Molecular similarity and complementarity based on the theory of atoms in molecules

Popelier, Paul L. A.

doi:10.1007/978-94-011-1350-2_9

Cited by 30 publications

(36 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Ultimately, any molecular similarity method must incorporate conformational flexibility requiring special techniques that avoid typical combinatorial explosions. A recent discussion of a fair cross-section of methods can be found in a book by Dean . In this paper we focus on similarity measures operating on quantum mechanical information.…”

Section: Quantum Molecular Similarity Measuresmentioning

confidence: 99%

See 1 more Smart Citation

Quantum Molecular Similarity. 1. BCP Space

1999

Self Cite

View full text Add to dashboard Cite

We propose a new similarity measure operating in an abstract space spanned by properties evaluated at bond critical points defined by the theory of Atoms in Molecules. Consequently, we represent molecules compactly and reliably, extracting the relevant information from their ab initio wave function. Typical problems of continuous quantum similarity measures are thereby avoided. The practical use of this novel method is adequately illustrated via the Hammett equation for para and meta substituted benzoic acids. On the basis of our definition of distances between molecules in BCP (Bond Critical Point) space, we are able to reproduce the experimental sequence of acidities determined by the well-known σ constant of a set of substituted congeners. Moreover, our approach points out where the common reactive center of the molecules is. Due to these promising results we embark on a research program systematically addressing further issues outlined in this work. The generality and feasibility of our approach will enable predictions in medically related QSARs.

show abstract

Section: Quantum Molecular Similarity Measuresmentioning

confidence: 99%

“…In other words, using the data of one molecule's action we can predict the action of another closely related molecule by merely comparing how similar the original molecule is to the other one. This is the basis of the molecular similarity postulate, which we adopt in this and future work.…”

Section: Introductionmentioning

confidence: 97%

Quantum Molecular Similarity. 1. BCP Space

1999

Self Cite

View full text Add to dashboard Cite

show abstract

“…QTAIM analyses provide properties for uniquely and physically quantifying local and regional properties of molecules. − QTAIM properties are helpful not only for interpretation but also for prediction, when used as QSAR descriptors, for example. − QTAIM properties can also be useful metrics for quantifying local and regional differences between the same molecule using different computational methods, which is the primary use to which they shall be put to here.…”

Section: Resultsmentioning

confidence: 99%

Subshell Fitting of Relativistic Atomic Core Electron Densities for Use in QTAIM Analyses of ECP-Based Wave Functions

Keith¹,

Frisch²

2011

J. Phys. Chem. A

View full text Add to dashboard Cite

Scalar-relativistic, all-electron density functional theory (DFT) calculations were done for free, neutral atoms of all elements of the periodic table using the universal Gaussian basis set. Each core, closed-subshell contribution to a total atomic electron density distribution was separately fitted to a spherical electron density function: a linear combination of s-type Gaussian functions. The resulting core subshell electron densities are useful for systematically and compactly approximating total core electron densities of atoms in molecules, for any atomic core defined in terms of closed subshells. When used to augment the electron density from a wave function based on a calculation using effective core potentials (ECPs) in the Hamiltonian, the atomic core electron densities are sufficient to restore the otherwise-absent electron density maxima at the nuclear positions and eliminate spurious critical points in the neighborhood of the atom, thus enabling quantum theory of atoms in molecules (QTAIM) analyses to be done in the neighborhoods of atoms for which ECPs were used. Comparison of results from QTAIM analyses with all-electron, relativistic and nonrelativistic molecular wave functions validates the use of the atomic core electron densities for augmenting electron densities from ECP-based wave functions. For an atom in a molecule for which a small-core or medium-core ECPs is used, simply representing the core using a simplistic, tightly localized electron density function is actually sufficient to obtain a correct electron density topology and perform QTAIM analyses to obtain at least semiquantitatively meaningful results, but this is often not true when a large-core ECP is used. Comparison of QTAIM results from augmenting ECP-based molecular wave functions with the realistic atomic core electron densities presented here versus augmenting with the limiting case of tight core densities may be useful for diagnosing the reliability of large-core ECP models in particular cases. For molecules containing atoms of any elements of the periodic table, the production of extended wave function files that include the appropriate atomic core densities for ECP-based calculations, and the use of these wave functions for QTAIM analyses, has been automated.

show abstract

“…Calculated 3D ESP maps of π-conjugated cores (Br-BC16 and Br-NC16, Figure 3a,d) and quantum theory of atoms in molecules (QTAIM) of Bader [72,73] obtained by DFT calculations were used to reveal the formation of intermolecular type-I Br•••Br contact and HB. The results show that a pair of intermolecular H•••Br HBs in each dimer control the structural formation.…”

Section: The Effect Of Geometry Symmetry Of π-Conjugated Cores Along the C−br Bondmentioning

confidence: 99%

Halogen Bonds Fabricate 2D Molecular Self-Assembled Nanostructures by Scanning Tunneling Microscopy

2020

View full text Add to dashboard Cite

Halogen bonds are currently new noncovalent interactions due to their moderate strength and high directionality, which are widely investigated in crystal engineering. The study about supramolecular two-dimensional architectures on solid surfaces fabricated by halogen bonding has been performed recently. Scanning tunneling microscopy (STM) has the advantages of realizing in situ, real-time, and atomic-level characterization. Our group has carried out molecular self-assembly induced by halogen bonds at the liquid–solid interface for about ten years. In this review, we mainly describe the concept and history of halogen bonding and the progress in the self-assembly of halogen-based organic molecules at the liquid/graphite interface in our laboratory. Our focus is mainly on (1) the effect of position, number, and type of halogen substituent on the formation of nanostructures; (2) the competition and cooperation of the halogen bond and the hydrogen bond; (3) solution concentration and solvent effects on the molecular assembly; and (4) a deep understanding of the self-assembled mechanism by density functional theory (DFT) calculations.

show abstract

Molecular similarity and complementarity based on the theory of atoms in molecules

Cited by 30 publications

References 62 publications

Quantum Molecular Similarity. 1. BCP Space

Quantum Molecular Similarity. 1. BCP Space

Subshell Fitting of Relativistic Atomic Core Electron Densities for Use in QTAIM Analyses of ECP-Based Wave Functions

Halogen Bonds Fabricate 2D Molecular Self-Assembled Nanostructures by Scanning Tunneling Microscopy

Contact Info

Product

Resources

About