Stability, polarity, intramolecular interactions and π-electron delocalization for all eighteen tautomers rotamers of uracil. DFT studies in the gas phase

2009 ◽  
Vol 74 (1) ◽  
pp. 57-72 ◽  
Author(s):  
Ewa D. Raczyńska ◽  
Katarzyna Zientara ◽  
Tomasz M. Stępniewski ◽  
Katarzyna Kolczyńska
Keyword(s):  
Gas Phase ◽  
Functional Groups ◽  
Intramolecular Interactions ◽  
Electron Delocalization ◽  
Dft Studies ◽  
Tautomeric Equilibria ◽  
Aromatic Character ◽  
Stability Order ◽  
The Stability ◽  
Main Factor

Complete tautomeric equilibria were investigated for uracil at the DFT(B3LYP)/6-311+G(d,p) level to establish the stability order of all possible 18 tautomers-rotamers in the gas phase and to characterize their internal effects, polarity and aromatic character. Although the di-NH form strongly predominates (100%) in the mixture, the NH–OH, di-OH and CH–NH forms can be also considered. The favored tautomer is moderately stabilized by intramolecular interactions (attractions of the NH and C=O groups); it is also moderately polar and moderately delocalized. Stability of the functional groups (both amide functions) seems to be more important than intramolecular interactions, polarity and aromaticity. This is probably the main factor that dictates the tautomeric preferences in the uracil molecule.

Homoselenocysteine — An oxygen or selenium acid in the gas phase?

2010 ◽  
Vol 88 (8) ◽  
pp. 744-753 ◽  
Author(s):  
Marcela Hurtado ◽  
Otilia Mó ◽  
Manuel Yáñez
Keyword(s):  
Gas Phase ◽  
Global Minimum ◽  
Group Structure ◽  
Hydroxyl Group ◽  
Amino Group ◽  
Deprotonated Form ◽  
Protonated Amino Group ◽  
Stability Order ◽  
The Stability ◽  
Intramolecular Hydrogen

The potential energy surface of l-homoselenocysteine (HSEC) has been explored through the use of B3LYP/6-311+G(d,p) calculations. In this survey, seventy-seven different conformers have been located. These local minima can be classified in four groups, A–D. Structures A, B, and D are stabilized by intramolecular hydrogen bonds (IMHBs) with the amino group acting as the hydrogen bond (HB) donor and the carbonyl group (structures A and D) or the hydroxyl group (structure B) as HB acceptors. The structures in set C present an IMHB with the amino group acting as the HB acceptor and the hydroxyl group as the HB donor. The stability order decreases in the following order: A > B > C > D. From their relative stabilities it can be concluded that only three of these conformers, namely A1, A4, and A5, would exist in the gas phase at room temperature. The most stable deprotonated form corresponds to a Se-deprotated species stabilized by a strong IMHB between the hydroxyl group and the Se atom. However, a direct deprotonation of the most stable neutrals lead to O-deprotonated species, which eventually isomerize to yield the global minimum. Hence, we can conclude that, quite unexpectedly, HSEC behaves as a Se acid in the gas phase, its intrinsic acidity being 1374 kJ mol–1 at the B3LYP/6-311++G(3df,2p) level of theory. The most stable protonated forms are systematically the N-protonated ones, the global minimum being a structure stabilized through an IMHB involving the protonated amino group as the HB donor and the SeH group as the HB acceptor. The calculated gas-phase proton affinity (PA) at the B3LYP/6-311++G(3df,2p) level of theory is 930 kJ mol–1.

Radical Capture at Ni(II) Complexes: C-C, C-N, and C-O Bond Formation

2019 ◽  
Author(s):  
Abolghasem (Gus) Bakhoda ◽  
Stefan Wiese ◽  
Christine Greene ◽  
Bryan C. Figula ◽  
Jeffery A. Bertke ◽  
...  
Keyword(s):  
Functional Groups ◽  
Bond Formation ◽  
Dft Studies ◽  
Bond Forming ◽  
Aryl Amines ◽  
Shed Light ◽  
Competing Pathways

<p>The dinuclear b-diketiminato Ni<sup>II</sup><i>tert</i>-butoxide {[Me<sub>3</sub>NN]Ni}<sub>2</sub>(<i>μ</i>-O<i><sup>t</sup></i>Bu)<sub>2 </sub>(<b>2</b>), synthesized from [Me<sub>3</sub>NN]Ni(2,4-lutidine) (<b>1</b>) and di-<i>tert</i>-butylperoxide, is a versatile precursor for the synthesis of a series of Ni<sup>II</sup>complexes [Me<sub>3</sub>NN]Ni-FG to illustrate C-C, C-N, and C-O bond formation at Ni<sup>II </sup>via radicals. {[Me<sub>3</sub>NN]Ni}<sub>2</sub>(<i>μ</i>-O<i><sup>t</sup></i>Bu)<sub>2 </sub>reacts with nitromethane, alkyl and aryl amines, acetophenone, benzamide, ammonia and phenols to deliver corresponding mono- or dinuclear [Me<sub>3</sub>NN]Ni-FG species (FG = O<sub>2</sub>NCH<sub>2</sub>, R-NH, ArNH, PhC(O)NH, PhC(O)CH<sub>2</sub>, NH<sub>2</sub>and OAr). Many of these Ni<sup>II </sup>complexes are capable of capturing the benzylic radical PhCH(•)CH<sub>3 </sub>to deliver corresponding PhCH(FG)CH<sub>3 </sub>products featuring C-C, C-N or C-O bonds. DFT studies shed light on the mechanism of these transformations and suggest two competing pathways that depend on the nature of the functional groups. These radical capture reactions at [Ni<sup>II</sup>]-FG complexes outline key C-C, C-N, and C-O bond forming steps and suggest new families of nickel radical relay catalysts.</p>

Carbo-[3]oxocarbon and its isomers: evaluation of the stability and of the electron delocalization

2008 ◽  
Vol 10 (24) ◽  
pp. 3578 ◽  
Author(s):  
Mickaël Gicquel ◽  
Jean-Louis Heully ◽  
Christine Lepetit ◽  
Remi Chauvin
Keyword(s):  
Electron Delocalization ◽  
The Stability

scholarly journals Functional Groups Required for the Stability of Yeast RNA Triphosphatasein Vitroandin Vivo

2001 ◽  
Vol 276 (32) ◽  
pp. 30514-30520 ◽  
Author(s):  
Martin Bisaillon ◽  
Stewart Shuman
Keyword(s):  
Functional Groups ◽  
The Stability

The influence of the chlorine-hydrogen ratio in the gas phase on the stability of the {113} faces of silicon in Si-H-Cl CVD

1990 ◽  
Vol 102 (1-2) ◽  
pp. 233-244 ◽  
Author(s):  
J.G.E. Gardeniers ◽  
M.M.W. Mooren ◽  
M.H.J.M. De Croon ◽  
L.J. Giling
Keyword(s):  
Gas Phase ◽  
The Stability

The search for formal electrostatic effects on molecular conformation and crystal packing: crystal structure of 2,2′′-disubstituted (HversusPPh2) 1,1′-(1,2-phenylene)bis(3-methyl-1H-imidazol-3-ium) bis(trifluoromethanesulfonate)

2016 ◽  
Vol 72 (3) ◽  
pp. 198-202
Author(s):  
Carine Duhayon ◽  
Yves Canac ◽  
Laurent Dubrulle ◽  
Carine Maaliki ◽  
Remi Chauvin
Keyword(s):  
Crystal Structure ◽  
Electrostatic Interactions ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Relative Orientation ◽  
Electron Delocalization ◽  
Electrostatic Effects ◽  
Conformational Freedom ◽  
The Stability ◽  
Bond Character

Electrostatic interactions between localized integral charges make the stability and structure of highly charged small and rigid organics intriguing. Can σ/π-electron delocalization compensate reduced conformational freedom by lowering the repulsion between identical charges? The crystal structure of the title salt, C14H16N42+·2CF3SO3−, (2), is described and compared with that of the 2,2′′-bis(diphenylphosphanyl) derivative, (4). The conformations of the dications and their interactions with neighbouring trifluoromethanesulfonate anions are first analyzed from the standpoint of formal electrostatic effects. Neither cation exhibits any geometrical strain induced by the intrinsic repulsion between the positive charges. In contrast, the relative orientation of the imidazolium rings [i.e. antifor (2) andsynfor (4)] is controlled by different configurations of the interactions with the closest trifluoromethanesulfonate anions. The long-range arrangement is also found to be specific: beyond the formal electrostatic packing, C—H...O and C—H...F contacts have no definite `hydrogen-bond' character but allow the delineation of layers, which are either pleated or flat in the packing of (2) or (4), respectively.

scholarly journals Concomitant polymorphs of aryl-ether amine via catemer and dimer carboxylic acid supramolecular interactions and their effect on optical properties

2021 ◽  
Author(s):  
Mehboobali Pannipara ◽  
Abdullah G Al-Sehemi
Keyword(s):  
Optical Properties ◽  
Carboxylic Acid ◽  
Crystal Lattice ◽  
Functional Groups ◽  
Molecular Orbital ◽  
Acid Group ◽  
Supramolecular Interactions ◽  
Aryl Ether ◽  
Stability Calculation ◽  
The Stability

Abstract Carboxylic acid supramolecular synthon exhibited dimer or catemer motifs in the crystal lattice depend on the substituent and other functional groups present in the structure. In general, presence of other competing functional groups produced catemer motifs whereas unsubstituted acids showed dimer. In this manuscript, we have synthesized a new aryl ether amine-based Schiff base with carboxylic acid functionality ( 1 ) and demonstrated polymorphic structure via catemer ( 1a ) and dimer ( 1b ) motifs in the solid state. In both the structure, carboxylic acid group adopted different orientation in the crystal lattice. The different H-bonding lead to modulation of optical properties that was further supported highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) calculation. Further the stability calculation indicates that catemer structure was more stable by 8.54 kcal/mole relative to dimer motifs. In contrast, naphthyl group attached carboxylic acid structure did not show neither dimer nor catemer motifs in the crystal lattice as compared to diethylaminophenyl group, which confirm the presence of other substituent or competing functional groups strongly influence on the motifs of supramolecular interactions.

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