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Chemical Intuition (chemical + intuition)

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Chemistry100%

Selected Abstracts

Are the Hirshfeld and Mulliken population analysis schemes consistent with chemical intuition?

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2009
Soumen Saha
Abstract In the present article, we report a comparative study between the Hirshfeld and Mulliken population analysis schemes (abbreviated as HPA and MPA, respectively). Trends of atomic charges derived from these two population analysis schemes are compared with those expected from other commonly used chemical concepts like electronegativity, inductive effects, and resonance effects. Although previous studies on intramolecular reactivity sequences demonstrated that HPA generates reliable and non-negative (and thus physically more realistic) condensed Fukui function (FF) values, the present study reveals problems with the HPA charge partitioning technique. Specifically, HPA fails to reproduce reliable intermolecular and intramolecular charge trends in several systems. Reasons for the success and failure of HPA are discussed and a method for improving the Hirshfeld charge partitioning is proposed. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source]

The Binding Mode of Progesterone to Its Receptor Deduced from Molecular Dynamics Simulations

CHEMBIOCHEM, Issue 2-3 2003
Tiziana Mordasini Dr.
Abstract An unambiguous understanding of the binding mode of human progesterone to its receptor still eludes experimental search. According to the X-ray structure of the ligand-binding domain, only one (O3) of the two keto groups at the ligand ends (O3 and O20) should play a role. This result is in conflict with chemical intuition and the results of site-directed mutagenesis experiments. Herein, we report classical molecular dynamics simulations that reveal the dynamic nature of the binding in solution, elucidate the reasons why X-ray studies failed to determine the role of O20, and clarify the effects of the mutations. The predictive power of the force field is ensured by the consistent introduction of a first-principles representation of the ligand. [source]

Solid,Solid Phase Transitions: Interface Controlled Reactivity and Formation of Intermediate Structures

CHEMISTRY - A EUROPEAN JOURNAL, Issue 36 2007
Stefano Leoni Dr.
Abstract Finding new pathways to novel materials is an open challenge in modern solid-state chemistry. Among the reasons that still prevent a rational planning of synthetic routes is the lack of an atomistic understanding at the moment of phase formation. Metastable phases are, in this respect, powerful points of access to new materials. For the synthetic efforts to fully take advantage of such peculiar intermediates, a precise atomistic understanding of critical processes in the solid state in its many facets, that is, nucleation patterns, formation and propagation of interfaces, intermediate structures, and phase growth, is mandatory. Recently we have started a systematic theoretical study of phase transitions, especially of processes with first-order thermodynamics, to reach a firm understanding of the atomistic mechanisms governing polymorphism in the solid state. A clear picture is emerging of the interplay between nucleation patterns, the evolution of domain interfaces and final material morphology. Therein intermediate metastable structural motifs with distinct atomic patterns are identified, which become exciting targets for chemical synthesis. Accordingly, a new way of implementing simulation strategies as a powerful support to the chemical intuition is emerging. Simulations of real materials under conditions corresponding to the experiments are shedding light onto yet elusive aspects of solid,solid transformations. Particularly, sharp insights into local nucleation and growth events allow the formulation of new concepts for rationalizing interfaces formed during phase nucleation and growth. Structurally different and confined in space, metastable interfaces occurring during polymorph transformations bring about distinct diffusion behavior of the chemical species involved. More generally, stable structures emerge as a result of the concurrence of the transformation mechanism and of chemical reactions within the phase-growth fronts. [source]

Atomic Properties of Amino Acids: Computed Atom Types as a Guide for Future Force-Field Design

CHEMPHYSCHEM, Issue 8 2003
Paul L. A. Popelier Dr.
Abstract The quantum chemical topology (QCT) is able to propose atom types by direct computation rather than by chemical intuition. In previous work, molecular electron densities of 20 amino acids and smaller derived molecules were partitioned into a set of 760 topological atoms. Each atom was characterised by seven atomic properties and subjected to cluster analysis element by element, that is, C, H, O, N, and S. From the respective dendrograms, 21 carbon atom types were distinguished, 7 hydrogen, 2 nitrogen, 6 oxygen, and 6 sulfur atom types. Herein, we contrast the QCT atom types with those of the assisted model building with energy refinement (AMBER) force field. We conclude that in spite of fair agreement between QCT and AMBER atom types, the latter are sometimes underdifferentiated and sometimes overdifferentiated. In summary, we suggest that QCT is a useful guide in designing new force fields or improving existing ones. The computational origin of QCT atom types makes their determination unbiased compared to atom type determination by chemical intuition and a priori assumptions. We provide a list of specific recommendations. [source]