Two acetylamino derivatives of 2,4-bis(trichloromethyl)-1,3-benzdioxin showing different types of hydrogen bonding: (a) (C13C)CH?O=C and (b) N-H?O=C

1992 ◽  
Vol 22 (5) ◽  
pp. 533-540 ◽  
Author(s):  
Anne Irving
Keyword(s):  
Hydrogen Bonding ◽  
Different Types ◽  
Derivatives Of

Two-dimensional condensation of nucleobases: A comparative study of halogen derivatives of cytosine

2009 ◽  
Vol 74 (11-12) ◽  
pp. 1611-1622 ◽  
Author(s):  
Lukáš Fojt ◽  
Vladimír Vetterl ◽  
Thomas Doneux
Keyword(s):  
Hydrogen Bonding ◽  
Intermolecular Interactions ◽  
Electrostatic Interactions ◽  
Dispersion Forces ◽  
Two Dimensional ◽  
Electrode Surfaces ◽  
Different Types ◽  
Self Association ◽  
Derivatives Of ◽  
Third Derivative

The high ability of self-association of nucleic acid components leads to a two-dimensional (2D) condensation at electrode surfaces. The driving force of the process resides in the intermolecular interactions, such as dispersion forces, hydrogen bonding or electrostatic interactions. In this study, the condensation of 5-halogen cytosine derivatives (5-fluorocytosine, 5-bromocytosine and 5-iodocytosine) at the hanging mercury drop electrode was investigated to evaluate the influence of the different types of intermolecular interactions in the phenomenon. All of these derivatives form 2D capacitance pits, but in distinct conditions of pH, concentrations and temperature. Dispersion forces are identified as the main contributor to the 2D condensation of 5-iodocytosine, while for 5-fluorocytosine this is hydrogen bonding in hemiprotonated dimers. The third derivative, 5-bromocytosine, is an intermediate case between the two formers.

Quasi-Barrierless Submolecular Motion in Mechanically Interlocked Carbon Nanotubes

2020 ◽  
Author(s):  
Julia Villalva ◽  
Belén Nieto-Ortega ◽  
Manuel Melle-Franco ◽  
Emilio Pérez
Keyword(s):  
Density Functional ◽  
Close Contact ◽  
Tight Binding ◽  
Energetic Cost ◽  
Molecular Fragments ◽  
Activation Barriers ◽  
Flat Surfaces ◽  
Different Types ◽  
Atomically Flat ◽  
Derivatives Of

The motion of molecular fragments in close contact with atomically flat surfaces is still not fully understood. Does a more favourable interaction imply a larger barrier towards motion even if there are no obvious minima? Here, we use mechanically interlocked rotaxane-type derivatives of SWNTs (MINTs) featuring four different types of macrocycles with significantly different affinities for the SWNT thread as models to study this problem. Using molecular dynamics, we find that there is no direct correlation between the interaction energy of the macrocycle with the SWNT and its ability to move along or around it. Density functional tight-binding calculations reveal small (<2.5 Kcal·mol-1) activation barriers, the height of which correlates with the commensurability of the aromatic moieties in the macrocycle with the SWNT. Our results show that macrocycles in MINTs rotate and translate freely around and along SWNTs at room temperature, with an energetic cost lower than the rotation around the C−C bond in ethane.<br>

scholarly journals Hydrated metal(II) complexes of N-(6-amino-3,4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl) derivatives of glycine, glycylglycine, threonine, serine, valine and methionine: a monomeric complex and coordination polymers in one, two and three dimensions linked by hydrogen bonding. Corrigendum

2006 ◽  
Vol 62 (1) ◽  
pp. 165-165
Author(s):  
M. Luz Godino Salido ◽  
Paloma Arranz Mascarós ◽  
Rafaél López Garzón ◽  
M. Dolores Gutiérrez Valero ◽  
John N. Low ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Synchrotron Radiation ◽  
Data Collection ◽  
Coordination Polymers ◽  
Data Reduction ◽  
Three Dimensions ◽  
Compound Viii ◽  
Monomeric Complex ◽  
Cell Refinement ◽  
Derivatives Of

Some of the data collection details for compound (VIII) were incorrectly given in Table 1 of Godino Salido et al. (2004). The data for compound VIII in this paper were collected using synchrotron radiation at the Daresbury SRS station 9.8, λ = 0.6935 Å (Cernik et al., 1997; Clegg, 2000). The data were collected using a Bruker SMART 1K CCD diffractometer using ω rotation with narrow frames. The computer program used in the data collection was SMART (Bruker, 2001) and for cell refinement and data reduction SAINT (Bruker, 2001).

Proton spin–spin coupling constants and intramolecular hydrogen bonding in bromine derivatives of 1,3-dihydroxybenzene

1976 ◽  
Vol 54 (14) ◽  
pp. 2228-2230 ◽  
Author(s):  
Ted Schaefer ◽  
J. Brian Rowbotham
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Proton Spin ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Hydroxyl Groups ◽  
Oh Groups ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling ◽  
Derivatives Of

The conformational preferences in CCl4 solution at 32 °C of the hydroxyl groups in bromine derivatives of 1,3-dihydroxybenzene are deduced from the long-range spin–spin coupling constants between hydroxyl protons and ring protons over five bonds. Two hydroxyl groups hydrogen bond to the same bromine substituent in 2-bromo-1,3-dihydroxybenzene but prefer to hydrogen bond to different bromine substituents when available, as in 2,4-dibromo-1,3-dihydroxybenzene. When the OH groups can each choose between two ortho bromine atoms, as in 2,4,6-tribromoresorcinol, they apparently do so in a very nearly statistical manner except that they avoid hydrogen bonding to the common bromine atom.

Beziehungen zwischen Rotationsisomerie, Wasserstoffbrücken-Bindung und Substituenteneffekten der organischen Chemie / Relations between Rotational Isomerism, Hydrogen Bonding, and Substituent Effects in Organic Chemistry

1972 ◽  
Vol 27 (6) ◽  
pp. 663-674 ◽  
Author(s):  
Gotthard H. Krause ◽  
Herbert Hoyer
Keyword(s):  
Hydrogen Bonding ◽  
Substituent Effects ◽  
Intramolecular Hydrogen Bonding ◽  
Rotational Isomerism ◽  
Proton Acceptor ◽  
Single Bond ◽  
Free Enthalpy ◽  
Acceptor Group ◽  
Intramolecular Hydrogen ◽  
Derivatives Of

The change of free enthalpy involved in intramolecular hydrogen bonding is smaller if the proton acceptor group can rotate round a single bond, as compared to proton acceptor groups which are fixed in a position optimal for hydrogen bonding. Also, the free enthalpy change is altered when the rotation of the proton acceptor is sterically restricted. This is demonstrated by comparing the absorptions of carbonyl stretching vibrations in the infrared spectra of certain compounds showing rotational isomerism. In the present study derivatives of 5-hydroxy-2,2-dimethyl-6-carbomethoxychromanone- (4), 3-nitrosalicylaldehyde and 3-nitro-2-hydroxy-acetophenones substituted in the position 5 and 6 are examined.

scholarly journals Crystal structures of four dimeric manganese(II) bromide coordination complexes with various derivatives of pyridine N-oxide

2019 ◽  
Vol 75 (8) ◽  
pp. 1284-1290
Author(s):  
Sheridan Lynch ◽  
Genevieve Lynch ◽  
Will E. Lynch ◽  
Clifford W. Padgett
Keyword(s):  
Hydrogen Bonding ◽  
Solvent Molecule ◽  
Bound Water ◽  
Manganese Atom ◽  
Coordination Complexes ◽  
Water Molecules ◽  
Inversion Center ◽  
Dimeric Complex ◽  
Bromide Ions ◽  
Derivatives Of

Four manganese(II) bromide coordination complexes have been prepared with four pyridine N-oxides, viz. pyridine N-oxide (PNO), 2-methylpyridine N-oxide (2MePNO), 3-methylpyridine N-oxide (3MePNO), and 4-methylpyridine N-oxide (4MePNO). The compounds are bis(μ-pyridine N-oxide)bis[aquadibromido(pyridine N-oxide)manganese(II)], [Mn2Br4(C5H5NO)4(H2O)2] (I), bis(μ-2-methylpyridine N-oxide)bis[diaquadibromidomanganese(II)]–2-methylpyridine N-oxide (1/2), [Mn2Br4(C6H7NO)2(H2O)4]·2C6H7NO (II), bis(μ-3-methylpyridine N-oxide)bis[aquadibromido(3-methylpyridine N-oxide)manganese(II)], [Mn2Br4(C6H7NO)4(H2O)2] (III), and bis(μ-4-methylpyridine N-oxide)bis[dibromidomethanol(4-methylpyridine N-oxide)manganese(II)], [Mn2Br4(C6H7NO)4(CH3OH)2] (IV). All the compounds have one unique MnII atom and form a dimeric complex that contains two MnII atoms related by a crystallographic inversion center. Pseudo-octahedral six-coordinate manganese(II) centers are found in all four compounds. All four compounds form dimers of Mn atoms bridged by the oxygen atom of the PNO ligand. Compounds I, II and III exhibit a bound water of solvation, whereas compound IV contains a bound methanol molecule of solvation. Compounds I, III and IV exhibit the same arrangement of molecules around each manganese atom, ligated by two bromide ions, oxygen atoms of two PNO ligands and one solvent molecule, whereas in compound II each manganese atom is ligated by two bromide ions, one O atom of a PNO ligand and two water molecules with a second PNO molecule interacting with the complex via hydrogen bonding through the bound water molecules. All of the compounds form extended hydrogen-bonding networks, and compounds I, II, and IV exhibit offset π-stacking between PNO ligands of neighboring dimers.

scholarly journals A computational study on how structure influences the optical properties in model crystal structures of amyloid fibrils

2017 ◽  
Vol 19 (5) ◽  
pp. 4030-4040 ◽  
Author(s):  
Luca Grisanti ◽  
Dorothea Pinotsi ◽  
Ralph Gebauer ◽  
Gabriele S. Kaminski Schierle ◽  
Ali A. Hassanali
Keyword(s):  
Optical Properties ◽  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Crystal Structures ◽  
Amyloid Fibrils ◽  
Computational Study ◽  
Model Systems ◽  
Hydrogen Bonding Interactions ◽  
Model Crystal ◽  
Different Types

Different types of hydrogen bonding interactions that occur in amyloids model systems and molecular factors that control the susceptibility of the protons to undergo proton transfer and how this couples to the optical properties.

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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