Properties of Chemically Interesting Potential Energy Surfaces

Heidrich, Dietmar; Kliesch, Wolfgang; Quapp, Wolfgang

doi:10.1007/978-3-642-93499-5

Cited by 94 publications

(87 citation statements)

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“…For a small molecule, or molecules consisting of a few essentially rigid building blocks, one can employ low-dimensional projections of the landscape to highlight important features of e.g. the transition path during a conformational change or a chemical reaction [44]. For larger molecules, finding reduced coordinates has led to the application of the so-called principal coordinate analysis (PCA) to the configurations that represent local minima [45].…”

Section: Visualization Techniques In Energy Landscapes Representationmentioning

confidence: 99%

Structure Prediction for PbS and ZnO at Different Pressures and Visualization of the Energy Landscapes

et al. 2011

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An important issue in modern solid state chemistry is the development of a general methodology to predict the possible (meta)-stable modifications of a solid. This requires the global exploration of the energy landscape of the chemical system, since each stable phase corresponds to a locally ergodic region of the landscape. The global search in the lead sulfide system has been performed with simulated annealing on the ab initio level, while zinc oxide was studied with an empirical potential using simulated annealing, both at standard and elevated pressure (up to 100 GPa). The local optimization of the modifications found in the PbS system was performed using various density functionals. Next, the energy E(V ) and enthalpy H(p) as function of volume and pressure, respectively, were computed for these modifications and their electronic structure was analyzed. The structures found for ZnO were locally optimized on ab initio level (DFT and Hartree-Fock). In both systems the structures found were in good agreement with the experiment. Furthermore, we employed the threshold algorithm to explore the barrier structure of the landscape of ZnO as function of the number of formula units in the simulation cell. Based on the barrier and minima information 2-D models of the energy landscape were constructed.

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Section: Visualization Techniques In Energy Landscapes Representationmentioning

confidence: 99%

Structure Prediction for PbS and ZnO at Different Pressures and Visualization of the Energy Landscapes

et al. 2011

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“…Adjacent conformations differ by insertion or deletion of a single base pair, arranging the secondary structures in an undirected graph. Heidrich et al 1991), which describe the system at the level of spatial coordinates of individual atoms.…”

Section: Theory Energy Landscapes For Rna Foldingmentioning

confidence: 99%

BarMap: RNA folding on dynamic energy landscapes

Hofacker¹,

Flamm²,

Heine³

et al. 2010

RNA

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Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, especially in time-variable and externally triggered systems, are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we describe the theoretical foundations of a generic approach that not only allows the direct computation of approximate population densities but also reduces the efforts required to analyze the folding energy landscapes to a one-time preprocessing step. The basic idea is to consider the kinetics on individual landscapes and to model external triggers and environmental changes as small but discrete changes in the landscapes. A ''barmap'' links macrostates of temporally adjacent landscapes and defines the transfer of population densities from one ''snapshot'' to the next. Implemented in the BarMap software, this approach makes it feasible to study folding processes at the level of basins, saddle points, and barriers for many nonstationary scenarios, including temperature changes, cotranscriptional folding, refolding in consequence to degradation, and mechanically constrained kinetics, as in the case of the translocation of a polymer through a pore.

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“…For projector (4) we can measure the zero of equation (5) directly in the n-dimensional curvilinear metric. This version of n P r is used in section 7.…”

Section: Definition Of Rgf Curvesmentioning

confidence: 99%

“…The concept of the minimum energy path (MEP) or reaction path (RP) of an adiabatic potential energy surface (PES) is the usual approach to the theoretical kinetics of larger chemical systems [1][2][3][4][5][6]. It is roughly defined as a line in coordinate space, which connects two minima by passing the saddle point (SP) (the transition structure) of a PES.…”

Section: Introductionmentioning

confidence: 99%

Newton Trajectories in the Curvilinear Metric of Internal Coordinates

Quapp

2004

Journal of Mathematical Chemistry

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The reaction path is an important concept of theoretical chemistry. We discuss the definition with the help of the following of the reduced gradient (RGF) [see Quapp et al., Theoret. Chem. Acc. 100 (1998) 285], also named the Newton trajectory. All the important features of the potential energy surface are definable independently of the coordinate system. We demonstrate it for the Newton trajectory. We design a numerical scheme for the RGF method including the intrinsic curvilinear metric of internal coordinates. For the path following we extend the previous method to the use of a generalized singular value decomposition (SVD). An example of the HCN isomerization pathway is discussed.

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Properties of Chemically Interesting Potential Energy Surfaces

Cited by 94 publications

References 0 publications

Structure Prediction for PbS and ZnO at Different Pressures and Visualization of the Energy Landscapes

Structure Prediction for PbS and ZnO at Different Pressures and Visualization of the Energy Landscapes

BarMap: RNA folding on dynamic energy landscapes

Newton Trajectories in the Curvilinear Metric of Internal Coordinates

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