Direct measurement of single-molecule dynamics and reaction kinetics in confinement using time-resolved transmission electron microscopy

We report experimental methodologies utilising transmission electron microscopy (TEM) as an imaging tool for reaction kinetics at the single molecule level, in direct space and with spatiotemporal continuity. Using reactions of perchlorocoronene (PCC) in nanotubes of different diameters and at different temperatures, we found a period of molecular movement to precede the intermolecular addition of PCC, with a stronger dependence of the reaction rate on the nanotube diameter, controlling the local environments around molecules, than on the reaction temperature (-175, 23 or 400 °C). Once initiated, polymerisation of PCC follows zero-order reaction kinetics with the observed reaction cross section σ_obs of 1.13 × 10^-9 nm² (11.3 ± 0.6 barn), determined directly from time-resolved TEM image series acquired with a rate of 100 frames per second. Polymerisation was shown to proceed from a single point, with molecules reacting sequentially, as in a domino effect, due to the strict conformational requirement of the Diels-Alder cycloaddition creating the bottleneck for the reaction. The reaction mechanism was corroborated by correlating structures of reaction intermediates observed in TEM images, with molecular weights measured by using mass spectrometry (MS) when the same reaction was triggered by UV irradiation. The approaches developed in this study bring the imaging of chemical reactions at the single-molecule level closer to traditional concepts of chemistry.

Quantum Chemical Characterization and Design of Quantum Dots for Sensing Applications

The ability to tune the optoelectronic properties of quantum dots (QDs) makes them ideally suited for the use as fluorescence sensing probes. The vast structural diversity in terms of the composition and size of QDs can make designing a QD for a specific sensing application a challenging process. Quantum chemical calculations have the potential to aid this process through the characterization of the properties of QDs, leading to their in silico design. This is explored in the context of QDs for the fluorescence sensing of dopamine based upon density functional theory and time-dependent density functional theory (TDDFT) calculations. The excited states of hydrogenated carbon, silicon, and germanium QDs are characterized through TDDFT calculations. Analysis of the molecular orbital diagrams for the isolated molecules and calculations of the excited states of the dopamine-functionalized quantum dots establish the possibility of a photoinduced electron-transfer process by determining the relative energies of the electronic states formed from a local excitation on the QD and the lowest QD → dopamine electron-transfer state. The results suggest that the Si₁₆₅H₁₀₀ and Ge₈₄H₆₄ QDs have the potential to act as fluorescent markers that could distinguish between the oxidized and reduced forms of dopamine, where the fluorescence would be quenched for the oxidized form. The work contributes to a better understanding of the optical and electronic behavior of QD-based sensors and illustrates how quantum chemical calculations can be used to inform the design of QDs for specific fluorescent sensing applications.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

Density Functional Theory Calculations of Core-Electron Binding Energies at the K-Edge of Heavier Elements

The capability to determine core-electron binding energies (CEBEs) is vital in the analysis of X-ray photoelectron spectroscopy, and the continued development of light sources has made inner shell spectroscopy of heavier elements increasingly accessible. Density functional theory is widely used to determine CEBEs of lighter elements (boron-fluorine). It is shown that good performance of exchange-correlation functionals for these elements does not necessarily translate to the calculation of CEBEs for the heavier elements from the next row of the periodic table, and in general, larger errors are observed. Two strategies are explored that improve the accuracy of the calculated CEBEs. The first is to apply element and functional dependent energy corrections, and the second is a reparametrization of a short-range corrected functional. This functional is able to reproduce experimental phosphorus and sulfur K-edge CEBEs with an average error of 0.15 eV demonstrating the importance of reducing the self-interaction error associated with the core electrons and represents progress toward a density functional theory calculation that performs equally well for ionization at the K-edge of all elements.

Risuteganib Protects against Hydroquinone-induced Injury in Human RPE Cells

Purpose

Cigarette smoking has been implicated in the pathogenesis of AMD. Integrin dysfunctions have been associated with AMD. Herein, we investigate the effect of risuteganib (RSG), an integrin regulator, on RPE cell injury induced by hydroquinone (HQ), an important oxidant in cigarette smoke.

Methods

Cultured human RPE cells were treated with HQ in the presence or absence of RSG. Cell death, mitochondrial respiration, reactive oxygen species production, and mitochondrial membrane potential were measured by flow cytometry, XFe24 analyzer, and fluorescence plate reader, respectively. Whole transcriptome analysis and gene expression were analyzed by Illumina RNA sequencing and quantitative PCR, respectively. F-actin aggregation was visualized with phalloidin. Levels of heme oxygenase-1, P38, and heat shock protein 27 proteins were measured by Western blot.

Results

HQ induced necrosis and apoptosis, decreased mitochondrial bioenergetics, increased reactive oxygen species levels, decreased mitochondrial membrane potential, increased F-actin aggregates, and induced phosphorylation of P38 and heat shock protein 27. HQ, but not RSG alone, induced substantial transcriptome changes that were regulated by RSG cotreatment. RSG cotreatment significantly protected against HQ-induced necrosis and apoptosis, prevented HQ-reduced mitochondrial bioenergetics, decreased HQ-induced reactive oxygen species production, improved HQ-disrupted mitochondrial membrane potential, reduced F-actin aggregates, decreased phosphorylation of P38 and heat shock protein 27, and further upregulated HQ-induced heme oxygenase-1 protein levels.

Conclusions

RSG has no detectable adverse effects on healthy RPE cells, whereas RSG cotreatment protects against HQ-induced injury, mitochondrial dysfunction, and actin reorganization, suggesting a potential role for RSG therapy to treat retinal diseases such as AMD.

Simulation of vibrationally resolved absorption spectra of neutral and cationic polyaromatic hydrocarbons

The identification of the carriers of the absorption features associated with the diffuse interstellar bands (DIBs) is a long-standing problem in astronomical spectroscopy. Computational simulations can contribute to the assignment of the carriers of DIBs since variations in molecular structure and charge state can be studied more readily than through experimental measurements. Polyaromatic hydrocarbons have been proposed as potential carriers of these bands, and it is shown that simulations based upon density functional theory and time-dependent density functional theory calculations can describe the vibrational structure observed in experiment for neutral and cationic naphthalene and pyrene. The vibrational structure arises from a small number of vibrational modes involving in-plane atomic motions, and the Franck–Condon–Herzberg–Teller approximation improves the predicted spectra in comparison with the Franck–Condon approximation. The study also highlights the challenges for the calculations to enable the assignment in the absence of experimental data, namely prediction of the energy separation between the different electronic states to a sufficient level of accuracy and performing vibrational analysis for higher-lying electronic states.

Observation of Double Excitations in the Resonant Inelastic X-ray Scattering of Nitric Oxide

The nitrogen K-edge resonant inelastic X-ray scattering (RIXS) map of nitric oxide (NO) has been measured and simulated to provide a detailed analysis of the observed features. High-resolution experimental RIXS maps were collected using an in situ gas flow cell and a high-transmission soft X-ray spectrometer. Accurate descriptions of the ground, excited, and core-excited states are based upon restricted active space self-consistent-field calculations using second order multiconfigurational perturbation theory. The nitrogen K-edge RIXS map of NO shows a range of features that can be assigned to intermediate states arising from 1s → π* and 1s → Rydberg excitations; additional bands are attributed to doubly excited intermediate states comprising 1s → π* and π → π* excitations. These results provide a detailed picture of RIXS for an open-shell molecule and an extensive description of the core-excited electronic structure of NO, an important molecule in many chemical and biological processes.

Resveratrol Protects Against Hydroquinone-Induced Oxidative Threat in Retinal Pigment Epithelial Cells

Purpose

Oxidative stress in retinal pigment epithelial (RPE) cells is associated with age-related macular degeneration (AMD). Resveratrol exerts a range of protective biologic effects, but its mechanism(s) are not well understood. The aim of this study was to investigate how resveratrol could affect biologic pathways in oxidatively stressed RPE cells.

Methods

Cultured human RPE cells were treated with hydroquinone (HQ) in the presence or absence of resveratrol. Cell viability was determined with WST-1 reagent and trypan blue exclusion. Mitochondrial function was measured with the XFe24 Extracellular Flux Analyzer. Expression of heme oxygenase-1 (HO-1) and glutamate cysteine ligase catalytic subunit was evaluated by qPCR. Endoplasmic reticulum stress protein expression was measured by Western blot. Potential reactions between HQ and resveratrol were investigated using high-performance liquid chromatography mass spectrometry with resveratrol and additional oxidants for comparison.

Results

RPE cells treated with the combination of resveratrol and HQ had significantly increased cell viability and improved mitochondrial function when compared with HQ-treated cells alone. Resveratrol in combination with HQ significantly upregulated HO-1 mRNA expression above that of HQ-treated cells alone. Resveratrol in combination with HQ upregulated C/EBP homologous protein and spliced X-box binding protein 1. Additionally, new compounds were formed from resveratrol and HQ coincubation.

Conclusions

Resveratrol can ameliorate HQ-induced toxicity in RPE cells through improved mitochondrial bioenergetics, upregulated antioxidant genes, stimulated unfolded protein response, and direct oxidant interaction. This study provides insight into pathways through which resveratrol can protect RPE cells from oxidative damage, a factor thought to contribute to AMD pathogenesis.

Density Functional Theory Based Methods for the Calculation of X-ray Spectroscopy

The availability of new light sources combined with the realization of the unique capabilities of spectroscopy in the X-ray region has driven tremendous advances in the field of X-ray spectroscopy. Currently, these techniques are emerging as powerful analytical tools for the study of a wide range of problems encompassing liquids, materials, and biological systems. Time-resolved measurements add a further dimension to X-ray spectroscopy, opening up the potential to resolve ultrafast chemical processes at an atomic level. X-ray spectroscopy encompasses a range of techniques which provide complementary information, and these include X-ray photoelectron spectroscopy (XPS), X-ray absorption spectroscopy (XAS), X-ray emission spectroscopy (XES), and resonant inelastic X-ray scattering (RIXS). In many studies, the interpretation of the experimental data relies upon calculations to enable the nature of the underlying molecular structure, electronic structure, and bonding to be revealed. Density functional theory (DFT) based methods are some of the most widely used methods for the simulation of X-ray spectra. In this Account, we focus on our recent contributions to the simulation of a range of X-ray spectroscopic techniques using DFT and linear-response time-dependent density functional theory (TDDFT) and show how these methods can provide a computational toolkit for the simulation of X-ray spectroscopy. The importance of the exchange-correlation functional for the calculation of XAS is discussed, and the introduction of short-range corrected functionals is described. The application of these calculations to study large systems through the use of efficient implementations of TDDFT will be highlighted, with the use of these methods illustrated through studies of ionic liquids and transition metal complexes. The extension of TDDFT to calculate XES through the use of a reference determinant for the core-ionized state will be described, and the factors that affect the accuracy of the computed spectra discussed. The application of these approaches will be illustrated through the study of a range of organic molecules and transition metal complexes, which also show how going beyond the dipole approximation in determining the transition intensities can be critical. The application of these approaches to the simulation of the RIXS spectrum of water will also be described, highlighting how ultrafast dynamics on the femtoscale time scale are evident in the measured spectra. In these calculations, the description of the core-ionized and core-excited states becomes increasingly important, and the role of the basis set in accurately describing these states will be explored.

Influence of molecular design on radical spin multiplicity: characterisation of BODIPY dyad and triad radical anions

A strategy to create organic molecules with high degrees of radical spin multiplicity is reported in which molecular design is correlated with the behaviour of radical anions in a series of BODIPY dyads. Upon reduction of each BODIPY moiety radical anions are formed which are shown to have different spin multiplicities by electron paramagnetic resonance (EPR) spectroscopy and distinct profiles in their cyclic voltammograms and UV-visible spectra. The relationship between structure and multiplicity is demonstrated showing that the balance between singlet, biradical or triplet states in the dyads depends on relative orientation and connectivity of the BODIPY groups. The strategy is applied to the synthesis of a BODIPY triad which adopts an unusual quartet state upon reduction to its radical trianion.

Probing the electronic structure of ether functionalised ionic liquids using X-ray photoelectron spectroscopy

The charge distribution associated with individual components in functionalised ionic liquids (ILs) can be tuned by careful manipulation of the substituent groups incorporated into the ions. Here we use X-ray photoelectron spectroscopy to investigate the impact of substituent atoms on the electronic structure of similar imidazolium-based systems each paired with a common anion, [Tf₂N]^-. The experimental measurements revealed an unexpected variation in the charge density distribution within the IL cation when the oxygen atom in a poly-ether containing side chain is moved by just one atomic position. This surprising observation is supported by density functional theory calculations.

Zinc 1s Valence-to-Core X-ray Emission Spectroscopy of Halozincate Complexes

The Zn 1s valence-to-core (VtC) X-ray emission spectra of seven ionic liquids have been measured experimentally and simulated on the basis of time-dependent density-functional theory (TDDFT) calculations. Six of the ionic liquids were made by mixing [C₈C₁Im]X and Zn(II)X₂ at three different ZnX₂ mole fractions (0.33, 0.50, or 0.67) for X = Cl or Br, and a further ionic liquid was made by mixing [P_6,6,6,14]Cl and a mole fraction of ZnCl₂ of 0.33. Calculations were performed for the [ZnX₄]^2-, [Zn₂X₆]^2-, and [Zn₄X₁₀]^2- ions to capture the expected metal complex speciation. The VtC emission spectra showed three bands arising from single-electron processes that can be assigned to emission from ligand p-type orbitals, zinc d-orbitals, and ligand s-type orbitals. For all seven ionic liquids, the highest occupied molecular orbital arises from the ligand p orbitals, and the spectra for the different size metal complexes for the same X were found to be very similar, in terms of both relative peak intensities and peak energies. For both experiments and TDDFT calculations, there was an energy difference of 0.5 eV between the Cl-based and Br-based metal complexes for the ligand s and p orbitals, while the Zn 3d orbital energies were relatively unaffected by the identity of the ligand. The TDDFT calculations find that for the ions with symmetrically equivalent zinc atoms ([Zn₂X₆]^2- and [Zn₄X₁₀]^2-), the most appropriate core-ionized reference state has a core-hole that is localized on a single zinc atom. In this framework, the spectra for the larger ions can be viewed as a sum of spectra for the tetrahedral complex with a single zinc atom with small variations in the structure of the coordinating ligands. Because the spectra are relatively insensitive to small changes in the geometry of the ligands, this is consistent with the small variation in the spectra measured in the experiment.

AIRBED: A Simplified Density Functional Theory Model for Physisorption on Surfaces

Dispersion interactions are commonly included in density functional theory (DFT) calculations through the addition of an empirical correction. In this study, a modification is made to the damping function in DFT-D2 calculations to describe repulsion at small internuclear distances. The resulting Atomic Interactions Represented By Empirical Dispersion (AIRBED) approach is used to model the physisorption of molecules on surfaces such as graphene and hexagonal boron nitride, where the constituent atoms of the surface are no longer required to be included explicitly in the density functional theory calculation but are represented by a point charge to capture electrostatic effects. It is shown that this model can reproduce the structures predicted by full DFT-D2 calculations to a high degree of accuracy. The significant reduction in computational cost allows much larger systems to be studied, including molecular arrays on surfaces and sandwich complexes involving organic molecules between two surface layers.

Probing Elusive Cations: Infrared Spectroscopy of Protonated Acetic Acid

Protonated carboxylic acids, (RCOOH)H⁺, are the initial intermediates in acid-catalyzed (Fischer) esterification reactions. However, the identity of the isomeric form has been debated. Surprisingly, no optical spectra have been reported for any isomer of the protonated carboxylic acid monomer, despite it being a fundamental organic cation. Here, we address these issues by using a new approach to prepare cold He-tagged cations of protonated acetic acid (AA), which entails electron ionization of helium nanodroplets containing metastable dimers of AA. The protonated species is subsequently probed using infrared photodissociation spectroscopy, and following a comparison with calculations, we identify the two isomers whose roles in Fischer esterification are debated. These are the carbonyl-protonated E, Z isomer and the metastable hydroxyl-protonated isomer. Our technique provides a novel approach that can be applied to other elusive ionic species.

Synthesis and characterisation of rylene diimide dimers using molecular handcuffs

Mechanically interlocked handcuffs provide a strategy to study rylene diimide dimers and to investigate their electronic and magnetic properties.

A strategy for positioning, and loosely connecting, molecules in close proximity using mechanically interlocked handcuffs is described. The strategy is demonstrated using rylene diimides, creating dimeric structures in which two components are linked through pillar[5]arene/imidazolium rotaxanes. Investigation of the resulting molecules demonstrates intriguing and new properties that arise from placing these redox active dye molecules together, allowing interactions, whilst allowing the molecules to separate as required. In particular we observe excimer emission from a perylene diimide dimer handcuff and the formation of an unusual radical anion π-dimer upon double reduction of the same molecule. The latter exhibits a unique visible absorption profile for a PDI-based molecule. We demonstrate the flexibility of our approach by making an unprecedented mixed perylene diimide/naphthalene diimide dimer which also reveals interactions between the two components. Our synthetic strategy facilitates the creation of unusual dimeric structures and allows the investigation of intermolecular interactions and the effects they have on electronic and magnetic properties.

Dimers of acetic acid in helium nanodroplets

Two metastable dimers are created inside superfluid helium and studied using infrared spectroscopy to provide insight into condensed phase structures.

Quantum chemical study of the structure, spectroscopy and reactivity of NO+.(H2O) n=1-5 clusters

Quantum chemical methods including Møller-Plesset perturbation (MP2) theory and density functional theory (DFT) have been used to study the structure, spectroscopy and reactivity of NO⁺(H₂O) _n=1-5 clusters. MP2/6-311++G** calculations are shown to describe the structure and spectroscopy of the clusters well. DFT calculations with exchange-correlation functionals with a low fraction of Hartree-Fock exchange give a binding energy of NO⁺(H₂O) that is too high and incorrectly predict the lowest energy structure of NO⁺(H₂O)₂, and this error may be associated with a delocalization of charge onto the water molecule directly binding to NO⁺ Ab initio molecular dynamics (AIMD) simulations were performed to study the NO⁺(H₂O)₅ [Formula: see text] H⁺(H₂O)₄ + HONO reaction to investigate the formation of HONO from NO⁺(H₂O)₅ Whether an intracluster reaction to form HONO is observed depends on the level of electronic structure theory used. Of note is that methods that accurately describe the relative energies of the product and reactant clusters did not show reactions on the timescales studied. This suggests that in the upper atmosphere the reaction may occur owing to the energy present in the NO⁺(H₂O)₅ complex following its formation.This article is part of the theme issue 'Modern theoretical chemistry'.

Simulation of the Raman spectroscopy of multi-layered carbon nanomaterials

A empirical potential based model for simulating the Raman spectroscopy of layered carbon nanomaterials is introduced.

Reactivity of the O2+·(H2O)n and NO+·(H2O)n cluster ions in the D-region of the ionosphere

Ab initio molecular dynamics simulations reveal different reactivities of NO⁺·(H₂O)_n and O₂⁺·(H₂O)_n cluster ions in the D-region of the ionosphere.

The growth and fluorescence of phthalocyanine monolayers, thin films and multilayers on hexagonal boron nitride

Free-base phthalocyanine forms distinct interfacial phases and thin films on hexagonal boron nitride including a monolayer arrangement as determined using high resolution atomic force microscopy.

The impact of sulfur functionalisation on nitrogen-based ionic liquid cations

XPS is used to investigate the impact of sulfur containing substituents on the electronic structure of a series of N-based cations, all with a common anion, [NTf₂]⁻. The experimental data is complex and cannot be easily deconstructed, DFT provides critical insight into bonding and electronic structure for each system studied.

Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin

The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two‐dimensional ultraviolet spectroscopy experiments have determined the rates of tryptophan → heme electron transfer and excitation energy transfer for the two tryptophan residues in myoglobin (Consani et al., Science, 2013, 339, 1586). Here, we show that accurate prediction of these rates can be achieved using Marcus theory in conjunction with time‐dependent density functional theory. Key intermediate residues between the donor and acceptor are identified, and in particular the residues Val68 and Ile75 play a critical role in calculations of the electron coupling matrix elements. Our calculations demonstrate how small changes in structure can have a large effect on the rates, and show that the different rates of electron transfer are dictated by the distance between the heme and tryptophan residues, while for excitation energy transfer the orientation of the tryptophan residues relative to the heme is important. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

NEXAFS spectroscopy of ionic liquids: experiments versus calculations

Experimental N 1s and S 1s NEXAFS spectra are compared to TD-DFT calculated spectra for 12 ionic liquids.

A QM/MM study of the nature of the entatic state in plastocyanin

Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study, the nature of the entatic state is investigated through density functional theory‐based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12.8 kcal/mol and 14.5 kcal/mol for the oxidized and reduced forms of the protein, indicating that the active site has an intermediate structure. It is shown that the energy gap between the oxidized and reduced forms varies significantly with the fluctuations in the structure of the active site at room temperature. An accurate determination of the reorganization energy requires averaging over conformation and a large region of the protein around the active site to be treated at the quantum mechanical level. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

X-ray and Electron Spectroscopy of Water

Here we present an overview of recent developments of X-ray and electron spectroscopy to probe water at different temperatures. Photon-induced ionization followed by detection of electrons from either the O 1s level or the valence band is the basis of photoelectron spectroscopy. Excitation between the O 1s and the unoccupied states or occupied states is utilized in X-ray absorption and X-ray emission spectroscopies. These techniques probe the electronic structure of the liquid phase and show sensitivity to the local hydrogen-bonding structure. Both experimental aspects related to the measurements and theoretical simulations to assist in the interpretation are discussed in detail. Different model systems are presented such as the different bulk phases of ice and various adsorbed monolayer structures on metal surfaces.

Quantum Chemical Calculations of X-ray Emission Spectroscopy

The calculation of X-ray emission spectroscopy with equation of motion coupled cluster theory (EOM-CCSD), time-dependent density functional theory (TDDFT), and resolution of the identity single excitation configuration interaction with second-order perturbation theory (RI-CIS(D)) is studied. These methods can be applied to calculate X-ray emission transitions by using a reference determinant with a core-hole, and they provide a convenient approach to compute the X-ray emission spectroscopy of large systems since all of the required states can be obtained within a single calculation, removing the need to perform a separate calculation for each state. For all of the methods, basis sets with the inclusion of additional basis functions to describe core orbitals are necessary, particularly when studying transitions involving the 1s orbitals of heavier nuclei. EOM-CCSD predicts accurate transition energies when compared with experiment; however, its application to larger systems is restricted by its computational cost and difficulty in converging the CCSD equations for a core-hole reference determinant, which become increasing problematic as the size of the system studied increases. While RI-CIS(D) gives accurate transition energies for small molecules containing first row nuclei, its application to larger systems is limited by the CIS states providing a poor zeroth-order reference for perturbation theory which leads to very large errors in the computed transition energies for some states. TDDFT with standard exchange-correlation functionals predicts transition energies that are much larger than experiment. Optimization of a hybrid and short-range corrected functional to predict the X-ray emission transitions results in much closer agreement with EOM-CCSD. The most accurate exchange-correlation functional identified is a modified B3LYP hybrid functional with 66% Hartree-Fock exchange, denoted B(66)LYP, which predicts X-ray emission spectra for a range of molecules including fluorobenzene, nitrobenzene, acetone, dimethyl sulfoxide, and CF3Cl in good agreement with experiment.

van der Waals-Induced Chromatic Shifts in Hydrogen-Bonded Two-Dimensional Porphyrin Arrays on Boron Nitride

The fluorescence of a two-dimensional supramolecular network of 5,10,15,20-tetrakis(4-carboxylphenyl)porphyrin (TCPP) adsorbed on hexagonal boron nitride (hBN) is red-shifted due to, primarily, adsorbate-substrate van der Waals interactions. TCPP is deposited from solution on hBN and forms faceted islands with typical dimensions of 100 nm and either square or hexagonal symmetry. The molecular arrangement is stabilized by in-plane hydrogen bonding as determined by a combination of molecular-resolution atomic force microscopy performed under ambient conditions and density functional theory; a similar structure is observed on MoS2 and graphite. The fluorescence spectra of submonolayers of TCPP on hBN are red-shifted by ∼30 nm due to the distortion of the molecule arising from van der Waals interactions, in agreement with time-dependent density functional theory calculations. Fluorescence intensity variations are observed due to coherent partial reflections at the hBN interface, implying that such hybrid structures have potential in photonic applications.