18 research outputs found

    Fast and Reasonable Geometry Optimization of Lanthanoid Complexes with an Extended Tight Binding Quantum Chemical Method

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    The recently developed tight binding electronic structure approach GFN-xTB is tested in a comprehensive and diverse lanthanoid geometry optimization benchmark containing 80 lanthanoid complexes. The results are evaluated with reference to high-quality X-ray molecular structures obtained from the Cambridge Structural Database and theoretical DFT-D3­(BJ) optimized structures for a few Pm (<i>Z</i> = 61) containing systems. The average structural heavy-atom root-mean-square deviation of GFN-xTB (0.65 Å) is smaller compared to its competitors, the Sparkle/PM6 (0.86 Å) and HF-3c (0.68 Å) quantum chemical methods. It is shown that GFN-xTB yields chemically reasonable structures, less outliers, and performs well in terms of overall computational speed compared to other low-cost methods. The good reproduction of large lanthanoid complex structures corroborates the wide applicability of the GFN-xTB approach and its value as an efficient low-cost quantum chemical method. Its main purpose is the search for energetically low-lying complex conformations in the elucidation of reaction mechanisms

    Co–C Bond Dissociation Energies in Cobalamin Derivatives and Dispersion Effects: Anomaly or Just Challenging?

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    Accurate Co–C bond dissociation energies (BDEs) of large cobalamin derivatives in the gas phase and solution are crucial for understanding bond activation mechanisms in various enzymatic reactions. However, they are challenging for both experiment and theory as indicated by an obvious discrepancy between experimental and theoretical gas phase data for adenosylcobinamide. State-of-the-art dispersion-corrected DFT and LPNO-CCSD calculations are conducted for the Co–C BDEs of some neutral and positively charged cobalamin derivatives with adenosyl and methyl ligands and compared with available experimental gas phase and solution data to resolve the controversy. Our results from various levels of electronic structure theory are fully consistent with chemical and physical reasoning. We show undoubtedly that the Co–C bonds in complexes with the bulky adenosyl ligand are indirectly enhanced by many ligand-host noncovalent interactions and that the overall BDE are <i>larger</i> than those with the small methyl ligand in the gas phase. The additional intramolecular dispersion and hydrogen-bond interactions are significantly but not fully quenched in aqueous solution. The theoretical results including standard continuum solvation and dispersion corrections to DFT are in full accordance with experimental solution data. This is in agreement with several successful joined experimental/theoretical studies in recent years employing similar quantum chemical methodology. We see therefore no empirical basis for questioning the reliability of current dispersion corrections like D3 or VV10 to standard density functional approximations neither for these compounds nor for organometallic chemistry in general

    Comprehensive Thermochemical Benchmark Set of Realistic Closed-Shell Metal Organic Reactions

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    We introduce the new MOR41 benchmark set consisting of 41 closed-shell organometallic reactions resembling many important chemical transformations commonly used in transition metal chemistry and catalysis. It includes significantly larger molecules than presented in other transition metal test sets and covers a broad range of bonding motifs. Recent progress in linear-scaling coupled cluster theory allowed for the calculation of accurate DLPNO-CCSD­(T)/CBS­(def2-TZVPP/def2-QZVPP) reference energies for 3d,4d,5d-transition metal compounds with up to 120 atoms. Furthermore, 41 density functionals, including seven GGAs, three meta-GGAs, 14 hybrid functionals, and 17 double-hybrid functionals combined with two different London dispersion corrections, are benchmarked with respect to their performance for the newly compiled MOR41 reaction energies. A few wave function-based post-HF methods as, e.g., MP2 or RPA with similar computational demands are also tested and in total, 90 methods were considered. The double-hybrid functional PWPB95-D3­(BJ) outperformed all other assessed methods with an MAD of 1.9 kcal/mol, followed by the hybrids ωB97X-V (2.2 kcal/mol) and mPW1B95-D3­(BJ) (2.4 kcal/mol). The popular PBE0-D3­(BJ) hybrid also performs well (2.8 kcal/mol). Within the meta-GGA class, the recently published SCAN-D3­(BJ) functional as well as TPSS-D3­(BJ) perform best (MAD of 3.2 and 3.3 kcal/mol, respectively). Many popular methods like BP86-D3­(BJ) (4.9 kcal/mol) or B3LYP-D3­(BJ) (4.9 kcal/mol) provide significantly worse reaction energies and are not recommended for organometallic thermochemistry considering the availability of better methods with the same computational cost. The results regarding the performance of different functional approximations are consistent with conclusions from previous main-group thermochemistry benchmark studies

    Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

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    We have created a benchmark set of quantum chemical structure–energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO–CCSD­(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0χ<sub>OL3</sub> force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of ∼0.4–0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields

    Crystal Packing Induced Carbon–Carbon Double–Triple Bond Isomerization in a Zirconocene Complex

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    We present a combined theoretical and experimental analysis of the carbon–carbon bond character in two prototypical zirconocene complexes. The two cyclic seven-membered ring zirconium compounds <b>2a</b> and <b>2b</b> differ by the substitution of a <i>tert</i>-butyl by a trimethylsilyl group. Due to the coordination of the π-system to the metal atom, a formally forbidden (η<sup>2</sup>-allenyl)/enamido-Zr to (η<sup>2</sup>-alkyne)/κ<i>N</i>-imine-Zr complex isomerization is feasible. State-of-the-art dispersion-corrected density functional theory (DFT-D3) is used in both the solid and condensed phase to examine and quantify the experimental structures (X-ray diffraction) and <sup>13</sup>C NMR magnetic shielding. The complementary investigations demonstrate the importance of nonlocal London dispersion interactions. Both X-ray structures agree excellently with the results of the solid-state DFT-D3 calculations. Interestingly, <b>2b</b> exhibits a mixed allene–alkyne form in the solid state, while its gas phase structure has a strong allene character. The substitution leading to <b>2a</b> prevents this isomerization in the solid state by the intramolecular stabilization of the allene structure. NMR solid and liquid phase measurements confirm the theoretically proposed transition. By combining the experimental and theoretical information, the rather unusual triple/single to double/double-bond transition is attributed to an intermolecular London dispersion induced crystal packing effect

    Evidence of a Donor–Acceptor (Ir–H)→SiR<sub>3</sub> Interaction in a Trapped Ir(III) Silane Catalytic Intermediate

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    The ionic iridacycle [(2-phenylenepyridine-κ<i>N</i>,κ<i>C</i>)­IrCp*­(NCMe)]­[BArF<sub>24</sub>] ([<b>2</b>]­[BArF<sub>24</sub>]) displays a remarkable capability to catalyze the O-dehydrosilylation of alcohols at room temperature (0.4 × 10<sup>3</sup> < TON < 10<sup>3</sup>, 8 × 10<sup>3</sup> < TOF<sub><i>i</i></sub> < 1.9 × 10<sup>5</sup> h<sup>–1</sup> for primary alcohols) that is explained by its exothermic reaction with Et<sub>3</sub>SiH, which affords the new cationic hydrido-Ir­(III)-silylium species [<b>3</b>]­[BArF<sub>24</sub>]. Isothermal calorimetric titration (ITC) indicates that the reaction of [<b>2</b>]­[BArF<sub>24</sub>] with Et<sub>3</sub>SiH requires 3 equiv of the latter and releases an enthalpy of −46 kcal/mol in chlorobenzene. Density functional theory (DFT) calculations indicate that the thermochemistry of this reaction is largely dominated by the concomitant bis-hydrosilylation of the released MeCN ligand. Attempts to produce [<b>3</b>]­[BF<sub>4</sub>] and [<b>3</b>]­[OTf] salts resulted in the formation of a known neutral hydrido-iridium­(III) complex, i.e. <b>4</b>, and the release of Et<sub>3</sub>SiF and Et<sub>3</sub>SiOTf, respectively. In both cases formation of the cationic μ-hydrido-bridged bis-iridacyclic complexes [<b>5</b>]­[BF<sub>4</sub>] and [<b>5</b>]­[OTf], respectively, was observed. The structure of [<b>5</b>]­[OTf] was established by X-ray diffraction analysis. Conversion of [<b>3</b>]­[BArF<sub>24</sub>] into <b>4</b> upon reaction with either 4-<i>N</i>,<i>N</i>-dimethylaminopyridine or [<i>n</i>Bu<sub>4</sub>]­[OTf] indicates that the Ir center holds a +III formal oxidation state and that the Et<sub>3</sub>Si<sup>+</sup> moiety behaves as a Z-type ligand according to Green’s formalism. [<b>3</b>]­[BArF<sub>24</sub>], which was trapped and structurally characterized and its electronic structure investigated by state-of-the-art DFT methods (DFT-D, EDA, ETS-NOCV, QTAIM, ELF, NCI plots and NBO), displays the features of a cohesive hydridoiridium­(III)→silylium donor–acceptor complex. This study suggests that the fate of [<b>3</b>]<sup>+</sup> in the O-dehydrosilylation of alcohols is conditioned by the nature of the associated counteranion and by the absence of Lewis base in the medium capable of irreversibly capturing the silylium species

    Flexible Phenanthracene Nanotubes for Explosive Detection

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    Phenanthracene nanotubes with arylene-ethynylene-butadiynylene rims and phenanthracene walls are synthesized in a modular bottom-up approach. One of the rims carries hexadecyloxy side chains, mediating the affinity to highly oriented pyrolytic graphite. Molecular dynamics simulations show that the nanotubes are much more flexible than their structural formulas suggest: In 12, the phenanthracene units act as hinges that flip the two macrocycles relative to each other to one of two possible sites, as quantum mechanical models suggest and scanning tunneling microscopy investigations prove. Unexpectedly, both theory and experiment show for 13 that the three phenanthracene hinges are deflected from the upright position, accompanied by a deformation of both macrocycles from their idealized sturdy macroporous geometry. This flexibility together with their affinity to carbon-rich substrates allows for an efficient host–guest chemistry at the solid/gas interface opening the potential for applications in single-walled carbon nanotube-based sensing, and the applicability to build new sensors for the detection of 2,4,6-trinitrotoluene via nitroaromatic markers is shown

    Flexible Phenanthracene Nanotubes for Explosive Detection

    No full text
    Phenanthracene nanotubes with arylene-ethynylene-butadiynylene rims and phenanthracene walls are synthesized in a modular bottom-up approach. One of the rims carries hexadecyloxy side chains, mediating the affinity to highly oriented pyrolytic graphite. Molecular dynamics simulations show that the nanotubes are much more flexible than their structural formulas suggest: In 12, the phenanthracene units act as hinges that flip the two macrocycles relative to each other to one of two possible sites, as quantum mechanical models suggest and scanning tunneling microscopy investigations prove. Unexpectedly, both theory and experiment show for 13 that the three phenanthracene hinges are deflected from the upright position, accompanied by a deformation of both macrocycles from their idealized sturdy macroporous geometry. This flexibility together with their affinity to carbon-rich substrates allows for an efficient host–guest chemistry at the solid/gas interface opening the potential for applications in single-walled carbon nanotube-based sensing, and the applicability to build new sensors for the detection of 2,4,6-trinitrotoluene via nitroaromatic markers is shown

    Flexible Phenanthracene Nanotubes for Explosive Detection

    No full text
    Phenanthracene nanotubes with arylene-ethynylene-butadiynylene rims and phenanthracene walls are synthesized in a modular bottom-up approach. One of the rims carries hexadecyloxy side chains, mediating the affinity to highly oriented pyrolytic graphite. Molecular dynamics simulations show that the nanotubes are much more flexible than their structural formulas suggest: In 12, the phenanthracene units act as hinges that flip the two macrocycles relative to each other to one of two possible sites, as quantum mechanical models suggest and scanning tunneling microscopy investigations prove. Unexpectedly, both theory and experiment show for 13 that the three phenanthracene hinges are deflected from the upright position, accompanied by a deformation of both macrocycles from their idealized sturdy macroporous geometry. This flexibility together with their affinity to carbon-rich substrates allows for an efficient host–guest chemistry at the solid/gas interface opening the potential for applications in single-walled carbon nanotube-based sensing, and the applicability to build new sensors for the detection of 2,4,6-trinitrotoluene via nitroaromatic markers is shown

    Flexible Phenanthracene Nanotubes for Explosive Detection

    No full text
    Phenanthracene nanotubes with arylene-ethynylene-butadiynylene rims and phenanthracene walls are synthesized in a modular bottom-up approach. One of the rims carries hexadecyloxy side chains, mediating the affinity to highly oriented pyrolytic graphite. Molecular dynamics simulations show that the nanotubes are much more flexible than their structural formulas suggest: In 12, the phenanthracene units act as hinges that flip the two macrocycles relative to each other to one of two possible sites, as quantum mechanical models suggest and scanning tunneling microscopy investigations prove. Unexpectedly, both theory and experiment show for 13 that the three phenanthracene hinges are deflected from the upright position, accompanied by a deformation of both macrocycles from their idealized sturdy macroporous geometry. This flexibility together with their affinity to carbon-rich substrates allows for an efficient host–guest chemistry at the solid/gas interface opening the potential for applications in single-walled carbon nanotube-based sensing, and the applicability to build new sensors for the detection of 2,4,6-trinitrotoluene via nitroaromatic markers is shown
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