Molecular design strategy of fluorogenic probes based on quantum chemical prediction of intramolecular spirocyclization.

Fluorogenic probes are essential tools for real-time visualization of dynamic intracellular processes in living cells, but so far, their design has been largely dependent on trial-and-error methods. Here we propose a quantum chemical calculation-based method for rational prediction of the fluorescence properties of hydroxymethyl rhodamine (HMR)-based fluorogenic probes. Our computational analysis of the intramolecular spirocyclization reaction, which switches the fluorescence properties of HMR derivatives, reveals that consideration of the explicit water molecules is essential for accurate estimation of the free energy difference between the open (fluorescent) and closed (non-fluorescent) forms.

Bridged Stilbenes: AIEgens Designed via a Simple Strategy to Control the Non-radiative Decay Pathway.

To broaden the application of aggregation-induced emission (AIE) luminogens (AIEgens), the design of novel small-molecular dyes that exhibit high fluorescence quantum yield (Φ ) in the solid state is required. Considering that the mechanism of AIE can be rationalized based on steric avoidance of non-radiative decay pathways, a series of bridged stilbenes was designed, and their non-radiative decay pathways were investigated theoretically. Bridged stilbenes with short alkyl chains exhibited a strong fluorescence emission in solution and in the solid state, while bridged stilbenes with long alkyl chains exhibited AIE.

Roles of Closed- and Open-Loop Conformations in Large-Scale Structural Transitions of l-Lactate Dehydrogenase.

The mechanism of l-lactate generation from pyruvate by l-lactate dehydrogenase (LDH) from the rabbit muscle was studied theoretically by the multistructural microiteration (MSM) method combined with the quantum mechanics/molecular mechanics (QM/MM)-ONIOM method, where the MSM method describes the MM environment as a weighted average of multiple different structures that are fully relaxed during geometry optimization or a reaction path calculation for the QM part. The results showed that the substrate binding and product states were stabilized only in the open-loop conformation of LDH and the reaction occurred in the closed-loop conformation. In other words, before and after the chemical reaction, a large-scale structural transition from the open-loop conformation to the closed-loop conformation and vice versa occurred.

Synthesis of fluorescent polycarbonates with highly twisted ,-bis(dialkylamino)anthracene AIE luminogens in the main chain.

A synthetic route to embed aggregation-induced-emission-(AIE)-active luminophores in polycarbonates (PCs) in various ratios is reported. The AIE-active monomer is based on the structure of 9,10-bis(piperidyl)anthracene. The obtained PCs display good film-forming properties, similar to those observed in poly(bisphenol A carbonate) (Ba-PC).

An Unexpected Ireland-Claisen Rearrangement Cascade During the Synthesis of the Tricyclic Core of Curcusone C: Mechanistic Elucidation by Trial-and-Error and Automatic Artificial Force-Induced Reaction (AFIR) Computations.

In the course of a total synthesis effort directed toward the natural product curcusone C, the Stoltz group discovered an unexpected thermal rearrangement of a divinylcyclopropane to the product of a formal Cope/1,3-sigmatropic shift sequence. Since the involvement of a thermally forbidden 1,3-shift seemed unlikely, theoretical studies involving two approaches, the "trial-and-error" testing of various conceivable mechanisms (Houk group) and an "automatic" approach using the Maeda-Morokuma AFIR method (Morokuma group) were applied to explore the mechanism. Eventually, both approaches converged on a cascade mechanism shown to have some partial literature precedent: Cope rearrangement/1,5-sigmatropic silyl shift/Claisen rearrangement/retro-Claisen rearrangement/1,5-sigmatropic silyl shift, comprising a quintet of five sequential thermally allowed pericyclic rearrangements.

Computational study on the luminescence quantum yields of terbium complexes with 2,2'-bipyridine derivative ligands.

Terbium complexes are widely used as luminescent materials because of their bright green emission and sharp emission spectra and the independence of their emission wavelengths from the surrounding environment. The luminescence quantum yield (LQY), however, heavily depends on the surroundings, and an appropriate ligand design is indispensable. In this study, we focus on a Tb complex coordinated by a 2,2'-bipyridine derivative ligand (L1), whose LQY is almost zero at room temperature [M.

DFT and AFIR Study on the Mechanism and the Origin of Enantioselectivity in Iron-Catalyzed Cross-Coupling Reactions.

The mechanism of the full catalytic cycle for Fe-chiral-bisphosphine-catalyzed cross-coupling reaction between alkyl halides and Grignard reagents (Nakamura and co-workers, J. Am. Chem.

Exploring the full catalytic cycle of rhodium(i)-BINAP-catalysed isomerisation of allylic amines: a graph theory approach for path optimisation.

We explored the reaction mechanism of the cationic rhodium(i)-BINAP complex catalysed isomerisation of allylic amines using the artificial force induced reaction method with the global reaction route mapping strategy, which enabled us to search for various reaction paths without assumption of transition states. The entire reaction network was reproduced in the form of a graph, and reasonable paths were selected from the complicated network using Prim's algorithm. As a result, a new dissociative reaction mechanism was proposed.

The K-Region in Pyrenes as a Key Position to Activate Aggregation-Induced Emission: Effects of Introducing Highly Twisted N,N-Dimethylamines.

A new design strategy to activate aggregation-induced emission (AIE) in pyrene chromophores is reported. In a previous report, we demonstrated that highly twisted N,N-dialkylamines of anthracene and naphthalene induce drastic AIE when these donors are introduced at appropriate positions to stabilize the S/S minimum energy conical intersection (MECI). In the present study, this design strategy was applied to pyrene: the introduction of N,N-dimethylamine substituents at the 4,5-positions of pyrene, the so-called K-region, are likely to stabilize MECIs.

Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems.

We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non-reaction-center (surrounding) part is optimized by fixing atoms in the reaction-center part before displacements of the reaction-center atoms.

Organic linkers control the thermosensitivity of the emission intensities from Tb(iii) and Eu(iii) in a chameleon polymer.

Thermometers whose emission color gradually changes with temperature are called chameleon emitters. In this study, we discuss the mechanism of the thermosensitivity of the emission color of polymers that contain two lanthanides (Ln), , [TbEu(hfa)(linker)] , where the Ln(hfa) complexes (hfa: hexafluoro acetylacetonato) are connected by a phosphine oxide "linker" molecule. First, the difference in the thermosensitivities of the emissions from Tb and Eu are discussed.

Trihydroborates and Dihydroboranes Bearing a Pentacoordinated Phosphorus Atom: Double Ring Expansion To Balance the Coordination States.

The first trihydroborate bearing a pentacoordinated phosphorus atom was synthesized as a new P-B bonded compound. Hydride abstraction of the trihydroborate gave an intermediary dihydroborane, which showed hydroboration reactivity and was trapped with pyridine whilst maintaining the P-B bond. The dihydroborane underwent a rearrangement, which involved a double ring expansion to compensate for the unbalanced coordination states of the phosphorus and boron atoms, to give a new fused bicyclic phosphine-boronate.

Theoretical Study of Addition Reactions of LM(M = Rh, Ir) and LM(M = Pd, Pt) to Li@C.

The addition reaction of M(Cl)(CO)(PPh) (M = Rh, Ir) and M(PPh) (M = Pd, Pt) fragments with X@C (X = 0, Li) were characterized by density functional theory (DFT) and the artificial force-induced reaction (AFIR) method. The calculated free energy profiles suggested that the η[6:6]-addition is the most favorable reaction, which is consistent with the experimental observations. In the presence of Li ion, the reaction is highly exothermic, leading to η[6:6] product of LIrLi@C.

Different conical intersections control nonadiabatic photochemistry of fluorene light-driven molecular rotary motor: A CASSCF and spin-flip DFT study.

We report the light-driven isomerization mechanism of a fluorene-based light-driven rotary motor (corresponding to Feringa's 2nd generation rotary motor, [M. M. Pollard et al.

Artificial Force Induced Reaction Method for Systematic Determination of Complex Reaction Mechanisms.

Nowadays, computational studies are very important for the elucidation of reaction mechanisms and selectivity of complex reactions. However, traditional computational methods usually require an estimated reaction path, mainly driven by limited experimental implications, intuition, and assumptions of stationary points. However, the artificial force induced reaction (AFIR) method in the global reaction route mapping (GRRM) strategy can be used for unbiased and automatic reaction path searches for complex reactions.

Artificial Force Induced Reaction (AFIR) Method for Exploring Quantum Chemical Potential Energy Surfaces.

In this account, a technical overview of the artificial force induced reaction (AFIR) method is presented. The AFIR method is one of the automated reaction-path search methods developed by the authors, and has been applied extensively to a variety of chemical reactions, such as organocatalysis, organometallic catalysis, and photoreactions. There are two modes in the AFIR method, i.

Palladium-catalyzed regioselective and stereo-invertive ring-opening borylation of 2-arylaziridines with bis(pinacolato)diboron: experimental and computational studies.

A palladium catalyzed regioselective borylative ring opening reaction of 2-arylaziridines to give β-amino-β-arylethylborates was developed. The reaction reported herein represents the first example of ring-opening borylation of non-vinylic aziridines and direct borylative C(sp)-N bond cleavage of neutral organic substrates. NMR studies and density functional theory (DFT) calculations suggested that the active intermediate for the reaction is a PdL complex [L = P(-Bu)Me].

Theoretical insight into the wavelength-dependent photodissociation mechanism of nitric acid.

Photodissociation pathways of HNO3 involving the four lowest electronic singlet states (S0, S1, S2 and S3) were studied by the MS-CAS(12e,8o)PT2/6-31+G* method. All critical points, i.e.

Highly Twisted N,N-Dialkylamines as a Design Strategy to Tune Simple Aromatic Hydrocarbons as Steric Environment-Sensitive Fluorophores.

The steric-environment sensitivity of fluorescence of 9,10-bis(N,N-dialkylamino)anthracenes (BDAAs) was studied experimentally and theoretically. A new design strategy to tune simple aromatic hydrocarbons as efficient aggregation-induced emission (AIE) luminogens and molecular rotors is proposed. For a variety of BDAAs, prominent Stokes shifts and efficient solid-state fluorescence were observed.

Computational Catalysis Using the Artificial Force Induced Reaction Method.

The artificial force induced reaction (AFIR) method in the global reaction route mapping (GRRM) strategy is an automatic approach to explore all important reaction paths of complex reactions. Most traditional methods in computational catalysis require guess reaction paths. On the other hand, the AFIR approach locates local minima (LMs) and transition states (TSs) of reaction paths without a guess, and therefore finds unanticipated as well as anticipated reaction paths.

Computational SN 2-Type Mechanism for the Difluoromethylation of Lithium Enolate with Fluoroform through Bimetallic C-F Bond Dual Activation.

The reaction mechanism for difluoromethylation of lithium enolates with fluoroform was analyzed computationally (DFT calculations with the artificial force induced reaction (AFIR) method and solvation model based on density (SMD) solvation model (THF)), showing an SN 2-type carbon-carbon bond formation; the "bimetallic" lithium enolate and lithium trifluoromethyl carbenoid exert the C-F bond "dual" activation, in contrast to the monometallic butterfly-shaped carbenoid in the Simmons-Smith reaction. Lithium enolates, generated by the reaction of 2 equiv. of lithium hexamethyldisilazide (rather than 1 or 3 equiv.

Trimeric cluster of lithium amidoborane-the smallest unit for the modeling of hydrogen release mechanism.

A detailed first-principle DFT M06/6-311++G(d.p) study of dehydrogenation mechanism of trimeric cluster of lithium amidoborane is presented. The first step of the reaction is association of two LiNH2 BH3 molecules in the cluster.

QM/MD studies on graphene growth from small islands on the Ni(111) surface.

Quantum chemical molecular dynamics simulations of graphene growth from small island precursors in different carbon nucleation densities on the Ni(111) surface at high temperatures have been conducted. The results indicate that small islands are not static, i.e.

Mechanisms of Hydrogen Generation from Tetrameric Clusters of Lithium Amidoborane.

The first-principles study of dehydrogenation mechanism of tetrameric clusters of lithium amidoborane LiNH2BH3, (LiAB)4, is presented. The choice of tetramer is based on the suspicion that dimeric cluster models used in previous theoretical studies are too small to capture the essence of the reaction. Dehydrogenation pathways starting from three isomers of (LiAB)4 tetramers were explored by applying the artificial force induced reaction (AFIR) method at the M06 level of theory.

Exploring the Reaction Coordinates for f-f Emission and Quenching of Lanthanide Complexes - Thermosensitivity of Terbium(III) Luminescence.

Lanthanide complexes with temperature dependent f-f emission intensities are commonly used as temperature sensors. The thermosensitivity can be controlled by the ligands, but their effects are difficult to predict. To clarify the origin of the differences in thermosensitivity, we propose a new theoretical strategy, the energy shift method, and use it to find crossing points between two states where intersystem crossing and excitation energy transfer take place.