The hydrogen perturbation in molecular connectivity computations

Pogliani, Lionello

doi:10.1002/jcc.20375

Cited by 18 publications

(30 citation statements)

References 23 publications

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“…Despite the good results obtained by Pogliani [55][56][57] the isoelectric point pI for 21 amino acids was analyzed by our group [45,47]. The use of (1+ n/n T ) = 1/2 for Arg, 4/3 for Asp and Glu, 2/3 for His and Lys and one for all others improved the fit: The correlation coefficient represents the 96.8% of the one of the correlation of the means (np = 4, r = 0.997).…”

Section: Results For Amino Acids and Proteinsmentioning

confidence: 52%

“…The fitting line corresponds to the 21 amino acids; once However, the model is inadequate for proteins because G 4 V increases with n A and n B . Although the results are comparable to those of Pogliani [55][56][57], the interest is in the separation of the predicted results for those amino acids with isoelectric point pI~6, to check later if this splitting is meaningful for proteins. The pIs [calculated with Equation (8) and experimental] for the 21 amino acids are displayed in Fig.…”

Section: Results For Amino Acids and Proteinsmentioning

confidence: 79%

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Topological Charge-Transfer Indices: From Small Molecules to Proteins

Torrens¹,

Castellano²

2009

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Valence-topological charge-transfer indices are applied to the calculation of dipole moment-pH at the isoelectric point. Dipole moments calculated by algebraic-vector semisums of charge-transfer indices are defined. The ability of indices, for the description of molecular charge distribution, is established by comparing them with the dipole moment of the valence-isoelectronic series of cyclopentadiene-benzene-styrene. Both charge-transfer indices are proposed: vector semisums μ vec -μ vec V . The μ vec V is intermediate between μ vec and μ experiment . The steric effect is almost constant along series and the dominating effect is electronic. The indices are applied to the calculation of the dipole moments of the homologous series of percutaneous enhancers and the isoelectric point of 21 amino acids. In most fits no superimposition of the corresponding G k -J k /G k V -J k V pairs is observed, which diminishes the risk of collinearity. The inclusion of heteroatoms in the -electron systems is beneficial for the description of isoelectric point, because of either the role of additional p-orbitals provided by heteroatom or the role of steric factors in the -electron conjugation. The use of (valence) chargetransfer indices gives limited results for amino-acid isoelectric points. The inclusion of the number of acidic/basic groups improves the models, especially for amino acids with more than two functional groups. The fitting line for 21 amino acids is used to estimate the lysozyme isoelectric point by replacing (1+ n/n T ) with (M+ n)/n T . The lysozyme fragment results can estimate the isoelectric point of the whole protein within 1-13% error.

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Section: Results For Amino Acids and Proteinsmentioning

confidence: 52%

Section: Results For Amino Acids and Proteinsmentioning

confidence: 79%

Topological Charge-Transfer Indices: From Small Molecules to Proteins

Torrens¹,

Castellano²

2009

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“…K 0 graphs may be used to encode the depleted hydrogen atoms. In fact, the depleted hydrogen atoms (or K 0 graphs) can be encoded by the aid of the following fractional perturbation term, [16][17][18] Exponent n is no optimization parameter, it just quantifies the importance of the hydrogen atoms in a model study, i.e., the higher the n values the lower the importance of the perturbation introduced by the hydrogen atoms. Different values of n give rise to different sets of indices, where in each set n is constant, i.e., the corresponding d v is constant.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Model of twelve properties of a set of organic solvents with graph‐theoretical and/or experimental parameters

Pogliani

2009

J Comput Chem

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Twelve properties of a highly heterogeneous class of organic solvents have been modeled with a graph-theoretical molecular connectivity modified (MC) method, which allows to encode the core electrons and the hydrogen atoms. The graph-theoretical method uses the concepts of simple, general, and complete graphs, where these last types of graphs are used to encode the core electrons. The hydrogen atoms have been encoded by the aid of a graph-theoretical perturbation parameter, which contributes to the definition of the valence delta, delta(v), a key parameter in molecular connectivity studies. The model of the twelve properties done with a stepwise search algorithm is always satisfactory, and it allows to check the influence of the hydrogen content of the solvent molecules on the choice of the type of descriptor. A similar argument holds for the influence of the halogen atoms on the type of core electron representation. In some cases the molar mass, and in a minor way, special "ad hoc" parameters have been used to improve the model. A very good model of the surface tension could be obtained by the aid of five experimental parameters. A mixed model method based on experimental parameters plus molecular connectivity indices achieved, instead, to consistently improve the model quality of five properties. To underline is the importance of the boiling point temperatures as descriptors in these last two model methodologies.

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“…One of the goals of MC theory—the description of the molecular world with graph‐theoretical concepts—is about as grand as it gets but its theoretical evolution has been rather fragmentary. Some “fragments” in MC theory, which will be reviewed in this study, have been tackled only in the last 15 years, like the cis‐trans problem,13 the extension of the MC indices,14–17 the electron‐core problem,18–21 and the hydrogen atom problem 22. The issue of delineating a complete MC theory is no secondary task as MC theory is central in many QSPR/QSAR model studies, which try to predict properties and activities of drugs, as exemplified by a growing series of articles appearing in the current literature, among which References 23–32 are of particular interest.…”

Section: Introductionmentioning

confidence: 99%