Publisher’s Note: “A modified next reaction method for simulating chemical systems with time dependent propensities and delays” [J. Chem. Phys. 127, 214107 (2007)]

2008 ◽  
Vol 128 (10) ◽  
pp. 109903 ◽  
Author(s):  
David F. Anderson
Keyword(s):  
Chem Phys ◽  
Time Dependent ◽  
Reaction Method ◽  
Chemical Systems

RESONANCES IN H+HLi SCATTERING FOR NONZERO TOTAL ANGULAR MOMENTUM (J > 0): A TIME-DEPENDENT WAVE PACKET APPROACH

2006 ◽  
Vol 05 (04) ◽  
pp. 871-885 ◽  
Author(s):  
R. PADMANABAN ◽  
S. MAHAPATRA
Keyword(s):  
Angular Momentum ◽  
Wave Packet ◽  
Total Angular Momentum ◽  
Energy Surface ◽  
Chem Phys ◽  
Time Dependent ◽  
Coriolis Coupling ◽  
Initial State ◽  
Sudden Approximation ◽  
Franck Condon

The resonances in H + HLi scattering for nonzero total angular momentum (J > 0) are examined here by a time-dependent wave packet approach employing an ab initio potential energy surface (PES) [Dunne LJ, Murrell JN, Jemmer P, Chem Phys Lett336: 1, 2001] of the system. The resonances are identified by calculating a set of pseudospectra corresponding to the Franck–Condon transition of a hypothetical initial state to the interaction region of the H + HLi PES. The resonances are characterized by calculating their eigenfunctions and linewidth lifetimes. The resonances for J ≠ 0 are discussed in relation to their counterpart for J = 0. The effect of Coriolis coupling on the resonances obtained from the centrifugal sudden approximation for J = 2 and for K = 0,1,2 is examined.

Chemical Tests as Alternatives to Animal Tests in Research on Late Symptoms in Diabetes

2002 ◽  
Vol 30 (3) ◽  
pp. 341-348
Author(s):  
Mette Nielsen ◽  
Jørgen Clausen
Keyword(s):  
Heavy Metals ◽  
Free Radicals ◽  
Free Radical ◽  
Time Dependent ◽  
Advanced Glycation ◽  
Chemical Systems ◽  
In Vitro Systems ◽  
Free Radical Formation ◽  
Animal Tests

Glycation reactions, such as those seen in late diabetes, can be mimicked in purely chemical systems. The glycation is time-dependent, and in in vitro systems it may continue for days. Ascorbate seems to enhance the reactions. The reactions are associated with free-radical formation through transformation of an Amadori product to (deoxy-)glycoson, catalysed by heavy metals. Ascorbate enhances the reaction by a factor of 5–10 compared with in vitro systems without ascorbate. In vitro systems containing bovine serum albumin retard the formation of free-radicals, because of the formation of advanced glycation products.

Independent gradient model based on Hirshfeld partition (IGMH): A new method for visual study of interactions in chemical systems

2021 ◽  
Author(s):  
Tian Lu ◽  
Qinxue Chen
Keyword(s):  
Visual Analysis ◽  
Weak Interactions ◽  
Chem Phys ◽  
Noncovalent Interaction ◽  
Chemical Systems ◽  
Gradient Model ◽  
Atom Pairs ◽  
New Variant ◽  
Physical Background ◽  
User Friendly

The independent gradient model (IGM) originally proposed in Phys. Chem. Chem. Phys., 19, 17928 (2017) has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years, and it has many clear advantages over the widely employed noncovalent interaction (NCI) method, such as intrafragment and interfragment interactions can be elegantly isolated and thus separately studied, the isosurfaces are smoother and less jaggy. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we first present a detailed overview of the IGM analysis, and then propose our new variant of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free-state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. In addition, we describe some indices defined on the top of IGM or IGMH framework to quantify contributions from various atoms or atom pairs to interaction between specific fragments. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been efficiently supported in our freely available and user-friendly wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn), and a detailed tutorial is presented. We hope that IGMH will become a new popular method among chemists for exploring interactions in wide variety of chemical systems.

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