The characterization of atomic interactions
01 Mar 1984-Journal of Chemical Physics (American Institute of Physics)-Vol. 80, Iss: 5, pp 1943-1960
TL;DR: In this paper, the authors derived the sign of the Laplacian of the charge density ρ to the relative magnitudes of the local contributions of the potential and kinetic energy densities to their virial theorem averages.
Abstract: The theory of molecular structure determined by the gradient vector field of the charge density ρ identifies the set of atomic interactions present in a molecule. The interactions so defined are characterized in terms of the properties of the Laplacian of the charge density ∇2ρ(r). A scalar field is concentrated in those regions of space where its Laplacian is negative and depleted in those where it is positive. An expression derived from the quantum mechanical stress tensor relates the sign of the Laplacian of ρ to the relative magnitudes of the local contributions of the potential and kinetic energy densities to their virial theorem averages. By obtaining a map of those regions where ∇2ρ(r) 0. The mechanics are characterized by the relatively large value of the kinetic energy, particularly the component parallel to the interaction line. In the closed‐shell interactions, the regions of dominant potential energy contributions are separately localized within the boundaries of each of the interacting atoms or molecules. In the shared interactions, a region of low potential energy is contiguous over the basins of both of the interacting atoms. The problem of further classifying a given interaction as belonging to a bound or unbound state of a system is also considered, first from the electrostatic point of view wherein the regions of charge concentration as determined by the Laplacian of ρ are related to the forces acting on the nuclei. This is followed by and linked to a discussion of the energetics of interactions in terms of the regions of dominant potential and kinetic energy contributions to the virial as again determined by the Laplacian of ρ. The properties of the Laplacian of the electronic charge thus yield a unified view of atomic interactions, one which incorporates the understandings afforded by both the Hellmann–Feynman and virial theorems.
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TL;DR: This work develops an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives, which provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids.
Abstract: Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
5,731 citations
TL;DR: In this paper, the Hartree-Fock parallel spin probability was used to identify localized electronic groups in atomic and molecular systems, which is completely independent of unitary orbital transformations.
Abstract: We introduce in this work a new approach to the identification of localized electronic groups in atomic and molecular systems. Our approach is based on local behavior of the Hartree–Fock parallel‐spin pair probability and is completely independent of unitary orbital transformations. We derive a simple ‘‘electron localization function’’ (ELF) which easily reveals atomic shell structure and core, binding, and lone electron pairs in simple molecular systems as well.
5,039 citations
TL;DR: This chapter discusses the development of DFT as a tool for Calculating Atomic andMolecular Properties and its applications, as well as some of the fundamental and Computational aspects.
Abstract: I. Introduction: Conceptual vs Fundamental andComputational Aspects of DFT1793II. Fundamental and Computational Aspects of DFT 1795A. The Basics of DFT: The Hohenberg−KohnTheorems1795B. DFT as a Tool for Calculating Atomic andMolecular Properties: The Kohn−ShamEquations1796C. Electronic Chemical Potential andElectronegativity: Bridging Computational andConceptual DFT1797III. DFT-Based Concepts and Principles 1798A. General Scheme: Nalewajski’s ChargeSensitivity Analysis1798B. Concepts and Their Calculation 18001. Electronegativity and the ElectronicChemical Potential18002. Global Hardness and Softness 18023. The Electronic Fukui Function, LocalSoftness, and Softness Kernel18074. Local Hardness and Hardness Kernel 18135. The Molecular Shape FunctionsSimilarity 18146. The Nuclear Fukui Function and ItsDerivatives18167. Spin-Polarized Generalizations 18198. Solvent Effects 18209. Time Evolution of Reactivity Indices 1821C. Principles 18221. Sanderson’s Electronegativity EqualizationPrinciple18222. Pearson’s Hard and Soft Acids andBases Principle18253. The Maximum Hardness Principle 1829IV. Applications 1833A. Atoms and Functional Groups 1833B. Molecular Properties 18381. Dipole Moment, Hardness, Softness, andRelated Properties18382. Conformation 18403. Aromaticity 1840C. Reactivity 18421. Introduction 18422. Comparison of Intramolecular ReactivitySequences18443. Comparison of Intermolecular ReactivitySequences18494. Excited States 1857D. Clusters and Catalysis 1858V. Conclusions 1860VI. Glossary of Most Important Symbols andAcronyms1860VII. Acknowledgments 1861VIII. Note Added in Proof 1862IX. References 1865
3,890 citations
TL;DR: In this article, the topological properties of ρ(r) at the intermolecular critical points of 83 experimentally observed hydrogen bonds [X-H⋯O (X=C,N,O)], using accurate X-ray diffraction experiments, were analyzed.
2,675 citations
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TL;DR: In this article, it was shown that the force on a nucleus in an atomic system is just the classical electrostatic force that would be exerted on this nucleus by other nuclei and by the electrons' charge distribution.
Abstract: Formulas have been developed to calculate the forces in a molecular system directly, rather than indirectly through the agency of energy. This permits an independent calculation of the slope of the curves of energy vs. position of the nuclei, and may thus increase the accuracy, or decrease the labor involved in the calculation of these curves. The force on a nucleus in an atomic system is shown to be just the classical electrostatic force that would be exerted on this nucleus by other nuclei and by the electrons' charge distribution. Qualitative implications of this are discussed.
2,832 citations
TL;DR: In this paper, an algorithm for the calculation of the average properties of an atom in a molecule is described. But this algorithm is restricted to the case where the atom is defined within the topological theory of molecular structure, a theory which defines atoms, bonds, structure and structural stability in terms of a system's charge distribution.
Abstract: This article describes an algorithm for the calculation of the average properties of an atom in a molecule. The atom is defined within the topological theory of molecular structure, a theory which defines atoms, bonds, structure, and structural stability in terms of the topological properties of a system's charge distribution. The average properties of the atom so defined are uniquely determined by quantum mechanics. Results for a number of hydrocarbon molecules, obtained by the program PROAIM (properties of atoms in molecules) which implements this algorithm, are given. In general, this program enables one to calculate the average energy of an atom in a molecule to an accuracy of ±1 kcal/mol.
1,250 citations