Jaroslaw Kalinowski

The development of Laue techniques for single-pulse diffraction of chemical complexes: time-resolved Laue diffraction on a binuclear rhodium metal-organic complex

A modified Laue method is shown to produce excited-state structures at atomic resolution of a quality competitive with those from monochromatic experiments. The much faster data collection allows the use of only one or a few X-ray pulses per data frame, which minimizes crystal damage caused by laser exposure of the samples and optimizes the attainable time resolution. The method has been applied to crystals of the α-modification of Rh(2)(μ-PNP)(2)(PNP)(2) (BPh(4))(2) [PNP = CH(3)N(P(OCH(3))(2))(2), Ph = phenyl]. The experimental results show a shortening of the Rh-Rh distance in the organometallic complex of 0.136 (8) Å on excitation and are quantitatively supported by quantum-mechanical (QM)/molecular-mechanics (MM) theoretical calculations which take into account the confining effect of the crystal environment, but not by theoretical results on the isolated complex, demonstrating the defining effect of the crystal matrix.

Isomerization and Decomposition of a Criegee Intermediate in the Ozonolysis of Alkenes: Dynamics Using a Multireference Potential

The isomerization and decomposition dynamics of the simplest Criegee intermediate CH2 OO have been studied by classical trajectory simulations using the multireference ab initio MR-PT2 potential on the fly. A new, accelerated algorithm for dynamics with MR-PT2 was used. For an initial temperature of 300 K, starting from the transition state from CH2 OO→CH2 O2  , the system reaches the dioxirane structure in around 50 fs, then isomerizes to formic acid (in ca. 2800 fs), and decomposes into CO+H2 O at around 2900 fs. The contributions of different configurations to the multiconfigurational total electronic wave function vary dramatically along the trajectory, with diradical contributions being important for transition states corresponding to H-atom transfers, while being only moderately significant for CH2 OO. The implications for reactions of Criegee intermediates are discussed.

The LaueUtil toolkit for Laue photocrystallography. I. Rapid orientation matrix determination for intermediate-size-unit-cell Laue data

A new method for determination of the orientation matrix of Laue X-ray data is presented. The method is based on matching of the experimental patterns of central reciprocal lattice rows projected on a unit sphere centered on the origin of the reciprocal lattice with the corresponding pattern of a monochromatic data set on the same material. This technique is applied to the complete data set and thus eliminates problems often encountered when single frames with a limited number of peaks are to be used for orientation matrix determination. Application of the method to a series of Laue data sets on organometallic crystals is described. The corresponding program is available under a Mozilla Public License-like open-source license.

Infrared Identification of Proton-Bound Rare-Gas Dimers (XeHXe)+, (KrHKr)+, and (KrHXe)+ and Their Deuterated Species in Solid Hydrogen

Proton-bound rare-gas dimer (RgHRg)(+), in which Rg represents a rare-gas atom, serves as a prototypical system for proton solvation by inert-gas atoms. Until now, only centrosymmetric species with Rg = Ar, Kr, or Xe have been identified with infrared spectra. We employed electron bombardment during deposition of a mixture of Xe (or Kr) in p-H2 at 3.2 K to prepare (RgHRg)(+). Lines at 847.0 and 972.1 cm(-1) are assigned as the Rg-H-Rg antisymmetric stretching (ν3) mode and its combination with the Rg-H-Rg symmetric stretching (ν1 + ν3) mode of (XeHXe)(+) in solid p-H2, respectively. Lines at 871.1 and 974.0 cm(-1) are assigned as the ν3 and ν1 + ν3 modes of (KrHKr)(+) in solid p-H2, respectively. Slightly shifted and broadened lines were observed for these species in solid n-H2. These results agree satisfactorily with reported experimental values of (XeHXe)(+) and (KrHKr)(+) in solid Xe, Kr, and Ar, and with the quantum-chemically predicted anharmonic vibrational wavenumbers of these species in the gaseous phase; the significant spectral shifts in various matrixes are rationalized with the proton affinities of the hosts. When a mixture of Xe and Kr in p-H2 was used, an additional broad feature at 1284 cm(-1) was observed and assigned as the ν3 mode of (KrHXe)(+) in solid p-H2. This line shifted to 1280 cm(-1) in solid n-H2 and the corresponding line of (KrDXe)(+) was observed at 954 cm(-1) in n-D2. The observations of these lines are new; the wavenumbers significantly blue shifted from those of the centrosymmetric (RgHRg)(+) agree with the quantum-chemically predicted anharmonic vibrational wavenumbers of 1279 cm(-1) for (KrHXe)(+) and 916 cm(-1) for (KrDXe)(+). Analysis of the computational results shows that electronic correlation effects play a much greater role for the asymmetric than for the symmetric species. An interpretation for this is provided.

Hybrid MP2/MP4 potential surfaces in VSCF calculations of IR spectra: applications for organic molecules.

This study introduces an improved hybrid MP2/MP4 ab initio potential for vibrational spectroscopy calculations which is very accurate, yet without high computational demands. The method uses harmonic vibrational calculations with the MP4(SDQ) potential to construct an improved MP2 potential by coordinate scaling. This improved MP2 potential is used for the anharmonic VSCF calculation. The method was tested spectroscopically for four molecules: butane, acetone, ethylene and glycine. Very good agreement with experiment was found. For most of the systems, the more accurate harmonic treatment considerably improved the MP2 anharmonic results.

The LaueUtil toolkit for Laue photocrystallography. II. Spot finding and integration.

A spot-integration method is described which does not require prior indexing of the reflections. It is based on statistical analysis of the values from each of the pixels on successive frames, followed for each frame by morphological analysis to identify clusters of high value pixels which form an appropriate mask corresponding to a reflection peak. The method does not require prior assumptions such as fitting of a profile or definition of an integration box. The results are compared with those of the seed-skewness method which is based on minimizing the skewness of the intensity distribution within a peaks integration box. Applications in Laue photocrystallography are presented.

Stability of Criegee intermediates formed by ozonolysis of different double bonds.

The formation of Criegee intermediates by ozonolysis of different species containing C═N and C═P bonds is studied computationally. Electronic structure calculations are carried out for the energetics of ozonolysis, and the lifetime of the Criegee intermediate formed is computed by transition state theory. All calculations are carried out for formation of CH2OO, the simplest Criegee intermediate. Extremely large differences are found for the lifetime of CH2OO depending on the specific C═N, C═P, and C═C precursor, due to the great variations in the exoergicity of the ozonolysis. The largest lifetimes of CH2OO are found to be up to a millisecond range for a Schiff base precursor, being orders of magnitude greater than for C═C and C═P precursors at the same conditions. The results provide insights into the role of the precursor in determining the stability of the Criegee species formed and suggest an approach for preparing Criegee intermediates of relatively long lifetimes.

Electron localization function study on intramolecular electron transfer in the QTTFQ and DBTTFI radical anions.

The unsymmetrical distribution of the unpaired electron in the ground state of the DBTTFI(•-) radical anion (bi(6-n-butyl-5,7-dioxo-6,7-dihydro-5H-[1,3]dithiolo[4,5-f]isoindole-2-ylidene) is theoretically predicted using the M06-2X/6-31+G(d,p) level of calculations. The results are additionally confirmed by single point calculations at B3LYP/aug-cc-pVTZ, LC-ωPBE/aug-cc-pVTZ, and M06-2X/aug-cc-pVTZ levels. DBTTFI, containing the TTF (tetrathiafulvalene) fragment, may be used in the construction of organic microelectronic devices, similarly to the radical anion of QTTFQ. The unsymmetrical distribution of spin density in (QTTFQ)(•-) has been confirmed using M06-2X/aug-cc-pVTZ calculations, with subsequent study using topological analysis of electron localization function (ELF). The reorganization of the chemical bonds during intramolecular electron transfer in (QTTFQ)(•-) and (DBTTFI)(•-) has been analyzed using bonding evolution theory (BET). The reaction path has been simulated by the IRC procedure, and the evolution of valence basins has been described using catastrophe theory. The simple mechanisms: (QTTFQ)(•-): η-1-3-CC(+)-0: (-•)(QTTFQ) and (DBTTFI)(•-): η-1-3-[F](4)[F(+)](4)-0: (-•)(DBTTFI), each consisting of three steps, have been observed. Two cusp or 4-fold catastrophes occur immediately after the TS. Our study shows that potential future microelectronic devices, constructed on the basis of the (QTTFQ)(•-) and (DBTTFI)(•-) systems, should exploit the properties of the C═C bond.

Dynamics and spectroscopy of CH₂OO excited electronic states.

The excited states of the Criegee intermediate CH2OO are studied in molecular dynamics simulations using directly potentials from multi-reference perturbation theory (MR-PT2). The photoexcitation of the species is simulated, and trajectories are propagated in time on the excited state. Some of the photoexcitation events lead to direct fragmentation of the molecule, but other trajectories describe at least several vibrations in the excited state, that may terminate by relaxation to the ground electronic state. Limits on the role of non-adiabatic contributions to the process are estimated by two different simulations, one that forces surface-hopping at potential crossings, and another that ignores surface hopping altogether. The effect of non-adiabatic transitions is found to be small. Spectroscopic implications and consequences for the interpretation of experimental results are discussed.