Johannes M. Dieterich

Preparation of RSn(I)–Sn(I)R with Two Unsymmetrically Coordinated Sn(I) Atoms and Subsequent Gentle Activation of P4

This article reports the reduction of [{2,6-iPr(2)C(6)H(3)NC(CH(3))}(2)C(6)H(3)SnCl] (1) with potassium graphite to afford a new distannyne [{2,6-iPr(2)C(6)H(3)NC(CH(3))}(2)C(6)H(3)Sn](2) (2) with a Sn-Sn bond. The most striking phenomenon of 2 is the presence of two differently coordinated Sn atoms (one is three-coordinated, the other is four-coordinated). The Sn-Sn bond length in 2 is 2.8981(9) Å, which is very close to that of a Sn-Sn single bond (2.97-3.06 Å). To elucidate the nature of the Sn-Sn bond, DFT calculation is carried out that shows there is no multiple bond character in 2. Furthermore, the reaction of 2 with white P(4) affords the tetraphosphabicylobutane derivative 3. This is the first example of gentle activation of white phosphorus by a compound with low valent Sn atoms. Note that, unlike 2, in 3 both Sn atoms are four-coordinated.

Automated Diffraction Tomography for the Structure Elucidation of Twinned, Sub‐micrometer Crystals of a Highly Porous, Catalytically Active Bismuth Metal–Organic Framework

The number of metal–organic framework (MOF) compounds has increased almost exponentially over the last decade as a consequence of their fascinating structures and potential applications. They are composed of inorganic building units, such as metal ions or clusters, which are connected through organic linker molecules to form a porous three-dimensional network. Most of the MOFs are based on rigid polycarboxylate linker molecules, but a large variety of metal ions, mainly transition-metal ions, have also been incorporated. The chemical and thermal stability of metal carboxylate based MOFs is crucial for potential applications and depends on the metal ions incorporated. In general, metal ions in higher oxidation states lead to more stable structures. While the use of divalent metal ions often results in the formation of single crystals, whose structures can be routinely determined by single-crystal X-ray diffraction, triand tetravalent metal carboxylates are mostly obtained as microcrystalline powders and the determination of their structures poses immense challenges. 4c,5] Direct methods have been successfully employed, but complicated structures with large unit cells necessitate the use of nonstandard approaches. Thus, computational assisted structure determination, namely, the AASBU approach (assembling of secondary building units), the ligand-replacement strategy, and DFT calculations have been applied. Recently automated diffraction tomography (ADT) has been introduced as a new method for collecting three-dimensional electron diffraction data from single nanosized crystals, thus allowing singlecrystal analysis even for porous and organic sub-microcrystalline samples. A trivalent metal that exhibits interesting catalytic properties is bismuth. It is nontoxic, noncarcinogenic, and for a rare metal relatively inexpensive, and thus bismuth compounds are used as green catalysts. Despite these characteristics, the number of bismuth-based MOFs is rather limited and only a few compounds with limited porosity have been described. This is in contrast to the many known bismuth-oxo clusters, which could possibly be used for the construction of new MOFs. Here, we present the synthesis of the first highly crystalline, porous, and catalytically active bismuth-based MOF Bi(BTB) (BTB = 1,3,5-benzenetrisbenzoate), whose structure was elucidated by a combination of electron diffraction, Rietveld refinement, and DFT calculations. Bi(BTB), denoted as CAU-7 (CAU = ChristianAlbrechts-Universit t) was synthesized by using conventional as well as microwave (MW) assisted heating. The reaction of Bi(NO3)3·5 H2O with H3BTB in methanol at 120 8C led to phase-pure CAU-7 (for a detailed synthesis procedure see the Supporting Information). The reaction time can be reduced from 12 h to 20 min by using MW-assisted instead of conventional heating, but this leads to the formation of 10–20 mm large agglomerates of strongly intergrown elongated crystals of about 100 nm (see Figures S2–S4 in the Supporting Information). The addition of DMF in the conventional synthesis results in the formation of larger rodlike crystals ranging from 200 to 300 nm in length. Transmission electron microscopy confirmed that isolated CAU-7 crystals have a typical rodlike shape with different length/diameter ratios (see Figure S5 in the Supporting Information). Such isolated rods were used to collect electron diffraction data by automated diffraction tomography (ATD). Single-crystal ADT electron diffraction datasets were collected using a cryo holder cooled to 120 K and mild illumination conditions. To prevent beam damage and improve the signal intensity, the diffraction data were acquired in the precession mode. The three-dimensional diffraction space reconstruction leads to lattice parameters a = 32 , b = 28 , c = 4 , a = b = g = 908, and extinction group Pb-a. The reconstructed reciprocal space is shown in Figure 1. [*] M. Feyand, T. Reimer, Prof. Dr. N. Stock Institut f r Anorganische Chemie Christian Albrechts Universit t zu Kiel Max-Eyth Strasse 2, 24118 Kiel (Germany) E-mail: stock@ac.uni-kiel.de

OGOLEM: Global cluster structure optimisation for arbitrary mixtures of flexible molecules. A multiscaling, object-oriented approach

In practical applications, global cluster structure optimisation has so far been limited largely to homogeneous clusters of atoms or small molecules, with little or no choice in the calculation of inter-particle forces. We eliminate these limitations by presenting a new program suite OGOLEM that is universal by design, both in cluster composition (including arbitrarily heterogeneous clusters of complicated molecules) and in its interfaces to force calculation backends. This is demonstrated by exemplary applications in two novel fields: strongly heterogeneous Lennard–Jones clusters (ternary, quaternary, quinary) and mixed clusters of the aminoglycoside Kanamycin A with sodium cations.

Composition-induced structural transitions in mixed Lennard-Jones clusters: Global reparametrization and optimization

As extended benchmarks to global cluster structure optimization methods, we provide a first systematic point of entry into the world of strongly mixed rare gas clusters. A new set of generalized Lennard‐Jones pair potentials is generated for this purpose, by fitting them to high‐end ab initio reference data. Employing these potentials in our genetic algorithm‐based global structure optimization framework, we examined various systems from binary to quinary mixtures of atom types. A central result from this study is that the famous fcc structure for 38 atoms can survive for certain binary mixtures but appears to be prone to collapsing into the dominating icosahedral structure, which we observed upon introduction of one single atom of a ternary type.

Monomeric Sn(II) and Ge(II) hydrides supported by a tridentate pincer-based ligand

Herein we report the syntheses of terminal Sn(II) (3) and Ge(II) (4) hydrides from the corresponding chloride precursors [{2,6-iPr(2)C(6)H(3)NCMe}(2)C(6)H(3)MCl] (M = Sn (1), Ge (2)) using [K{B(sec-Bu)(3)}H] as a hydrogenating agent. Combination of steric shielding and intramolecular N → M interactions resulted in the protection of M(II)-H bonds.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

A push-and-pull model for allosteric anion binding in cage complexes

A series of electronic structure calculations has been carried out on an artificial anion binding host. The compound with four Pd(II) cations and a total of eight bis-monodentate pyridyl ligands forms by self-assembly an interpenetrated double cage with three binding pockets. Through the use of a simple push-and-pull model connecting the potentials of the different sites, we are able to explain the allosteric effect observed in anion binding. Two factors seem to be particularly significant in the latter, namely the flatness of the potential in each binding pocket as well as the length of the ligand. Our results are found to be in excellent agreement with the experimentally observed structures.

Structural diversity in sodium doped water trimers

The structures of sodium doped water trimers are characterized on the basis of their infrared action spectra in the OH-stretching region and a global optimization approach to identify the lowest energy minima. The most stable structure is an open ring with two contacts of terminal water molecules to the Na atom. This structure explains the dominating feature in the IR depletion spectrum around 3410 cm(-1). Three additional isomer classes were found in an energy window of 12 kJ mol(-1) with vertical ionization energies ranging from ∼3.83 eV to ∼4.36 eV. These structures show different hydrogen bonding and sodium coordination patterns and are identified by specific spectral features in the IR spectra. The significant abundance of closed rings with an external Na atom, resembling the undoped water trimer, suggests that for larger clusters the picture of the sodium atom being situated on the cluster surface seems adequate.

Bond Dissociation Energies of C10 and C18 Methyl Esters from Local Multireference Averaged-Coupled Pair Functional Theory

We previously developed a fast, local, reduced scaling Cholesky-decomposed multireference averaged-coupled pair functional (CD-LMRACPF2) method, which takes advantage of the locality of dynamic correlation and numerical approximations such as Cholesky decomposition and integral screening. Motivated by the desire to study large biodiesel methyl ester molecules, here we validate CD-LMRACPF2 for the computation of bond dissociation energies (BDEs) in a suite of oxygenated molecules, and show that the low-cost method is very accurate compared to the conventional variant. We then demonstrate the power of CD-LMRACPF2 for fast and accurate computation of energies of molecules containing up to 13 second-row atoms within a polarized triple-ζ (cc-pVTZ) basis set. We use biodiesel methyl esters as a chemically interesting model system and furnish BDEs of C10 and C18 methyl esters, with the latter performed within a cc-pVDZ basis set. We describe trends in the BDEs and explain how structural (isomeric) differences affect BDEs, as well as discuss implications of BDE trends for biodiesel physical and chemical properties.

Atomdroid: A Computational Chemistry Tool for Mobile Platforms

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.