Fragment Transferability Studied Theoretically and Experimentally with QTAIM – Implications for Electron Density and Invariom Modeling

Luger, Peter; Dittrich, Birger

doi:10.1002/9783527610709.ch12

Cited by 6 publications

(3 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, through the Ehrenfest and Feynman theorems, one has the tools that are needed to describe the forces acting in any system and, through the virial theorem, to relate these forces to the system’s energy and its potential and kinetic contributions . This is the physics underlying all bonded interactions, and when combined with the properties of the electron and energy densities at a bond critical point, it provides one with a classification scheme that establishes trends and the distinguishing features of atomic interactions over the entire spectrum of bonding. , It is widely employed in the analysis of experimental densities ,,,− and has an ever widening range of application as exemplified by its recent novel use in establishing a classification scheme based on the covalent, ionic, and resonance components of valence bond theory . Anyone possessed with knowledge of Schrödinger’s equation may derive QTAIM and its theorems without knowledge of its derivation from Schwinger’s principle of stationary action, making the theory accessible to all …”

Section: Why Go From Bonds To Bonding?mentioning

confidence: 99%

Bond Paths Are Not Chemical Bonds

2009

View full text Add to dashboard Cite

This account takes to task papers that criticize the definition of a bond path as a criterion for the bonding between the atoms it links by mistakenly identifying it with a chemical bond. It is argued that the notion of a chemical bond is too restrictive to account for the physics underlying the broad spectrum of interactions between atoms and molecules that determine the properties of matter. A bond path on the other hand, as well as being accessible to experimental verification and subject to the theorems of quantum mechanics, is applicable to any and all of the interactions that account for the properties of matter. It is shown that one may define a bond path operator as a Dirac obserVable, making the bond path the measurable expectation Value of a quantum mechanical operator. Particular attention is given to van der Waals interactions that traditionally are assumed to represent attractive interactions that are distinct from chemical bonding. They are assumed by some to act in concert with Pauli repulsions to account for the existence of condensed states of molecules. It is such dichotomies of interpretation that are resolved by the experimental detection of bond paths and the delineation of their properties in molecular crystals. Specific criticisms of the stabilization afforded by the presence of bond paths derived from spectroscopic measurements performed on dideuteriophenanthrene are shown to be physically unsound. The concept of a bond path as a "bridge of density" linking bonded atoms was introduced by London in 1928 following the definition of the electron density by Schrödinger in 1926. These papers marked the beginning of the theory of atoms in molecules linked by bond paths.

show abstract

Section: Why Go From Bonds To Bonding?mentioning

confidence: 99%

Bond Paths Are Not Chemical Bonds

2009

View full text Add to dashboard Cite

show abstract

“…Only the properties of the atoms directly involved in the tautomerization are significantly affected, the carbon and remaining atoms of the residue bonded to Cα for example exhibiting a change in population less than 0.00e. The constancy in the atomic properties of the atoms forming the backbone of a polypeptide, found in spite of the very different attached residues including those bearing net charges, has led to the construction of aspherical scattering models to replace the independent atom model in the determination of the electron density from high resolution crystallographic work. , This important and emerging field of crystallography is a result of the experimental verification of the transferability of atoms and groupings of atoms defined as proper open systems. The creation of a vacancy in a solid does not lead to any difficulties in applying QTAIM, as to the crystal face of MoS 2 in a study of its catalytic properties …”

Section: Transferability In Solids Ionic and Otherwisementioning

confidence: 99%

Nearsightedness of Electronic Matter As Seen by a Physicist and a Chemist

Bader

2008

J. Phys. Chem. A

View full text Add to dashboard Cite

The theorem of Hohenberg and Kohn, that the electron density is a unique functional of the external potential, applies to a closed system with a fixed number of electrons. Transferability of the electron density of an atom between two systems, necessary to account for the fundamental role of a functional group with characteristic properties in chemistry, however, is a problem in the physics of an open system. Transferability in chemistry requires a new theorem stated in terms of the density: that the electron density of an atom in a molecule or crystal determines its additive contribution to all properties of the total system, its transferability being determined by a paralleling degree of transferability in the atom's virial field, the virial of the Ehrenfest force exerted on its electron density. Transferability of the virial field is found in spite of unavoidable changes in the external potential that occur on transfer. The properties of an atom in a molecule are determined by the Heisenberg equation of motion for a "proper open system" derived from the principle of stationary action. The theorem is grounded in the common sense observation that two atoms that "look the same", i.e., have the same charge distribution, must possess identical properties. Transferability is discussed in terms of the properties of the electron density, the one-density and the two-density matrix, the latter demonstrating that both the Coulombic and exchange contributions to the energy of a group are separately transferable. It is demonstrated that the exchange indices determined by the two-density matrix provide a readily determinable measure of the effective range of the exchange energy.

show abstract

“…As a result, the determination of very accurate electron density maps from x-ray crystallography has become accessible to numerous research laboratories in the world. QTAIM, having its starting point the electron density, has quickly acquired the status of the single most important theory used to analyze experimental density maps nowadays [30,31,[120][121][122][123][124][125][126][127]. Experimental densities are currently analyzed by several software, we mention among them XD [128] and MOPRO [129,130] as examples.…”

Section: Future Perspectivementioning

confidence: 99%

Electron-Density Descriptors as Predictors in Quantitative Structure–Activity/Property Relationships and Drug Design

Matta

Arabi

2011

Future Med. Chem.

View full text Add to dashboard Cite

The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

show abstract

Fragment Transferability Studied Theoretically and Experimentally with QTAIM – Implications for Electron Density and Invariom Modeling

Cited by 6 publications

References 39 publications

Bond Paths Are Not Chemical Bonds

Bond Paths Are Not Chemical Bonds

Nearsightedness of Electronic Matter As Seen by a Physicist and a Chemist

Electron-Density Descriptors as Predictors in Quantitative Structure–Activity/Property Relationships and Drug Design

Contact Info

Product

Resources

About