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We define a nomenclature for the classification of porous organic cage molecules, enumerating the 20 most probable topologies, 12 of which have been synthetically realised to date. We then discuss the computational challenges encountered when trying to predict the most likely topological outcomes from dynamic covalent chemistry (DCC) reactions of organic building blocks. This allows us to explore the extent to which comparing the internal energies of possible reaction outcomes is successful in predicting the topology for a series of 10 different building block combinations.

We present the first unconstrained nonadiabatic molecular dynamics (NAMD) simulations of photocatalytic water oxidation by small hydrated TiO2 nanoparticles using Tully surface hopping and time-dependent density functional theory. The results indicate that ultrafast electron–proton transfer from physisorbed water to the photohole initiates the photo-oxidation on the S1 potential energy surface. The new mechanism readily explains the observation of mobile hydroxyl radicals in recent experiments. Two key driving forces for the photo-oxidation reaction are identified: localization of the electron–hole pair and stabilization of the photohole by hydrogen bonding interaction. Our findings illustrate the scope of recent advances in NAMD methods and emphasize the importance of explicit simulation of electronic excitations.

Supramolecular self-assembly has allowed the synthesis of beautiful and complex molecular architectures, such as cages, macrocycles, knots, catenanes, and rotaxanes. We focus here on porous organic cages, which are molecules that have an intrinsic cavity and multiple windows. These cages have been shown to be highly effective at molecular separations and encapsulations. We investigate the possibility of complexes where one cage sits within the cavity of another. We term this a `nested cage' complex. The design of such complexes is highly challenging, so we use computational screening to explore 8712 different pair combinations, running almost 0.5M calculations to sample the phase space of the cage conformations. Through analysing the binding energies of the assemblies, we identify highly energetically favourable pairs of cages in nested cage complexes. The vast majority of the most favourable complexes include the large imine cage reported by Gawronski and co-workers using a [8+12] reaction of 4-tert-butyl-2,6-diformylphenol and cis,cis-1,3,5-triaminocyclohexane. The most energetically favourable nested cage complex combines the Gawronski cage with a dodecaamide cage that has six vertices, which can sit in the six windows of the larger cage. We also identify cages that have favourable binding energies for self-catenation.

A structurally diverse family of 39 covalent triazine-based framework materials (CTFs) is synthesized by Suzuki-Miyaura polycondensation and tested as hydrogen evolution photocatalysts using a high-throughput workflow. The two best-performing CTFs are based on benzonitrile and dibenzo[b,d]thiophene sulfone linkers, respectively, with catalytic activities that are among the highest for this material class. The activities of the different CTFs are rationalized in terms of four variables: the predicted electron affinity, the predicted ionization potential, the optical gap, and the dispersibility of the CTFs particles in solution, as measured by optical transmittance. The electron affinity and dispersibility in solution are the best predictors of photocatalytic hydrogen evolution activity.

A completely unsymmetrical porous organic cage was synthesized from a C2v symmetrical building block that was identified by a computational screen. The cage was formed through a 12-fold imine condensation of a tritopic C2v symmetric trialdehyde with a di-topic C2 symmetric diamine in a [4+6] reaction. The cage was rigid and microporous, as predicted by the simulations, with an apparent Brunauer-Emmett-Teller surface area of 578 m2 g-1. The reduced symmetry of the tritopic building block relative to its topicity meant there were 36 possible structural isomers of the cage. Experimental characterization suggests a single isomer with 12 unique imine environments, but techniques such as NMR could not conclusively identify the isomer. Computational structural and electronic analysis of the possible isomers was used to identify the most likely candidates, and hence to construct a 3-dimensional model of the amorphous solid. The rational design of unsymmetrical cages using building blocks with reduced symmetry offers new possibilities in controlling the degree of crystallinity, porosity, and solubility, of self-assembled materials.

An evolutionary algorithm is developed and used to search for shape persistent porous organic cages., The chemical and structural space of possible molecular materials is enormous, as they can, in principle, be built from any combination of organic building blocks. Here we have developed an evolutionary algorithm (EA) that can assist in the efficient exploration of chemical space for molecular materials, helping to guide synthesis to materials with promising applications. We demonstrate the utility of our EA to porous organic cages, predicting both promising targets and identifying the chemical features that emerge as important for a cage to be shape persistent or to adopt a particular cavity size. We identify that shape persistent cages require a low percentage of rotatable bonds in their precursors (

The hydrogen evolution activity of a polymeric photocatalyst was maximised by co-polymerisation, using both experimental and computational screening, for a family of 1,4-phenylene/2,5-thiophene co-polymers. The photocatalytic activity is the product of multiple material properties that are affected in different ways by the polymer composition and microstructure. For the first time, the photocatalytic activity was shown to be a function of the arrangement of the building blocks in the polymer chain as well as the overall composition. The maximum in hydrogen evolution for the co-polymer series appears to result from a trade-off between the fraction of light absorbed and the thermodynamic driving force for proton reduction and sacrificial electron donor oxidation, with the co-polymer of p-terphenyl and 2,5-thiophene showing the highest activity.

We propose a general high-throughput virtual screening approach for the optical and electronic properties of conjugated polymers. This approach makes use of the recently developed xTB family of low-computational-cost density functional tight-binding methods from Grimme and co-workers, calibrated here to (TD-)DFT data computed for a representative diverse set of (co-)polymers. Parameters drawn from the resulting calibration using a linear model can then be applied to the xTB derived results for new polymers, thus generating near DFT-quality data with orders of magnitude reduction in computational cost. As a result, after an initial computational investment for calibration, this approach can be used to quickly and accurately screen on the order of thousands of polymers for target applications. We also demonstrate that the (opto)electronic properties of the conjugated polymers show only a very minor variation when considering different conformers and that the results of high-throughput screening are therefore expected to be relatively insensitive with respect to the conformer search methodology applied.

A tool for the automated assembly, molecular optimization and property calculation of supramolecular materials is presented. stk is a modular, extensible and open‐source Python library that provides a simple Python API and integration with third party computational codes. stk currently supports the construction of linear polymers, small linear oligomers, organic cages in multiple topologies and covalent organic frameworks (COFs) in multiple framework topologies, but is designed to be easy to extend to new, unrelated, supramolecules or new topologies. Extension to metal–organic frameworks (MOFs), metallocycles or supramolecules, such as catenanes, would be straightforward. Through integration with third party codes, stk offers the user the opportunity to explore the potential energy landscape of the assembled supramolecule and then calculate the supramolecule's structural features and properties. stk provides support for high‐throughput screening of large batches of supramolecules at a time. The source code of the program can be found at https://github.com/supramolecular-toolkit/stk. © 2018 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

We study the vertical and adiabatic ionization potentials and electron affinities of bare and hydroxylated TiO

As also observed for conventional silicate glasses, water can be incorporated in the bulk interstitial regions of a bioactive glass (BG) matrix during the glass preparation and/or upon exposure to an aqueous environment. However, in the case of BGs, very little is known about the effect of hydration on the bulk structure, and then on key properties of these materials, such as biodegradation and bioactivity, that depend on the bulk structure itself. Here we employ a combination of atomistic simulation techniques to explore the nature and effects of water–BG interactions in the bulk of a bioactive glass. The fate of water inserted in the bulk interstitial region of 45S5 bioglass has been studied by ab initio geometry relaxations and Molecular Dynamics (AIMD) simulations. We probed the interaction of a water molecule with silica rings and cages of different size, as well as the stability of potentially relevant configurations involving manually dissociated water and opened rings. The local stability of selected configurations was further assessed by subjecting them to AIMD runs, in order to overcome possible kinetic barriers for water diffusion and dissociation. Small rings do not appear as favourable absorption sites in the bulk of a bioactive glass as they are for bioinert glasses. Moreover, water dissociation through rupture of Si–O bonds of silica rings formed in the bulk was thermodynamically unfavourable. However, a high-temperature AIMD run led to a dissociated state involving no broken Si–O bonds and a free hydroxyl: because re-optimization of this state produced the most favourable hydration energy identified in this study, dissociative absorption through this mechanism appears a likely outcome of the water–45S5 interaction at low water content. We discuss the structural and dynamical basis for the stability of this and other water–glass adducts identified, and the potential consequences of these interactions for the behaviour of the glass in a biological context.

Nonadiabatic molecular dynamics simulations suggest an excited state electron proton transfer mechanism and explain the observation of mobile hydroxyl radicals., We present the first unconstrained nonadiabatic molecular dynamics (NAMD) simulations of photocatalytic water oxidation by small hydrated TiO2 nanoparticles using Tully surface hopping and time-dependent density functional theory. The results indicate that ultrafast electron–proton transfer from physisorbed water to the photohole initiates the photo-oxidation on the S1 potential energy surface. The new mechanism readily explains the observation of mobile hydroxyl radicals in recent experiments. Two key driving forces for the photo-oxidation reaction are identified: localization of the electron–hole pair and stabilization of the photohole by hydrogen bonding interaction. Our findings illustrate the scope of recent advances in NAMD methods and emphasize the importance of explicit simulation of electronic excitations.

We investigate using a computational approach the physical and chemical processes underlying the application of organic (macro)molecules as fluorescence quenching sensors for explosives sensing. We concentrate on the use of amine molecular cages to sense nitroaromatic analytes, such as picric acid and 2,4-dinitrophenol, through fluorescence quenching. Our observations for this model system hold for many related systems. We consider the different possible mechanisms of fluorescence quenching: Förster resonance energy transfer, Dexter energy transfer and photoinduced electron transfer, and show that in the case of our model system, the fluorescence quenching is driven by the latter and involves stable supramolecular sensor-analyte host-guest complexes. Furthermore, we demonstrate that the experimentally observed selectivity of amine molecular cages for different explosives can be explained by the stability of these host-guest complexes and discuss how this is related to the geometry of the binding site in the sensor. Finally, we discuss what our observations mean for explosive sensing by fluorescence quenching in general and how this can help in future rational design of new supramolecular detection systems.

Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285In this chapter, we will rst review possible computational methods and then their applications in modeling the photochemistry and physics of nanostructures.

In this mini-review, we discuss what insight computational modelling can provide into the working of photocatalysts for solar fuel synthesis and how calculations can be used to screen for new promising materials for photocatalytic water splitting and carbon dioxide reduction. We will extensively discuss the different relevant (material) properties and the computational approaches (DFT, TD-DFT, GW/BSE) available to model them. We illustrate this with examples from the literature, focussing on polymeric and nanoparticle photocatalysts. We finish with a perspective on the outstanding conceptual and computational challenges.

The excitation energies of the four lowest-lying singlet excited states of the TiO2, Ti2O4, and Ti3O6 clusters are calculated by a variety of different Equation-of-Motion Coupled Cluster (EOM-CC) approaches in order to obtain benchmark values for the optical excitations of titanium dioxide clusters. More specifically we investigate what the effect is of the inclusion of triple excitations “triples” in the (EOM-)CC scheme on the calculated excited states of the clusters. While for the monomer and dimer the inclusion of triples is found to only cause a rigid shift in the excitation energies, in the case of the trimer the crossing of the excited states is observed. Coupled cluster approaches where triples are treated perturbatively were found to offer no advantage over EOM-CCSD, whereas the active-space methods (EOM-CCSDt(II/I)) were demonstrated to yield results very close to full EOM-CCSDT, but at a much reduced computational cost.

The reactivity of bioglasses, which is related to the dissolution of cations and orthosilicate groups in the physiological fluid, strongly depends on the key structural features present at the glass surfaces. On the basis of the composition and the synthetic routes employed to make the glass, surfaces with very different characteristics and thus presenting different mechanisms of dissolution can be observed. In this paper, the surface structures of two very different bioglass compositions, namely 45S5 (46.1 SiO2, 24.4 Na2O, 26.9 CaO, and 2.6 P2O5 mol %) and 77S (80.0 SiO2, 16.0 CaO, and 4.0 P2O5 mol %), have been investigated by means of periodic DFT calculations based on a PBE functional and localized Gaussian basis set as encoded in the CRYSTAL code. Our calculations show that the two glass surfaces differ by the relative amount of key structural sites such as NBOs, exposed ions, orthosilicate units, and small rings. We have demonstrated how the number of these sites affects the surface stability and reactivity (bioactivity).