Biomedical subjects

Andreas Heyden

Publications and source records attributed to Andreas Heyden.

5 recordsLinked to original sources

PubMed2006

Nitrous oxide decomposition over Fe-ZSM-5 in the presence of nitric oxide: a comprehensive DFT study.

A number of experimental studies have shown recently that ppm-level additions of nitric oxide (NO) enhance the rate of nitrous oxide (N(2)O) decomposition catalyzed by Fe-ZSM-5 at low temperatures. In the present work, the NO-assisted N(2)O decomposition over mononuclear iron sites in Fe-ZSM-5 was studied on a molecular level using density functional theory (DFT) and transition-state theory. A reaction network consisting of over 100 elementary reactions was considered. The structure and energies of potential-energy minima were determined for all stable species, as were the structures and energies of all transition states. Reactions involving changes in spin potential-energy surfaces were also taken into account. In the absence of NO and at temperatures below 690 K, most active single iron sites (Z(-)[FeO](+)) are poisoned by small concentrations of water in the gas phase; however, in the presence of NO, these poisoned sites are converted into a novel active iron center (Z(-)[FeOH](+)). These latter sites are capable of promoting the dissociation of N(2)O into a surface oxygen atom and gas-phase N(2). The surface oxygen atom is removed by reaction with NO or nitrogen dioxide (NO(2)). N(2)O dissociation is the rate-limiting step in the reaction mechanism. At higher temperatures, water desorbs from inactive iron sites and the reaction mechanism for N(2)O decomposition becomes independent of NO, reverting to the reaction mechanism previously reported by Heyden et al. [J. Phys. Chem. B 2005, 109, 1857].

Journal Article↗

PubMed2006

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Algorithms↗

PubMed2005

Efficient methods for finding transition states in chemical reactions: comparison of improved dimer method and partitioned rational function optimization method.

A combination of interpolation methods and local saddle-point search algorithms is probably the most efficient way of finding transition states in chemical reactions. Interpolation methods such as the growing-string method and the nudged-elastic band are able to find an approximation to the minimum-energy pathway and thereby provide a good initial guess for a transition state and imaginary mode connecting both reactant and product states. Since interpolation methods employ usually just a small number of configurations and converge slowly close to the minimum-energy pathway, local methods such as partitioned rational function optimization methods using either exact or approximate Hessians or minimum-mode-following methods such as the dimer or the Lanczos method have to be used to converge to the transition state. A modification to the original dimer method proposed by [Henkelman and Jonnson J. Chem. Phys. 111, 7010 (1999)] is presented, reducing the number of gradient calculations per cycle from six to four gradients or three gradients and one energy, and significantly improves the overall performance of the algorithm on quantum-chemical potential-energy surfaces, where forces are subject to numerical noise. A comparison is made between the dimer methods and the well-established partitioned rational function optimization methods for finding transition states after the use of interpolation methods. Results for 24 different small- to medium-sized chemical reactions covering a wide range of structural types demonstrate that the improved dimer method is an efficient alternative saddle-point search algorithm on medium-sized to large systems and is often even able to find transition states when partitioned rational function optimization methods fail to converge.

Journal Article↗

PubMed2005

Comprehensive DFT study of nitrous oxide decomposition over Fe-ZSM-5.

The reaction mechanism for nitrous oxide decomposition has been studied on hydrated and dehydrated mononuclear iron sites in Fe-ZSM-5 using density functional theory. In total, 46 different surface species with different spin states (spin multiplicity M(S) = 4 or 6) and 63 elementary reactions were considered. Heats of adsorption, activation barriers, reaction rates, and minimum energy pathways were determined. The approximate minimum energy pathways and transition states were calculated using the "growing string method" and a modified "dimer method". Spin surface crossing (e.g., O(2) desorption) was considered. The minimum potential energy structure on the seam of two potential energy surfaces was determined with a multiplier penalty function algorithm by Powell and approximate rates of spin surface crossings were calculated. It was found that nitrous oxide decomposition is first order with respect to nitrous oxide concentration and zero order with respect to oxygen concentration. Water impurities in the gas stream have a strong inhibiting effect. In the concentration range of 1-100 ppb, the presence of water vapor influences the surface composition and the apparent rate coefficient. This is especially relevant in the temperature range of 600-700 K where most experimental kinetic studies are performed. Apparent activation barriers determined over this temperature range vary from 28.4 (1 ppb H(2)O) to 54.8 kcal/mol (100 ppb H(2)O). These results give an explanation why different research groups and different catalyst pretreatments often result in very different activation barriers and preexponential factors. Altogether perfect agreement with experimental results could be achieved.

Journal Article↗

PubMed2004

A growing string method for determining transition states: comparison to the nudged elastic band and string methods.

Interpolation methods such as the nudged elastic band and string methods are widely used for calculating minimum energy pathways and transition states for chemical reactions. Both methods require an initial guess for the reaction pathway. A poorly chosen initial guess can cause slow convergence, convergence to an incorrect pathway, or even failed electronic structure force calculations along the guessed pathway. This paper presents a growing string method that can find minimum energy pathways and transition states without the requirement of an initial guess for the pathway. The growing string begins as two string fragments, one associated with the reactants and the other with the products. Each string fragment is grown separately until the fragments converge. Once the two fragments join, the full string moves toward the minimum energy pathway according to the algorithm for the string method. This paper compares the growing string method to the string method and to the nudged elastic band method using the alanine dipeptide rearrangement as an example. In this example, for which the linearly interpolated guess is far from the minimum energy pathway, the growing string method finds the saddle point with significantly fewer electronic structure force calculations than the string method or the nudged elastic band method.

Journal Article↗