Luscus: molecular viewer and editor for MOLCAS

The novel program for graphical display and editing of molecular systems, luscus, is described. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling

Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes?

The lytic polysaccharide monooxygenase (LPMO) enzymes boost polysaccharide depolymerization through oxidative chemistry, which has fueled the hope for more energy-efficient production of biofuel. We have recently proposed a mechanism for the oxidation of the polysaccharide substrate (Hedeg{\aa}rd & Ryde, Chem. Sci. 2018, 9, 3866). In this mechanism, complexes with superoxide, oxyl, as well as hydroxyl (i.e. [CuO2]+, [CuO]+ and [CuOH]2+) cores were involved. These complexes can have both singlet and triplet spin states, and both spin-states may be important for how LPMOs function during catalytic turnover. Previous calculations on LPMOs have exclusively been based on density functional theory (DFT). However, different DFT functionals are known to display large differences for spin-state splittings in transition-metal complexes, and this has also been an issue for LPMOs. In this paper, we study the accuracy of DFT for spin-state splittings in superoxide, oxyl, and hydroxyl intermediates involved in LPMO turnover. As reference we employ multiconfigurational perturbation theory (CASPT2).Comment: 29 pages, 5 figures, 5 table

Revised atomistic models of the crystal structure of C–S–H with high C/S ratio

The atomic structure of calcium-silicate-hydrate ( C 1.67 −S−H x ) has been studied. Atomistic C−S−H models suggested in our previous study have been revised in order to perform a direct comparison of energetic stability of the different structures. An extensive set of periodic structures of C−S−H with variation of water content was created, and then optimized using molecular dynamics with reactive force field ReaxFF and quantum chemical semiempirical method PM6. All models show organization of water molecules inside the structure of C−S−H . The new geometries of C−S−H , reported in this paper, show lower relative energy with respect to the geometries from the original definition of C−S−H models. Model that corresponds to calcium enriched tobermorite structure has the lowest relative energy and the density closest to the experimental values

Atomistic modeling of crystal structure of Ca1.67SiHx

The atomic structure of calcium-silicate-hydrate (C1.67-S-Hx) has been investigated by theoretical methods in order to establish a better insight into its structure. Three models for C-S-H all derived from tobermorite are proposed and a large number of structures were created within each model by making a random distribution of silica oligomers of different size within each structure. These structures were subjected to structural relaxation by geometry optimization and molecular dynamics steps. That resulted in a set of energies within each model. Despite an energy distribution between individual structures within each model, significant energy differences are observed between the three models. The C-S-H model related to the lowest energy is considered as the most probable. It turns out to be characterized by the distribution of dimeric and pentameric silicates and the absence of monomers. This model has mass density which is closest to the experimental one

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations

Automatic procedure for generating symmetry adapted wavefunctions

Automatic detection of point groups as well as symmetrisation of molecular geometry and wavefunctions are useful tools in computational quantum chemistry. Algorithms for developing these tools as well as an implementation are presented. The symmetry detection algorithm is a clustering algorithm for symmetry invariant properties, combined with logical deduction of possible symmetry elements using the geometry of sets of symmetrically equivalent atoms. An algorithm for determining the symmetry adapted linear combinations (SALCs) of atomic orbitals is also presented. The SALCs are constructed with the use of projection operators for the irreducible representations, as well as subgroups for determining splitting fields for a canonical basis. The character tables for the point groups are auto generated, and the algorithm is described. Symmetrisation of molecules use a projection into the totally symmetric space, whereas for wavefunctions projection as well and partner function determination and averaging is used. The software has been released as a stand-alone, open source library under the MIT license and integrated into both computational and molecular modelling software. Graphical abstract

The electronic structure of negatively charged fullerenes : From monomers to dimers

Multiconfigurational second order perturbation theory was employed in order to describe the ground and excited states of negatively charged fullerenes C60 and fullerene dimers C120. The calculations were performed for all possible spin states. The obtained results can be used to understand the electronic structure of fullerides

In Search of the reason for the breathing effect of MIL53 metal-organic framework : An ab initio multiconfigurational study

Multiconfigurational methods are applied to study electronic properties and structural changes in the highly flexible metal-organic framework MIL53(Cr). Via calculated bending potentials of angles, that change the most during phase transition, it is verified that the high flexibility of this material is not a question about special electronic properties in the coordination chemistry, but about overall linking of the framework. The complex posseses a demanding electronic structure with delocalized spin density, antifferomagnetic coupling and high multi-state character requiring multiconfigurational methods. Calculated properties are in good agreement with known experimental values confirming our chosen methods

Multiconfigurational Study of the Electronic Structure of Negatively Charged Fullerens

Multiconfigurational second order perturbation theory was employed in order to describe the ground and excited states of C_60^(-n). Different choices of the active spaces are discussed and the possibility to apply multiconfigurational theory to study C_120 is investigated. The calculations were performed for all possible spin states (for selected charge) and show the preference of low spin state. The energy difference between two C_60^(-3) and pairs C_60^(-1)- C_60^(-5) and C_60^(-2)- C_60^(-4) shows that the probability to create a charge alternation in fullerides is small

The preferred conformation of dipeptides in the context of biosynthesis

Globular proteins are folded polypeptide structures comprising stretches of secondary structures (helical (alpha- or 3(10) helix type), polyproline helix or beta-strands) interspersed by regions of less well-ordered structure ("random coil"). Protein fold prediction is a very active field impacting inte alia on protein engineering and misfolding studies. Apart from the many studies of protein refolding from the denatured state, there has been considerable interest in studying the initial formation of peptides during biosynthesis, when there are at the outset only a few residues in the emerging polypeptide. Although there have been many studies employing quantum chemical methods of the conformation of dipeptides, these have mostly been carried out in the gas phase or simulated water. None of these conditions really apply in the interior confines of the ribosome. In the present work, we are concerned with the conformation of dipeptides in this low dielectric environment. Furthermore, only the residue types glycine and alanine have been studied by previous authors, but we extend this repertoire to include leucine and isoleucine, position isomers which have very different structural propensities