Biomedical subjects

G J Kroes

Publications and source records attributed to G J Kroes.

11 recordsLinked to original sources

PubMed2006

Reactive and nonreactive scattering of N2 from Ru(0001): a six-dimensional adiabatic study.

We have studied the dissociative chemisorption and scattering of N(2) on and from Ru(0001), using a six-dimensional quasiclassical trajectory method. The potential energy surface, which depends on all the molecular degrees of freedom, has been built applying a modified Shepard interpolation method to a data set of results from density functional theory, employing the RPBE generalized gradient approximation. The frozen surface and Born-Oppenheimer [Ann. Phys. (Leipzig) 84, 457 (1927)] approximations were used, neglecting phonons and electron-hole pair excitations. Dissociative chemisorption probabilities are found to be very small even for translational energies much higher than the minimum reaction barrier, in good agreement with experiment. A comparison to previous low dimensional calculations shows the importance of taking into account the multidimensional effects of N(2) rotation and translation parallel to the surface. The new calculations strongly suggest a much smaller role of nonadiabatic effects than previously assumed on the basis of a comparison between low dimensional results and experiments [J. Chem. Phys. 115, 9028 (2001)]. Also in agreement with experiment, our theoretical results show a strong dependence of reaction on the initial vibrational state. Computed angular scattering distributions and parallel translation energy distributions are in good agreement with experiments on scattering, but the theory overestimates vibrational and rotational excitations in scattering.

Journal Article↗

PubMed2006

Predicting catalysis: understanding ammonia synthesis from first-principles calculations.

Here, we give a full account of a large collaborative effort toward an atomic-scale understanding of modern industrial ammonia production over ruthenium catalysts. We show that overall rates of ammonia production can be determined by applying various levels of theory (including transition state theory with or without tunneling corrections, and quantum dynamics) to a range of relevant elementary reaction steps, such as N(2) dissociation, H(2) dissociation, and hydrogenation of the intermediate reactants. A complete kinetic model based on the most relevant elementary steps can be established for any given point along an industrial reactor, and the kinetic results can be integrated over the catalyst bed to determine the industrial reactor yield. We find that, given the present uncertainties, the rate of ammonia production is well-determined directly from our atomic-scale calculations. Furthermore, our studies provide new insight into several related fields, for instance, gas-phase and electrochemical ammonia synthesis. The success of predicting the outcome of a catalytic reaction from first-principles calculations supports our point of view that, in the future, theory will be a fully integrated tool in the search for the next generation of catalysts.

Journal Article↗

PubMed2006

Multidimensional effects on dissociation of N2 on Ru(0001).

The applicability of the Born-Oppenheimer approximation to molecule-metal surface reactions is presently a topic of intense debate. We have performed classical trajectory calculations on a prototype activated dissociation reaction, of N2 on Ru(0001), using a potential energy surface based on density functional theory. The computed reaction probabilities are in good agreement with molecular beam experiments. Comparison to previous calculations shows that the rotation of N2 and its motion along the surface affect the reactivity of N2 much more than nonadiabatic effects.

Journal Article↗

PubMed2006

Multiconfiguration time-dependent Hartree method applied to molecular dissociation on surfaces: H2 + Pt(111).

Four-dimensional quantum dynamics calculations are performed on the dissociative chemisorption of H(2) on Pt(111) using the multiconfiguration time-dependent Hartree method. The aim of this work is to study the performance of the multiconfiguration time-dependent Hartree method for a gas-surface reaction by comparison with the standard time-dependent wave-packet propagation method. The initial-state resolved dissociation probability of H(2) is calculated within two four-dimensional models. The first four-dimensional model treats explicitly the rotational motion of the molecule and the H(2) dissociation is studied above two different sites of the Pt(111). For this model, only a potential-energy surface of general form was available. This potential was refitted to a sum of product form to allow efficient calculations with the multiconfiguration time-dependent Hartree method. The second model focuses on the description of the center-of-mass motion parallel to the surface, the rotational motion of the molecule being frozen. These four-dimensional quantum dynamics calculations yield important insights which can help with performing full six-dimensional calculations on H(2) dissociating on Pt(111). The multiconfiguration time-dependent Hartree method is shown to be particularly efficient for computing initial-state selective dissociation probabilities for the system studied, with a good accuracy and a reduced amount of memory and computational time when compared to the standard time-dependent wave-packet method.

Journal Article↗

PubMed2005

A classical dynamics method for H2 diffraction from metal surfaces.

We present a discretization method that allows one to interpret measurements on diffraction of diatomic molecules from solid surfaces using six-dimensional (6D) classical trajectory calculations. It has been applied to the D2NiAl(110) and H2Pd(111) systems (which are models for activated and nonactivated dissociative chemisorption, respectively) using realistic potential energy surfaces obtained from first principles. Comparisons with experimental results and 6D quantum dynamical calculations show that, in general, the method is able to predict the relative intensity of the most important diffraction peaks. We therefore conclude that classical mechanics can be an efficient guide for experimentalists in the search for the most significant diffraction channels.

Journal Article↗

PubMed2004

Reactive scattering of H2 from Cu(100): six-dimensional quantum dynamics results for reaction and scattering obtained with a new, accurately fitted potential-energy surface.

Six-dimensional quantum dynamical calculations are reported for the dissociative chemisorption of (v=0, 1, j=0) H(2) on Cu(100), and for rovibrationally inelastic scattering of (v=1, j=1) H(2) from Cu(100). The dynamics results were obtained using a new potential-energy surface (PES5), which was based on density-functional calculations using a slab representation of the adsorbate-substrate system and a generalized gradient approximation to the exchange-correlation energy. A very accurate method (the corrugation reducing procedure) was used to represent the density-functional theory data in a global potential-energy surface. With the new, more accurately fitted PES5, the agreement between the dynamics results and experimental results for reaction and rovibrationally elastic scattering is not as good as was obtained with a previous potential-energy surface (PES4), which was based on a subset of the density-functional theory data not yet including the results for the low-symmetry Cu sites. Preliminary density-functional theory results suggest that the agreement between theory and experiment will improve over that obtained with PES5 if the density-functional calculations are repeated using a larger basis set and using more copper layers than employed in PES4 and PES5.

Journal Article↗

PubMed2004

In-plane and out-of-plane diffraction of H(2) from metal surfaces.

We have measured in-plane and out-of-plane diffraction of H2 and D2 molecular beams scattered by reactive Pd(111) and nonreactive NiAl(110) surfaces at 140-150 meV. A comparison with six-dimensional quantum dynamics and classical trajectory calculations shows for the first time that accurate diffraction patterns can be obtained from state-of-the-art potential energy surfaces based on density functional theory. Our measurements show that, at general incidence conditions, out-of-plane diffraction is much more important than was assumed in previous experiments.

Journal Article↗

PubMed2004

Comparison of methods for finding saddle points without knowledge of the final states.

Within the harmonic approximation to transition state theory, the biggest challenge involved in finding the mechanism or rate of transitions is the location of the relevant saddle points on the multidimensional potential energy surface. The saddle point search is particularly challenging when the final state of the transition is not specified. In this article we report on a comparison of several methods for locating saddle points under these conditions and compare, in particular, the well-established rational function optimization (RFO) methods using either exact or approximate Hessians with the more recently proposed minimum mode following methods where only the minimum eigenvalue mode is found, either by the dimer or the Lanczos method. A test problem involving transitions in a seven-atom Pt island on a Pt(111) surface using a simple Morse pairwise potential function is used and the number of degrees of freedom varied by varying the number of movable atoms. In the full system, 175 atoms can move so 525 degrees of freedom need to be optimized to find the saddle points. For testing purposes, we have also restricted the number of movable atoms to 7 and 1. Our results indicate that if attempting to make a map of all relevant saddle points for a large system (as would be necessary when simulating the long time scale evolution of a thermal system) the minimum mode following methods are preferred. The minimum mode following methods are also more efficient when searching for the lowest saddle points in a large system, and if the force can be obtained cheaply. However, if only the lowest saddle points are sought and the calculation of the force is expensive but a good approximation for the Hessian at the starting position of the search can be obtained at low cost, then the RFO approaches employing an approximate Hessian represent the preferred choice. For small and medium sized systems where the force is expensive to calculate, the RFO approaches employing an approximate Hessian is also the more efficient, but when the force and Hessian can be obtained cheaply and only the lowest saddle points are sought the RFO approach using an exact Hessian is the better choice. These conclusions have been reached based on a comparison of the total computational effort needed to find the saddle points and the number of saddle points found for each of the methods. The RFO methods do not perform very well with respect to the latter aspect, but starting the searches further away from the initial minimum or using the hybrid RFO version presented here improves this behavior considerably in most cases.

Journal Article↗

PubMed2004

Sticking of CO to crystalline and amorphous ice surfaces.

We present results of classical trajectory calculations on the sticking of hyperthermal CO to the basal plane (0001) face of crystalline ice Ih and to the surface of amorphous ice Ia. The calculations were performed for normal incidence at a surface temperature Ts = 90 K for ice Ia, and at Ts = 90 and 150 K for ice Ih. For both surfaces, the sticking probability can be fitted to a simple exponentially decaying function of the incidence energy, Ei: Ps = 1.0e(-Ei(kJ/mol)/90(kJ/mol)) at Ts = 90 K. The energy transfer from the impinging molecule to the crystalline and the amorphous surface is found to be quite efficient, in agreement with the results of molecular beam experiments on the scattering of the similar molecule, N2, from crystalline and amorphous ice. However, the energy transfer is less efficient for amorphous than for crystalline ice. Our calculations predict that the sticking probability decreases with Ts for CO scattering from crystalline ice, as the energy transfer from the impinging molecule to the warmer surfaces becomes less efficient. At high Ei (up to 193 kJ/mol), no surface penetration occurs in the case of crystalline ice. However, for CO colliding with the amorphous surface, a penetrating trajectory was observed to occur into a large water pore. The molecular dynamics calculations predict that the average potential energy of CO adsorbed to ice Ih is -10.1 +/- 0.2 and -8.4 +/- 0.2 kJ/mol for CO adsorbed to ice Ia. These values are in agreement with previous experimental and theoretical data. The distribution of the potential energy of CO adsorbed to ice Ia was found to be wider (with a standard deviation sigma of 2.4 kJ/mol) than that of CO interacting with ice Ih (sigma = 2.0 kJ/mol). In collisions with ice Ia, the CO molecules scatter at larger angles and over a wider distribution of angles than in collisions with ice Ih.

Journal Article↗

PubMed2004

Application of the modified Shepard interpolation method to the determination of the potential energy surface for a molecule-surface reaction: H2 + Pt(111).

We have used a modified Shepard (MS) interpolation method, initially developed for gas phase reactions, to build a potential energy surface (PES) for studying the dissociative chemisorption of H2 on Pt(111). The aim was to study the efficiency and the accuracy of this interpolation method for an activated multidimensional molecule-surface reactive problem. The strategy used is based on previous applications of the MS method to gas phase reactions, but modified to take into account special features of molecule-surface reactions, like the presence of many similar reaction pathways which vary only slightly with surface site. The efficiency of the interpolation method was tested by using an already existing PES to provide the input data required for the construction of the new PES. The construction of the new PES required half as many ab initio data points as the construction of the old PES, and the comparison of the two PESs shows that the method is able to reproduce with good accuracy the most important features of the H2 + Pt(111) interaction potential. Finally, accuracy tests were done by comparing the results of dynamics simulations using the two different PESs. The good agreement obtained for reaction probabilities and probabilities for rotationally and diffractionally inelastic scattering shows clearly that the MS interpolation method can be used efficiently to yield accurate PESs for activated molecule-surface reactions.

Journal Article↗

PubMed2000

Quantum dynamics of the dissociation of H2 on Cu(100): dependence of the site-reactivity on initial rovibrational state.

We perform six-dimensional (6D) quantum wavepacket calculations for H2 dissociatively adsorbing on Cu(100) from a variety of rovibrational initial states. The calculations are performed on a new potential energy surface (PES), the construction of which is also detailed. Reaction probabilities are in good agreement with experimental findings. Using a new flux analysis method, we calculate the reaction probability density as a function of surface site and collision energy, for a variety of initial states. This approach is used to study the effects of rotation and vibration on reaction at specific surface sites. The results are explained in terms of characteristics of the PES and intrinsically dynamic effects. An important observation is that, even at low collision energies, reaction does not necessarily proceed predominantly in the region of the minimum potential barrier, but can occur almost exclusively at a site with a higher barrier. This suggests that experimental control of initial conditions could be used to selectively induce reaction at particular surface sites. Our predictions for site-reactivity could be tested using contemporary experimental methods: The calculations predict that, for reacting molecules, there will be a dependence of the quadrupole alignment of j on the incident vibrational state, v. This is a direct result of PES topography in the vicinity of the preferred reaction sites of v = 0 and v = 1 molecules. Invoking detailed balance, evidence for this difference in preferred reaction site of v = 0 and 1 molecules could be obtained through associative desorption experiments.

Journal Article↗