Cobaltocenium derivatives have shown great potential as components of anion exchange membranes in fuel cells because they exhibit excellent thermal and alkaline stability under operating conditions while allowing for high anion mobility. The properties of the cobaltocenium-anion complexes can be chemically tuned through the substituent groups on the cyclopentadienyl (Cp) rings of the cation CoCp2+. However, the synthesis and characterization of the full range of possible derivatives are very challenging and time-consuming, and while the computational tools can greatly expedite this process, full screening of the electronic structure at a high level of theory is still computationally intensive. Therefore, in this work, we consider the machine learning (ML) modeling as a tool of predicting stability of disubstituted [CoCp2]OH complexes measured by their bond-dissociation energy (BDE). The relevant process here is the dissociation of the cobaltocenium-hydroxide complex into fragments [CoCpY']OH and CpY, where Y and Y' each represent one out of 42 substituent groups of experimental interest. In agreement with the previous ML study of 120 mono- and selected disubstituted species [Wetthasinghe et al. J. Chem. Phys. A (2022) 126], our analysis of the data set expanded to all possible disubstituted cobaltoceniums, points to the highest occupied and lowest unoccupied molecular orbitals, along with the Hirshfeld charge on the singly substituted benzene, to be the key features predicting the BDE of the unseen complexes. Based on the examination of the outliers, the acidity of substituents ((CO)NH2 in our case) is found to be of special significance for the cobaltocenium stability and for the model development. Moreover, we demonstrate that upon the data set refinement, the conventional ML models are capable of predicting the BDE close to 1 kcal/mol based on the properties of just the fragments, thereby greatly reducing the total number of species and of the computational time of each calculation. Such fragment-based "combinatorial" approach to the BDE modeling is noteworthy, since the geometry optimization of complexes in solution is conceptually challenging and computationally demanding, even when leveraging high-performance computing resources.
Polymers incorporating cobaltocenium groups have received attention as promising components of anion-exchange membranes (AEMs), exhibiting a good balance of chemical stability and high ionic conductivity. In this work, we analyze the hydroxide diffusion in the presence of cobaltocenium cations in an aqueous environment based on the molecular dynamics of model systems confined in one dimension to mimic the AEM channels. In order to describe the proton hopping mechanism, the forces are obtained from the electronic structure computed at the density-functional tight-binding level. We find that the hydroxide diffusion depends on the channel size, modulation of the electrostatic interactions by the solvation shell, and its rearrangement ability. Hydroxide diffusion proceeds via both the vehicular and structural diffusion mechanisms with the latter playing a larger role at low diffusion coefficients. The highest diffusion coefficient is observed under moderate water densities (around half the density of liquid water) when there are enough water molecules to form the solvation shell, reducing the electrostatic interaction between ions, yet there is enough space for the water rearrangements during the proton hopping. The effects of cobaltocenium separation, orientation, chemical modifications, and the role of nuclear quantum effects are also discussed.
Cooperative behavior and orthogonal responses of two classes of coordinatively integrated photochromic molecules towards distinct external stimuli were demonstrated on the first example of a photo-thermo-responsive hierarchical platform. Synergetic and orthogonal responses to temperature and excitation wavelength are achieved by confining the stimuli-responsive moieties within a metal-organic framework (MOF), leading to the preparation of a novel photo-thermo-responsive spiropyran-diarylethene based material. Synergistic behavior of two photoswitches enables the study of stimuli-responsive resonance energy transfer as well as control of the photoinduced charge transfer processes, milestones required to advance optoelectronics development. Spectroscopic studies in combination with theoretical modeling revealed a nonlinear effect on the material electronic structure arising from the coordinative integration of photoresponsive molecules with distinct photoisomerization mechanisms. Thus, the reported work covers multivariable facets of not only fundamental aspects of photoswitch cooperativity, but also provides a pathway to modulate photophysics and electronics of multidimensional functional materials exhibiting thermo-photochromism.
We present a quantum dynamics approach for molecular systems based on wave function factorization into components describing the light and heavy particles, such as electrons and nuclei. The dynamics of the nuclear subsystem can be viewed as motion of the trajectories defined in the nuclear subspace, evolving according to the average nuclear momentum of the full wave function. The probability density flow between the nuclear and electronic subsystems is facilitated by the imaginary potential, derived to ensure a physically meaningful normalization of the electronic wave function for each configuration of the nuclei, and conservation of the probability density associated with each trajectory in the Lagrangian frame of reference. The imaginary potential, defined in the nuclear subspace, depends on the momentum variance in the nuclear coordinates averaged over the electronic component of the wave function. An effective real potential, driving the dynamics of the nuclear subsystem, is defined to minimize motion of the electronic wave function in the nuclear degrees of freedom. Illustration and the analysis of the formalism are given for a two-dimensional model system of vibrationally nonadiabatic dynamics.
Confinement-imposed photophysics was probed for novel stimuli-responsive hydrazone-based compounds demonstrating a conceptual difference in their behavior within 2D versus 3D porous matrices for the first time. The challenges associated with photoswitch isomerization arising from host interactions with photochromic compounds in 2D scaffolds could be overcome in 3D materials. Solution-like photoisomerization rate constants were realized for sterically demanding hydrazone derivatives in the solid state through their coordinative immobilization in 3D scaffolds. According to steady-state and time-resolved photophysical measurements and theoretical modeling, this approach provides access to hydrazone-based materials with fast photoisomerization kinetics in the solid state. Fast isomerization of integrated hydrazone derivatives allows for probing and tailoring resonance energy transfer (ET) processes as a function of excitation wavelength, providing a novel pathway for ET modulation.
Herein, we report structural, computational, and conductivity studies on urea-directed self-assembled iodinated triphenylamine (TPA) derivatives. Despite numerous reports of conductive TPAs, the challenges of correlating their solid-state assembly with charge transport properties hinder the efficient design of new materials. In this work, we compare the assembled structures of a methylene urea bridged dimer of di-iodo TPA (1) and the corresponding methylene urea di-iodo TPA monomer (2) with a di-iodo mono aldehyde (3) control. These modifications lead to needle shaped crystals for 1 and 2 that are organized by urea hydrogen bonding, πâ¯π stacking, Iâ¯I, and Iâ¯π interactions as determined by SC-XRD, Hirshfeld surface analysis, and X-ray photoelectron spectroscopy (XPS). The long needle shaped crystals were robust enough to measure the conductivity by two contact probe methods with 2 exhibiting higher conductivity values (â¼6 × 10-7 S cm-1) compared to 1 (1.6 × 10-8 S cm-1). Upon UV-irradiation, 1 formed low quantities of persistent radicals with the simple methylurea 2 displaying less radical formation. The electronic properties of 1 were further investigated using valence band XPS, which revealed a significant shift in the valence band upon UV irradiation (0.5-1.9 eV), indicating the potential of these materials as dopant free p-type hole transporters. The electronic structure calculations suggest that the close packing of TPA promotes their electronic coupling and allows effective charge carrier transport. Our results show that ionic additives significantly improve the conductivity up to â¼2.0 × 10-6 S cm-1 in thin films, enabling their implementation in functional devices such as perovskite or solid-state dye sensitized solar cells.
An improved understanding of the P450 structure is relevant to the development of biomimetic catalysts and inhibitors for controlled CH-bond activation, an outstanding challenge of synthetic chemistry. Motivated by the experimental findings of an unusually short Fe-S bond of 2.18 Å for the wild-type (WT) OleT P450 decarboxylase relative to a cysteine pocket mutant form (A369P), a computational model that captures the effect of the thiolate axial ligand on the iron-sulfur distance is presented. With the computational efficiency and streamlined analysis in mind, this model combines a cluster representation of the enzymeâ40-110 atoms, depending on the heme and ligand truncation levelâwith a density functional theory (DFT) description of the electronic structure (ES) and is calibrated against the experimental data. The optimized Fe-S distances show a difference of 0.25 Å between the low and high spin states, in agreement with the crystallographic structures of the OleT WT and mutant forms. We speculate that this difference is attributable to the packing of the ligand; the mutant is bulkier due to an alanine-to-proline replacement, meaning that it is excluded from the energetically favored low-spin minimum because of steric constraints. The presence of pure spin-state pairs and the intersection of the low/high spin states for the enzyme model is indicative of the limitations of single-reference ES methods in such systems and emphasizes the significance of using the proper state when modeling the hydrogen atom transfer (HAT) reaction catalyzed by OleT. At the same time, the correct characterization of both the short and long Fe-S bonds within a small DFT-based model of 42 atoms paves the way for quantum dynamics modeling of the HAT step, which initiates the OleT decarboxylation reaction.
Heme , Iron , Cysteine/chemistry , Density Functional Theory , Heme/chemistry , Iron/chemistry , Ligands
Using a combination of experimental studies, theory, simulation, and modeling, we investigate the hydrogen atom transfer (HAT) reaction by the high-valent ferryl cytochrome P450 (CYP) intermediate known as Compound I, a species that is central to innumerable and important detoxification and biosynthetic reactions. The P450 decarboxylase known as OleT converts fatty acids, a sustainable biological feedstock, into terminal alkenes and thus is of high interest as a potential means to produce fungible biofuels. Previous experimental work has established the intermediacy of Compound I in the CâC scission reaction catalyzed by OleT and an unprecedented ability to monitor the HAT process in the presence of bound fatty acid substrates. Here, we leverage the kinetic simplicity of the OleT system to measure the activation barriers for CYP HAT and the temperature dependence of the substrate 2H kinetic isotope effect. Notably, neither measurement has been previously accessible for a CYP to date. Theoretical analysis alludes to the significance of substrate fatty acid coordination for generating the hydrogen donor/acceptor configurations that are most conducive for HAT to occur. The analysis of the two-dimensional potential energy surface, based on multireference electronic wave functions, illustrates the uncoupled character of the hydrogen motion. Quantum dynamics calculations along the hydrogen reaction path demonstrate that hydrogen tunneling is essential to qualitatively capture the experimental isotope effect, its temperature dependence, and appropriate activation energies. Overall, a more fundamental understanding of the OleT reaction coordinate contributes to the development of biomimetic catalysts for controlled CâH bond activation, an outstanding current challenge for (bio)synthetic chemistry.
Carboxy-Lyases , Cytochrome P-450 Enzyme System , Carboxy-Lyases/metabolism , Cytochrome P-450 Enzyme System/chemistry , Fatty Acids/chemistry , Hydrogen/chemistry , Isotopes , Kinetics
Cationic cobaltocenium derivatives are promising components of the anion exchange membranes because of their excellent thermal and alkaline stability under the operating conditions of a fuel cell. Here, we present an efficient modeling approach to assessing the chemical stability of substituted cobaltocenium CoCp2+, based on the computed electronic structure enhanced by machine learning techniques. Within the aqueous environment, the positive charge of the metal cation is balanced by the hydroxide anion through formation of the CoCp2+OH- complexes, whose dissociation is studied within the implicit solvent employing the density functional theory. The data set of about 118 the CoCp2+OH- complexes based on 42 substituent groups characterized by a range of electron-donating (ED) and electron-withdrawing (EW) properties is constructed and analyzed. Given 12 carefully chosen chemistry-informed descriptors of the complexes and relevant fragments, the stability of the complexes is found to strongly correlate with the energies of the highest occupied and lowest unoccupied molecular orbitals, modulated by a switching function of the Hirshfeld charge. The latter is used as a measure of the electron-withdrawing-donating character of the substituents. On the basis of this observation from the conventional regression analysis, two fully connected, feed-forward neural network (FNN) models with different unit structures, called the chemistry-informed (CINN) and the quadratic (QNN) neural networks, together with a support vector regression (SVR) model are developed. Both deep neural network models predict the bond dissociation energies of the cobaltocenium complexes with mean relative errors less than 10.56% and average absolute errors less than 1.63 kcal/mol, superior to the conventional regression and the SVR model prediction. The results show the potential of QNN to efficiently capture more complex relationships. The concept of incorporating the domain (chemical) knowledge/insight into the neural network structure paves the way to applications of machine learning techniques with small data sets, ultimately leading to better predictive models compared to the classical machine learning method SVR and conventional regression analysis.
Cobalt , Contraceptives, Oral, Combined , Electrons , Female , Humans , Machine Learning , Neural Networks, Computer
Metallocenium cations, used as a component in an anion exchange membrane of a fuel cell, demonstrate excellent thermal and alkaline stability, which can be improved by the chemical modification of the cyclopentadienyl rings with substituent groups. In this work, the relation between the bond dissociation energy (BDE) of the cobaltocenium (CoCp2+) derivatives, used as a measure of the cation stability, and chemistry-informed descriptors obtained from the electronic structural calculations is established. The analysis of 12 molecular descriptors for 118 derivatives reveals a nonlinear dependence of the BDE on the electron donating-withdrawing character of the substituent groups coupled to the energy of the frontier molecular orbitals. A chemistry-informed feed-forward neural network trained using k-fold cross-validation over the modest data set is able to predict the BDE from the molecular descriptors with the mean absolute error of about 1 kcal/mol. The theoretical analysis suggests some promising modifications of cobaltocenium for experimental research. The results demonstrate that even for modest data sets the incorporation of the chemistry knowledge into the neural network architecture, e.g., through mindful selection and screening of the descriptors and their interactions, paves the way to gain new insight into molecular properties.
The efficient delivery of reactive and toxic gaseous reagents to organic reactions was studied using metal-organic frameworks (MOFs). The simultaneous cargo vehicle and catalytic capabilities of several MOFs were probed for the first time using the examples of aromatization, aminocarbonylation, and carbonylative Suzuki-Miyaura coupling reactions. These reactions highlight that MOFs can serve a dual role as a gas cargo vehicle and a catalyst, leading to product formation with yields similar to reactions employing pure gases. Furthermore, the MOFs can be recycled without sacrificing product yield, while simultaneously maintaining crystallinity. The reported findings were supported crystallographically and spectroscopically (e.g., diffuse reflectance infrared Fourier transform spectroscopy), foreshadowing a pathway for the development of multifunctional MOF-based reagent-catalyst cargo vessels for reactive gas reagents as an attractive alternative to the use of toxic pure gases or gas generators.
Absorption of electronic acceptors in the accessible channels of an assembled triphenylamine (TPA) bis-urea macrocycle 1 enabled the study of electron transfer from the walls of the TPA framework to the encapsulated guests. The TPA host is isoskeletal in all host-guest structures analyzed with guests 2,1,3-benzothiadiazole, 2,5-dichlorobenzoquinone and I2 loading in single-crystal-to-single-crystal transformations. Analysis of the crystal structures highlights how the spatial proximity and orientation of the TPA host and the entrapped guests influence their resulting photophysical properties and allow direct comparison of the different donor-acceptor complexes. Diffuse reflectance spectroscopy shows that upon complex formation 1·2,5-dichlorobenzoquinone exhibits a charge transfer (CT) transition. Whereas, the 1·2,1,3-benzothiadiazole complex undergoes a photoinduced electron transfer (PET) upon irradiation with 365 nm LEDs. The CT absorptions were also identified with the aid of time dependent density functional theory (TD-DFT) calculations. Cyclic voltammetry experiments show that 2,1,3-benzothiadiazole undergoes reversible reduction within the host-guest complex. Moreover, the optical band gaps of the host 1·2,5-dichlorobenzoquinone (1.66 eV), and host 1·2,1,3-benzothiadiazole (2.15 eV) complexes are significantly smaller as compared to the free host 1 material (3.19 eV). Overall, understanding this supramolecular electron transfer strategy should pave the way towards designing lower band gap inclusion complexes.
The Madelung-de Broglie-Bohm formulation of the Schrödinger equation casts the time-evolution of a wave function as dynamics of an ensemble of quantum, or Bohmian, trajectories, interacting via the nonlocal quantum potential. This trajectory perspective gives insight into the quantumness (or classicality) of a given system due to clear partitioning of the energy into classical and quantum components. Here, we propose a system-independent measure of the quantumness of dynamics, based on the energy time-change, referred to as "quantum power". This measure is local in the coordinate space. Based on applications to model chemical systems, we argue that during the transition from the quantum to classical regime, defined as compression of quantization, the quantum features in dynamics do not "disappear" but are pushed forward in time. This feature may be used to gauge the validity of the semiclassical and other approximate dynamics approaches in applications to anharmonic systems.
Unprecedented one-step C[double bond, length as m-dash]C bond cleavage leading to opening of the buckybowl (π-bowl), that could provide access to carbon-rich structures with previously inaccessible topologies, is reported; highlighting the possibility to implement drastically different synthetic routes to π-bowls in contrast to conventional ones applied for polycyclic aromatic hydrocarbons. Through theoretical modeling, we evaluated the mechanistic pathways feasible for π-bowl planarization and factors that could affect such a transformation including strain and released energies. Through employment of Marcus theory, optical spectroscopy, and crystallographic analysis, we estimated the possibility of charge transfer and electron coupling between "open" corannulene and a strong electron acceptor such as 7,7,8,8-tetracyanoquinodimethane. Alternative to a one-pot solid-state corannulene "unzipping" route, we reported a nine-step solution-based approach for preparation of novel planar "open" corannulene-based derivatives in which electronic structures and photophysical profiles were estimated through the energies and isosurfaces of the frontier natural transition orbitals.
Herein we probe the effects of crystalline structure and geometry on benzophenone photophysics, self-quenching, and the regenerable formation of persistent triplet radical pairs at room temperature. Radical pairs are not observed in solution but appear via an emergent pathway within the solid-state assembly. Single crystal X-ray diffraction (SC-XRD) of two sets of constitutional isomers, benzophenone bis-urea macrocycles, and methylene urea-tethered dibenzophenones are compared. Upon irradiation with 365 nm light-emitting diodes (LEDs), each forms photogenerated radicals as monitored by electron paramagnetic resonance (EPR). Once generated, the radicals exhibit half-lives from 2 to 60 days before returning to starting material without degradation. Re-exposure to light regenerates the radicals with similar efficiency. Subtle differences in the structure of the crystalline frameworks modulates the maximum concentration of photogenerated radicals, phosphorescence quantum efficiency (φ), and n-type self-quenching as observed using laser flash photolysis (LFP). These studies along with the electronic structure analysis based on the time-dependent density functional theory (TD-DFT) suggest the microenvironment surrounding benzophenone largely dictates the favorability of self-quenching or radical formation and affords insights into structure/function correlations. Advances in understanding how structure determines the excited state pathway solid-state materials undertake will aid in the design of new radical initiators, components of OLEDs, and NMR polarizing agents.
An efficient basis representation of time-dependent wavefunctions is essential for theoretical studies of high-dimensional molecular systems exhibiting large-amplitude motion. For fully coupled anharmonic systems, the complexity of a general wavefunction scales exponentially with the system size; therefore, for practical reasons, it is desirable to adapt the basis to the time-dependent wavefunction at hand. Often times on this quest for a minimal basis representation, time-dependent Gaussians are employed, in part because of their localization in both configuration and momentum spaces and also because of their direct connection to classical and semiclassical dynamics, guiding the evolution of the basis function parameters. In this work, the quantum-trajectory guided adaptable Gaussian (QTAG) bases method [ J. Chem. Theory Comput. 2020, 16, 18-34] is generalized to include correlated, i.e., non-factorizable, basis functions, and the performance of the QTAG dynamics is assessed on benchmark system/bath tunneling models of up to 20 dimensions. For the popular choice of initial conditions describing tunneling between the reactant/product wells, the minimal "semiclassical" description of the bath modes using essentially a single multidimensional basis function combined with the multi-Gaussian representation of the tunneling mode is shown to capture the dominant features of dynamics in a highly efficient manner.
Photophysics tunability through alteration of framework aperture (metal-organic framework (MOF) = variable; guest = constant) was probed for the first time in comparison with previously explored concepts (MOF = constant; guest = variable). In particular, analysis of the confinement effect on a photophysical response of integrated 5-(3-chlorobenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one (Cl-BI) chromophore allowed us to establish a photophysics-aperture relationship. To shed light on the observed correlation, the framework confined environment was replicated using a molecular cage, Pd6(TPT)4 (TPT = 2,4,6-tri(pyridin-4-yl)-1,3,5-triazine), thus allowing for utilization of crystallography, spectroscopy, and theoretical simulations to reveal the effect a confined space has on the chromophore's molecular conformation (including disruption of strong hydrogen bonding and novel conformer formation) and any associated changes on a photophysical response. Furthermore, the chosen Cl-oHBI@Pd6(TPT)4 (Cl-oHBI = 5-(5-chloro-2-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one, chromophore) system was applied as a tool for targeted cargo delivery of a chromophore to the confined space of DNA, which resulted in promotion of chromophore-DNA interactions through a well-established intercalation mechanism. Moreover, the developed principles were applied toward utilizing a HBI-based chromophore as a fluorescent probe on the example of macrophage cells. For the first time, suppression of non-radiative decay pathways of a chromophore was tested by anchoring the chromophore to a framework metal node, portending a potential avenue to develop an alternative to natural biomarkers. Overall, these studies are among the first attempts to demonstrate the unrevealed potential of a confined scaffold environment for tailoring a material's photophysical response.
DNA/chemistry , Fluorescent Dyes/chemistry , Imidazoles/chemistry , Metal-Organic Frameworks/chemistry , Triazines/chemistry , Fluorescent Dyes/radiation effects , HeLa Cells , Humans , Imidazoles/radiation effects , Intercalating Agents/chemistry , Intercalating Agents/radiation effects , Light , Molecular Conformation
The effect of donor (D)-acceptor (A) alignment on the materials electronic structure was probed for the first time using novel purely organic porous crystalline materials with covalently bound two- and three-dimensional acceptors. The first studies towards estimation of charge transfer rates as a function of acceptor stacking are in line with the experimentally observed drastic, eight-fold conductivity enhancement. The first evaluation of redox behavior of buckyball- or tetracyanoquinodimethane-integrated crystalline was conducted. In parallel with tailoring the D-A alignment responsible for "static" changes in materials properties, an external stimulus was applied for "dynamic" control of the electronic profiles. Overall, the presented D-A strategic design, with stimuli-controlled electronic behavior, redox activity, and modularity could be used as a blueprint for the development of electroactive and conductive multidimensional and multifunctional crystalline porous materials.
Metal node engineering in combination with modularity, topological diversity, and porosity of metal-organic frameworks (MOFs) could advance energy and optoelectronic sectors. In this study, we focus on MOFs with multinuclear heterometallic nodes for establishing metal-property trends, i.e., connecting atomic scale changes with macroscopic material properties by utilization of inductively coupled plasma mass spectrometry, conductivity measurements, X-ray photoelectron and diffuse reflectance spectroscopies, and density functional theory calculations. The results of Bader charge analysis and studies employing the Voronoi-Dirichlet partition of crystal structures are also presented. As an example of frameworks with different nodal arrangements, we have chosen MOFs with mononuclear, binuclear, and pentanuclear nodes, primarily consisting of first-row transition metals, that are incorporated in HHTP-, BTC-, and NIP-systems, respectively (HHTP3- = triphenylene-2,3,6,7,10,11-hexaone; BTC3- = 1,3,5-benzenetricarboxylate; and NIP2- = 5-nitroisophthalate). Through probing framework electronic profiles, we demonstrate structure-property relationships, and also highlight the necessity for both comprehensive analysis of trends in metal properties, and novel avenues for preparation of heterometallic multinuclear isoreticular structures, which are critical components for on-demand tailoring of properties in heterometallic systems.
The computational cost of describing a general quantum system fully coupled by anharmonic interactions scales exponentially with the system size. Thus, an efficient basis representation of wave functions is essential, and when it comes to the large-amplitude motion of high-dimensional systems, the dynamic bases of Gaussian functions are often employed. The time dependence of such bases is determined from the variational principle or from classical dynamics; the former is challenging in implementation due to singular matrices, while the latter may not cover the configuration space relevant to quantum dynamics. Here we describe a method using Quantum Trajectory-guided Adaptable Gaussian (QTAG) bases "tuned"-including the basis position, phase, and width-to the wave function evolution, thanks to the continuity of the probability density in the course of the quantum trajectory dynamics. Thus, an efficient basis in configuration space is generated, bypassing the variational equations on the parameters of the Gaussians. We also propose a time propagator with basis transformation by projections which lends efficiency and stability to the QTAG dynamics, as demonstrated on standard tests and the ammonia inversion model.
