular charges.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

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

2019

Self Cite

View full text Add to dashboard Cite

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 (E es ) 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 E es . To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (E EML ) 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 E EML and E es . However, strong relation between E EML and the charge penetration component of E es 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.

show abstract

Section: Qtaim Analysismentioning

confidence: 97%

Section: Crystal Charge Density Modelsmentioning

confidence: 99%

Section: Crystal Charge Density Modelsmentioning

confidence: 99%

“…The following interaction energies for isolated dimers with geometry as found in studied crystals were taken from [30] and continued to be analysed in this paper:…”

Section: Intermolecular Interaction Energies and Electrostatic Contrimentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

2019

Self Cite

View full text Add to dashboard Cite

show abstract

Energetic, Topological and Electric Field Analyses of Cation‐Cation Nucleic Acid Interactions in Watson‐Crick Disposition

et al. 2018

View full text Add to dashboard Cite

A theoretical study of the effect of the diprotonation on the nucleic acid bases (A : U, A : T and G : C) in Watson‐Crick conformation has been carried out by means of DFT computational methods in vacuum. In addition, the corresponding neutral and monoprotonated binary complexes have been considered. Most of the diprotonated species studied are stable, even though the binding energy is positive due to the overall repulsive electrostatic term. Local electrostatic attractive forces in the regions of hydrogen bonds (HBs) are responsible for equilibrium geometries, as shown by the electric field lines connecting the electrophilic and nucleophilic sites involved in the HB interactions. Secondary electrostatic effects also affect the assembling of the nucleic acid complexes in either neutral or cationic form. In particular, the electric field lines flowing from electrophilic sites in one base to nucleophilic sites in the other reinforce the linking between them. Hence, when the nucleophilic site concerns the free lone pair of the heteroatom involved in the HB interaction as acceptor, the HB distance shortens. However, if the free lone pair of the HB acceptor interacts with an electrophilic site in the same molecule, the HB distance elongates, weakening the HB interaction. The topological analysis of the electron density distribution in HB regions indicates that neutral, monoprotonated and diprotonated complexes show no differences in the nature of their HB's.

show abstract

Electron density is not spherical: the many applications of the transferable aspherical atom model

Kulik

Dominiak

2022

Computational and Structural Biotechnology Journal

View full text Add to dashboard Cite

Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions

Cited by 12 publications

References 142 publications

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

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

Energetic, Topological and Electric Field Analyses of Cation‐Cation Nucleic Acid Interactions in Watson‐Crick Disposition

Electron density is not spherical: the many applications of the transferable aspherical atom model

Contact Info

Product

Resources

About