Force-field parametrization based on radial and energy distribution functions

We propose a novel force-field-parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher-level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Aromaticity Relocation in Perylene Derivatives upon Two‐Electron Oxidation To Form Anthracene and Phenanthrene

We prepared perylene dications 1 ²⁺ and 2 ²⁺ by using “capped” perylene derivatives, and for the first time, successfully obtained single crystals of a perylene dication 1 ²⁺ that enabled us to perform its structural analysis. We realized that the substituted aryl groups on perylene control the positions of positive charges, thus the remaining electronic system satisfies Clar's sextet rule toward the highest number of localized sextets. Experimental and theoretical evidence proved that Clar's aromatic π‐sextet rule could be applied even for the dicationic perylenes in a very simple way.     

Visible-Light-Induced Heptacene Generation under Ambient Conditions: Utilization of Single-crystal Interior as an Isolated Reaction Site

The photo-induced generation of unstable molecules generally requires stringent conditions to prevent oxidation and the concomitant decomposition of the products. The visible-light-induced conversion of two heptacene precursors to heptacene was studied. Single crystals of bis- and mono-α-diketone-type heptacene precursors ( 7-DK2 and 7-DK1 , respectively), were prepared to investigate the effect of precursor structure on reactivity. The photoirradiation of a 7-DK2 single crystal cleaved only one α-diketone group, forming an intermediate bearing a pentacene subunit, while that of a 7-DK1 single crystal gave rise to characteristic absorption peaks of heptacene and their increase in intensity with photoirradiation time, indicating the generation of heptacene without decomposition. Heptacene production was not observed when the precursors were photoirradiated in solution, implying that the single crystal interior provided isolation from the external environment, thus preventing heptacene oxidation.     

Synthesis and Metalation of Doubly o‐Phenylene‐Bridged Cyclic Bis(dipyrrin)s with Highly Bent Skeleton of Dibenzoporphyrin(2.1.2.1)

Facile synthesis of dibenzoporphyrins(2.1.2.1) has been successfully reported by the simple condensation reaction of o‐dipyrrolylbenzene with various aldehydes in the presence of a Lewis acid. This reaction enables the preparation of various dibenzoporphyrin(2.1.2.1) derivatives with p‐substituted phenyl groups, five‐membered heterocycles, and ethynyl groups at the meso‐positions. Dibenzoporphyrins(2.1.2.1) consist of two dipyrrin units that are connected by o‐phenylene bridges, which adopt highly bent saddle‐shaped structures; this was confirmed by X‐ray diffraction analysis. We found that dibenzoporphyrin(2.1.2.1) can be described as a 20π antiaromatic conjugated system, but practically, it is not an antiaromatic macrocycle, which we revealed by ¹H NMR spectroscopy. The redox potentials had good correlations with Hammett substituent constant (σ_p) of the substituents at the meso‐positions. The free‐base dibenzoporphyrin(2.1.2.1) was able to form the metal complexes with nickel(II), copper(II), palladium(II), platinum(II), and tin(IV) ions. These results suggested that dibenzoporphyrin(2.1.2.1) derivatives can be utilized as novel macrocyclic dianionic tetradentate ligands for various metal ions to give complexes with varying optical and electrochemical properties.     

Extension of the LP-Newton method to conic programming problems via semi-infinite representation

Numerical Algorithms - The LP-Newton method solves linear programming (LP) problems by repeatedly projecting a current point onto a certain relevant polytope. In this paper, we extend the...     

Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Regioselective protection of sugars catalyzed by dimethyltin dichloride

The first catalytic process for protection of hydroxyl groups in sugars has been developed. Highly regioselective protection was accomplished along with high chemical yield. The regioselectivity of the benzoylation was realized as an intrinsic character of sugars based on a stereorelationship among their hydroxyl groups. Furthermore, complete protection of alpha-methyl glucoside and beta-methyl xyloside was accomplished.     

Enhanced Four-Electron Oxygen Reduction Selectivity of Clamp-Shaped Cobalt(II) Porphyrin(2.1.2.1) Complexes

The molecular structure, electrochemistry, spectroelectrochemistry and electrocatalytic oxygen reduction reaction (ORR) features of two Co^II porphyrin(2.1.2.1) complexes bearing Ph or F₅Ph groups at the two meso-positions of the macrocycle are examined. Single crystal X-ray analysis reveal a highly bent, nonplanar macrocyclic conformation of the complex resulting in clamp-shaped molecular structures. Cyclic voltammetry paired with UV/Vis spectroelectrochemistry in PhCN/0.1 M TBAP suggest that the first electron addition corresponds to a macrocyclic-centered reduction while spectral changes observed during the first oxidation are consistent with a metal-centered Co^II/Co^III process. The activity of the clamp-shaped complexes towards heterogeneous ORR in 0.1 M KOH show selectivity towards the 4e⁻ ORR pathway giving H₂O. DFT first-principle calculations on the porphyrin catalyst indicates a lower overpotential for 4e⁻ ORR as compared to the 2e⁻ pathway, consistent with experimental data.     

N=8 Armchair Graphene Nanoribbons: Solution Synthesis and High Charge Carrier Mobility**

Structurally defined graphene nanoribbons (GNRs) have emerged as promising candidates for nanoelectronic devices. Low band gap (<1 eV) GNRs are particularly important when considering the Schottky barrier in device performance. Here, we demonstrate the first solution synthesis of 8-AGNRs through a carefully designed arylated polynaphthalene precursor. The efficiency of the oxidative cyclodehydrogenation of the tailor-made polymer precursor into 8-AGNRs was validated by FT-IR, Raman, and UV/Vis-near-infrared (NIR) absorption spectroscopy, and further supported by the synthesis of naphtho[1,2,3,4-ghi]perylene derivatives ( 1 and 2 ) as subunits of 8-AGNR , with a width of 0.86 nm as suggested by the X-ray single crystal analysis. Low-temperature scanning tunneling microscopy (STM) and solid-state NMR analyses provided further structural support for 8-AGNR . The resulting 8-AGNR exhibited a remarkable NIR absorption extending up to ∼2400 nm, corresponding to an optical band gap as low as ∼0.52 eV. Moreover, optical-pump TeraHertz-probe spectroscopy revealed charge-carrier mobility in the dc limit of ∼270 cm² V⁻¹ s⁻¹ for the 8-AGNR .