JEDI: A versatile code for strain analysis of molecular and periodic systems under deformation.

Stretching or compression can induce significant energetic, geometric, and spectroscopic changes in materials. To fully exploit these effects in the design of mechano- or piezo-chromic materials, self-healing polymers, and other mechanoresponsive devices, a detailed knowledge about the distribution of mechanical strain in the material is essential. Within the past decade, Judgement of Energy DIstribution (JEDI) analysis has emerged as a useful tool for this purpose. Based on the harmonic approximation, the strain energy in each bond length, bond angle, and dihedral angle of the deformed system is calculated using quantum chemical methods. This allows the identification of the force-bearing scaffold of the system, leading to an understanding of mechanochemical processes at the most fundamental level. Here, we present a publicly available code that generalizes the JEDI analysis, which has previously only been available for isolated molecules. Now, the code has been extended to two- and three-dimensional periodic systems, supramolecular clusters, and substructures of chemical systems under various types of deformation. Due to the implementation of JEDI into the Atomic Simulation Environment, the JEDI analysis can be interfaced with a plethora of program packages that allow the calculation of electronic energies for molecular systems and systems with periodic boundary conditions. The automated generation of a color-coded three-dimensional structure via the Visual Molecular Dynamics program allows insightful visual analyses of the force-bearing scaffold of the strained system.

Emergent Properties in Chemistry - Relating Molecular Properties to Bulk Behavior.

Certain properties of an object only emerge when a sufficient number of those objects are present in a definite arrangement. For example, one or two water molecules cannot said to be in a liquid state, but a drop of water can be. This concept of emergence has been studied extensively, but only occasionally discussed explicitly in the context of chemistry. In this paper, we aim to show the fruitfulness of the concept of emergence for chemical inquiry by considering four case studies of emergent chemical properties, i. e., the liquidity and freezing of water, structural properties of crystals, thermodynamical phase transitions and quantum mechanical phenomena. We show that some of these properties emerge gradually, some at discrete points, and some should be taken to emerge only when the number of constituents tends to infinity. We argue that studying the way in which chemical properties emerge presents a useful avenue for research that promises greater insight into the nature of those properties.

CREST-A program for the exploration of low-energy molecular chemical space.

Conformer-rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Chem. Phys. 22, 7169 (2020)] as an automated driver for calculations at the extended tight-binding level (xTB), it offers a variety of molecular- and metadynamics simulations, geometry optimization, and molecular structure analysis capabilities. Implemented algorithms include automated procedures for conformational sampling, explicit solvation studies, the calculation of absolute molecular entropy, and the identification of molecular protonation and deprotonation sites. Calculations are set up to run concurrently, providing efficient single-node parallelization. CREST is designed to require minimal user input and comes with an implementation of the GFNn-xTB Hamiltonians and the GFN-FF force-field. Furthermore, interfaces to any quantum chemistry and force-field software can easily be created. In this article, we present recent developments in the CREST code and show a selection of applications for the most important features of the program. An important novelty is the refactored calculation backend, which provides significant speed-up for sampling of small or medium-sized drug molecules and allows for more sophisticated setups, for example, quantum mechanics/molecular mechanics and minimum energy crossing point calculations.

Calculating high-pressure vibrational frequencies analytically with the extended hydrostatic compression force field approach.

We report the implementation of the analytical Hessian for the mechanochemical extended hydrostatic compression force field method in the Q-Chem program package. To verify the implementation, the analytical Hessian was compared with finite difference calculations. In addition, we calculated the pressure dependency of the Raman active vibrational modes of methane, ethane, and hydrogen, as well as all IR and Raman active modes of Buckminsterfullerene, and compared the results with experimental and theoretical data. Our implementation paves the way for the analysis of geometric points on a pressure-deformed potential energy surface and provides a straightforward model to calculate the vibrational properties of molecules under high pressure.

Boosting quantum yields and circularly polarized luminescence of penta- and hexahelicenes by doping with two BN-groups.

The incorporation of boron-nitrogen (BN) units into polycyclic aromatic hydrocarbons (PAHs) as an isoelectronic replacement of two carbon atoms can significantly improve their optical properties, while the geometries are mostly retained. We report the first non-π-extended penta- and hexahelicenes comprising two aromatic 1,2-azaborinine rings. Comparing them with their all-carbon analogs regarding structural, spectral and (chir)optical properties allowed us to quantify the impact of the heteroatoms. In particular, BN-hexahelicene BN[6] exhibited a crystal structure congruent with its analog CC[6], but displayed a fivefold higher fluorescence quantum yield (φfl = 0.17) and an outstanding luminescence dissymmetry factor (|glum| = 1.33 × 10-2). Such an unusual magnification of both properties at the same time makes BN-helicenes suitable candidates as circularly polarized luminescence emitters for applications in materials science.

Investigating the accuracy of density functional methods for molecules in electric fields.

The use of oriented external electric fields (OEEFs) as a potential tool for catalyzing chemical reactions has gained traction in recent years. Electronic structure calculations using OEEFs are commonly done using methods based on density functional theory (DFT), but until now, the performance of DFT methods for calculating molecules in OEEFs had not been assessed in a more general scope. Looking at the accuracy of molecular geometries, electronic energies, and electric dipole moments compared to accurate coupled-cluster with perturbative triples data, we have investigated a wide variety of density functionals using different basis sets to determine how well the individual functionals perform on various types of chemical bonds. We found that most functionals accurately calculate geometries in OEEFs and that small basis sets are sufficient in many cases. Calculations of electronic energies show a significant error introduced by the OEEF, which the use of a larger basis set helps mitigate. Our findings show that DFT methods can be used for accurate calculations in OEEFs, allowing researchers to make full use of the advantages that they bring.

Synthesis and crystal structure of 2-(anthracen-9-yl)-1-(tert-butyl-dimethyl-sil-yl)-3,6-di-hydro-1λ4,2λ4-aza-borinine.

The title compound, C24H30BNSi (I), is an asymmetric 1,2,3,6-tetra-hydro-1,2-aza-borinine consisting of a BN-substituted cyclo-hexa-diene analog with a B-anthracenyl substituent. A ring-closing metathesis with subsequent substitution of the obtained BCl 1,2-aza-borinine using anthracenyl lithium yielded the title compound I. The asymmetric unit (Z = 8) belongs to the ortho-rhom-bic space group Pbca and shows an elongated N-C bond compared to previously reported BN-1,4-cyclo-hexa-diene [Abbey et al. (2008 ▸) J. Am. Chem. Soc. 130, 7250-7252]. The primarily contributing surface inter-actions are H⋯H and C⋯H/H⋯C (as elucidated by Hirshfeld surface analysis) which are dominated by van der Waals forces. Moreover, the non-aromatic BN heterocycle and the protecting group exhibit intra- and inter-molecular C-H⋯π inter-actions, respectively, with the anthracenyl substituent.

Using oriented external electric fields to manipulate rupture forces of mechanophores.

Oriented external electric fields (OEEFs) can facilitate chemical reactions by selectively weakening bonds. This makes them a topic of interest in mechanochemistry, where mechanical force is used to rupture specific bonds in molecules. Using electronic structure calculations based on density functional theory (DFT), we investigate the effect of OEEFs on the mechanical force required to activate mechanophores. We demonstrate that OEEFs can greatly lower the rupture force of mechanophores, and that the degree of this effect highly depends on the angle relative to the mechanical force at which the field is being applied. The greatest lowering of the rupture force does not always occur at the point of perfect alignment between OEEF and the vector of mechanical force. Using natural bond orbital analysis, we show that mechanical force amplifies the effect that an OEEF has on the scissile bond of a mechanophore. By combining methods to simulate molecules in OEEFs with methods applying mechanical force, we present an effective tool for analyzing mechanophores in OEEFs and show that computationally determining optimal OEEFs for mechanophore activation can assist in the development of future experimental studies.

An in-silico NMR laboratory for nuclear magnetic shieldings computed via finite fields: Exploring nucleus-specific renormalizations of MP2 and MP3.

We developed and implemented a method-independent, fully numerical, finite difference approach to calculating nuclear magnetic resonance shieldings, using gauge-including atomic orbitals. The resulting capability can be used to explore non-standard methods, given only the energy as a function of finite-applied magnetic fields and nuclear spins. For example, standard second-order Møller-Plesset theory (MP2) has well-known efficacy for 1H and 13C shieldings and known limitations for other nuclei such as 15N and 17O. It is, therefore, interesting to seek methods that offer good accuracy for 15N and 17O shieldings without greatly increased compute costs, as well as exploring whether such methods can further improve 1H and 13C shieldings. Using a small molecule test set of 28 species, we assessed two alternatives: κ regularized MP2 (κ-MP2), which provides energy-dependent damping of large amplitudes, and MP2.X, which includes a variable fraction, X, of third-order correlation (MP3). The aug-cc-pVTZ basis was used, and coupled cluster with singles and doubles and perturbative triples [CCSD(T)] results were taken as reference values. Our κ-MP2 results reveal significant improvements over MP2 for 13C and 15N, with the optimal κ value being element-specific. κ-MP2 with κ = 2 offers a 30% rms error reduction over MP2. For 15N, κ-MP2 with κ = 1.1 provides a 90% error reduction vs MP2 and a 60% error reduction vs CCSD. On the other hand, MP2.X with a scaling factor of 0.6 outperformed CCSD for all heavy nuclei. These results can be understood as providing renormalization of doubles amplitudes to partially account for neglected triple and higher substitutions and offer promising opportunities for future applications.

Trapping the Transition State in a [2,3]-Sigmatropic Rearrangement by Applying Pressure.

Transition states are of central importance in chemistry. While they are, by definition, transient species, it has been shown before that it is possible to "trap" transition states by applying stretching forces. We here demonstrate that the task of transforming the transition state of a chemical reaction into a minimum on the potential energy surface can be achieved using hydrostatic pressure. We apply the computational extended hydrostatic compression force field (X-HCFF) approach to the educt of a [2,3]-sigmatropic rearrangement in both static and dynamic calculations and find that the five-membered cyclic transition state of this reaction becomes a minimum at pressures in the range between 100 and 150 GPa. Born-Oppenheimer molecular dynamics (BOMD) simulations suggest that slow decompression leads to a 70:30 mix of the product and the educt of the sigmatropic rearrangement. Our findings are discussed in terms of geometric parameters and electronic rearrangements throughout the reaction. To provide reference data for experimental investigations, we simulated the IR, Raman, and time-resolved UV/vis absorption spectra for the educt, transition state, and product. We speculate that the trapping of transition states by using pressure is generally possible if the transition state of a chemical reaction has a more condensed geometry than both the educt and the product, which paves the way for new ways of initiating chemical reactions.

An efficient implementation of the GOSTSHYP pressure model by applying shell-bounding Gaussian 1-electron-3-center integral screening.

We implemented a screening algorithm for one-electron-three-center overlap integrals over contracted Gaussian-type orbitals into the Q-Chem program package. The respective bounds were derived using shell-bounding Gaussians and the Obara-Saika recurrence relations. Using integral screening, we reduced the computational scaling of the Gaussians On Surface Tesserae Simulate HYdrostatic Pressure (GOSTSHYP) model in terms of calculation time and memory usage to a linear relationship with the tesserae used to discretize the surface area. Further code improvements allowed for additional performance boosts. To demonstrate the algorithm's better performance, we calculated the compressibility of fullerenes up to C180, where we were originally limited to C40 due to the high RAM usage of GOSTSHYP.

Alliacane-Type Secondary Metabolites from Submerged Cultures of the Basidiomycete Clitocybe nebularis.

Seven sesquiterpenoids, named nebucanes A-G (1-7), featuring a rare alliacane scaffold with unprecedented furan or pyrrole functions, were isolated from the fermentation broth of Clitocybe nebularis. Their structures were established on the basis of 1D/2D NMR spectroscopic analyses, HR-(+)-ESIMS spectra, and comparison of measured and calculated CD spectra for determination of the absolute configuration. Assessing the biological activities, nebucane D (4) exhibited antifungal effects against Rhodotorula glutinis, while nebucane G (7) displayed significant cytotoxicity against MCF-7 and A431 cell lines.

Can a Finite Chain of Hydrogen Cyanide Molecules Model a Crystal?

When calculating structural or spectroscopic properties of molecular crystals, the question arises whether it is sufficient to simulate only a single molecule or a small molecular cluster or whether the simulation of the entire crystal is indispensable. In this work we juxtapose calculations on the high-pressure structural properties of the (periodic) HCN crystal and chains of HCN molecules of finite length. We find that, in most cases, the behavior of the crystal can be reproduced by computational methods simulating only around 15 molecules. The pressure-induced lengthening of the C-H bond in HCN found in calculations on both the periodic and finite material are explained in terms of orbital interaction. Our results pave the way for a more thorough understanding of high-pressure structural properties of materials and give incentives for the design of materials that expand under pressure. In addition, they shed light on the complementarity between calculations on periodic materials and systems of finite size.

BN-Substitution in Dithienylpyrenes Prevents Excimer Formation in Solution and in the Solid State.

Boron-nitrogen substitutions in polycyclic aromatic hydrocarbons (PAHs) have a strong impact on the optical properties of the molecules due to a significantly more heterogeneous electron distribution. However, besides these single-molecule properties, the observed optical properties of PAHs critically depend on the degree of intermolecular interactions such as π-π-stacking, dipolar interactions, or the formation of dimers in the excited state. Pyrene is the most prominent example showing the latter as it exhibits a broadened and strongly bathochromically shifted emission band at high concentrations in solution compared to the respective monomers. In the solid state, the impact of intermolecular interactions is even higher as it determines the crystal packing crucially. In this work, a thiophene-flanked BN-pyrene (BNP) was synthesized and compared with its all-carbon analogue (CCP) in solution and in the solid state by means of crystallography, NMR spectroscopy, UV-vis spectroscopy, and photoluminescence (PL) spectroscopy. In solution, PL spectroscopy revealed the solvent-dependent presence of excimers of CCP at high concentrations. In contrast, no excimers were found in BNP. Clear differences were also observed in the single-crystal packing motifs. While CCP revealed overlapped pyrene planes with centroid distances in the range of classical π-stacking interactions, the BNP scaffolds were displaced and significantly more spatially separated.