ChemInform Abstract: New “Proton Sponge” Compounds. Part 5. “Proton Sponges” and the Geometry of Hydrogen Bonds: Aromatic Nitrogen Bases with Exceptional Basicities

ChemInform ◽  
1988 ◽  
Vol 19 (42) ◽  
Author(s):  
H. A. STAAB ◽  
T. SAUPE
2011 ◽  
Vol 1005 (1-3) ◽  
pp. 12-16 ◽  
Author(s):  
L.Z. Boiko ◽  
V.I. Sorokin ◽  
E.A. Filatova ◽  
Z.A. Starikova ◽  
V.A. Ozeryanskii ◽  
...  

2016 ◽  
Vol 16 (4) ◽  
pp. 2112-2122 ◽  
Author(s):  
Lynne H. Thomas ◽  
Andrew O. F. Jones ◽  
Andras A. Kallay ◽  
Garry J. McIntyre ◽  
Chick C. Wilson

2019 ◽  
pp. 56-62 ◽  
Author(s):  
Gennadiy Vladimirovich Zhizhin

The geometry of the neighborhood of the compound of two nucleic acid helices with nitrogen bases was investigated. It is proved that this neighborhood is a cross-polytope of dimension 13 (polytope of hereditary information), in the coordinate planes of which there are complementary hydrogen bonds of nitrogenous bases. The structure of this polytope is defined, its image is given. The total incident flows from the low-dimensional elements to the higher-dimensional elements and vice versa of the hereditary information polytope are calculated equal to each other. High values of these flows indicate a high intensity of information exchange in the polytope of hereditary information that ensures the transfer of this information


2014 ◽  
Vol 47 (6) ◽  
pp. 2100-2104 ◽  
Author(s):  
Anders Østergaard Madsen ◽  
Anna A. Hoser

A major update of theSHADEserver (http://shade.ki.ku.dk) is presented. In addition to all of the previous options for estimating H-atom anisotropic displacement parameters (ADPs) that were offered bySHADE2, the newest version offers two new methods. The first method combines the original translation–libration–screw analysis with input from periodicab initiocalculations. The second method allows the user to input experimental information from spectroscopic measurements or from neutron diffraction experiments on related structures and utilize this information to evaluate ADPs of H atoms. Tools are provided to set up theab initiocalculations and to derive the internal motion from the calculations. The new server was tested on a range of compounds where neutron diffraction data were available. In most cases, the results are significantly better than previous estimates, and for strong hydrogen bonds in proton sponges, theab initiocalculations become crucial.


Author(s):  
Gennadiy Vladimirovich Zhizhin

The representations of the sugar molecule and the residue of phosphoric acid in the form of polytopes of higher dimension are used. Based on these ideas and their simplified three-dimensional images, a three-dimensional image of nucleic acids is constructed. The geometry of the neighborhood of the compound of two nucleic acid helices with nitrogen bases has been investigated in detail. It is proved that this neighborhood is a cross-polytope of dimension 13 (polytope of hereditary information), in the coordinate planes of which there are complementary hydrogen bonds of nitrogenous bases. The structure of this polytope is defined, and its image is given. The total incident flows from the low-dimensional elements to the higher-dimensional elements and vice versa of the hereditary information polytope are calculated equal to each other. High values of these flows indicate a high intensity of information exchange in the polytope of hereditary information that ensures the transfer of this information.


1998 ◽  
Vol 76 (5) ◽  
pp. 583-611 ◽  
Author(s):  
Katherine N Robertson ◽  
Pradip K Bakshi ◽  
Susanne D Lantos ◽  
T Stanley Cameron ◽  
Osvald Knop

In organoammonium cations containing two or more N atoms, the H(N) atom introduced by the protonation may engage in an N→H(N)...Y bond to an external acceptor (anion or solvent molecule); in an intra-cation (intra-annular) N→H(N)...N' bond; or in a branched N→H(N)...N',Y bond(s), simultaneously intra-cation and to one or more external acceptors. The outcome of the competition for these bond types is determined by various factors, e.g., the size of the ring to be closed by insertion of the H(N) atom, steric accessibility of H(N), and the H-bond-forming strength of Y. Some of these are discussed in considerable detail and are exemplified by the hitherto unreported crystal structures of the tetraphenylborates (solvated or unsolvated) of the 2,2':6',2"-terpyridinium (1), 2,3-bis(2-pyridyl)pyrazinium (2), 2,2'-dipyridylammonium (3), 6,7-dihydro[b,j][1,10]phenanthrolinium (9), 2,4,7-triamino-6-pteridinium (triamterenium, 10), proton-sponge (1-Me2N-8-Me2NH-naphthalene, 11, 12), and 9-amino-1,2,3,4-tetrahydroacridinium (tacrinium, 13) cations. The crystal structures of the comparison compounds 2,3-bis(2-pyridyl)pyrazine (4) and its mono- (2A) and diprotonated (3) chlorides, and of 2-phenylpyridinium (6) and 7,8-benzoquinolinium (7, 8) tetraphenylborates, have also been determined. The many interesting features of these crystal structures, such as the X→H(X)...phenyl bonding (X = N, O, C), are commented upon and crystallographic comparisons with numerous literature compounds are offered. Included in the discussion are the monoprotonated intrabridgehead cations of the bicyclic diamines of Alder et al., the N-H(N)-N' angle of which has been shown, analytically, to be dominated by the size of the smallest of the rings in these tricyclic systems.Key words: crystal structures, hydrogen bonding, intrabridgehead cations, proton sponges, tetraphenylborates.


2016 ◽  
Vol 81 (13) ◽  
pp. 5574-5587 ◽  
Author(s):  
Alexander F. Pozharskii ◽  
Valery A. Ozeryanskii ◽  
Vladimir Y. Mikshiev ◽  
Alexander S. Antonov ◽  
Anatoly V. Chernyshev ◽  
...  

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