Hydrogen Bonding in Mimics of Watson–Crick Base Pairs Involving CH Proton Donor and F Proton Acceptor Groups: A Theoretical Study

ChemPhysChem ◽  
2004 ◽  
Vol 5 (4) ◽  
pp. 481-487 ◽  
Author(s):  
Célia Fonseca Guerra ◽  
F. Matthias Bickelhaupt ◽  
Evert Jan Baerends
Keyword(s):  
Hydrogen Bonding ◽  
Theoretical Study ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Base Pairs

Hydrogen bonding. Part 9. Solute proton donor and proton acceptor scales for use in drug design

1989 ◽  
pp. 1355 ◽  
Author(s):  
Michael H. Abraham ◽  
Philip P. Duce ◽  
David V. Prior ◽  
Derek G. Barratt ◽  
Jeffrey J. Morris ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Drug Design ◽  
Proton Donor ◽  
Proton Acceptor

scholarly journals Detection of Proton-Acceptor Sites of Hydrogen Bonding in Adenine · Uracil Base Pairs by the Use of 15N Magnetic Resonance

2005 ◽  
Vol 117 (3) ◽  
pp. 553-558 ◽  
Author(s):  
Mayumi WATANABE ◽  
Hiromu SUGETA ◽  
Hideo IWAHASHI ◽  
Yoshimasa KYOGOKU ◽  
Masatsune KAINOSHO
Keyword(s):  
Hydrogen Bonding ◽  
Magnetic Resonance ◽  
Proton Acceptor ◽  
Base Pairs ◽  
Uracil Base

A novel supramolecular polymer fabricated via stronger hydrogen-bonding interactions between substituted amide groups: design, synthesis, properties and mechanism

RSC Advances ◽  
2015 ◽  
Vol 5 (102) ◽  
pp. 84104-84112 ◽  
Author(s):  
Ze-Hui Dai ◽  
Lu Qiang ◽  
Li-ming Tang ◽  
Bao-Hua Guo
Keyword(s):  
Hydrogen Bonding ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Supramolecular Polymer ◽  
Cooling Process ◽  
Electron Densities ◽  
Design Synthesis ◽  
Hydrogen Bonding Interactions ◽  
Synthesis Properties

By modulating the electron densities of substitutes of both a proton donor (N–H) and proton acceptor (CO), the molecules of DPCHP-DODE assemble into a supramolecular polymer during the cooling process of the melt DPCHP-DODE.

scholarly journals 7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization

2020 ◽  
Vol 76 (5) ◽  
pp. 513-523
Author(s):  
Dasharath Kondhare ◽  
Simone Budow-Busse ◽  
Constantin Daniliuc ◽  
Frank Seela
Keyword(s):  
Base Pair ◽  
Crystal Packing ◽  
Donor Site ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Acceptor Site ◽  
Base Pairs ◽  
Purine Base ◽  
Value Differences ◽  
Ribose Moiety

The positional change of nitrogen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-deazaguanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′-endo) for the ribose moiety, with an antiperiplanar orientation of the 5′-hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2′ of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H...O and N—H...O). The concept of pK-value differences to evaluate base-pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.

scholarly journals Thermochemistry of Solution, Solvation, and Hydrogen Bonding of Cyclic Amides in Proton Acceptor and Donor Solvents. Amide Cycle Size Effect

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1411
Author(s):  
Ilnaz T. Rakipov ◽  
Artem A. Petrov ◽  
Aydar A. Akhmadiyarov ◽  
Artashes A. Khachatrian ◽  
Timur A. Mukhametzyanov ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Size Effect ◽  
Infinite Dilution ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Solvation Enthalpy ◽  
Specific Contribution

In the present work, the thermochemistry of solution, solvation, and hydrogen bonding of cyclic amides in proton acceptor (B) and proton donor (RXH) solvents were studied. The infinite dilution solution enthalpies of δ-valerolactam, N-methylvalerolactam, ε-caprolactam, and N-methylcaprolactam were measured at 298.15 K. The solvation enthalpies of cyclic amides were calculated based on the measured solution enthalpies and sublimation/vaporization enthalpies from literature. The enthalpies of hydrogen bonding between cyclic amides and proton acceptor and donor solvents were then calculated as a difference between the total solvation enthalpy and the non-specific contribution. The latter was estimated via two different approaches in proton donor and proton accepting solvents. The effect of the cycle size on the strength of hydrogen bonding of the cyclic amides in solution is discussed.

A theoretical study of 3,5-diazido-1,2,4-triazole: the role of the hydrogen bonding interaction in stabilizing the molecular system

2014 ◽  
Vol 92 (9) ◽  
pp. 896-903 ◽  
Author(s):  
Junqing Yang ◽  
Xuedong Gong ◽  
Guixiang Wang
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Density Functional ◽  
Molecular System ◽  
Polarizable Continuum Model ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Good Thermal Stability ◽  
The Stability ◽  
Dynamics Simulations

3,5-Diazido-1, 2, 4-triazole (DATZ) is a compound that has a good thermal stability and can be used to produce high energetic ionic salts. The conformations of DATZ were searched by the molecular dynamics simulations and optimized by the molecular mechanics and dispersion-corrected density functional theory methods. The dimer and trimer of DATZ were constructed from the most stable monomer. The hydrogen bonding interactions, which were found to be critically important in increasing the stability of the dimer and trimer, were investigated with the help of the natural bond orbital and the quantum theory of atoms in molecules analyses. The changes in thermodynamic functions, stabilization interaction energies, and hydrogen-bonding energies show that the trimer is most likely the existing form of DATZ. The intramolecular, intermolecular, and water catalytic proton transfer processes were simulated to investigate the proton transfer mechanism. The intermolecular transfer process requires the lowest activation energy (42.56 kJ mol−1) and is the most likely process of proton transfer. DATZ is not only a proton acceptor but also a proton donor. Its weak acidity was quantified as pKa = 10.16. The solvation energy estimated using the conductor-like polarizable continuum model in water is the largest (−99.96 kJ mol−1), revealing that DATZ is more stable in water than in another seven solvents.

Substituent Effects on Hydrogen Bonding in Watson–Crick Base Pairs. A Theoretical Study

2005 ◽  
Vol 16 (3) ◽  
pp. 211-221 ◽  
Author(s):  
Célia Fonseca Guerra ◽  
Tushar van der Wijst ◽  
F. Matthias Bickelhaupt
Keyword(s):  
Hydrogen Bonding ◽  
Theoretical Study ◽  
Substituent Effects ◽  
Base Pairs

Syntheses and Luminescent Behavior of π-Extended [Ru(bpy)3]2+ Derivatives through Triple Hydrogen Bonds as an Organic-Inorganic Hybridized Material

2006 ◽  
Vol 11-12 ◽  
pp. 277-280 ◽  
Author(s):  
Tomohiro Ozawa ◽  
Y. Kishi ◽  
K. Miyamoto ◽  
Y. Wasada-Tsutsui ◽  
Yasuhiro Funahashi ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Energy Transfer ◽  
High Performance ◽  
Electron System ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Intense Luminescence ◽  
Luminescent Spectra ◽  
Luminescent Behavior

Two new bipyridine derivative ligands with an extended π electron system and a triple hydrogen bond group, 2,4-diaminopyrimido[5,6-b]dipyrido[2,3-f:2’,3’-h]quinoxaline (DAPQ) and 2,4(1H,3H)-pyrimidinedion[5,6-b]dipyrido[2,3-f:2’3’-h]quinoxaline (PDPQ), were synthesized in order to construct high-performance Ru(II) complexes. The two Ru(II) complexes composed of dapq or pdpq and two 2,2’-bipyridine (BPY) ligands showed characteristic luminescent spectra with a peak maximum at ca. 610 nm. The octahedral Ru(II) complexes with a D-A-D (D: proton donor; A: proton acceptor) type triple hydrogen bond indicated intense luminescence in comparison with the corresponding Ru(II) complex composed of three BPY ligands. When the triple hydrogen bond was formed with a Co(III) complex with the D-A-D type hydrogen bonding group, the luminescence was quenched. This result was explained in terms of an energy transfer from an excited Ru(II) complex to the Co(III) complex.

A novel hydrogen-bonding N-oxide–sulfonamide–nitro N—H...O synthon determining the architecture of benzenesulfonamide cocrystals

2022 ◽  
Vol 78 (1) ◽  
Author(s):  
Kinga Wzgarda-Raj ◽  
Agnieszka J. Rybarczyk-Pirek ◽  
Sławomir Wojtulewski ◽  
Marcin Palusiak
Keyword(s):  
Hydrogen Bonding ◽  
Quantum Theory ◽  
Hydrogen Bonds ◽  
Detailed Analysis ◽  
Ternary Complex ◽  
Proton Donor ◽  
Proton Acceptor ◽  
X Ray ◽  
Oxide Group ◽  
Sulfonamide Group

The structures of novel cocrystals of 4-nitropyridine N-oxide with benzenesulfonamide derivatives, namely, 4-nitrobenzenesulfonamide–4-nitropyridine N-oxide (1/1), C5H4N2O3·C6H6N2O4S, and 4-chlorobenzenesulfonamide–4-nitropyridine N-oxide (1/1), C6H6ClNO2S·C5H4N2O3, are stabilized by N—H...O hydrogen bonds, with the sulfonamide group acting as a proton donor. The O atoms of the N-oxide and nitro groups are acceptors in these interactions. The latter is a double acceptor of bifurcated hydrogen bonds. Previous studies on similar crystal structures indicated competition between these functional groups in the formation of hydrogen bonds, with the priority being for the N-oxide group. In contrast, the present X-ray studies indicate the existence of a hydrogen-bonding synthon including N—H...O(N-oxide) and N—H...O(nitro) bridges. We present here a more detailed analysis of the N-oxide–sulfonamide–nitro N—H...O ternary complex with quantum theory computations and the Quantum Theory of Atoms in Molecules (QTAIM) approach. Both interactions are present in the crystals, but the O atom of the N-oxide group is found to be a more effective proton acceptor in hydrogen bonds, with an interaction energy about twice that of the nitro-group O atoms.

Structure of N,4-dinitroaniline and its complex with sulfolane at 85 K; on the proton donor–acceptor affinity of the primary nitramine (HNNO2) group

2001 ◽  
Vol 58 (1) ◽  
pp. 109-115
Author(s):  
J. Zaleski ◽  
Z. Daszkiewicz ◽  
J. B. Kyzioł
Keyword(s):  
Hydrogen Bonding ◽  
Aromatic Ring ◽  
Crystal Packing ◽  
Valence Angle ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Torsion Angles ◽  
Donor Acceptor ◽  
Weak Electron ◽  
Analogous Effect

The NNO2 group of the title compound is significantly less twisted with respect to the aromatic ring in comparison to a typical secondary nitramine. The amide nitrogen is trigonally hybridized. The nitramino group is almost planar. The C—C—N—N torsion angles vary between ca 13 and 42°, whereas the twist along the N—N bond is much smaller and amounts to between ca 1 and 15°. Those twist angles are governed by a crystal packing and are much larger in the case of crystals of pure N,4-dinitroaniline in comparison to that of its complex with sulfolane. The deviations of the internal angles of the aromatic ring from 120° do not exceed 3°. The presence of the nitro group increases the C—C—C valence angle of ca 2.0–2.6°, whereas an analogous effect associated with the nitramino group is much smaller (ca 0.3–1.3°), pointing to its weak electron-withdrawing properties. The nitramino group displays no tendency to conjugate with an electron-demanding substituent across the ring. It participates in hydrogen bonding only as a hydrogen-bonding donor. It does not act as a proton acceptor, despite the fact that nitramine rearrangement is catalysed by acids.

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