On the Harmonic Oscillator Model of Electron Delocalization (HOMED) Index and its Application to Heteroatomic π-Electron Systems

Raczyńska, Ewa D.; Hallman, Małgorzata; Kolczyńska, Katarzyna; Stępniewski, Tomasz M.

doi:10.3390/sym2031485

Cited by 142 publications

(236 citation statements)

References 56 publications

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“…To properly determine the distribution of p-and nelectrons for all tautomers/rotamers of cytosine and to well describe the variations of electron delocalization, the geometry-based HOMED (harmonic oscillator model of electron delocalization) procedure [63,64] was applied to the geometries optimized at the DFT(B3LYP)/6-311?G(d,p) level. The abbreviation HOMED was proposed in 2006 for the modified index [63], but it may also be abbreviated as moHOMA (modified original HOMA) or simply HOMA.…”

Section: Methodsmentioning

confidence: 99%

“…The abbreviation HOMED was proposed in 2006 for the modified index [63], but it may also be abbreviated as moHOMA (modified original HOMA) or simply HOMA. The HOMA (harmonic oscillator model of aromaticity) index [65,66], reformulated by Krygowski [67], and the HOMHED (harmonic oscillator model of heterocyclic electron delocalization) index, proposed by Frizzo and Martins in 2012 [68] and based on hypotheses of the HOMED index [64], were not applied here for cytosine. The reasons were discussed previously [53,69].…”

Section: Methodsmentioning

confidence: 99%

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DFT studies on the favored and rare tautomers of neutral and redox cytosine

Raczyńska

Sapuła²,

Zientara‐Rytter³

et al. 2015

Struct Chem

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The complete tautomeric mixture consisting of nine prototropic tautomers has been studied in the gas phase at the DFT(B3LYP)/6-311?G(d,p) level for neutral, oxidized, and reduced cytosine. Rotational isomerism of the exo -OH group and geometrical isomerism of the exo =NH group have also been considered. Tautomeric conversions possible for cytosine have been compared with those for its structural models, 4-amino-and 2-hydroxypyrimidine. Effects of intramolecular interactions between neighboring groups for cytosine are analogous to those observed for model compounds. Although they are not very strong, they are sufficient to influence tautomeric equilibria and relative stabilities of individual tautomers. One-electron oxidation and one-electron reduction change tautomeric preferences. Tautomers that are rare forms for neutral cytosine become favored ones for oxidized and reduced cytosine. Aromaticity is not the main factor that dictates the tautomeric preferences. Stability of functional groups seems to be more important than full electron delocalization.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

DFT studies on the favored and rare tautomers of neutral and redox cytosine

Raczyńska

Sapuła²,

Zientara‐Rytter³

et al. 2015

Struct Chem

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“…1b) atoms of solvents including the data for nonequilibrium complexes. The obtained data for formamide (IVa, IVb) and formic acid (IIIb, IIId) are outliers since in these cases, the binding energy is affected by a resonance effect due to n-p conjugation HY- [32,36].…”

Section: Interactions With Cationsmentioning

confidence: 99%

Interactions of polar hydrogen bond donor solvents with ions: a theoretical study

et al. 2016

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Intermolecular interactions between molecules of protic solvents (water, methanol, formic acid, formamide, methylamine and ammonia) and monatomic ions (Li ? , Na ? , K ? , F -, Cl -and Br -) were characterized by the total energy of interaction (E total ) and the amount of charge which is transferred between the solvent molecule and the ion (CT). For the studied systems, linear relationships between E total and ln(CT) were observed and explained. In the case of complexes with metal cations, a good linear correlation between E total and the molar enthalpy of ion solvation (DH o i;solv ), obtained from experimental data for water, methanol, formamide and ammonia, was found. On the other hand, for complexes with anions, a planar regression between E total and two explanatory parameters: DH o i;solv and DH vap (molar heat of vaporization for a given solvent), was established. The latter shows an important role played by solvent-solvent interactions around anions, which is in agreement with some literature predictions based on the mean spherical approximation.

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“…In case of an even number of bonds, the normalization constant,  CC , from the HOMED theory reduces to the rHOMA normalization constant,  (Raczyńska et al, 2010). The normalization constant, , for each type of bond was calculated according to the rHOMA theory from Eq.…”

Section: Computational Detailsmentioning

confidence: 99%

“…The concept of HOMA was taken by Jug and Koester in 1993 to propose reformulated HOMA (rHOMA), which has been applied to various cyclic and acyclic conjugated systems (Jug and Koester, 1990). Discrepancies of the rHOMA index led Raczyńska et al to introduce a new Harmonic Oscillator Model of Electron Delocalization (HOMED) index (Raczyńska et al, 2010). Quantum mechanical methods have been used to estimate the bond lengths for the reference molecules as well as for the different π-electron delocalized acyclic and cyclic compounds containing C-C, C-N and C-O bonds including heteroaromatic systems.…”

Section: Introductionmentioning

confidence: 99%

Quantum-chemical study of molecular structure and relative stability of trans and cis isomers of model anilide derivatives

Cagardová

Poliak

Lukeš

2017

Acta Chimica Slovaca

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Derivatives of anilide were studied systematically by the density functional theory (DFT) using the B3LYP hybrid functional and the 6-311+G(3df,2p) basis set. Characteristic frequencies of N-H and C=O stretching modes for cis and trans conformers distinguishing were compared with available experimental and theoretical data. Effect of substitution in ortho position and acidic residue group is discussed with respect to the bond length changes in the aromatic ring and aromaticity indexes. Energy differences between cis and trans conformations allow estimating the effect of intramolecular hydrogen bonds stabilizing the studied conformations. The trans conformation of parent formanilide is stabilized via the C ( . The selected anilide series represent model compounds for drug design.

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On the Harmonic Oscillator Model of Electron Delocalization (HOMED) Index and its Application to Heteroatomic π-Electron Systems

Cited by 142 publications

References 56 publications

DFT studies on the favored and rare tautomers of neutral and redox cytosine

DFT studies on the favored and rare tautomers of neutral and redox cytosine

Interactions of polar hydrogen bond donor solvents with ions: a theoretical study

Quantum-chemical study of molecular structure and relative stability of trans and cis isomers of model anilide derivatives

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