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.     

Optical tweezers applied to a microfluidic system

We will demonstrate how optical tweezers can be combined with a microfluidic system to create a versatile microlaboratory. Cells are moved between reservoirs filled with different media by means of optical tweezers. We show that the cells, on a timescale of a few seconds, can be moved from one reservoir to another without the media being dragged along with them. The system is demonstrated with an experiment where we expose E. coli bacteria to different fluorescent markers. We will also discuss how the system can be used as an advanced cell sorter. It can favorably be used to sort out a small fraction of cells from a large population, in particular when advanced microscopic techniques are required to distinguish various cells. Patterns of channels and reservoirs were generated in a computer and transferred to a mask using either a sophisticated electron beam technique or a standard laser printer. Lithographic methods were applied to create microchannels in rubber silicon (PDMS). Media were transported in the channels using electroosmotic flow. The optical system consisted of a combined confocal and epi-fluorescence microscope, dual optical tweezers and a laser scalpel.     

Systematic studies on the determination of Hg-labelled proteins using laser ablation-ICPMS and isotope dilution analysis

A method was developed for the precise and accurate determination of ovalbumin labelled with p-hydroxy-mercuribenzoic acid (pHMB) using polyacrylamide gel electrophoresis with ns-laser ablation–inductively coupled plasma mass spectrometry. Following systematic optimisation of the ablation process in terms of detection sensitivity, two different quantification strategies were applied: external calibration using standards of the derivatized protein after ¹³C⁺ normalization and, as a proof of concept, label-specific isotope dilution analysis (IDA) using pHMB enriched in the isotope ¹⁹⁹Hg. Due to the inhomogeneous distribution of the protein within the gel bands, it could be demonstrated that the IDA approach was superior in terms of precision and accuracy. Furthermore, it permits a reliable quantification, if more complex separation protocols are applied, as typically occurring analyte loss and degradation can be compensated for as soon as complete mixture of spike and sample is achieved. The estimated limit of detection was 160 fmol in the case of ovalbumin. In contrast to earlier studies using metals naturally present in proteins, no loss of mercury was observed during separation under denaturing conditions and other sample preparation steps. Using label-specific IDA, the measured isotope ratios in the gel corresponded to recoveries between 95% and 103%.     

High-performance liquid chromatography of levomepromazine (methotrimeprazine) and its main metabolites

The phenothiazine drug levomepromazine (methotrimeprazine) has five metabolites which previously have been identified in plasma from psychiatric patients. These are formed by sulphoxidation, N-demethylation, O-demethylation and aromatic hydroxylation in two different positions. A high-performance liquid chromatographic system is described for the analysis of levomepromazine and its main metabolites on a Supelcosil C18-DB column, based on ion-pair formation with sodium docecyl sulphate. The effects of variations in pH, buffer concentration, counter-ion concentration, temperature and concentration and composition of the organic solvent were examined. The six components may be analysed in 27.4 min at room temperature using 25 mM sodium dodecyl sulphate in 500 mM ammonium acetate buffer (pH 5.0)-5% v/v tetrahydrofuran in acetonitrile (50:50, v/v) as the mobile phase.     

PURE SINGLET OXYGEN CYTOTOXICITY FOR BACTERIA

We have modified the separated-surface-sensitizer singlet oxygen generating system previously described (Midden and Wang, 1983) for the efficient exposure to pure singlet oxygen of bacteria collected on membrane filters. Physical separation of the photosensitizer and the bacteria eliminates the possibility of direct interaction between bacteria and photoexcited sensitizers that could lead to Type I (non-singlet oxygen) photooxidation processes. This system was used to examine the bacterial cytotoxicity of singlet oxygen. The role of singlet oxygen was confirmed by measuring the decrease in cytotoxicity as the distance between the singlet oxygen source and the bacteria was increased. The gas phase half-life of the intermediate responsible for cell killing, determined from this distance dependence analysis (24 ± 6 ms), is the same as that calculated from literature data for the gas phase half-life of singlet oxygen (53 ± 37 ms). Killing of various strains of Salmonella lyphimurium and Escherichia coli was compared at the same dose of singlet oxygen. Bacteria were killed by singlet oxygen at levels several orders of magnitude lower than those effective in killing by H₂O₂. Altered DNA repair capacities (uvrB, recA, xth, nth , pKM101) did not affect survival. Incomplete cell wall lipopolysaccharide formation decreased survival following singlet oxygen exposure. Overproduction of the singlet oxygen quencher histidine increased survival, as did accumulation of the dipeptide carnosine (β-alanyl-L-histidine). No evidence for mutagenicity of exogenous singlet oxygen exposure was obtained in a variety of S. typhimurium strains killed to 35% survival.     

A CNDO-MO calculation of VCl4

The electronic structure of the tetrahedral molecule VCL₄ is investigated within the CNDO-MO approximations. The metal and ligand valence orbitals, 3d, 4s, 4p; and 3s, 3p; respectively, have been systematically varied in an attempt to minimize the total energy; “optimum” V 4s(χ₄ = 1.10) and 4p(d ³ p ²) orbitals have been established, but V 3d(d ⁿ ) and Cl(-δ) valence orbitals are only seen to favor lower energy for expanded orbitals. Since determining the one-electron molecular orbital level which is occupied by the vanadium lone electron is a major aspect of this investigation, all calculations have been performed in triplicate: calculations assuming the unpaired electron occupies the 3a ₁, 2 _e and 4t ₂ molecular orbital (ground state electronic configurations² A ₁,² E, and² T ₂, respectively). The Hartree-Fock equations have been solved by Roothaan's SCF method for open shells, but off-diagonal multipliers between filled and partly filled molecular orbitals of the same symmetry have been neglected. As a qualitative estimate of the error introduced by this simplification, the pertinent overlap integrals between the eigenfunctions from calculations for the three possible configurations,² A ₁,² E, and² T ₂, are investigated as functions of the component 3d(d ⁿ ) and Cl(-δ) valence orbitals. The overlap integrals from the relevant² A ₁ and² T ₂ calculations are reasonably small, but the neglect of off-diagonal multipliers in calculations on the² E state is found to be a poor approximation. An ordering of the non-filled molecular orbitals in VCl₄ of 4t ₂ < 3a ₁ < 2e < 5t ₂ seems most consistent with the numerous calculations. This suggested ground state electronic configuration of² T ₂ introduces new aspects to the consideration of a (dynamic) Jahn-Teller effect in VCl₄. Experimental data pertinent to the electronic structure of VCl₄ has been briefly summarized, but unfortunately it is inadequate to confirm or deny the present calculations.     

Side Products in Nucleotide Chemistry

Abstract

Alkyl bisaminophosphorodiamidites¹ (1) has been shown to be versatile reagents for in situ preparation of d-nucleoside-3-phosphoramidites^2,3,4 (2.)     

Finite size effects in stimulated laser pair production

We consider stimulated pair production employing strong-field QED in a high-intensity laser background. In an infinite plane wave, we show that light-cone quasi-momentum can only be transferred to the created pair as a multiple of the laser frequency, i.e. by a higher harmonic. This translates into discrete resonance conditions providing the support of the pair creation probability which becomes a delta-comb. These findings corroborate the usual interpretation of multi-photon production of pairs with an effective mass. In a pulse, the momentum transfer is continuous, leading to broadening of the resonances and sub-threshold behaviour. The peaks remain visible as long as the number of cycles per pulse exceeds unity. The resonance patterns in pulses are analogous to those of a diffraction process based on interference of the produced pairs. We finally comment on the dependence of the peak positions, and in turn the effective mass, on the pulse shape.     

3J(PCNH) in phosphorus substituted thioformamides as a configurational probe

Coupling between P and (N)? H has been observed in the ¹H{¹⁴N}NMR spectra of a series of phosphorus substituted thioformamides, R¹₂/P(X)C(S)NHR². For R² = H one of the two couplings constants ³J(PCNH) is much larger than the other. The larger constant is assumed to be ³J(PCNH) (trans) and the magnitude of ³J(PCNH) for several compounds with R² = Me or Ph is used to assign the configuration about the C(S)? N bond.