Similarity of atoms in molecules

Ciosłowski, Jerzy; Nanayakkara, Asiri

doi:10.1021/ja00077a020

Cited by 67 publications

(54 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Both the Carbó index and the Hodgkin-Richards index were used by Boon et al 107 , whereas in the applications of AIM, the Cioslowski similarity measure was used. 131,132,154 For the atom-centered approach, we can use all similarity indices. In all cases, maximal similarity is obtained if the two atoms being compared are coincident.…”

Section: Atom-centered Basis Function Approachmentioning

confidence: 99%

Molecular Quantum Similarity: Theory and Applications

Bultinck¹,

Gironés²,

Carbó‐Dorcaz³

2005

Reviews in Computational Chemistry

119

View full text Add to dashboard Cite

Section: Atom-centered Basis Function Approachmentioning

confidence: 99%

Molecular Quantum Similarity: Theory and Applications

Bultinck¹,

Gironés²,

Carbó‐Dorcaz³

2005

Reviews in Computational Chemistry

119

View full text Add to dashboard Cite

“…The newly developed variational approach (14) to the determination of atomic surfaces were used, producing properties of atoms in molecules with accuracy exceeding (au). Calculations of the atomic similarity index (15) were carried out with the recently proposed algorithm (16).…”

Section: Details Of Calculationmentioning

confidence: 99%

“…The difference between the shapes of two atoms A and B that are parts of molecules X and Y, respectively, can be readily assessed with the similarity measures obtained by maximizing the similarity index (15) over all possible angular orientations of A with respect to B. In eq.…”

Section: Shapes Of Oxygen Atoms In Carbonyl Compoundsmentioning

confidence: 99%

See 1 more Smart Citation

Variability of shapes and properties of atoms in molecules: a case study of the carbonyl oxygen

Stefanov¹,

Ciosłowski²

1996

Can. J. Chem.

Self Cite

View full text Add to dashboard Cite

A comparative study of carbonyl oxygen atoms in diverse molecular environments is presented. The variability of shapes of oxygen atoms is quantified with a newly developed similarity measure that confirms the qualitative conclusions of visual assessment. Electronic properties of these atoms, such as charges, energies, and dipole moments, are computed and their possible correlations with the atomic shapes are studied. Factors that affect atomic shapes are investigated and found to be distinct from those influencing electronic properties of atoms in molecules. The kinetic energies of the atoms under study correlate poorly with the atomic charges. The second-neighbor effects on the atomic energies and charges are approximately additive. Both the theoretical considerations and the numerical results definitively rule out the possibility of the shapes of atomic basins unambiguously determining the properties of atoms in molecules. The consequences of this observation for the recently contemplated approaches to the prediction of electronic properties of large molecules are discussed.Key words: atoms in molecules, properties of -; similarity of -; transferability of -.Resume : On prCsente les rCsultats d'une Ctude comparative des atornes d'oxygkne de carbonyles dans divers environnements moltculaires. On a quantifiC la variabilitC des formes des atornes d'oxygkne ? i l'aide d'une mesure de similaritt dtveloppCe rCcemment qui confirme les conclusions qualitatives de l'attribution visuelle. On a calculC les propriCtCs Clectroniques de ces atomes, telles que les charges, les Cnergies et les moments dipolaires et on a CtudiC leurs corrClations possibles avec les formes atorniques et on a trouvC qu'elles sont diffkrentes de celles qui influencent les propriCtCs Clectroniques des atomes dans les molCcules. La relation entre les Cnergies cinCtiques des atomes examints et leurs charges atomiques n'est pas bonne. Les effets du deuxikme voisin sur les Cnergies et les charges atomiques sont approximativement additifs. Les considCrations thCoriques ainsi que les rCsultats numCriques permettent d'Climiner dtfinitivement la possibilitC d'utiliser les formes des bassins atomiques pour dCterminer sans ambigu'itk les propriCtCs des atomes dans les molCcules. On discute des consCquences de cette observation sur les approches contemplCes rCcemment pour prCdire les propriCtCs Clectroniques de grosses molCcules.

show abstract

“…In this way the computational time would only increase linearly with the number of subunits. Furthermore, to extend this strategy to homologous organic molecules, according to the transferability and molecular similarity of atomic groups, [16][17][18][19][20][21][22] we have studied the approximately transferable property of the correlation energies of methyl and methylene groups along the series of linear alkanes and developed the group additive scheme for general applicability. 23 In this paper, we analyze the variability and transferability of correlation energy contributions in terms of functional groups in CH 3 (CH 2 ) m OH (m＝0-4) linear alkyl alcohols.…”

Section: Introductionmentioning

confidence: 99%

Group Contribution Model for Estimate of Correlation Energies of Linear Alkyl Alcohols

Zhuo¹,

Wei

2008

Chin. J. Chem.

View full text Add to dashboard Cite

The correlation energy contribution of a polar group in a molecular system was defined and the contributions of HO, CH 3 , and CH 2 groups in CH 3 (CH 2 ) m OH (m＝0-4) linear alkyl alcohols were calculated and studied at MP2-OPT2/6-311＋＋G(d) level. It is revealed that the E corr (HO) and E corr (CH 3 ) values of two terminal groups decrease somewhat with increase of number m in CH 3 (CH 2 ) m OH (m＝0-4) series. The value of E corr (CH 2 ) in the α position is larger than those values of methylene groups in other positions in the same system, and the farther the CH 2 from HO group in the molecule, the smaller the value of E corr (CH 2 ) in CH 3 (CH 2 ) m OH (m＝1-4) systems. Therefore, it was predicted that with the increase of number m in CH 3 (CH 2 ) m OH systems the values of E corr (CH 2 ) that are those of CH 2 groups relatively far from the terminal HO group would show a converging trend to that of a "standard" CH 2 group and its value of E corr (CH 2 ) would be transferable in CH 3 (CH 2 ) m OH homologous systems. The excellent fitting relationships between the total correlation energy and the number of (m-1) where m is the number of methylene groups were obtained from both results at MP2-OPT2/6-311＋＋G(d) level for CH 3 (CH 2 ) m OH (m＝ 2-4) systems by Meld program and at MP2/6-311＋＋G(d)//HF/6-311＋＋G(d) level for CH 3 (CH 2 ) m OH (m＝2-7) systems by Gaussian 98 program, which show that the total correlation energy is a linear function of the number of (m-1).

show abstract

Similarity of atoms in molecules

Cited by 67 publications

References 23 publications

Molecular Quantum Similarity: Theory and Applications

Molecular Quantum Similarity: Theory and Applications

Variability of shapes and properties of atoms in molecules: a case study of the carbonyl oxygen

Group Contribution Model for Estimate of Correlation Energies of Linear Alkyl Alcohols

Contact Info

Product

Resources

About