QM/MM Simulations of Afatinib-EGFR Addition: The Role of ß-Dimethylaminomethyl Substitution.

Acrylamides are the most commonly used warheads of targeted covalent inhibitors (TCIs) directed at cysteines; however, the reaction mechanisms of acrylamides in proteins remain controversial, particularly for those involving protonated or unreactive cysteines. Using the combined semiempirical quantum mechanics (QM)/molecular mechanics (MM) free energy simulations, we investigated the reaction between afatinib, the first TCI drug for cancer treatment, and Cys797 in the EGFR kinase. Afatinib contains a ß-dimethylaminomethyl (ß-DMAM) substitution which has been shown to enhance the intrinsic reactivity and potency against EGFR for related inhibitors. Two hypothesized reaction mechanisms were tested. Our data suggest that Cys797 becomes deprotonated in the presence of afatinib, and the reaction proceeds via a classical Michael addition mechanism, with Asp800 stabilizing the ion-pair reactant state ß-DMAM+/C797- and the transition state of the nucleophilic attack. Our work elucidates an important structure-activity relationship of acrylamides in proteins.

QM/MM simulations of EFGR with afatinib reveal the role of the ß-dimethylaminomethyl substitution.

Acrylamides are the most commonly used warheads of targeted covalent inhibitors (TCIs) directed at cysteines; however, the reaction mechanisms of acrylamides in proteins remain controversial, particularly for those involving protonated or unreactive cysteines. Using the combined semiempirical quantum mechanics (QM)/molecular mechanics (MM) free energy simulations, we investigated the reaction between afatinib, the first TCI drug for cancer treatment, and Cys797 in the EGFR kinase. Afatinib contains a ß-dimethylaminomethyl (ß-DMAM) substitution which has been shown to enhance the intrinsic reactivity and potency against EGFR for related inhibitors. Two hypothesized reaction mechanisms were tested. Our data suggest that Cys797 becomes deprotonated in the presence of afatinib and the reaction proceeds via a classical Michael addition mechanism, with Asp800 stabilizing the ion-pair reactant state ß-DMAM+/C797- and the transition state of the nucleophilic attack. Our work elucidates an important structure-activity relationship of acrylamides in proteins.

Uranium(iv) alkyl cations: synthesis, structures, comparison with thorium(iv) analogues, and the influence of arene-coordination on thermal stability and ethylene polymerization activity.

Reaction of [(XA2)U(CH2SiMe3)2] (1; XA2 = 4,5-bis(2,6-diisopropylanilido)-2,7-di-tert-butyl-9,9-dimethylxanthene) with 1 equivalent of [Ph3C][B(C6F5)4] in arene solvents afforded the arene-coordinated uranium alkyl cations, [(XA2)U(CH2SiMe3)(η n -arene)][B(C6F5)4] {arene = benzene (2), toluene (3), bromobenzene (4) and fluorobenzene (5)}. Compounds 2, 3, and 5 were crystallographically characterized, and in all cases the arene is π-coordinated. Solution NMR studies of 2-5 suggest that the binding preferences of the [(XA2)U(CH2SiMe3)]+ cation follow the order: toluene ≈ benzene > bromobenzene > fluorobenzene. Compounds 2-4 generated in C6H5R (R = H, Me or Br, respectively) showed no polymerization activity under 1 atm of ethylene. By contrast, 5 and 5-Th (the thorium analogue of 5) in fluorobenzene at 20 and 70 °C achieved ethylene polymerization activities between 16 800 and 139 200 g mol-1 h-1 atm-1, highlighting the extent to which common arene solvents such as toluene can suppress ethylene polymerization activity in sterically open f-element complexes. However, activation of [(XA2)An(CH2SiMe3)2] {M = U (1) or Th (1-Th)} with [Ph3C][B(C6F5)4] in n-alkane solvents did not afford an active polymerization catalyst due to catalyst decomposition, illustrating the critical role of PhX (X = H, Me, Br or F) coordination for alkyl cation stabilization. Gas phase DFT calculations, including fragment interaction calculations with energy decomposition and ETS-NOCV analysis, were carried out on the cationic portion of 2'-Th, 2', 3' and 5' (analogues of 2-Th, 2, 3 and 5 with hydrogen atoms in place of ligand backbone methyl and tert-butyl groups), providing insight into the nature of actinide-arene bonding, which decreases in strength in the order 2'-Th > 2' ≈ 3' > 5'.

Tuning Structural and Optical Properties of Porphyrin-based Hydrogen-Bonded Organic Frameworks by Metal Insertion.

Herein, a simple way of tuning the optical and structural properties of porphyrin-based hydrogen-bonded organic frameworks (HOFs) is reported. By inserting transition metal ions into the porphyrin cores of GTUB-5 (p-H8 -TPPA (5,10,15,20-Tetrakis[p-phenylphosphonic acid] HOF), the authors show that it is possible to generate HOFs with different band gaps, photoluminescence (PL) life times, and textural properties. The band gaps of the resulting HOFs (viz., Cu-, Ni-, Pd-, and Zn-GTUB-5) are measured by diffuse reflectance and PL spectroscopy, as well as calculated via DFT, and the PL lifetimes are measured. Across the series, the band gaps vary over a narrow range from 1.37 to 1.62 eV, while the PL lifetimes vary over a wide range from 2.3 to 83 ns. These differences ultimately arise from metal-induced structural changes, viz., changes in the metal-to-nitrogen distances, number of hydrogen bonds, and pore volumes. DFT reveals that the band gaps of Cu-, Zn-, and Pd- GTUB-5 are governed by highest occupied/lowest unoccupied crystal orbitals (HOCO/LUCO) composed of π- orbitals on the porphyrin linkers, while that of Ni-GTUB-5 is governed by a HOCO and LUCO composed of Ni dorbitals. Overall, our findings show that metal-insertion can be used to optimize HOFs for optoelectronics and small-molecule capture applications.

Coordination-Induced Band Gap Reduction in a Metal-Organic Framework.

Herein, we report on the synthesis of a microporous, three-dimensional phosphonate metal-organic framework (MOF) with the composition Cu3 (H5 -MTPPA)2 ⋅ 2 NMP (H8 -MTPPA=methane tetra-p-phenylphosphonic acid and NMP=N-methyl-2-pyrrolidone). This MOF, termed TUB1, has a unique one-dimensional inorganic building unit composed of square planar and distorted trigonal bipyramidal copper atoms. It possesses a (calculated) BET surface area of 766.2 m2 /g after removal of the solvents from the voids. The Tauc plot for TUB1 yields indirect and direct band gaps of 2.4 eV and 2.7 eV, respectively. DFT calculations reveal the existence of two spin-dependent gaps of 2.60 eV and 0.48 eV for the alpha and beta spins, respectively, with the lowest unoccupied crystal orbital for both gaps predominantly residing on the square planar copper atoms. The projected density of states suggests that the presence of the square planar copper atoms reduces the overall band gap of TUB1, as the beta-gap for the trigonal bipyramidal copper atoms is 3.72 eV.

Semiconductive microporous hydrogen-bonded organophosphonic acid frameworks.

Herein, we report a semiconductive, proton-conductive, microporous hydrogen-bonded organic framework (HOF) derived from phenylphosphonic acid and 5,10,15,20-tetrakis[p-phenylphosphonic acid] porphyrin (GTUB5). The structure of GTUB5 was characterized using single crystal X-ray diffraction. A narrow band gap of 1.56 eV was extracted from a UV-Vis spectrum of pure GTUB5 crystals, in excellent agreement with the 1.65 eV band gap obtained from DFT calculations. The same band gap was also measured for GTUB5 in DMSO. The proton conductivity of GTUB5 was measured to be 3.00 × 10-6 S cm-1 at 75 °C and 75% relative humidity. The surface area was estimated to be 422 m2 g-1 from grand canonical Monte Carlo simulations. XRD showed that GTUB5 is thermally stable under relative humidities of up to 90% at 90 °C. These findings pave the way for a new family of organic, microporous, and semiconducting materials with high surface areas and high thermal stabilities.

Phosphonate Metal-Organic Frameworks: A Novel Family of Semiconductors.

Herein, the first semiconducting and magnetic phosphonate metal-organic framework (MOF), TUB75, is reported, which contains a 1D inorganic building unit composed of a zigzag chain of corner-sharing copper dimers. The solid-state UV-vis spectrum of TUB75 reveals the existence of a narrow bandgap of 1.4 eV, which agrees well with the density functional theory (DFT)-calculated bandgap of 1.77 eV. Single-crystal conductivity measurements for different orientations of the individual crystals yield a range of conductances from 10-3 to 103 S m-1 at room temperature, pointing to the directional nature of the electrical conductivity in TUB75. Magnetization measurements show that TUB75 is composed of antiferromagnetically coupled copper dimer chains. Due to their rich structural chemistry and exceptionally high thermal/chemical stabilities, phosphonate MOFs like TUB75 may open new vistas in engineerable electrodes for supercapacitors.

Implementation of the SM12 Solvation Model into ADF and Comparison with COSMO.

In this article, an implementation of the newest iteration of the Minnesota solvation model, SM12, into the Amsterdam density functional (ADF) computational package is presented. ADF makes exclusive use of Slater-type orbitals (STO), which correctly represent the true atomic orbitals for atoms, whereas SM12 and the underlying charge model 5 (CM5) have previously only been tested on Gaussian-type orbitals (GTO). This new implementation is used to prove the basis set independence of both CM5 and SM12. A detailed comparison of the SM12 and COSMO solvation models, as implemented in ADF, is also presented. We show that this new implementation of SM12 has a mean unsigned error (MUE) of 0.68 kcal/mol for 272 molecules in water solvent, 4.10 kcal/mol MUE for 112 charged ions in water, and 0.92 kcal/mol MUE for 197 solvent calculations of various molecules. SM12 outperforms COSMO for all neutral molecules and performs as well as COSMO for cationic molecules, only falling short when anionic molecules are taken into consideration, likely due to CM5's use of Hirshfeld charges and their poor description of anionic molecules, though CM5 seems to improve upon this discrepancy.