Zeolitic Imidazolate Frameworks as Solid-State Nanomachines.

Machines have continually developed with the needs of daily life and industrial applications. While the careful design of molecular-scale devices often displays enhanced properties along with mechanical movements, controlling mechanics within solid-state molecular structures remains a significant challenge. Here, we explore the distinct mechanical properties of zeolitic imidazolate frameworks (ZIFs) - frameworks that contain hidden mechanical components. Using a combination of experimental and theoretical approaches, we uncover the machine-like capabilities of ZIFs, wherein connected composite building units operate similarly to a mechanical linkage system. Importantly, this research suggests that certain ZIF subunits act as core mechanical components, paving an innovative view for the future design of solid-state molecular machines.

Formulation of transition dipole gradients for non-adiabatic dynamics with polaritonic states.

A general formulation of the strong coupling between photons confined in a cavity and molecular electronic states is developed for the state-interaction state-average spin-restricted ensemble-referenced Kohn-Sham method. The light-matter interaction is included in the Jaynes-Cummings model, which requires the derivation and implementation of the analytical derivatives of the transition dipole moments between the molecular electronic states. The developed formalism is tested in the simulations of the nonadiabatic dynamics in the polaritonic states resulting from the strong coupling between the cavity photon mode and the ground and excited states of the penta-2,4-dieniminium cation, also known as PSB3. Comparison with the field-free simulations of the excited-state decay dynamics in PSB3 reveals that the light-matter coupling can considerably alter the decay dynamics by increasing the excited state lifetime and hindering photochemically induced torsion about the C=C double bonds of PSB3. The necessity of obtaining analytical transition dipole gradients for the accurate propagation of the dynamics is underlined.

Gaussian Process Regression-Based Near-Infrared d-Luciferin Analogue Design Using Mutation-Controlled Graph-Based Genetic Algorithm.

Molecular discovery is central to the field of chemical informatics. Although optimization approaches have been developed that target-specific molecular properties in combination with machine learning techniques, optimization using databases of limited size is challenging for efficient molecular design. We present a molecular design method with a Gaussian process regression model and a graph-based genetic algorithm (GB-GA) from a data set comprising a small number of compounds by introducing mutation probability control in the genetic algorithm to enhance the optimization capability and speed up the convergence to the optimal solution. In addition, we propose reducing the number of parameters in the conventional GB-GA focusing on efficient molecular design from a small database. We generated a target-specific database by combining active learning and iterative design in the evolutionary methodologies and chose Gaussian process regression as the prediction model for molecular properties. We show that the proposed scheme is more efficient for optimization toward the target properties from goal-directed benchmarks with several drug-like molecules compared to the conventional GB-GA method. Finally, we provide a demonstration whereby we designed D-luciferin analogues with near-infrared fluorescence for bioimaging, which is desirable for effective in vivo light sources, from a small-size data set.

Extension of molecules with an inverted singlet-triplet gap with conjugated branches to alter the oscillator strength.

Molecules that violate Hund's rule and possess negative singlet-triplet gaps (ΔEST) have been actively studied for their potential usage in organic light emitting diodes without the need for thermal activation. However, the weak oscillator strength from the symmetry of such molecules has been recognized as their shortcoming for their application in optoelectronic devices. A group of molecules with a common structural motif involving the original molecule with an inverted gap having branches consisting of conjugated molecules of varied structures and extent of conjugation have been predicted to have desirable oscillator strength, but only few detailed and comprehensive studies regarding the form of excited states and the reason behind the improved oscillator strength have been carried out. We show in this work a series of analyses that suggest that the increase of oscillator strength is correlated with the nature of the excited state changing from a localized excitation to a delocalized excitation involving the central molecule and the branches. The resulting oscillator strength thus depends on the energetic matching of the branching molecule and the central molecule, rather than solely the oscillator strength of the central molecule. From the ΔEST inversion point of view, the static correlation with low-lying doubly excited configurations, the key mechanism behind the inversion in the localized excited state, weakens as the excited states delocalize. As a consequence, the dynamic correlation has a more decisive effect in determining the singlet-triplet gap.

Origamic metal-organic framework toward mechanical metamaterial.

Origami, known as paper folding has become a fascinating research topic recently. Origami-inspired materials often establish mechanical properties that are difficult to achieve in conventional materials. However, the materials based on origami tessellation at the molecular level have been significantly underexplored. Herein, we report a two-dimensional (2D) porphyrinic metal-organic framework (MOF), self-assembled from Zn nodes and flexible porphyrin linkers, displaying folding motions based on origami tessellation. A combined experimental and theoretical investigation demonstrated the origami mechanism of the 2D porphyrinic MOF, whereby the flexible linker acts as a pivoting point. The discovery of the 2D tessellation hidden in the 2D MOF unveils origami mechanics at the molecular level.

Symmetry-Mismatched SBU Transformation in MOFs: Postsynthetic Metal Exchange from Zn to Fe and Its Effects on Gas Adsorption and Dye Selectivity.

This research explores the alteration of metal-organic frameworks (MOFs) using a method called postsynthetic metal exchange. We focus on the shift from a Zn-based MOF containing a [Zn4O(COO)6] secondary building unit (SBU) of octahedral site symmetry (ANT-1(Zn)) to a Fe-based one with a [Fe3IIIO(COO)6]+ SBU of trigonal prismatic site symmetry (ANT-1(Fe)). The symmetry-mismatched SBU transformation cleverly maintains the MOF's overall structure by adjusting the conformation of the flexible 1,3,5-benzenetribenzoate linker to alleviate the framework strain. The process triggers a decrease in the framework volume and pore size alongside a change in the framework's charge. These alterations influence the MOF's ability to adsorb gas and dye. During the transformation, core-shell MOFs (ANT-1(Zn@Fe)) are formed as intermediate products, demonstrating unique gas sorption traits and adjusted dye adsorption preferences due to the structural modifications at the core-shell interface. Heteronuclear clusters, located at the framework interfaces, enhance the heat of CO2 adsorption. Furthermore, they also influence the selectivity of the dye size. This research provides valuable insights into fabricating novel MOFs with unique properties by modifying the SBU of a MOF with flexible organic linkers from one site symmetry to another.

Real-Space and Real-Time Propagation for Correlated Electron-Nuclear Dynamics Based on Exact Factorization.

We present coupled equations of motion for correlated electron-nuclear dynamics for real-space and real-time propagation with a proper electron-nuclear correlation (ENC) from the exact factorization. Since the original ENC term from the exact factorization is non-Hermitian, the numerical instability arises as we propagate an electronic wave function. In this paper, we propose a Hermitian-type ENC term which depends on the electron density matrix and the nuclear quantum momentum. Moreover, we show that the Hermitian property of the electron-nuclear correlation term can capture quantum (de)coherence with a stable numerical real-space and real-time propagation. As an application, we demonstrate a real-space and real-time propagation of an electronic wave function coupled to trajectory-based nuclear motion for a one-dimensional model Hamiltonian. Our approach can capture nonadiabatic phenomena as well as quantum decoherence in excited state molecular dynamics. In addition, we propose a scheme to extend the current approach to many-body electronic states based on real-time time-dependent density functional theory, testing the nonadiabatic dynamics of a simple molecular system.

Calculation of exciton couplings based on density functional tight-binding coupled to state-interaction state-averaged ensemble-referenced Kohn-Sham approach.

We introduce the combination of the density functional tight binding (DFTB) approach, including onsite correction (OC) and long-range corrected (LC) functional and the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method with extended active space involving four electrons and four orbitals [LC-OC-DFTB/SSR(4,4)], to investigate exciton couplings in multichromophoric systems, such as organic crystals and molecular aggregates. We employ the LC-OC-DFTB/SSR(4,4) method to calculate the excitonic coupling in anthracene and tetracene. As a result, the LC-OC-DFTB/SSR(4,4) method provides a reliable description of the locally excited (LE) state in a single chromophore and the excitonic couplings between chromophores with reasonable accuracy compared to the experiment and the conventional SSR(4,4) method. In addition, the thermal fluctuation of excitonic couplings from dynamic nuclear motion in an anthracene crystal with LC-OC-DFTB/SSR(4,4) shows a similar fluctuation of excitonic coupling and spectral density with those of first-principle calculations. We conclude that LC-OC-DFTB/SSR(4,4) is capable of providing reasonable features related to LE states, such as Frenkel exciton with efficient computational cost.

Atomic transistors based on seamless lateral metal-semiconductor junctions with a sub-1-nm transfer length.

The edge-to-edge connected metal-semiconductor junction (MSJ) for two-dimensional (2D) transistors has the potential to reduce the contact length while improving the performance of the devices. However, typical 2D materials are thermally and chemically unstable, which impedes the reproducible achievement of high-quality edge contacts. Here we present a scalable synthetic strategy to fabricate low-resistance edge contacts to atomic transistors using a thermally stable 2D metal, PtTe2. The use of PtTe2 as an epitaxial template enables the lateral growth of monolayer MoS2 to achieve a PtTe2-MoS2 MSJ with the thinnest possible, seamless atomic interface. The synthesized lateral heterojunction enables the reduced dimensions of Schottky barriers and enhanced carrier injection compared to counterparts composed of a vertical 3D metal contact. Furthermore, facile position-selected growth of PtTe2-MoS2 MSJ arrays using conventional lithography can facilitate the design of device layouts with high processability, while providing low contact resistivity and ultrashort transfer length on wafer scales.

Singlet Oxygen Generation from Polyaminoglycerol by Spin-Flip-Based Electron Transfer.

Reactive oxygen species have drawn attention owing to their strong oxidation ability. In particular, the singlet oxygen (1O2) produced by energy transfer is the predominant species for controlling oxidation reactions efficiently. However, conventional 1O2 generators, which rely on enhanced energy transfer, frequently suffer from poor solubility, low stability, and low biocompatibility. Herein, we introduce a hyperbranched aliphatic polyaminoglycerol (hPAG) as a 1O2 generator, which relies on spin-flip-based electron transfer. The coexistence of a lone pair electron on the nitrogen atom and a hydrogen-bonding donor (the protonated form of nitrogen and hydroxyl group) affords proximity between hPAG and O2. Subsequent direct electron transfer after photo-irradiation induces hPAG•+-O2 •- formation, and the following spin-flip process generates 1O2. The spin-flip-based electron transfer pathway is analyzed by a series of photophysical, electrochemical, and computational studies. The 1O2 generator, hPAG, is successfully employed in photodynamic therapy and as an antimicrobial reagent.

Independent trajectory mixed quantum-classical approaches based on the exact factorization.

Mixed quantum-classical dynamics based on the exact factorization exploits the "derived" electron-nuclear correlation (ENC) term, aiming for the description of quantum coherences. The ENC contains interactions between the phase of electronic states and nuclear quantum momenta, which depend on the spatial shape of the nuclear density. The original surface hopping based on the exact factorization (SHXF) [Ha et al., J. Phys. Chem. Lett. 9, 1097 (2018)] exploits frozen Gaussian functions to construct the nuclear density in the ENC term, while the phase of electronic states is approximated as a fictitious nuclear momentum change. However, in reality, the width of nuclear wave packets varies in time depending on the shape of potential energy surfaces. In this work, we present a modified SHXF approach and a newly developed Ehrenfest dynamics based on the exact factorization (EhXF) with time-dependent Gaussian functions and phases by enforcing total energy conservation. We perform numerical tests for various one-dimensional two-state model Hamiltonians. Overall, the time-dependent width of Gaussian functions and the energy conserving phase show a reliable decoherence compared to the original frozen Gaussian-based SHXF and the exact quantum mechanical calculation. In particular, the energy conserving phase is crucial for EhXF to reproduce the correct quantum dynamics.

Generalized Formulation of the Density Functional Tight Binding-Based Restricted Ensemble Kohn-Sham Method with Onsite Correction to Long-Range Correction.

We present a generalized formulation for the combination of the density functional tight binding (DFTB) approach and the state-interaction state-average spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method by considering onsite correction (OC) as well as the long-range corrected (LC) functional. The OC contribution provides more accurate energies and analytic gradients for individual microstates, while the multireference character of the SSR provides the correct description for conical intersections. We benchmark the LC-OC-DFTB/SSR method against various DFTB calculation methods for excitation energies and conical intersection structures with π/π* or n/π* characters. Furthermore, we perform excited-state molecular dynamics simulations with a molecular rotary motor with variations of LC-OC-DFTB/SSR approaches. We show that the OC contribution to the LC functional is crucial to obtain the correct geometry of conical intersections.

Spatial distribution modulation of mixed building blocks in metal-organic frameworks.

The placement of mixed building blocks at precise locations in metal-organic frameworks is critical to creating pore environments suitable for advanced applications. Here we show that the spatial distribution of mixed building blocks in metal-organic frameworks can be modulated by exploiting the different temperature sensitivities of the diffusion coefficients and exchange rate constants of the building blocks. By tuning the reaction temperature of the forward linker exchange from one metal-organic framework to another isoreticular metal-organic framework, core-shell microstructural and uniform microstructural metal-organic frameworks are obtained. The strategy can be extended to the fabrication of inverted core-shell microstructures and multi-shell microstructures and applied for the modulation of the spatial distribution of framework metal ions during the post-synthetic metal exchange process of a Zn-based metal-organic framework to an isostructural Ni-based metal-organic framework.

Proton affinity and gas phase basicity of diamandoid molecules: diamantane to C131H116.

Calculated proton affinities (PAs) and gas phase basicities (GPBs) are reported for diamantane (C14H20), triamantane (C18H24), 'globular and planar' isomers of tetramantane (C22H28) and pentamantane (C26H32), and for one 'globular' isomer of each of the larger diamondoid molecules: C51H58, C78H72, C102H90, and C131H116. Assuming CxHy as the parent diamondoid molecule, we calculated PA and GPB values for a variety of CxHy+1+ isomers, as well as for the reaction CxHy + H+ yielding CxHy-1+ + H2(g); the latter is slightly favored based on GPB values for diamantane through pentamantane, but less favored compared to certain CxHy+1+ isomers of C51H58, C102H90, and C131H116. Indeed, the GPB values of C51H58, C102H90, and C131H116 classifiy them as 'superbases'. Calculations that had the initial location of the proton in an interstitial site inside the diamondoid molecule always showed the H having moved to the outside of the diamondoid molecule; for this reason, we focused on testing a variety of initial configurations with the proton placed in an initial position on the surface. Additional protons were added to determine the limiting number that could be, per these calculations, taken up by the diamondoid molecules and the maximum number of protons are shown in parentheses: C14H20(2), C18H24(3), C22H28(3), C26H32(3), C51H58(4). Bader charge distributions obtained for CxHy+1+ isomers (for diamantane through pentamantane) suggest that the positive charge is essentially completely delocalized over all the H atoms. NMR spectra were calculated for different isomers of C14H19+, and compared to the published NMR spectrum for when diamantane was mixed with magic acid and H2(g) was produced.

Coupled- and Independent-Trajectory Approaches Based on the Exact Factorization Using the PyUNIxMD Package.

We present mixed quantum-classical approaches based on the exact factorization framework. The electron-nuclear correlation term in the exact factorization enables us to deal with quantum coherences by accounting for electronic and nuclear nonadiabatic couplings effectively within classical nuclei approximation. We compare coupled- and independent-trajectory approximations with each other to understand algorithms in description of the bifurcation of nuclear wave packets and the correct spatial distribution of electronic wave functions along with nuclear trajectories. Finally, we show numerical results for comparisons of coupled- and independent-trajectory approaches for the photoisomerization of a protonated Schiff base from excited state molecular dynamics (ESMD) simulations with the recently developed Python-based ESMD code, namely, the PyUNIxMD program.

PyUNIxMD: A Python-based excited state molecular dynamics package.

Theoretical/computational description of excited state molecular dynamics is nowadays a crucial tool for understanding light-matter interactions in many materials. Here we present an open-source Python-based nonadiabatic molecular dynamics program package, namely PyUNIxMD, to deal with mixed quantum-classical dynamics for correlated electron-nuclear propagation. The PyUNIxMD provides many interfaces for quantum chemical calculation methods with commercial and noncommercial ab initio and semiempirical quantum chemistry programs. In addition, the PyUNIxMD offers many nonadiabatic molecular dynamics algorithms such as fewest-switch surface hopping and its derivatives as well as decoherence-induced surface hopping based on the exact factorization (DISH-XF) and coupled-trajectory mixed quantum-classical dynamics (CTMQC) for general purposes. Detailed structures and flows of PyUNIxMD are explained for the further implementations by developers. We perform a nonadiabatic molecular dynamics simulation for a molecular motor system as a simple demonstration.

Study of the Decoherence Correction Derived from the Exact Factorization Approach for Nonadiabatic Dynamics.

We present a detailed study of the decoherence correction to surface hopping that was recently derived from the exact factorization approach. Ab initio multiple spawning calculations that use the same initial conditions and the same electronic structure method are used as a reference for three molecules: ethylene, the methaniminium cation, and fulvene, for which nonadiabatic dynamics follows a photoexcitation. A comparison with the Granucci-Persico energy-based decoherence correction and the augmented fewest-switches surface-hopping scheme shows that the three decoherence-corrected methods operate on individual trajectories in a qualitatively different way, but the results averaged over trajectories are similar for these systems.

pH-Responsive Amphiphilic Polyether Micelles with Superior Stability for Smart Drug Delivery.

Despite widespread interest in the amphiphilic polymeric micelles for drug delivery systems, it is highly desirable to achieve high loading capacity and high efficiency to reduce the side effects of therapeutic agents while maximizing their efficacy. Here, we present a novel hydrophobic epoxide monomer, cyclohexyloxy ethyl glycidyl ether (CHGE), containing an acetal group as a pH-responsive cleavable linkage. A series of its homopolymers, poly(cyclohexyloxy ethyl glycidyl ether)s (PCHGEs), and block copolymers, poly(ethylene glycol)-block-poly(cyclohexyloxy ethyl glycidyl ether)s (mPEG-b-PCHGE), were synthesized via anionic ring-opening polymerization in a controlled manner. Subsequently, the self-assembled polymeric micelles of mPEG-b-PCHGE demonstrated high loading capacity, excellent stability in biological media, tunable release efficiency, and high cell viability. Importantly, quantum mechanical calculations performed by considering prolonged hydrolysis of the acetal group in CHGE indicated that the CHGE monomer had higher hydrophobicity than three other functional epoxide monomer analogues developed. Furthermore, the preferential cellular uptake and in vivo therapeutic efficacy confirmed the enhanced stability and the pH-responsive degradation of the amphiphilic block copolymer micelles. This study provides a new platform for the development of versatile smart polymeric drug delivery systems with high loading efficiency and tailorable release profiles.

Machine Learning-Assisted Excited State Molecular Dynamics with the State-Interaction State-Averaged Spin-Restricted Ensemble-Referenced Kohn-Sham Approach.

We present a machine learning-assisted excited state molecular dynamics (ML-ESMD) based on the ensemble density functional theory framework. Since we represent a diabatic Hamiltonian in terms of generalized valence bond ansatz within the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS) method, we can avoid singularities near conical intersections, which are crucial in excited state molecular dynamics simulations. We train the diabatic Hamiltonian elements and their analytical gradients with the SchNet architecture to construct machine learning models, while the phase freedom of off-diagonal elements of the Hamiltonian is cured by introducing the phase-less loss function. Our machine learning models show reasonable accuracy with mean absolute errors of ∼0.1 kcal/mol and ∼0.5 kcal/mol/Šfor the diabatic Hamiltonian elements and their gradients, respectively, for penta-2,4-dieniminium cation. Moreover, by exploiting the diabatic representation, our models can predict correct conical intersection structures and their topologies. In addition, our ML-ESMD simulations give almost identical result with a direct dynamics at the same level of theory.

Self-Assembly of Mitochondria-Targeted Photosensitizer to Increase Photostability and Photodynamic Therapeutic Efficacy in Hypoxia.

The development of photosensitizers for cancer photodynamic therapy has been challenging due to their low photostability and therapeutic inefficacy in hypoxic tumor microenvironments. To overcome these issues, we have developed a mitochondria-targeted photosensitizer consisting of an indocyanine moiety with triphenylphosphonium arms, which can self-assemble into spherical micelles directed to mitochondria. Self-assembly of the photosensitizer resulted in a higher photostability by preventing free rotation of the indoline ring of the indocyanine moiety. The mitochondria targeting capability of the photosensitizer allowed it to utilize intramitochondrial oxygen. We found that the mitochondria-targeted photosensitizer localized to mitochondria and induced apoptosis of cancer cells both normoxic and hypoxic conditions through generation of ROS. The micellar self-assemblies of the photosensitizer were further confirmed to selectively localize to tumor tissues in a xenograft tumor mouse model through passive targeting and showed efficient tumor growth inhibition.