Accurate treatment of nonbonded interactions within systematic molecular fragmentation

The accuracy of the systematic fragment approach to the estimation of molecular electronic energies is enhanced by a significantly improved treatment of nonbonded interactions between molecular fragments. Distributed electrostatic interactions, pairwise dispersion interactions, and many-body induction are evaluated from ab initio calculations of small molecular fragments. The accuracy of the complete approach is reported for a large sample of typical neutral organic molecules.We are grateful to the Australian Research Council for funding and the National Computational Infrastructure for a generous allocation of computer time

Extension of the universal force field for metal–organic frameworks

We have extended the Universal Force Field for Metal-Organic Frameworks (UFF4MOF) to cover all moieties present in the most extensive framework library to date, i.e. the Computation-Ready Experimental(CoRE) database (Chem. Mater. 26, 6185 (2014)). Thus, we have extended the parameters to include the fourth and fifth row transition metals, lanthanides and an additional atom type for Sulphur, while the parameters of original UFF and of UFF4MOF are not modified. Employing the new parameters signicantly enlarges the number of structures that may be subjected to a UFF calculation, i.e. more than doubling accessible MOFs of the CoRE structures and thus reaching over 99% of CoRE structure coverage. In turn, 95% of optimized cell parameters are within 10% of their experimental values. We contend these parameters will be most useful for the generation and rapid prototyping of hypothetical MOF structures from SBU databases

Explicit treatment of hydrogen bonds in the universal force field: Validation and application for metal-organic frameworks, hydrates, and host-guest complexes

A straightforward means to include explicit hydrogen bonds within the Universal Force Field (UFF) is presented. Instead of treating hydrogen bonds as non-bonded interaction subjected to electrostatic and Lennard-Jones potentials, we introduce an explicit bond with a negligible bond order, thus maintaining the structural integrity of the H-bonded complexes and avoiding the necessity to assign arbitrary charges to the system. The explicit hydrogen bond changes the coordination number of the acceptor site and the approach is thus most suitable for systems with under-coordinated atoms, such as many metalorganic frameworks; however, it also shows an excellent performance for other systems involving a hydrogen-bonded framework. In particular, it is an excellent means for creating starting structures for molecular dynamics and for investigations employing more sophisticated methods. The approach is validated for the hydrogen bonded complexes in the S22 dataset and then employed for a set of metal-organic frameworks from the Computation-Ready Experimental database and several hydrogen bonded crystals including water ice and clathrates. We show that the direct inclusion of hydrogen bonds reduces the maximum error in predicted cell parameters from 66% to only 14%, and the mean unsigned error is similarly reduced from 14% to only 4%. We posit that with the inclusion of hydrogen bonding, the solvent-mediated breathing of frameworks such as MIL-53 is nowaccessible to rapid UFF calculations, which will further the aim of rapid computational scanning of metal-organic frameworks while providing better starting points for electronic structure calculations

The SMFA program for quantum chemistry calculations on large molecules

SMFA is a general program package for performing quantum chemistry calculations on large molecules, using an energy-based fragmentation approach. The program can calculate electronic energies, energy gradients and second derivatives; perform geometry optimization; find first order saddle points (transition states); perform energy optimized scans along a user-defined path; and evaluate various molecular properties. The program can use any of the following quantum chemistry packages: GAMESS(US), GAUSSIAN, NWChem and Q-Chem. In addition, SMFA provides a number of utility programs that, inter alia, calculate vibrational frequencies and infrared spectra with isotopic substitutions, the electrostatic potential on the solvent-accessible-surface, and isodesmic and higher order near-iso-energetic reaction schemes. Calculations of the electronic energy and related properties can be carried out using a scheme that provides a computation time that is linearly dependent on the size of the molecule or, if the user has enough processing units available, in a walltime that is independent of the size of the molecule

How do Black Bream move through the fish gate on the Vasse Surge Barrier?

This study determined how Black Bream used the fish gate on the Vasse Surge Barrier by tagging them state of the art internal electronic tags. The tags, known as PIT tags, detected fish that passaged upstream and downstream through the fish gate over an 18 month period in 2017 and 2018. The local community helped us tag and release 322 Black Bream. The study revealed that movements through the fish gate were unrelated to spawning activity of this species and supported early work that the Vasse Estuary is not a key breeding site; instead they use the Deadwater to reproduce. Up until May 2018, Bream passaged through the fish gate 440 times (265 downstream and 175 upstream). Black Bream preferred to passage when the water velocity in the fish gate chute were lowest, which occurred when the water levels upstream and downstream of the surge barrier were relatively similar. When the dissolved oxygen upstream of the surge barrier was good, fewer fish passaged downstream to the Wonnerup Inlet although this was a relatively weak effect. However, the dissolved oxygen around the Vasse Suge Barrier during the current analysis period was relatively high compared to other years and therefore we anticipate that the effect of low dissolved oxygen on fish passage would be even stronger in those years. They also preferred to pass downstream through the fish gate during the evening, whereas upstream passages mostly occurred during the dawn and dusk periods. The findings greatly increase our understanding of the conditions that Black Bream require or prefer to use the fish gate on the Vasse Surge Barrier. However, as the PIT tags last for 20 years, additional data analysis is recommended to compare the factors influencing the passage of the species over multiple years of fish gate operation; including those years that experience poor oxygen levels. It is also recommended that additional fish PIT tagging occur, including other species, so that long-term fish passage through the structure may be further quantified

Excited states of Nb3N2 and Nb3C2: Density functional theory, CASSCF, and MRCI studies

Complete active space self-consistent field (CASSCF) and multireference configuration interaction (MRCI) methods are used to investigate the Nb(3)N(2) and Nb(3)C(2) clusters in order to determine the agreement between multireference methods, density functional theory (DFT), and experiment. These two clusters are ideal candidates to study as the known spectroscopy can serve to validate the computational results, yet there is still room for the calculations to inform further spectroscopic experiments. We find that the MRCI leading configuration for each of the ground states is in agreement with that predicted by DFT but only accounts for up to 70% of the total configuration. CASSCF and DFT geometries are also in general agreement. Transition energies between the neutral and cationic manifolds are found to be poorly predicted by MRCI relative to the computationally cheap DFT method. For Nb(3)C(2) we find that a higher energy isomer may have an electronic transition in the spectral vicinity as the lowest energy isomer.Matthew A. Addicoat and Gregory F. Meth

Catalytic activity towards hydrogen evolution dependent of the degree of conjugation and absorption of six organic chromophores

Conjugated materials can, in many cases, absorb visible light because of their delocalized π electron system. Such materials have been widely used as a photoactive layers in organic photovoltaic devices and as photosensitizers in dye‐sensitized solar cells. Additionally, these materials have been reported for applications in solar fuel production, working as photocatalysts for the hydrogen evolution reaction (HER). The synthesis of three flexible vinyl groups‐containing chromophores is reported. The catalytic activity towards hydrogen evolution of these chromophores has been investigated and compared to their non‐vinyl‐containing analogues. The catalytic effect was confirmed using two different approaches: electrochemical, using the chromophores to modify a working electrode, and photocatalytic, using the chromophores combined with platinum nanoparticles. A relationship between the degree of conjugation and the catalytic activity of the chromophores has been observed with the electrochemical method, while a relationship between the UV absorption in the solid state and the photocatalytic effect with platinum nanoparticles was observed

Triazine functionalized porous covalent organic framework for photo-organocatalytic E–Z isomerization of olefins

Visible light-mediated photocatalytic organic transformation has drawn significant attention as an alternative process for replacing thermal reactions. Although precious metal/organic dyes based homogeneous photocatalysts have been developed, their toxic and nonreusable nature makes them inappropriate for large-scale production. Therefore, we have synthesized a triazine and a keto functionalized nonmetal based covalent organic framework (TpTt) for heterogeneous photocatalysis. As the catalyst shows significant absorption of visible light, it has been applied for the photocatalytic uphill conversion of trans-stilbene to cis-stilbene in the presence of blue light-emitting diodes with broad substrate scope via an energy transfer process

Performance of GFN1-xTB for periodic optimization of metal organic frameworks

Tight-binding approaches bridge the gap between force field methods and Density Functional Theory (DFT). Density Functional Tight Binding (DFTB) has been employed for a wide range of systems including proteins, clays and 2D and 3D materials. DFTB is 2–3 orders of magnitude faster than DFT, allowing calculations containing up to ca. 5000 atoms. The efficiency of DFTB comes via pre-computed integrals, which are parameterized for each pair of atoms, and the requirement for this parameterization has previously prevented widespread use of DFTB for Metal–Organic Frameworks. The GFN-xTB (Geometries, Frequencies, and Non-covalent interactions Tight Binding) method provides parameters for elements up to Z ≤ 86. We have therefore employed GFN-xTB to periodic optimizations of the Computation Ready Experimental (CoRE) database of MOF structures. We find that 75% of all cell parameters remain within 5% of the reference (experimental) value and that bonds containing metal atoms are typically well conserved with a mean average deviation of 0.187 Å. Therefore GFN-xTB provides the ability to calculate MOF structures more accurately than force fields, and ca. 2 orders of magnitude faster than DFT. We therefore propose that GFN-xTB is a suitable method for screening of hypothetical MOFs (Z ≤ 86), with the advantage of accurate binding energies for adsorption applications

O(-)---C interactions and bond formation in 1-naphtholate anions with peri-located electrophilic carbon centres

The first peri interactions between naphtholate oxyanions and electrophilic double bonds are described. Tetramethylguanidine forms crystalline salts with 8-acetyl- and 8-benzoyl-naphthol which show O---C distances for the anions in the range 2.558-2.618 Å and small increases in carbonyl pyramidalities over the corresponding naphthols, whereas DMAP forms only hydrogen bonded complexes. Replacement of the acyl group with an alkene leads to intramolecular O-C bond formation for just the most electron deficient alkenes, with long peri O-C bonds (1.508 and 1.521 Å) observed in one case. However, both cyclised and uncyclised examples can be deprotonated to give cyclic structures according to NMR, and DFT calculations suggest very long peri- O-C bond lengths of 1.540 and 1.622 Å for two of these anions