Benjamin Fiedler

Understanding Stacking Interactions between an Aromatic Ring and Nucleobases in Aqueous Solution: Experimental and Theoretical Study.

Stacking interactions between aromatic compounds and nucleobases are crucial in recognition of nucleotides and nucleic acids, but a comprehensive understanding of the strength and selectivity of these interactions in aqueous solution has been elusive. To this end, model complexes have been designed and analyzed by experiment and theory. For the first time, stacking free energies between five nucleobases and anthracene were determined experimentally from thermodynamic double mutant cycles. Three different experimental methods were proposed and evaluated. The dye prefers to bind nucleobases in the order (kcal/mol): G (1.3) > T (0.9) > U (0.8) > C (0.5) > A (0.3). The respective trend of interaction free energies extracted from DFT calculations correlates to that obtained experimentally. Analysis of the data suggests that stacking interactions dominate over hydrophobic effects in an aqueous solution and can be predicted with DFT calculations.

Molecular Dipole Moments within the Incremental Scheme Using the Domain-Specific Basis-Set Approach

We present the first implementation of the fully automated incremental scheme for CCSD unrelaxed dipole moments using the domain-specific basis-set approach. Truncation parameters are varied, and the accuracy of the method is statistically analyzed for a test set of 20 molecules. The local approximations introduce small errors at second order and negligible ones at third order. For a third-order incremental CCSD expansion with a CC2 error correction, a cc-pVDZ/SV domain-specific basis set (tmain = 3.5 Bohr), and the truncation parameter f = 30 Bohr, we obtain a mean error of 0.00 mau (-0.20 mau) and a standard deviation of 1.95 mau (2.17 mau) for the total dipole moments (Cartesian components of the dipole vectors). By analyzing incremental CCSD energies, we demonstrate that the MP2 and CC2 error correction schemes are an exclusive correction for the domain-specific basis-set error. Our implementation of the incremental scheme provides fully automated computations of highly accurate dipole moments at reduced computational cost and is fully parallelized in terms of the calculation of the increments. Therefore, one can utilize the incremental scheme, on the same hardware, to extend the basis set in comparison to standard CCSD and thus obtain a better total accuracy.

4,5‐Dihydro‐1,2,3‐oxadiazole: A Very Elusive Key Intermediate in Various Important Chemical Transformations

4,5-Dihydro-1,2,3-oxadiazoles are postulated to be key intermediates in the industrial synthesis of ketones from alkenes, in the alkylation of DNA in vivo, and in the decomposition of N-nitrosoureas; they are also a subject of great interest for theoretical chemists. In the presented report, the formation of 4,5-dihydro-1,2,3-oxadiazole and the subsequent decay into secondary products have been studied by NMR monitoring analysis. The elusive properties evading characterization have now been confirmed by (1) H, (13) C, and (15) N NMR spectroscopy, and relevant 2D experiments at very low temperatures. Our experiments with suitably substituted N-nitrosoureas using thallium(I) alkoxides as bases under apolar conditions answer important questions on the existence and the secondary products of 4,5-dihydro-1,2,3-oxadiazole.

Combining Accuracy and Efficiency: An Incremental Focal-Point Method Based on Pair Natural Orbitals

In this work, we present a new pair natural orbitals (PNO)-based incremental scheme to calculate CCSD(T) and CCSD(T0) reaction, interaction, and binding energies. We perform an extensive analysis, which shows small incremental errors similar to previous non-PNO calculations. Furthermore, slight PNO errors are obtained by using TPNO = TTNO with appropriate values of 10-7 to 10-8 for reactions and 10-8 for interaction or binding energies. The combination with the efficient MP2 focal-point approach yields chemical accuracy relative to the complete basis-set (CBS) limit. In this method, small basis sets (cc-pVDZ, def2-TZVP) for the CCSD(T) part are sufficient in case of reactions or interactions, while some larger ones (e.g., (aug)-cc-pVTZ) are necessary for molecular clusters. For these larger basis sets, we show the very high efficiency of our scheme. We obtain not only tremendous decreases of the wall times (i.e., factors >102) due to the parallelization of the increment calculations as well as of the total times due to the application of PNOs (i.e., compared to the normal incremental scheme) but also smaller total times with respect to the standard PNO method. That way, our new method features a perfect applicability by combining an excellent accuracy with a very high efficiency as well as the accessibility to larger systems due to the separation of the full computation into several small increments.

The incremental method – theory and applications in chemistry and physics

A review of different methodical approaches for the implementation of the incremental scheme in quantum mechanics is presented. These methods represent a very important group among the wide range of local correlation methods. Originally introduced by Stoll in 1992 for a treatment of bulk solids, their applicability has been successfully extended to molecular systems on high levels of theory over the last decade. The incremental CCSD(T) approach provides a significantly increased efficiency in combination with a negligible loss of accuracy, compared to standard calculations. Furthermore, due to the reduced scaling with respect to the number of orbitals and the full parallelizability in terms of single increments, larger systems and basis sets are possible and a higher overall accuracy can be reached. Beside the highly accurate computation of absolute and various relative energies (cohesion, adsorption, weak interactions, chemical reactions), also other properties (lattice constants, bulk moduli, dipole moments, (hyper)polarizabilities) are obtainable.

Experimental observation and quantum chemical investigation of thallium(I) (Z)-methanediazotate: synthesis of a long sought and highly reactive species

For the first time, successful synthesis and characterisation of the missing (Z)-isomer of thallium(I) methanediazotate has been accomplished, utilising low-temperature NMR monitoring analysis. The title compound was synthesised from N-methyl-N-nitrosourea and thallium(I) propoxide, under sub-ambient temperature conditions, as a highly moisture sensitive entity. Quantum chemical calculations, performed at the CCSD(T) level, depict excellent conformity to experimental results. Indeed, compared to its (E) counterpart, the formation of the title compound is thermodynamically less favoured, but preferred by means of kinetic control owing to a hindered isomerisation.

A More Stable Template Localization for an Incremental Focal-Point Approach - Implementation and Application to the Intramolecular Decomposition of Tris-perfluoro-tert-butoxyalane

We present a new implementation of the template localization for the fully automated and parallizable incremental method, which excludes failures of this important step within the domain-specific basis set approach and thus ensures a higher reliability of the scheme, preserving its very high accuracy. Furthermore, we combine our method with an efficient focal-point ansatz to reach the complete basis set limit and carefully assess this approach for the first time with regard to reaction energies. For a test set of 51 reactions the incremental focal-point method with a basis set of moderate size provides a very high accuracy with respect to the complete basis set limit. That way, we are finally able to apply the scheme as a benchmark method (e.g., for density functionals) in the context of a relevant chemical topic, the intramolecular decomposition of tris-perfluoro-tert-butoxyalane (43 heavy atoms, 352 electrons).

Frontispiece: 4,5‐Dihydro‐1,2,3‐oxadiazole: A Very Elusive Key Intermediate in Various Important Chemical Transformations

Reactive Intermediates. The very weak NO bond of 4,5-dihydro-1,2,3-oxadiazole is most probably responsible for the elusive properties of this heterocycle. Thus, it cannot be directly detected even by low-temperature NMR monitoring. However, the formation of the secondary products ethylene oxide, acetaldehyde, and diazomethane is strong evidence for the generation of the five-membered heterocycle, as reported by K. Banert, J. Friedrich et al. in their Communication on page 15092 ff. The parent compound and bicyclic 4,5-dihydro-1,2,3-oxadiazoles are discussed as short-lived intermediates in medicinal chemistry and industrial processes, respectively.