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

Covalently linked organic networks

In this review, we intend to give an overview of the synthesis of well-defined covalently bound organic network materials such as covalent organic frameworks, conjugated microporous frameworks, and other "ideal polymer networks" and discuss the different approaches in their synthesis and their potential applications. In addition we will describe the common computational approaches and highlight recent achievements in the computational study of their structure and properties. For further information, the interested reader is referred to several excellent and more detailed reviews dealing with the synthesis (Dawson et al., 2012; Ding andWang, 2013; Feng et al., 2012) and computational aspects (Han et al., 2009; Colón and Snurr, 2014) of the materials presented here

Two-dimensional sp2 carbon–conjugated covalent organic frameworks

We synthesized a two-dimensional (2D) crystalline covalent organic framework (sp2c-COF) that was designed to be fully π-conjugated and constructed from all sp2-carbons by C=C condensation reactions of tetrakis(4-formylphenyl)pyrene and 1,4-phenylenediacetonitrile. The C=C linkages topologically connect pyrene knots at regular intervals into a 2D lattice with π-conjugations extended along both x and y directions, and develop an eclipsed layer framework rather than the more conventionally obtained disordered structures. The sp2c-COF is a semiconductor with a discrete band gap of 1.9 eV and can be chemically oxidized to enhance conductivity by 12 orders of magnitude. The generated radicals are confined on the pyrene knots, enabling the formation of a paramagnetic carbon structure with high spin density. The sp2-carbon framework induces ferromagnetic phase transition to develop spin-spin coherence and align spins unidirectionally across the material

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

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

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