Marek Sierka

Fast evaluation of the Coulomb potential for electron densities using multipole accelerated resolution of identity approximation

A new computational approach is presented that allows for an accurate and efficient treatment of the electronic Coulomb term in density functional methods. This multipole accelerated resolution of identity for J (MARI-J) method partitions the Coulomb interactions into the near- and far-field parts. The calculation of the far-field part is performed by a straightforward application of the multipole expansions and the near-field part is evaluated employing expansion of molecular electron densities in atom-centered auxiliary basis sets (RI-J approximation). Compared to full RI-J calculations, up to 6.5-fold CPU time savings are reported for systems with about 1000 atoms without any significant loss of accuracy. Other multipole-based methods are compared with regard to reduction of the CPU times versus the conventional treatment of the Coulomb term. The MARI-J approach compares favorably and offers speedups approaching two orders of magnitude for molecules with about 400 atoms and more than 5000 basis functio...

Application of semiempirical long‐range dispersion corrections to periodic systems in density functional theory

Ewald summation is used to apply semiempirical long‐range dispersion corrections (Grimme, J Comput Chem 2006, 27, 1787; 2004, 25, 1463) to periodic systems in density functional theory. Using the parameters determined before for molecules and the Perdew‐Burke‐Ernzerhof functional, structure parameters and binding energies for solid methane, graphite, and vanadium pentoxide are determined in close agreement with observed values. For methane, a lattice constant a of 580 pm and a sublimation energy of 11 kJ mol−1 are calculated. For the layered solids graphite and vanadia, the interlayer distances are 320 pm and 450 pm, respectively, whereas the graphite interlayer energy is −5.5 kJ mol−1 per carbon atom and layer. Only when adding the semiempirical dispersion corrections, realistic values are obtained for the energies of adsorption of C4 alkenes in microporous silica (−66 to −73 kJ mol−1) and the adsorption and chemisorption (alkoxide formation) of isobutene on acidic sites in the micropores of zeolite ferrierite (−78 to −94 kJ mol−1). As expected, errors due to missing self‐interaction correction as in the energy for the proton transfer from the acidic site to the alkene forming a carbenium ion are not affected by the dispersion term. The adsorption and reaction energies are compared with the results from Møller‐Plesset second‐order perturbation theory with basis set extrapolation.

Coordination and siting of Cu+ ions in ZSM-5: A combined quantum mechanics/interatomic potential function study

Siting and coordination of Cu+ ions in zeolite ZSM-5 have been studied by a combined quantum mechanics/interatomic potential function technique. A new Cu(I)–O interaction potential has been parameterized based on abinitio data which is compatible with abinitio-parametrized shell model potentials for zeolites. Several different sites of Cu+ inside ZSM-5 have been found. The structure of the site and the coordination of the Cu+ ion depend on the T-site where the Si atom is replaced by an Al atom. If Al is at the edge of the main and sinusoidal channels the Cu+ ion prefers to occupy thc open space in the channel intersection and it is coordinated to two oxygen atoms of the AlO4 tetrahedron. The largest binding energy of Cu+ with ZSM-5 was found for Cu+ located inside a six-membered ring on the wall of the sinusoidal channel, where it can coordinate to three or four oxygen atoms of the zeolite framework. The Cu+ sites predicted are in accord with available experimental results.

The Atomic Structure of a Metal-Supported Vitreous Thin Silica Film**

Clear as glass: The atomic structure of a metal-supported vitreous thin silica film was resolved using low-temperature scanning tunneling microscopy (STM). Based on the STM image, a model was constructed and the atomic arrangement of the thin silica glass determined (see picture). The total pair correlation function of the structural model shows good agreement with diffraction experiments performed on vitreous silica.

Finding transition structures in extended systems: A strategy based on a combined quantum mechanics–empirical valence bond approach

A method for efficient localization and description of stationary points on the potential energy surface of extended systems is presented. It is based on Warshel’s empirical valence bond approach, for which we propose a modification, and combines the potential function description of the total system with a quantum mechanical description of the reaction site (QM-Pot). We describe the implementation of the method in the QMPOT program, which is basically an optimizer for minima and saddle points and has interfaces to existing quantum mechanical (e.g., TURBOMOLE, GAUSSIAN94) and interatomic potential function codes (e.g., GULP, DISCOVER). The power of the method is demonstrated for proton transfer reactions in zeolite catalysts, which may have as many as 289 atoms in the unit cell. As a test case the zeolite chabazite is considered in this study. Its limited unit cell size (37 atoms) makes comparison with the full periodic ab initio limit possible. The inclusion of long-range effects due to the periodic crys...

Gas phase vibrational spectroscopy of mass-selected vanadium oxide anions

The vibrational spectra of vanadium oxide anions ranging from V(2)O(6)(-) to V(8)O(20)(-) are studied in the region from 555 to 1670 cm(-1) by infrared multiple photon photodissociation (IRMPD) spectroscopy. The cluster structures are assigned and structural trends identified by comparison of the experimental IRMPD spectra with simulated linear IR absorption spectra derived from density functional calculations, aided by energy calculations at higher levels of theory. Overall, the IR absorption of the V(m)O(n)(-) clusters can be grouped in three spectral regions. The transitions of (i) superoxo, (ii) vanadyl and (iii) V-O-V and V-O single bond modes are found at approximately 1100 cm(-1), 1020 to 870 cm(-1), and 950 to 580 cm(-1), respectively. A structural transition from open structures, including at least one vanadium atom forming two vanadyl bonds, to caged structures, with only one vanadyl bond per vanadium atom, is observed in-between tri- and tetravanadium oxide anions. Both the closed shell (V(2)O(5))(2,3)VO(3)(-) and open shell (V(2)O(5))(2-4)(-) anions prefer cage-like structures. The (V(2)O(5))(3,4)(-) anions have symmetry-broken minimum energy structures (C(s)) connected by low-energy transition structures of C(2v) symmetry. These double well potentials for V-O-V modes lead to IR transitions substantially red-shifted from their harmonic values. For the oxygen rich clusters, the IRMPD spectra prove the presence of a superoxo group in V(2)O(7)(-), but the absence of the expected peroxo group in V(4)O(11)(-). For V(4)O(11)(-), use of a genetic algorithm was necessary for finding a non-intuitive energy minimum structure with sufficient agreement between experiment and theory.

Structures and Properties of Spherical 90-Vertex Fullerene-Like Nanoballs

By applying the proper stoichiometry of 1:2 to [Cp(R)Fe(eta(5)-P(5))] and CuX (X=Cl, Br) and dilution conditions in mixtures of CH(3)CN and solvents like CH(2)Cl(2), 1,2-Cl(2)C(6)H(4), toluene, and THF, nine spherical giant molecules having the simplified general formula [Cp(R)Fe(eta(5)-P(5))]@[{Cp(R)Fe(eta(5)-P(5))}(12){CuX}(25)(CH(3)CN)(10)] (Cp(R)=eta(5)-C(5)Me(5) (Cp*); eta(5)-C(5)Me(4)Et (Cp(Et)); X=Cl, Br) have been synthesized and structurally characterized. The products consist of 90-vertex frameworks consisting of non-carbon atoms and forming fullerene-like structural motifs. Besides the mostly neutral products, some charged derivatives have been isolated. These spherical giant molecules show an outer diameter of 2.24 (X=Cl) to 2.26 nm (X=Br) and have inner cavities of 1.28 (X=Cl) and 1.20 nm (X=Br) in size. In most instances the inner voids of these nanoballs encapsulate one molecule of [Cp*Fe(eta(5)-P(5))], which reveals preferred orientations of pi-pi stacking between the cyclo-P(5) rings of the guest and those of the host molecules. Moreover, pi-pi and sigma-pi interactions are also found in the packing motifs of the balls in the crystal lattice. Electrochemical investigations of these soluble molecules reveal one irreversible multi-electron oxidation at E(p)=0.615 V and two reduction steps (-1.10 and -2.0 V), the first of which corresponds to about 12 electrons. Density functional calculations reveal that during oxidation and reduction the electrons are withdrawn or added to the surface of the spherical nanomolecules, and no Cu(2+) species are involved.

Thin silica films on Ru(0001): monolayer, bilayer and three-dimensional networks of [SiO4] tetrahedra

The atomic structure of thin silica films grown over a Ru(0001) substrate was studied by X-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, low energy electron diffraction, helium ion scattering spectroscopy, CO temperature programmed desorption, and scanning tunneling microscopy in combination with density functional theory calculations. The films were prepared by Si vapor deposition and subsequent oxidation at high temperatures. The silica film first grows as a monolayer of corner-sharing [SiO(4)] tetrahedra strongly bonded to the Ru(0001) surface through the Si-O-Ru linkages. At increasing amounts of Si, the film forms a bilayer of corner-sharing [SiO(4)] tetrahedra which is weakly bonded to Ru(0001). The bilayer film can be grown in either the crystalline or vitreous state, or both coexisting. Further increasing the film thickness leads to the formation of vitreous silica exhibiting a three-dimensional network of [SiO(4)]. The principal structure of the films can be monitored by infrared spectroscopy, as each structure shows a characteristic vibrational band, i.e., ∼1135 cm(-1) for a monolayer film, ∼1300 cm(-1) for the bilayer structures, and ∼1250 cm(-1) for the bulk-like vitreous silica.

Modellierung von Zeolithen durch zweidimensionale Aluminosilicatfilme auf Metallunterlagen

Zeolites are one of the most widely used materials in heterogeneous catalysis. However, the current understanding of the relation between structure and reactivity of these complex and highly porous materials mostly comes from studies employing bulk-sensitive techniques and from theoretical calculations based on educated assumptions about the inner surface within the pores present in the framework. Zeolite frameworks are formed by ordered arrangements of [SiO4/2] and [AlO4/2 ] tetrahedra, conferring the characteristic negative charge to the system, which is typically compensated by extra-framework metal cations M or H. Modeling such materials under controlled conditions, and taking advantage of the analytical tools commonly used in surface science, would provide a new playground for exploring structures and chemical reactions on zeolites. The preparation of welldefined aluminosilicate thin films was first reported using a Mo(112) substrate. It was shown that this film consists of a single layer network of corner-sharing [SiO4/2] tetrahedra and [AlO3/2] units, and the film is strongly bound to the Mo(112) surface by Si-O-Mo linkages (Figure 1a). Certainly, for those monolayer films the metal support has to be explicitly included in the proper description of the system. Furthermore, this film lacks the negative framework charge present in zeolites, which is responsible for the presence of acidic OH groups. To create a more adequate model system, herein we present the preparation of aluminosilicate films that a) are constituted of tetrahedral [SiO4] and [AlO4 ] building blocks, b) are weakly bound to the underlying metal support, and c) expose highly acidic OH species. Our results open up an avenue for experimental and theoretical modeling of zeolite surfaces that is aimed at a fundamental understanding of structure–reactivity relationships in those materials. As a starting point for the preparation of the aluminosilicate films, we used the recently reported preparation of a silica bilayer film weakly bound to a metal, in this case, Ru(0001) (see Figure 1b). The structure allows oxygen atoms to reversibly adsorb directly on the metal surface underneath the silica film, which can be grown either in the crystalline or vitreous state. 6] We will refer to all these films as silica films. For aluminosilicate films, reported here (see Experimental Section), the sum of the molar amounts of Si and Al was equal to the amounts of Si necessary to prepare the bilayer silica film. The structural characterization was performed by X-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and infrared reflection–absorption spectroscopy (IRAS), in combination with density functional theory (DFT) calculations. Using a silica film as a reference sample, the XPS results show that both Si and Al are in the highest oxidation states. For the O1s core level, a signal at about 530.7 eV develops as a shoulder to the main peak at 531.7 eV that originates from the O atoms surrounded solely by Si in the silica films (Supporting Information, Figure S1). This shoulder becomes more prominent at increasing Al/Si ratios and it has previously been assigned to the Al-O-Si linkage. The fact that the integral O1s signal intensity remains practically constant upon Al doping is consistent with Al substituting Si in the [SiO4] tetrahedra, giving an AlxSi(1 x)O2 composition, where x is the Al molar fraction. At low Al/Si ratios, the resulting aluminosilicate surfaces show only (2 2) LEED patterns and are nearly atomically flat. STM images of an Al0.12Si0.88O2 film, revealed irregularly shaped areas (marked A in Figure 2) with a slightly different Figure 1. Structural models of a) an AlSi7O19 film on Mo(112); b) a HAlSi7O16 film on O(2 1)/Ru(0001); and c) chabasite (H-CHA) with the proton on O1. Top and cross views are shown in (a) and (b), adsorbed CO are shown in (b) and (c). One of the surface O atoms on Ru(0001) underneath the film is not seen in the top view. Si yellow, O red, Al dark gray, C black, H white.

Structure determination of neutral MgO clusters—hexagonal nanotubes and cages

Structural information for neutral magnesium oxide clusters has been obtained by a comparison of their experimental vibrational spectra with predictions from theory. (MgO)(n) clusters with n = 3-16 have been studied in the gas phase with a tunable IR-UV two-color ionization scheme and size-selective infrared spectra have been measured. These IR spectra are compared to the calculated spectra of the global minimum structures predicted by a hybrid ab initio genetic algorithm. The comparison shows clear evidence that clusters of the composition (MgO)(3k) (k = 1-5) form hexagonal tubes, which confirm previous theoretical predictions. For the intermediate sizes (n≠ 3k) cage-like structures containing hexagonal (MgO)(3) rings are identified. Except for the cubic (MgO)(4) no evidence for bulk like structures is found.