Quantifying Fluctuations of Average Solvent Environments for Embedding Calculations

The viability and effectiveness of replacing an ensemble of embedded solute calculations by a single calculation using an average description of the solvent environment are evaluated. This work explores the fluctuations of the average description of the system obtained in two ways: from calculations on an ensemble of geometries and from an average environment constructed from the same ensemble. To this end, classical molecular dynamics simulations of a rigid acetone solute in SPCE water are performed in order to generate an ensemble of solvent environments. From this ensemble of solvent configurations, a number of different approaches for constructing an average solvent environment are employed. We perform a thorough numerical analysis of the fluctuations of the electrostatic potential experienced by the solute, as well as the resulting fluctuations of the solute's electronic density, measured through its dipole moment and fitted atomic point charges. At the same time, we inspect the accuracy of the methods used to construct average environments. Finally, the proposed method for generating the embedding potential from an average environment density is applied to estimate the solvatochromic shift of the first excitation of acetone. In order to account for quantum confinement effects, which may be important in certain cases, the fluctuations in the shift due to the interaction with the solvent are evaluated using frozen-density-embedding theory. Our results demonstrate that, for normally distributed environments, the constructed average environment is a reasonably good representation of a fluctuating molecular solvent environment. We then provide guidance for future comparisons between these theoretical treatments of solute/solvent systems to experimental measurements.

A post-HF approach to the sunscreen octyl methoxycinnamate

Octyl methoxycinnamate (2-ethylhexyl 4-methoxycinnamate, OMC) is a commercial sunscreen known as octinoxate with excellent UVB filter properties. However, it is known to undergo a series of photodegradation processes that decrease its effectiveness as a UVB filter. In particular, the trans (E) form-which is considered so far as the most stable isomer-converts to the cis (Z) form under the effect of light. In this work, by using post-Hartree-Fock approaches [CCSD, CCSD(t), and CCSD + T(CCSD)] on ground state OMC geometries optimized at the MP2 level, we show that the cis and trans forms of the gas-phase OMC molecule have comparable stability. Test calculations on the same structures with a series of dispersion-corrected density functional theory-based approaches including the B2PLYP double hybrid predict the trans structures to be energetically favored, missing the subtle stabilization of cis-OMC. Our results suggest that the cis form is stabilized by intra-molecular dispersion interactions, leading to a folded more compact structure than the trans isomer.

Precision Molecular Threading/Dethreading

The general principles guiding the design of molecular machines based on interlocked structures are well known. Nonetheless, the identification of suitable molecular components for a precise tuning of the energetic parameters that determine the mechanical link is still challenging. Indeed, what are the reasons of the "all-or-nothing" effect, which turns a molecular "speed-bump" into a stopper in pseudorotaxane-based architectures? Here we investigate the threading and dethreading processes for a representative class of molecular components, based on symmetric dibenzylammonium axles and dibenzo[24]crown-8 ether, with a joint experimental-computational strategy. From the analysis of quantitative data and an atomistic insight, we derive simple rules correlating the kinetic behaviour with the substitution pattern, and provide rational guidelines for the design of modules to be integrated in molecular switches and motors with sophisticated dynamic features.

Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels

Incorporation of biological systems in water nanodroplets has recently emerged as a new frontier to investigate structural changes of biomolecules, with perspective applications in ultra-fast drug delivery. We report on the molecular dynamics of the digestive protein Pepsin subjected to a double confinement. The double confinement stemmed from embedding the protein inside a water nanodroplet, which in turn was caged in a nanochannel mimicking the mesoporous silica SBA-15. The nano-bio-droplet, whose size fits with the pore diameter, behaved differently depending on the protonation state of the pore surface silanols. Neutral channel sections allowed for the droplet to flow, while deprotonated sections acted as anchoring piers for the droplet. Inside the droplet, the protein, not directly bonded to the surface, showed a behavior similar to that reported for bulk water solutions, indicating that double confinement should not alter its catalytic activity. Our results suggest that nanobiodroplets, recently fabricated in volatile environments, can be encapsulated and stored in mesoporous silicas.

Water in zeolite L and its MOF mimic

Confinement of molecules in one dimensional arrays of channel-shaped cavities has led to technologically interesting materials. However, the interactions governing the supramolecular aggregates still remain obscure, even for the most common guest molecule: water. Herein, we use computational chemistry methods (#compchem) to study the water organization inside two different channel-type environments: zeolite L – a widely used matrix for inclusion of dye molecules, and ZLMOF – the closest metal-organic-framework mimic of zeolite L. In ZLMOF, the methyl groups of the ligands protrude inside the channels, creating nearly isolated nanocavities. These cavities host well-separated ring-shaped clusters of water molecules, dominated mainly by water-water hydrogen bonds. ZLMOF provides arrays of “isolated supramolecule” environments, which might be exploited for the individual confinement of small species with interesting optical or catalytic properties. In contrast, the one dimensional channels of zeolite L contain a continuous supramolecular structure, governed by the water interactions with potassium cations and by water-water hydrogen bonds. Water imparts a significant energetic stabilization to both materials, which increases with the water content in ZLMOF and follows the opposite trend in zeolite L. The water network in zeolite L contains an intriguing hypercoordinated structure, where a water molecule is surrounded by five strong hydrogen bonds. Such a structure, here described for the first time in zeolites, can be considered as a water pre-dissociation complex and might explain the experimentally detected high proton activity in zeolite L nanochannels.

Entropy in multiple equilibria, compounds with different sites

The influence of entropy in multiple chemical equilibria is investigated for systems with different types of sites for the condition that the binding enthalpy of the species is the same within each type of sites and independent of those species that are already bonded. This allows splitting of the free reaction enthalpy into the particle distribution term and all other contributions for each type of sites separately and, hence, to evaluate this entropy contribution to the free reaction enthalpy. The situations for which this applies can be chemically very different, e.g. acid base, ligand exchange, isomerisation, conformational change, rearrangement of a ligand, ion exchange, adsorption of a species on the surface of a particle or a dendrimer, insertion of charged or neutral species into the cavities of a microporous or mesoporous host. We provide physical insight by discussing Xrc1{n1ABn2}Xrc2 systems. The number of coordination sites A and B are n1 and n2, respectively. The indices rc1 = 1, 2,…,n1 and rc2 = 1, 2,…,n2 count the number of X bonded to sites A and sites B, respectively. An important result is that the large number of equilibrium constants needed to describe those situations can be expressed as a function of two constants only. This allows studying systems quantitatively by experimental and theoretical means which otherwise might be difficult to handle. It has also implication for theoretical studies in the sense that it is sufficient to model only two reactions instead of many in order to describe a system. The results remain valid for systems with more than two types of different sites. The description of the entropy driven development of the fractional equilibrium coverage of the sites provides a new tool for understanding adsorption and ion exchange isotherms. The fractional equilibrium coverage of the sites can be described as a linear combination of individual Langmuir isotherms despite of the fact that such a linear combination has never the shape of the original Langmuir isotherm. This is remarkable and very useful. It provides us with new tools for describing and testing isotherms based on well defined, transparent physical ideas. Explicit solution for systems with 2, 3, 4, 5, 6, and 12 coordination sites are reported. Applications to a system with 12 coordination sites serve to illustrate information that can be obtained for complex situations.

Supramolecular Organization in Confined Nanospaces

Empty spaces are abhorred by nature, which immediately rushes in to fill the void. Humans have learnt pretty well how to make ordered empty nanocontainers, and to get useful products out of them. When such an order is imparted to molecules, new properties may appear, often yielding advanced applications. This review illustrates how the organized void space inherently present in various materials: zeolites, clathrates, mesoporous silica/organosilica, and metal organic frameworks (MOF), for example, can be exploited to create confined, organized, and self-assembled supramolecular structures of low dimensionality. Features of the confining matrices relevant to organization are presented with special focus on molecular-level aspects. Selected examples of confined supramolecular assemblies - from small molecules to quantum dots or luminescent species - are aimed to show the complexity and potential of this approach. Natural confinement (minerals) and hyperconfinement (high pressure) provide further opportunities to understand and master the atomistic-level interactions governing supramolecular organization under nanospace restrictions.

Direct observation of slow intersystem crossing in an aromatic ketone, fluorenone

Direct measurements of Single vibronic Level InterSystem Crossing (SLISC) have been performed on the fluorenone molecule in the gas phase, by time resolved photoelectron and photoion spectroscopy. Vibronic transitions above the S1 nπ* origin were excited in the 432-420 nm region and the decay of S1 and growth of T1(3)ππ* could be observed within a 10 ns time domain. The ionization potential is measured as 8.33 ± 0.04 eV. The energy of the first excited triplet state of fluorenone, T1 has been characterized directly at 18 640 ± 250 cm(-1). The internal conversion of S1 to S0 is found to amount to ∼15% of the population decay, thus ISC is the dominant electronic relaxation process. ISC, although favored by the S1(1)nπ*-T1(3)ππ* coupling scheme, is 3 orders of magnitude less efficient than in the similar molecule benzophenone. Thus, the planarity of the fluorenone molecule disfavors the exploration of the configuration space where surface crossings would create high ISC probability, which occurs in benzophenone through surface crossings. The time evolution of S1 fluorenone is well accounted for by the statistical decay of individual levels into a quasi-continuum of T1 vibronic levels.

Photochemistry and Photophysics in Silica-Based Materials: Ultrafast and Single Molecule Spectroscopy Observation

Silica-based materials (SBMs) are widely used in catalysis, photonics, and drug delivery. Their pores and cavities act as hosts of diverse guests ranging from classical dyes to drugs and quantum dots, allowing changes in the photochemical behavior of the confined guests. The heterogeneity of the guest populations as well as the confinement provided by these hosts affect the behavior of the formed hybrid materials. As a consequence, the observed reaction dynamics becomes significantly different and complex. Studying their photobehavior requires advanced laser-based spectroscopy and microscopy techniques as well as computational methods. Thanks to the development of ultrafast (spectroscopy and imaging) tools, we are witnessing an increasing interest of the scientific community to explore the intimate photobehavior of these composites. Here, we review the recent theoretical and ultrafast experimental studies of their photodynamics and discuss the results in comparison to those in homogeneous media. The discussion of the confined dynamics includes solvation and intra- and intermolecular proton-, electron-, and energy transfer events of the guest within the SBMs. Several examples of applications in photocatalysis, (photo)sensors, photonics, photovoltaics, and drug delivery demonstrate the vast potential of the SBMs in modern science and technology.

Entropy in multiple equilibria, theory and applications

Entropy controls the dependence of the equilibrium constants in the synthesis of host–guest composites on the occupation rc for channels of different length.

One-dimensional self-assembly of perylene-diimide dyes by unidirectional transit of zeolite channel openings

Confined supramolecular architectures of chromophores are key components in artificial antenna composites for solar energy harvesting and storage. A typical fabrication process, based on the insertion of dye molecules into zeolite channels, is still unknown at the molecular level. We show that slipping of perylene diimide dyes into the one-dimensional channels of zeolite L and travelling inside is only possible because of steric-interaction-induced cooperative vibrational modes of the host and the guest. The funnel-like structure of the channel opening, larger at the entrance, along with a directionally asymmetric entrance-exit probability, ensures a favorable self-assembly process of the perylene units.

Revealing electronic open quantum systems with subsystem TDDFT

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustrate the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.

Advances in theory and their application within the field of zeolite chemistry

Zeolites are versatile and fascinating materials which are vital for a wide range of industries, due to their unique structural and chemical properties, which are the basis of applications in gas separation, ion exchange and catalysis. Given their economic impact, there is a powerful incentive for smart design of new materials with enhanced functionalities to obtain the best material for a given application. Over the last decades, theoretical modeling has matured to a level that model guided design has become within reach. Major hurdles have been overcome to reach this point and almost all contemporary methods in computational materials chemistry are actively used in the field of modeling zeolite chemistry and applications. Integration of complementary modeling approaches is necessary to obtain reliable predictions and rationalizations from theory. A close synergy between experimentalists and theoreticians has led to a deep understanding of the complexity of the system at hand, but also allowed the identification of shortcomings in current theoretical approaches. Inspired by the importance of zeolite characterization which can now be performed at the single atom and single molecule level from experiment, computational spectroscopy has grown in importance in the last decade. In this review most of the currently available modeling tools are introduced and illustrated on the most challenging problems in zeolite science. Directions for future model developments will be given.

Host-guest interactions and orientation of dyes in the one-dimensional channels of zeolite L

A combined experimental and modeling study of methylacridine (MeAcr(+)) dye-zeolite L composites unravels the microscopic origin of their functional properties. The anisotropic orientation of the cationic dye inside the ZL channel is unambiguously determined and understood. The most stable orientation of MeAcr(+), which features both its long and short molecular axes nearly perpendicular to the channel axis, is mainly determined by dye-ZL electrostatic interactions but also depends on the cosolvent water. In ZL, MeAcr(+) is not hydrogen bonded to water or ZL framework oxygens and is hydrophobically solvated by water molecules. These findings further support the hypothesis that the cosolvent can importantly influence properties of dye-zeolite composites. Of relevance for a deeper comprehension of the physical chemistry of these hybrids is the observation that trivial energy transfer processes (self-absorption) are often playing a significant role in the optical properties of the composites.