Editorial

Editoria

MCPB.py: A Python Based Metal Center Parameter Builder

MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program’s ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling

Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions

Metal ions exist in almost half of the proteins in the protein databank, and they serve as structural, electron-transfer, and catalytic elements in the metabolic processes of organisms. Molecular dynamics (MD) simulation is a powerful tool that provides information about biomolecular systems at the atomic level. Coupled with the growth in computing power, algorithms like the particle mesh Ewald (PME) method have become the accepted standard when dealing with long-range interactions in MD simulations. The nonbonded model of metal ions consists of an electrostatic plus 12–6 Lennard-Jones (LJ) potential and is used largely because of its speed relative to more accurate models. In previous work we found that ideal parameters do not exist that reproduce several experimental properties for M­(II) ions simultaneously using the nonbonded model coupled with the PME method due to the underestimation of metal ion-ligand interactions. Via a consideration of the nature of the nonbonded model, we proposed that the observed error largely arises from overlooking charge-induced dipole interactions. The electrostatic plus 12–6 LJ potential model works reasonably well for neutral systems but does struggle with more highly charged systems. In the present work we designed and parametrized a new nonbonded model for metal ions by adding a 1/<i>r</i>⁴ term to the 12–6 model. We call it the 12–6–4 LJ-type nonbonded model due to its mathematical construction. Parameters were determined for 16 +2 metal ions for the TIP3P, SPC/E, and TIP4P_EW water models. The final parameters reproduce the experimental hydration free energies (HFE), ion-oxygen distances (IOD) in the first solvation shell, and coordination numbers (CN) accurately for most of the metal ions investigated. Preliminary tests on MgCl₂ at different concentrations in aqueous solution and Mg²⁺–nucleic acid systems show reasonable results suggesting that the present parameters can work in mixed systems. The 12–6–4 LJ-type nonbonded model is readily adopted into standard force fields like AMBER, CHARMM, and OPLS-AA with only a modest computational overhead. The new nonbonded model does not consider charge-transfer effects explicitly and, hence, may not be suitable for the simulation of systems where charge-transfer effects play a decisive role

Organocatalytic Enantioselective [1 + 4] Annulation of Morita–Baylis–Hillman Carbonates with Electron-Deficient Olefins: Access to Chiral 2,3-Dihydrofuran Derivatives

A reaction has been developed for the chiral phosphine-catalyzed enantioselective [1 + 4] annulation of Morita–Baylis–Hillman carbonates with electron-deficient olefins via a Michael alkylation process. Morita–Baylis–Hillman carbonates reacted smoothly with β,γ-unsaturated α-keto ester and α,β-unsaturated ketone substrates under 1,2-bis­[(2<i>R</i>,5<i>R</i>)-2,5-dimethylphospholano]­benzene monoxide catalysis to furnish a wide range of optically active 2,3-dihydrofurans in high yields (up to 95%) with excellent asymmetric induction (up to >99% ee, >20:1 dr). This protocol represents an efficient strategy for the synthesis of optically active multifunctional 2,3-dihydrofurans via an asymmetric Michael alkylation domino reaction

3‑Center-5-Electron Boryl Radicals with σ⁰π¹ Ground State Electronic Structure

Five- and six-membered boron heterocycle-based three-center-five-electron (<b>3c</b>–<b>5e</b>) type boryl radicals with unusual σ⁰π¹ ground state electronic structures are predicted theoretically. Compared to σ¹π⁰ analogs, their unique electronic structure leads to both lower reactivity toward H-atoms and stronger coordination with Lewis bases. The corresponding Lewis base-stabilized four-center-seven-electron (<b>4c</b>–<b>7e</b>) type boryl radicals are even more unreactive toward H-atoms than the conventional <b>4c</b>–<b>7e</b> ones

Double N,B-Type Bidentate Boryl Ligands Enabling a Highly Active Iridium Catalyst for C–H Borylation

Boryl ligands hold promise in catalysis due to their very high electron-donating property. In this communication double N,B-type boryl anions were designed as bidentate ligands to promote an sp² C–H borylation reaction. A symmetric pyridine-containing tetraamino­diborane(4) compound (<b>1</b>) was readily prepared as the ligand precursor that could be used, in combination with [Ir­(OMe)­(COD)]₂, to <i>in situ</i> generate a highly active catalyst for a broad range of (hetero)­arene substrates including highly electron-rich and/or sterically hindered ones. This work provides the first example of a bidentate boryl ligand in supporting homogeneous organometallic catalysis

Copper-Catalyzed Boron-Selective C(sp²)–C(sp³) Oxidative Cross-Coupling of Arylboronic Acids and Alkyltrifluoroborates Involving a Single-Electron Transmetalation Process

A rapid and highly selective oxidative cross-coupling reaction between readily available and shelf-stable arylboronic acids and primary or secondary potassium alkyltrifluoroborates was devised and developed, which works under mild conditions using copper­(II) acetate as the catalyst and silver oxide as the oxidant. Initial experimental results indicate that a single-electron transmetalation process is involved. This approach effectively bypasses the problems associated with the traditional cross-coupling reactions of alkylboronates and thus provides a complementary method in building C­(sp²)–C­(sp³) bonds

Stereocontrolled Construction of the Tricyclic Framework of Tiglianes and Daphnanes by an Oxidative Dearomatization Approach

An appropriately functionalized [5–7–6] tricyclic framework of tigliane and daphnane diterpenes containing seven contiguous stereocenters has been prepared in 10 steps from very simple building blocks in a modular and stereocontrolled fashion. The key features of this approach involve an efficient visible light-induced singlet oxygen oxidative dearomatization and an array of substrate-controlled highly diastereoselective transformations. This work provides a model strategy for rapid and diverted synthesis of natural and unnatural molecules sharing the common skeleton

Computational Analysis of Stable Hard Structures in the Ti–B System

The lowest energy crystalline structures of various stoichiometric titanium boride (Ti–B) intermetallic compounds are sought based on density functional theory combined with the particle-swarm optimization (PSO) technique. Besides three established experimental structures, i.e., FeB-type TiB, AlB₂-type, and Ta₃B₄-type Ti₃B₄, we predict additional six metastable phases at these stoichiometric ratios, namely, α- and β-phases for TiB, TiB₂, and Ti₃B₄, respectively. Moreover, we predict the most stable crystalline structures of four new titanium boride compounds with different stoichiometric ratios: Ti₂B–PS_A, Ti₂B₃–PS_B, TiB₃–PS_C, and TiB₄–PS_D. Notably, Ti₂B–PS_A is shown to have lower formation energy (thus higher stability) than the previously proposed Al₂Cu-type Ti₂B. The computed convex-hull and phonon dispersion relations confirm that all the newly predicted Ti–B intermetallic crystals are thermodynamically and dynamically stable. Remarkably, the predicted α-TiB₂ and β-TiB₂ show semi-metal-like electronic properties and possess high Vickers hardnesses (39.4 and 39.6 GPa), very close to the lower limit of <i>superhard materials</i> (40 GPa). Analyses of band structure, density of states, electronic localization function, and various elastic moduli provide further understanding of the electronic and mechanical properties of the intermetallic titanium borides. We hope the newly predicted hard intermetallic titanium borides coupled with desirable electronic properties and high elastic modulus will motivate future experimental synthesis for applications such as high-temperature structural materials