scholarly journals The Topological Analysis of the ELFx Localization Function: Quantitative Prediction of Hydrogen Bonds in the Guanine–Cytosine Pair

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3336
Author(s):  
Johanna Klein ◽  
Paul Fleurat-Lessard ◽  
Julien Pilmé
Keyword(s):  
Hydrogen Bonds ◽  
Global Minimum ◽  
Reaction Pathway ◽  
Topological Analysis ◽  
Stationary Points ◽  
Quantitative Prediction ◽  
Base Pairs ◽  
Localization Function ◽  
Favorable Reaction

In this contribution, we recall and test a new methodology designed to identify the favorable reaction pathway between two reactants. Applied to the formation of the DNA guanine (G) –cytosine (C) pair, we successfully predict the best orientation between the base pairs held together by hydrogen bonds and leading to the formation of the typical Watson Crick structure of the GC pair. Beyond the global minimum, some local stationary points of the targeted pair are also clearly identified.

scholarly journals Deciphering the Mechanism of Silver Catalysis of “Click” Chemistry in Water by Combining Experimental and MEDT Studies

Catalysts ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 956
Author(s):  
Hicham Ben El Ayouchia ◽  
Lahoucine Bahsis ◽  
Ismail Fichtali ◽  
Luis R. Domingo ◽  
Mar Ríos-Gutiérrez ◽  
...  
Keyword(s):  
Click Chemistry ◽  
Density Functional ◽  
Reaction Pathway ◽  
Topological Analysis ◽  
Intramolecular Interactions ◽  
Stationary Points ◽  
Ionic Character ◽  
Energy Barriers ◽  
Covalent Interaction ◽  
Mechanistic Pathway

A combined experimental study and molecular electron density theory (MEDT) analysis was carried out to investigate the click of 1,2,3-triazole derivatives by Ag(I)-catalyzed azide-alkyne cycloaddition (AgAAC) reaction as well as its corresponding mechanistic pathway. Such a synthetic protocol leads to the regioselective formation of 1,4-disubstituted-1,2,3-triazoles in the presence of AgCl as catalyst and water as reaction solvent at room temperature and pressure. The MEDT was performed by applying Density Functional Theory (DFT) calculations at both B3LYP/6-31G(d,p) (LANL2DZ for Ag) and ωB97XD/6-311G(d,p) (LANL2DZ for Ag) levels with a view to decipher the observed regioselectivity in AgAAC reactions, and so to set out the number of silver(I) species and their roles in the formation of 1,4-disubstituted-1,2,3-triazoles. The comparison of the values of the energy barriers for the mono- and dinuclear Ag(I)-acetylide in the AgAAC reaction paths shows that the calculated energy barriers of dinuclear processes are smaller than those of the mononuclear one. The type of intramolecular interactions in the investigated AgAAC click chemistry reaction accounts for the regioselective formation of the 1,4-regiosisomeric triazole isomer. The ionic character of the starting compounds, namely Ag-acetylide, is revealed for the first time. This finding rules out any type of covalent interaction, involving the silver(I) complexes, along the reaction pathway. Electron localization function (ELF) topological analysis of the electronic structure of the stationary points reaffirmed the zw-type (zwitterionic-type) mechanism of the AgAAC reactions.

The Order of Phase Transition of Solvable DNA Melting Models

2003 ◽  
Vol 17 (16) ◽  
pp. 885-896 ◽  
Author(s):  
Su-Long Nyeo ◽  
I-Ching Yang
Keyword(s):  
Phase Transition ◽  
Hydrogen Bonds ◽  
Short Range ◽  
Scaling Laws ◽  
Dna Melting ◽  
Thermodynamic Quantities ◽  
Base Pairs ◽  
Order Of Phase Transition ◽  
Exactly Solvable ◽  
Dna Models

The phase transition of DNA molecules is studied in an exactly solvable formalism with the Morse and Deng–Fan potentials for the interstrand hydrogen bonds of nucleotide base pairs. It is shown that although the two potentials have different short-range behaviors, the thermodynamic quantities of the DNA system in these potentials enjoy the same scaling laws with the associated critical exponents, which are explicitly calculated. These exactly solvable DNA models are shown to exhibit a phase transition of the second order and the results of the analysis agree with previous studies.

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Single Crystal ◽  
Diffraction Data ◽  
Density Functional ◽  
Quantitative Estimation ◽  
Topological Analysis ◽  
Pyroglutamic Acid ◽  
X Ray Diffraction ◽  
X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs

2017 ◽  
Vol 41 (20) ◽  
pp. 12104-12109 ◽  
Author(s):  
Yulei Shi ◽  
Wanrun Jiang ◽  
Zhiyuan Zhang ◽  
Zhigang Wang
Keyword(s):  
Hydrogen Bonds ◽  
Vibrational Properties ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs

For the AT pair, Symst and Strech peaks further shift toward the red, giving the H-bonds an amplified effect (orange arrows).

Three-centre C—H...O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures

1999 ◽  
Vol 55 (12) ◽  
pp. 2005-2012 ◽  
Author(s):  
Anirban Ghosh ◽  
Manju Bansal
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Base Pair ◽  
Minor Groove ◽  
Local Geometry ◽  
Data Sets ◽  
Base Pairs ◽  
Dna Minor Groove ◽  
Close Proximity ◽  
Using Data

AA·TT and GA·TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 Å) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA·TT and GA·TC steps the electropositive C2—H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C—H...O hydrogen bonds in the DNA minor groove. The C2—H2...O2 hydrogen bonds in the A·T base pairs could be a natural consequence of Watson–Crick pairing. However, the cross-strand interactions between the bases at the 3′-end of the AA·TT and GA·TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2...O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 Å) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A·T base pairs and the hydration of the minor groove, these C2—H2...O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA)·poly(dT).

scholarly journals Weak Hydrogen Bonds in Some Six- and Five-atom Interactions: An AIM Topological Analysis

2013 ◽  
Vol 2 (6) ◽  
pp. 343-346 ◽  
Author(s):  
Francisco Sánchez-Viesca ◽  
Fernando Cortés ◽  
Reina Gómez ◽  
Martha Berros
Keyword(s):  
Hydrogen Bonds ◽  
Topological Analysis ◽  
Weak Hydrogen Bonds

Charge density study of bis(clonixato)bis(ethanol) bis(imidazole)copper(II) complex

2018 ◽  
Vol 233 (9-10) ◽  
pp. 745-752
Author(s):  
Peter Herich ◽  
Lenka Kucková ◽  
Jan Moncol ◽  
Jozef Kožíšek
Keyword(s):  
Hydrogen Bonds ◽  
Copper Atom ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
Aim Analysis ◽  
Experimental Electron Density ◽  
Density Study ◽  
Imidazole Ligands ◽  
Oxygen Atoms

Abstract An experimental electronic structure of bis(clonixato)bis(ethanol) bis(imidazole)copper(II) complex, [Cu(cln)2(im)2(EtOH)2] (cln=clonixato, im=imidazole) (1) has been obtained from single-crystal X-ray diffraction data collected at 100 K using an Incoatec IμS Ag microfocus source. Metal-ligand (ML) bonds and hydrogen bonds (HBs) have been analysed using topological analysis of the experimental electron density with the atoms in molecules (AIM) approach. The central copper atom is octahedrally coordinated by two oxygen atoms from two clonixato anions and two nitrogen atoms from two imidazole ligands in equatorial plane. In axial positions are two oxygen atoms from two ethanol molecules. AIM analysis establishes that the central copper atom is bonded more strongly to the clonixato anion that to the imidazole or ethanol molecules. AIM analysis of two intramolecular and one intermolecular hydrogen bonds permits to estimate their strength. We show that the hydrogen bonds are strong enough to protect the molecule from decomposition in solvent media and to disable the more reactive imidazole-Cu-clonixato complex from interacting with e.g. a macromolecule. The electrostatic potential of the complex shows a highly positive value on the central atom, so the complex is highly reactive in an interaction with negative ligands.

scholarly journals Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

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