General trends in atomic and nuclear quantum similarity measures

Simple and accurate relationships between atomic and nuclear quantum similarity measures and their constituent elements were found. These results complement findings in previous studies in which quantum self‐similarity measures in atoms and nuclei were linked to the atomic and mass numbers, respectively. The models were validated on a large test set, and the general trends in the behavior of the quantum similarity measures for these quantum objects were made clear. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 685–692, 2000     

Commentaries on quantum similarity (1): Density gradient quantum similarity

Computation of density gradient quantum similarity integrals is analyzed, while comparing such integrals with overlap density quantum similarity measures. Gradient quantum similarity corresponds to another kind of numerical similarity assessment between a pair of molecular frames, which contrarily to the usual up to date quantum similarity definitions are not measures, that is: strictly positive definite integrals. As the density gradient quantum similarity integrals are defined as scalar products of three real functions, they appear to possess a richer structure than the corresponding positive definite density overlap quantum similarity measures, while preserving the overall similarity trends, when the molecular frames are relatively moved in three‐dimensional space. Similarity indices are also studied when simple cases are analyzed in order to perform more comparisons with density overlap quantum similarity. Multiple gradient quantum similarity integrals are also defined. General GTO formulae are given. Numerical results within the atomic shell approximation (ASA) framework are presented as simple examples showing the new performances of the gradient density quantum similarity. Fortran 90 programs illustrating the proposed theoretical development can be downloaded from appropriate websites. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Generation of Molecular Fields, Quantum Similarity Measures and Related Questions

A straightforward discussion on how to generate molecular fields is developed within the postulates of quantum mechanics. The theoretical formalism points towards the generalization and extension of the well-known molecular field forms, associated to density function and electrostatic molecular potential (EMP), including another category of fields associated to quantum molecular similarity measures. The results show that the new formalism can be easily applied to obtain an unlimited number of new information about molecular behavior.     

Non-linear Terms & Variational Approach in Quantum QSPR

The theoretical results presented in this work point out that quantitative structure–properties relationslips (QSPR) can be appropriately founded within the theoretical background of quantum mechanics. In this way, the deducible quantum QSPR (QQSPR) framework and the associated fundamental equation, furnish with a causal backup the structure–properties relationships old problem. Moreover, they also provide algorithms to obtain in a general manner, up to any approximation level and even from a variational point of view, unbiased and universal causal QSPR models for any chosen quantum object set.     

Quantum fidelity for analyzing atoms and fragments in molecule: Application to similarity,chirality, and aromaticity

Quantum information theory is applied to formulate a new technique for dealing with molecular similarity problems. In this technique, the so‐called quantum fidelity appears to be a counterpart of the conventional similarity measure due to Carbo (Carbo, R.; Leyda, L.; Arnau, M. Int J Quantum Chem 1980, 17, 1185). We define many‐body spin‐free density matrices for atoms and fragments in molecule, and compute corresponding fidelity measures for molecular subsystems. It allows us to treat the problem from the beginning within a many‐electron setting. The approach is employed for analyzing similarity between free atoms and atoms in molecule. A new chirality index, as based on the fidelity between molecule and its mirror image, is suggested to be an approximately additive nonnegative quantity. We also examine a local aromaticity by computing the fidelity measures for benzenoid fragments in polyaromatic hydrocarbons. A detailed study of the proposed indices is reported at the ab initio or semiempirical levels. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

How dependent are molecular and atomic properties on the electronic structure method? Comparison of Hartree‐Fock,DFT, and MP2 on a biologically relevant set of molecules

This article compares molecular properties and atomic properties defined by the quantum theory of atoms in molecules (QTAIM) obtained from three underlying levels of theory: MP2(full), density functional theory (DFT) (B3LYP), and Hartree‐Fock (H‐F). The same basis set (6‐311++G(d,p)) has been used throughout the study. The calculations and comparisons were applied to a set of 30 small molecules representing common fragments of biological molecules. The molecular properties investigated are the energies and the electrostatic moments (up to and including the quadrupoles), and the atomic properties include electron populations (and atomic charge), atomic dipolar and quadrupolar polarizations, atomic volumes, and corrected and raw atomic energies. The Cartesian distance between dipole vectors and the Frobenius distance between the quadrupole tensors calculated at the three levels of theory provide a measure of their correlation (or lack thereof). With the exception of energies (atomic and molecular), it is found that both DFT and H‐F are in excellent agreement with MP2, especially with regards to the electrostatic mutipoles up to the quadrupoles, but DFT and MP2 agree better in almost all studied properties (with the exception of molecular geometries). QTAIM properties whether obtained from H‐F, DFT(B3LYP), or MP2 calculations when used in the construction of empirical correlations with experiment such as quantitative structure‐activity‐(or property)‐relationships (QSAR/QSPR) are equivalent (because the properties calculated at the three levels are very highly correlated among themselves with r² typically >0.95, and therefore preserving trends). These results suggest that the massive volume of results that were published in the older literature at the H‐F level is valid especially when used to study trends or in QSAR or QSPR studies, and, as long as our test set of molecules is representative, there is no pressing need to re‐evaluate them at other levels of theory except when inadequate basis sets were used by today's standards. Extensive tabulation of molecular and atomic properties at the three theoretical levels is available in the Supporting Information, including optimized geometries, molecular energies, virial ratios, molecular electrostatic moments up to and including hexadecapoles, atomic populations, atomic volumes, atomic electrostatic moments up to and including the quadrupoles, and atomic energies. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Fully polarizable QM/MM calculations: An application to the nonbonded iodine–oxygen interaction in dimethyl‐2‐iodobenzoylphosphonate

The compound dimethyl‐2‐iodobenzoylphosphonate is unusual in that it forms well‐ordered crystals that clearly show short iodine‐oxygen interactions in which both the iodine and the oxygen are in their normal oxidation states. These interactions were studied using a new hybrid quantum mechanical–molecular mechanical approach that employs a polarizable molecular mechanics component. The electric field at the molecular mechanics atoms was calculated from a distributed multipole expansion of the wave function; this induced dipoles on the molecular mechanics atoms. The electrostatic potential in a spherical shell around the induced dipoles was reproduced through induced charges on the atomic center and those bonded to it using an analytical (rather than numerical) procedure. The new atomic charges (induced charges plus permanent charges) were then able to interact with the quantum mechanical entity and polarize the wave function. The procedure was iterated to convergence. The calculations show that the iodine atom becomes more positive in the crystal environment (modeled by a chain of three molecules of dimethyl‐2‐iodobenzoylphosphonate). Thus, while the cooperative effects of the crystal environment may not be the only feature stabilizing this unusual interaction, they do play a significant role in reducing the otherwise unfavourable iodine–oxygen monopole–monopole interaction. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 478–482, 2000     

Prediction on Critical Micelle Concentration of Nonionic Surfactants in Aqueous Solution： Quantitative Structure-Property Relationship Approach

IntroductionCriticalmicelleconcentration (cmc)ofsurfactantsinaqueoussolutionisoneofthemostusefulparametersforcharacterizingthepropertiesofsurfactants.Overaverynarrowconcentrationrangearoundthecmctransitionsoftheexistenceofsurfactantsoccurfrommonomer ,premicel lartomicellar .Andcompanyingthesetransitions ,manyotherimportantpropertiesofsurfactantsolution ,suchassurfacetension ,interfacialtension ,conductivity ,osmoticpressure ,detergency ,emulsification ,foamingandsoon ,alsochangesharplyatthepoi…     

一种新的分子拓扑指数及其在QSPR/QSAR研究中的应用

通过引入量子数、键参数,认为分子的性质与其中各原子的电负性、价电子数、成键电子数、价层主量子数及各化学键的键长有关,提出了一种新的分子拓扑指数mAY.采用该拓扑指数对饱和烷烃、烷基苯、烷氧氯硅烷、卤代苯、含氮杂环化合物、碱金属卤化物及卤化锡的性质/活性进行了相关关系的研究.结果表明,mAY与有机物和无机物的性质/活性间具有良好的相关性.