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E J Baerends

Publications and source records attributed to E J Baerends.

14 recordsLinked to original sources
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

Role of the Fermi surface in adsorbate-metal interactions: an energy decomposition analysis.

We present the result of a fragment-based energy decomposition analysis on some molecule-surface interactions. The analysis allows us to quantify the Pauli repulsion, its relief, and the attractive orbital interaction energy. In a metal, the existence of incompletely occupied energy bands causes significant relief of the Pauli repulsion due to escape of antibonding electrons to unoccupied states at the Fermi energy. This is the key electronic structure feature of metals that causes metal-molecule bond energies to be stronger and dissociation barriers of chemisorbed molecules to be much lower than those in comparable systems with no or one metal atom. As examples, we discuss the energy decomposition for the activated dissociation of hydrogen on the Cu surface and its unactivated dissociation on Pd, and for the (activated) chemisorption of N2 on W. We show that in all cases the relief of Pauli repulsion is of crucial importance for the chemisorption energy and for the low (or nonexistent) dissociation barriers. The barrier to the chemisorption well for nitrogen on tungsten is clearly related to a late relief of the Pauli repulsion. The relief of Pauli repulsion is important in lowering the barrier to dissociation of H2 on both Cu and Pd, but the difference in barrier heights for Cu and Pd appears to not be due to stronger relief of Pauli repulsion on Pd but primarily to the Pauli repulsion itself being stronger on Cu than on Pd, the relief energy being quite comparable on the two metals.

Journal Article↗
PubMed2005

Six-dimensional potential energy surface for H2 at Ru(0001).

The six-dimensional (6D) potential energy surface (PES) for the H(2) molecule interacting with a clean Ru(0001) surface has been computed accurately for the first time. Density functional theory (DFT) and a pseudopotential based periodic plane-wave approach have been used to calculate the electronic interactions between the molecule and the surface. Two different generalized gradient approximation (GGA) exchange-correlation functionals, PW91 and RPBE, have been adopted. Based on the DFT/GGA calculated potential energies, an analytical 6D PES has been constructed using the corrugation reducing procedure. A very accurate representation of the DFT/GGA data has been achieved, with an average error in the interpolation of about 3 meV and a maximum error not larger than about 30 meV. The top site is found to be the most reactive site for both functionals used, but PW91 predicts a higher reactivity than RPBE, with lower-energy and earlier-located dissociation barriers. The energetic corrugation displayed by the RPBE PES is larger than the PW91 PES while the geometric corrugation is smaller. The differences between the two PESs increase as the distance of the molecular center of mass to the surface decreases. A direct comparison with experimental investigations on H(2)/Ru(0001) could shed light on the suitability of these XC potentials often used in DFT calculations.

Adsorption↗
PubMed2005

Away from generalized gradient approximation: orbital-dependent exchange-correlation functionals.

The local-density approximation of density functional theory (DFT) is remarkably accurate, for instance, for geometries and frequencies, and the generalized gradient approximations have also made bond energies quite reliable. Sometimes, however, one meets with failure in individual cases. One of the possible routes towards better functionals would be the incorporation of orbital dependence (which is an implicit density dependency) in the functionals. We discuss this approach both for energies and for response properties. One possibility is the use of the Hartree-Fock-type exchange energy expression as orbital-dependent functional. We will argue that in spite of the increasing popularity of this approach, it does not offer any advantage over Hartree-Fock for energies. We will advocate not to apply the separation of exchange and correlation, which is so ingrained in quantum chemistry, but to model both simultaneously. For response properties the energies and shapes of the virtual orbitals are crucial. We will discuss the benefits that Kohn-Sham potentials can offer which are derived from either an orbital-dependent energy functional, including the exact-exchange functional, or which can be obtained directly as orbital-dependent functional. We highlight the similarity of the Hartree-Fock and Kohn-Sham occupied orbitals and orbital energies, and the essentially different meanings the virtual orbitals and orbital energies have in these two models. We will show that these differences are beneficial for DFT in the case of localized excitations (in a small molecule or in a fragment), but are detrimental for charge-transfer excitations. Again, orbital dependency, in this case in the exchange-correlation kernel, offers a solution.

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

Adsorption and diffusion on a stepped surface: atomic hydrogen on Pt(211).

We present density functional theory calculations for atomic hydrogen interacting with a stepped surface, the Pt(211) surface. The calculations have been performed at the generalized gradient approximation level, using a slab representation of the surface. This is the state-of-the-art method for calculating the interaction of atoms or molecules with metal surfaces, nevertheless only few studies have used it to study atoms or molecules interacting with stepped surfaces, and none, to the best of our knowledge, have considered hydrogen interacting with stepped platinum surfaces. Our goal has been to initiate a systematic study of this topic. We have calculated the full three-dimensional potential energy surface (PES) for the H/Pt(211) system together with the vibrational band structure and vibrational eigenfunctions of H. A deep global minimum of the PES is found for bridge-bonded hydrogen on the step edge, in agreement with experimental results for the similar H/Pt(533) system. All the local vibrational excitations at the global minimum have been identified, and this will serve as a helpful guide to the interpretation of future experiments on this (or similar) system(s). Furthermore, from the calculated PES and vibrational band structure, we identify a number of consequences for the interpretation or modelling of diffusion experiments studying the coverage and directional dependence of atomic hydrogen diffusion on stepped platinum surfaces.

Journal Article↗
PubMed2004

The spin-unrestricted molecular Kohn-Sham solution and the analogue of Koopmans's theorem for open-shell molecules.

Spin-unrestricted Kohn-Sham (KS) solutions are constructed from accurate ab initio spin densities for the prototype doublet molecules NO(2), ClO(2), and NF(2) with the iterative local updating procedure of van Leeuwen and Baerends (LB). A qualitative justification of the LB procedure is given with a "strong" form of the Hohenberg-Kohn theorem. The calculated energies epsilon(isigma) of the occupied KS spin orbitals provide numerical support to the analogue of Koopmans' theorem in spin-density functional theory. In particular, the energies -epsilon(ibeta) of the minor spin (beta) valence orbitals of the considered doublet molecules correspond fairly well to the experimental vertical ionization potentials (VIPs) I(i) (1) to the triplet cationic states. The energy -epsilon(Halpha) of the highest occupied (spin-unpaired) alpha orbital is equal to the first VIP I(H) (0) to the singlet cationic state. In turn, the energies -epsilon(ialpha) of the major spin (alpha) valence orbitals of the closed subshells correspond to a fifty-fifty average of the experimental VIPs I(i) (1) and I(i) (0) to the triplet and singlet states. For the Li atom we find that the exact spin densities are represented by a spin-polarized Kohn-Sham system which is not in its ground state, i.e., the orbital energy of the lowest unoccupied beta spin orbital is lower than that of the highest occupied alpha spin orbital ("a hole below the Fermi level"). The addition of a magnetic field in the -z direction will shift the beta levels up so as to restore the Aufbau principle. This is an example of the nonuniqueness of the mapping of the spin density on the KS spin-dependent potentials discussed recently in the literature. The KS potentials may no longer go to zero at infinity, and it is in general the differences nu(ssigma)( infinity )-epsilon(isigma) that can be interpreted as (averages of) ionization energies. In total, the present results suggest the spin-unrestricted KS theory as a natural one-electron independent-particle model for interpretation and assignment of the experimental photoelectron spectra of open-shell molecules.

Journal Article↗
PubMed2003

Optimized Slater-type basis sets for the elements 1-118.

Seven different types of Slater type basis sets for the elements H (Z = 1) up to E118 (Z = 118), ranging from a double zeta valence quality up to a quadruple zeta valence quality, are tested in their performance in neutral atomic and diatomic oxide calculations. The exponents of the Slater type functions are optimized for the use in (scalar relativistic) zeroth-order regular approximated (ZORA) equations. Atomic tests reveal that, on average, the absolute basis set error of 0.03 kcal/mol in the density functional calculation of the valence spinor energies of the neutral atoms with the largest all electron basis set of quadruple zeta quality is lower than the average absolute difference of 0.16 kcal/mol in these valence spinor energies if one compares the results of ZORA equation with those of the fully relativistic Dirac equation. This average absolute basis set error increases to about 1 kcal/mol for the all electron basis sets of triple zeta valence quality, and to approximately 4 kcal/mol for the all electron basis sets of double zeta quality. The molecular tests reveal that, on average, the calculated atomization energies of 118 neutral diatomic oxides MO, where the nuclear charge Z of M ranges from Z = 1-118, with the all electron basis sets of triple zeta quality with two polarization functions added are within 1-2 kcal/mol of the benchmark results with the much larger all electron basis sets, which are of quadruple zeta valence quality with four polarization functions added. The accuracy is reduced to about 4-5 kcal/mol if only one polarization function is used in the triple zeta basis sets, and further reduced to approximately 20 kcal/mol if the all electron basis sets of double zeta quality are used. The inclusion of g-type STOs to the large benchmark basis sets had an effect of less than 1 kcal/mol in the calculation of the atomization energies of the group 2 and group 14 diatomic oxides. The basis sets that are optimized for calculations using the frozen core approximation (frozen core basis sets) have a restricted basis set in the core region compared to the all electron basis sets. On average, the use of these frozen core basis sets give atomic basis set errors that are approximately twice as large as the corresponding all electron basis set errors and molecular atomization energies that are close to the corresponding all electron results. Only if spin-orbit coupling is included in the frozen core calculations larger errors are found, especially for the heavier elements, due to the additional approximation that is made that the basis functions are orthogonalized on scalar relativistic core orbitals.

Journal Article↗
PubMed2001

Exact exchange-correlation treatment of dissociated H(2) in density functional theory.

Whereas the wave function of the dissociated H(2) molecule is easily obtained, an exact treatment of this system has not yet been given in density functional theory. We propose an orbital dependent exchange-correlation functional that yields this exact Kohn-Sham solution. This type of functional offers an alternative to local-density and generalized gradient approximations and the prospects are indicated for treating with it some outstanding problems in density functional theory.

Journal Article↗
PubMed2001

DFT study of the active intermediate in the Fenton reaction.

Density functional theory has been used to investigate the nature of the oxidizing agent in the Fenton reaction. Starting from the primary intermediate [FeII(H2O)5H2O2]2+, we show that the oxygen-oxygen bond breaking mechanism has a small activation energy and could therefore demonstrate the catalytic effect of the metal complex. The O-O bond cleavage of the coordinated H2O2, however, does not lead to a free hydroxyl radical. Instead, the leaving hydroxyl radical abstracts a hydrogen from an adjacent coordinated water leading to the formation of a second Fe-OH bond and of a water molecule. Along this reaction path the primary intermediate transforms into the [FeIV(H2O)4(OH)2]2+ complex and in a second step into a more stable high valent ferryl-oxo complex [FeIV(H2O)5O]2+. We show that the energy profile along the reaction path is strongly affected by the presence of an extra water molecule located near the iron complex. The alternative intermediate [FeII(H2O)4(OOH-)(H3O+)]2+ suggested in the literature has been also investigated, but it is found to be unstable against the primary intermediate. Our results support a picture in which an FeIV-oxo complex is the most likely candidate as the active intermediate in the Fenton reaction, as indeed first proposed by Bray and Gorin already in 1932.

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↗
PubMed1994

A new model for the agonistic binding site on the histamine H2-receptor: the catalytic triad in serine proteases as a model for the binding site of histamine H2-receptor agonists.

The historical model for the agonistic binding site on the histamine H2-receptor is based on a postulated activation mechanism: it has been suggested that the histamine monocation binds to the histamine H2-receptor via the formation of three hydrogen bonds. The cationic ammonium group in the side chain and the -NH- group in the tau-position of the imidazole act as proton donors, whereas the =N- atom in the pi-position of the imidazole acts as a proton acceptor. Participation of the ammonium group in H-bonding with a presumed negative charge on the receptor leads to a decrease in positive charge, which is thought to induce a tautomeric change in the imidazole ring system from N tau-H to N pi-H. A consequence of this tautomeric shift is the donation of a proton from the receptor to the agonist on one side, while on the other side a proton is donated from the agonist to the receptor. The propose tautomeric shift has been suggested to trigger the H2-stimulating effect. However, this model for the constitution of the agonistic binding site and the accessory activation mechanism cannot explain the weak histamine H2-activity of beta-histine and the activity of several other recently synthesized H2-agonists. Based on a thorough literature study and with the aid of molecular electrostatic potentials (MEPs) we demonstrate that the sulphur atom present in histamine H2-agonists as dimaprit and 2-amino-5-(2-aminoethyl)thiazole does not function as a proton acceptor, which implicitly means that a tautomeric shift is not a prerequisite for H2-stimulation. As a consequence, the model for the agonistic binding site is adjusted, resulting in a strong resemblance to the nature and orientation of the amino acids constituting the catalytic triad in serine proteases. Within this concept, the N pi-H tautomer of histamine is the biologically active form, in contrast with the existing model in which the N tau-H tautomer is the active form.

Animals↗