On the brink of self-hydration: the water heptadecamer.

For pure, neutral, isolated molecular clusters, (H2O)17 marks the transition from structures with all water molecules on the cluster surface to water self-hydration, i.e., cluster structures around one central water molecule. Getting this right with water model potentials turns out to be challenging. Even the best water potentials currently available, which reproduce collective properties very well, still deliver contradicting results for (H2O)17, when different low-energy isomers from global structure optimizations are examined. Interestingly, ab initio quantum chemistry also struggles with the only seemingly simple question if (H2O)17 is all-surface or water-centered. Hence, although the long history of water potential development may be entering its final phase, it is not quite finished yet.

Comparison of Implicit and Explicit Solvent Approaches in Ab Initio Evaluation of Thermochemistry in Solution: Application in Studying Boron Isotope Fractionation in Water.

Evaluation of thermochemistry in solution plays a key role in numerous fields. For this task, the solvent effects are commonly included in theoretical computations based on either implicit or explicit solvent approaches. In the present study, we evaluate and compare the performance of some of the most widely applied methods based on these two approaches. For studying the solvent effect on thermochemistry with an explicit solvent, we demonstrate that partial normal mode analysis with frozen geometry of solvent molecules for multiple solute-solvent configurations can yield quite accurate and reliable results for a drastically reduced computational cost. As a case study, we consider the evaluation of the equilibrium constant for the boron isotope exchange between boric acid and borate (k3-4) in pure and saline water which is of high geochemical importance. Employing three different rigorous and high-precision theoretical approaches, we provide a reliable estimation of k3-4 which is a value within 1.028 to 1.030 for both pure and saline water which is in excellent agreement with experimental data.

Dependence of Vaporization Enthalpy on Molecular Surfaces and Temperature: Thermodynamically Effective Molecular Surfaces.

Approximation of molecular surfaces is of central importance in numerous scientific fields. In this study we theoretically derive a physical model to relate phase-change thermodynamics to molecular surfaces. The model allows accurately predicting vaporization enthalpy of compounds for a wide temperature range without requiring any empirical parameter. Through the new model, we conceptualize thermodynamically effective molecular surfaces and show that they, although only marginally different than van der Waals surfaces, substantially improve predictability of multiple thermodynamic quantities.

Graph-based Automated Macro-Molecule Assembly.

We present a general molecular framework assembly algorithm that takes a largely arbitrary molecular fragment database and a user-supplied target template graph as input. Automatic assembly of molecular fragments from the database, following a prescribed, user-supplied set of connection rules, then turns the template graph into an actual, chemically reasonable molecular framework. Assembly capabilities of our algorithm are tested by producing several abstract, closed-loop shapes. To indicate a few of many possible application areas we demonstrate a host-guest complex and a road toward catalysis. Postassembly substituent exchange can be used to produce electric fields of desired values at desired points inside the framework or at its surface as a stepping stone toward rationally designed, artificial heterogeneous catalysts.

Globally optimal catalytic fields for a Diels-Alder reaction.

In a previous paper [M. Dittner and B. Hartke, J. Chem. Theory Comput. 14, 3547 (2018)], we introduced a preliminary version of our GOCAT (globally optimal catalyst) concept in which electrostatic catalysts are designed for arbitrary reactions by global optimization of distributed point charges that surround the reaction. In this first version, a pre-defined reaction path was kept fixed. This unrealistic assumption allowed for only small catalytic effects. In the present work, we extend our GOCAT framework by a sophisticated and robust on-the-fly reaction path optimization, plus further concomitant algorithm adaptions. This allows smaller and larger excursions from a pre-defined reaction path under the influence of the GOCAT point-charge surrounding, all the way to drastic mechanistic changes. In contrast to the restricted first GOCAT version, this new version is able to address real-life catalysis. We demonstrate this by applying it to the electrostatic catalysis of a prototypical Diels-Alder reaction. Without using any prior information, this procedure re-discovers theoretically and experimentally established features of electrostatic catalysis of this very reaction, including a field-dependent transition from the synchronous, concerted textbook mechanism to a zwitterionic two-step mechanism, and diastereomeric discrimination by suitable electric field components.

Exploring self-organization of molecular tether molecules on a gold surface by global structure optimization.

We employ nondeterministic global cluster structure optimization, based on the evolutionary algorithms paradigm, to model the self-assembly of complex molecules on a surface. As a real-life application example directly related to many recent experiments, we use this approach for the assembly of triazatriangulene "platform" molecules on the Au(111) surface. Without additional restrictions like spatial discretizations, coarse-graining or precalculated adsorption poses, and despite the proof-of-principle character of this study, we achieve satisfactory qualitative agreement with several experimental observations and can provide answers to questions that experiments on these species had left open so far. © 2019 Wiley Periodicals, Inc.

Simulations of optically switchable molecular machines for particle transport.

A promising application for design and deployment of molecular machines is nanoscale transport, driven by artificial cilia. In this contribution, we present several further steps toward this goal, beyond our first-generation artificial cilium (Raeker et al., J. Phys. Chem. A 2012, 116, 11241). Promising new azobenzene-derivatives were tested for use as cilium motors. Using a QM/MM partitioning in on-the-fly photodynamics, excited-state surface-hopping trajectories were calculated for each isomerization direction and each motor version. The methods used were reparametrized semiempirical quantum chemistry together with floating-occupation configuration interaction as the QM part and the OPLSAA-L forcefield as MM part. In addition, we simulated actual particle transport by a single cilium attached to a model surface, with varying attachment strengths and modes, and with transport targets ranging from single atoms to multi-molecule arrangements. Our results provide valuable design guidelines for cilia-driven nanoscale transport and emphasize the need to carefully select the whole setup (not just the cilium itself, but also its surface attachment and the dynamic cilium-target interaction) to achieve true transport. © 2018 Wiley Periodicals, Inc.

Cluster structures influenced by interaction with a surface.

Clusters on surfaces are vitally important for nanotechnological applications. Clearly, cluster-surface interactions heavily influence the preferred cluster structures, compared to clusters in vacuum. Nevertheless, systematic explorations and an in-depth understanding of these interactions and how they determine the cluster structures are still lacking. Here we present an extension of our well-established non-deterministic global optimization package OGOLEM from isolated clusters to clusters on surfaces. Applying this approach to intentionally simple Lennard-Jones test systems, we produce a first systematic exploration that relates changes in cluster-surface interactions to resulting changes in adsorbed cluster structures.

Resonance dynamics of DCO (X̃ 2A') simulated with the dynamically pruned discrete variable representation (DP-DVR).

Selected resonance states of the deuterated formyl radical in the electronic ground state X̃ 2A' are computed using our recently introduced dynamically pruned discrete variable representation [H. R. Larsson, B. Hartke, and D. J. Tannor, J. Chem. Phys. 145, 204108 (2016)]. Their decay and asymptotic distributions are analyzed and, for selected resonances, compared to experimental results obtained by a combination of stimulated emission pumping and velocity-map imaging of the product D atoms. The theoretical results show good agreement with the experimental kinetic energy distributions. The intramolecular vibrational energy redistribution is analyzed and compared with previous results from an effective polyad Hamiltonian. Specifically, we analyzed the part of the wavefunction that remains in the interaction region during the decay. The results from the polyad Hamiltonian could mainly be confirmed. The C=O stretch quantum number is typically conserved, while the D-C=O bend quantum number decreases. Differences are due to strong anharmonic coupling such that all resonances have major contributions from several zero-order states. For some of the resonances, the coupling is so strong that no further zero-order states appear during the dynamics in the interaction region, even after propagating for 300 ps.

Ultrafast dynamics of UV-excited trans- and cis-ferulic acid in aqueous solutions.

The ultrafast UV-induced processes of the neutral, anionic and dianionic forms of trans- and cis-ferulic acid (FA) in aqueous solution were studied by static and femtosecond time-resolved emission and absorption spectroscopy combined with quantum chemical calculations. In all cases, initial excitation populates the first 1ππ* state. For the dianionic cis-isomer cFA2-, electronic deactivation takes place with a time constant of only 1.4 ps, whereas in all other cases, excited-state deactivation happens more than ten times slower, on a time scale of ≈20 ps. The data suggest sequential de-excitation pathways, where initial sub-picosecond solvent rearrangement and structural changes are followed by internal conversion to an intermediate excited electronic state from which deactivation to the ground state proceeds. Considering the time scales, barrierless excited-state pathways are suggested only in the case of cFA2-, where the observed formation of the isomerisation photoproduct tFA2- provides clear evidence for a cis ⇄ trans isomerisation coordinate. In the other cases, pathways with an excited-state energy barrier, presumably along the same coordinate, are likely, given the longer excited-state lifetimes.

Full-Dimensional Excited-State Intramolecular Proton Transfer Dynamics of Salicylic Acid.

Salicylic acid (SAc) and its excited-state intramolecular proton transfer (ESIPT) capabilities have been studied both experimentally and theoretically by static calculations. However, to our knowledge, no radiationless pathway has been proposed so far. Instead, excited-state deactivation was only investigated via fluorescence. Therefore, we will present full-dimensional photodynamics of SAc using the floating-occupation configuration-interaction (FOCI) treatment with single and paired double excitations based on the semiempirical RM1 Hamiltonian. To further clarify mechanistic details, the potential energy surface (PES) is scanned along the proton transfer coordinates in one and two dimensions. The time-evolution of relevant degrees of freedom (DOF), quantum yields and isomer populations are evaluated from 200 surface-hopping trajectories. It was found that a deactivation pathway from the excited state to the ground state is indeed accessible through a conical intersection, via rotation of the carboxyl group. Together with the ESIPT process, this rotation can also interchange the protons of the two (formal) OH groups, which makes the overall dynamics still more complex. Our full-dimensional photodynamics study provides a comprehensive overview of all these entangled steps.

Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields.

Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.

Efficient global optimization of reactive force-field parameters.

Reactive force fields make low-cost simulations of chemical reactions possible. However, optimizing them for a given chemical system is difficult and time-consuming. We present a high-performance implementation of global force-field parameter optimization, which delivers parameter sets of the same quality with much less effort and in far less time than before, and also offers excellent parallel scaling. We demonstrate these features with example applications targeting the ReaxFF force field. © 2015 Wiley Periodicals, Inc.

Reactive force fields made simple.

Generating a reactive force field for a given chemical reaction is turned from a many-months project for experts into a task of a few hours for a non-specialist, by joining the newly developed quantum-mechanically derived force field (QMDFF) and Warshel's time-tested empirical valence bond (EVB) idea. Three first example applications demonstrate that this works not just for simple atom exchange but also for more complicated reactions.

Observable-targeting global cluster structure optimization.

Traditionally, global cluster structure optimization is done by minimizing energy. As an alternative, we propose minimizing the difference between actual experimental observables and their simulated counterparts. To validate and explain this approach, test cases for small clusters are shown. Additionally, an application to real-life data for a larger cluster illustrates the advantages of this method: it provides direct links between properties and structure, and avoids problems both with insufficient accuracy in theoretical energy-ordering and with non-equilibrium conditions in experiment.

Pinpointing mechanochemical bond rupture by embedding the mechanophore into a macrocycle.

Mechanophores contain a mechanically labile bond that can be broken by an external mechanical force. Quantitative measurement and control of the applied force is possible through atomic force microscopy (AFM). A macrocycle was synthesized that contains both the mechanophore and an aliphatic chain that acts as a "safety line" upon bond breaking. This ring-opening mechanophore unit is linked to poly(ethylene glycol) spacers, which allow investigation by single molecule force spectroscopy. The length increase upon rupture of the mechanophore was measured and compared with quantum chemical calculations.

A graph-based short-cut to low-energy structures.

A new graph-based move class for global optimization of cluster structures is presented. Its performance and efficiency is analyzed for water clusters (H2O)n, n = 24, 61. This analysis indicates superior basin exploitation capabilities of the new move class for large clusters, compared to traditional moves.

Photochemical dynamics of E-methylfurylfulgide-kinematic effects on photorelaxation dynamics of furylfulgides.

With the present theoretical study of the photochemical switching of E-methylfurylfulgide we contribute an important step towards the understanding of the photochemical processes in furylfulgide-related molecules. We have carried out large-scale, full-dimensional direct semiempirical configuration-interaction surface-hopping dynamics of the photoinduced ring-closure reaction. Simulated static and dynamical UV/Vis-spectra show good agreement with experimental data of the same molecule. By a careful investigation of our dynamical data, we were able to identify marked differences to the dynamics of the previously studied E-isopropylfurylfulgide. With our simulations we can not only reproduce the experimentally observed quantum yield differences qualitatively but we can also pinpoint two reasons for them: kinematics and pre-orientation. With our analysis, we thus offer straightforward molecular explanations for the high sensitivity of the photodynamics towards seemingly minor changes in molecular constitution. Beyond the realm of furylfulgides, these insights provide additional guidance to the rational design of photochemically switchable molecules.

A size resolved investigation of large water clusters.

Size selected water clusters are generated by photoionizing sodium doped clusters close to the ionization threshold. This procedure is free of fragmentation. Upon infrared excitation, size- and isomer-specific OH-stretch spectra are obtained over a large range of cluster sizes. In one application of this method the infrared spectra of single water cluster sizes are investigated. A comparison with calculations, based on structures optimized by genetic algorithms, has been made to tentatively derive cluster structures which reproduce the experimental spectra. We identified a single all-surface structure for n = 25 and mixtures with one or two interior molecules for n = 24 and 32. In another application the sizes are determined at which the crystallization sets in. Surprisingly, this process strongly depends on the cluster temperature. The crystallization starts at sizes below n = 200 at higher temperatures and the onset is shifted to sizes above n = 400 at lower temperatures.

Global optimization of parameters in the reactive force field ReaxFF for SiOH.

We have used unbiased global optimization to fit a reactive force field to a given set of reference data. Specifically, we have employed genetic algorithms (GA) to fit ReaxFF to SiOH data, using an in-house GA code that is parallelized across reference data items via the message-passing interface (MPI). Details of GA tuning turn-ed out to be far less important for global optimization efficiency than using suitable ranges within which the parameters are varied. To establish these ranges, either prior knowledge can be used or successive stages of GA optimizations, each building upon the best parameter vectors and ranges found in the previous stage. We have finally arrive-ed at optimized force fields with smaller error measures than those published previously. Hence, this optimization approach will contribute to converting force-field fitting from a specialist task to an everyday commodity, even for the more difficult case of reactive force fields.