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

Numerical Research of Materials Crystal Lattice Parameters Based on Rare-Earth Metals

Geometrical parameters (coordinates and angles) of CeO2 crystal lattice by molecular dynamics method are calculated. Calculated parameters of crystal lattice are applied for definition the energy band structure via Hartree-Fock method in an approximation to CO LCAO (crystal orbitals as linear combination of atomic orbitals) and using the model of cyclic cluster. Calculated minimum energy band p-d is within the value range of experimental data. Valence band maximum is 4.2 while minimum energy band p-d width is 2.8 eV Quantum-chemical calculations are accelerated by Schwarz inequality and direct inversion method in iterative subspace. The obtained mathematical model is implemented into software package for calculating material properties

On the possibility of magneto-structural correlations: detailed studies of di-nickel carboxylate complexes

A series of water-bridged dinickel complexes of the general formula [Ni<sub>2</sub>(μ<sub>2</sub>-OH<sub>2</sub>)(μ2- O<sub>2</sub>C<sup>t</sup>Bu)<sub>2</sub>(O<sub>2</sub>C<sup>t</sup>Bu)2(L)(L0)] (L = HO<sub>2</sub>C<sup>t</sup>Bu, L0 = HO<sub>2</sub>C<sup>t</sup>Bu (1), pyridine (2), 3-methylpyridine (4); L = L0 = pyridine (3), 3-methylpyridine (5)) has been synthesized and structurally characterized by X-ray crystallography. The magnetic properties have been probed by magnetometry and EPR spectroscopy, and detailed measurements show that the axial zero-field splitting, D, of the nickel(ii) ions is on the same order as the isotropic exchange interaction, J, between the nickel sites. The isotropic exchange interaction can be related to the angle between the nickel centers and the bridging water molecule, while the magnitude of D can be related to the coordination sphere at the nickel sites

Emergence of comparable covalency in isostructural cerium(IV)- and uranium(IV)-carbon multiple bonds

We report comparable levels of covalency in cerium- and uranium-carbon multiple bonds in the isostructural carbene complexes [M(BIPMTMS)(ODipp)2] [M = Ce (1), U (2), Th (3); BIPMTMS = C(PPh2NSiMe3)2; Dipp = C6H3-2,6-Pri2] whereas for M = Th the M=C bond interaction is much more ionic. On the basis of single crystal X-ray diffraction, NMR, IR, EPR, and XANES spectroscopies, and SQUID magnetometry complexes 1-3 are confirmed formally as bona fide metal(IV) complexes. In order to avoid the deficiencies of orbital-based theoretical analysis approaches we probed the bonding of 1-3 via analysis of RASSCF- and CASSCF-derived densities that explicitly treats the orbital energy near-degeneracy and overlap contributions to covalency. For these complexes similar levels of covalency are found for cerium(IV) and uranium(IV), whereas thorium(IV) is found to be more ionic, and this trend is independently found in all computational methods employed. The computationally determined trends in covalency of Ce ~ U > Th are also reproduced in experimental exchange reactions of 1-3 with MCI4 salts where 1 and 2 do not exchange with ThCl4, but 3 does exchange with MCl4 (M = Ce, U) and 1 and 2 react with UCl4 and CeCl4, respectively, to establish equilibria. This study therefore provides complementary theoretical and experimental evidence that contrasts to the accepted description that generally lanthanide-ligand bonding in non-zero oxidation state complexes is overwhelmingly ionic but that of uranium is more covalent

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

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

Role of the Diamagnetic Zinc(II) Ion in Determining the Electronic Structure of Lanthanide Single-Ion Magnets.

Four complexes containing DyIII and PrIII ions and their LnIII -ZnII analogs have been synthesized in order to study the influence that a diamagnetic ZnII ion has on the electronic structure and hence, the magnetic properties of the DyIII and PrIII single ions. Single-crystal X-ray diffraction revealed the molecular structures as [DyIII (HL)2 (NO3 )3 ] (1), [PrIII (HL)2 (NO3 )3 ] (2), [ZnII DyIII (L)2 (CH3 CO2 )(NO3 )2 ] (3) and [ZnII2 PrIII (L)2 (CH3 CO2 )4 (NO3 )] (4) (where HL=2-methoxy-6-[(E)-phenyliminomethyl]phenol). The dc and ac magnetic data were collected for all four complexes. Compounds 1 and 3 display frequency dependent out-of-phase susceptibility signals (χM "), which is a characteristic signature for a single-molecule magnet (SMM). Although 1 and 3 are chemically similar, a fivefold increase in the anisotropic barrier (Ueff ) is observed experimentally for 3 (83 cm-1 ), compared to 1 (16 cm-1 ). To rationalize the larger anisotropic barrier (1 vs. 3), detailed ab initio calculations were performed. Although the ground state Kramer's doublet in both 1 and 3 are axial in nature (gzz =19.443 for 1 and 18.82 for 3), a significant difference in the energy gap (Ueff ) between the ground and first excited Kramer's doublet is calculated. This energy gap is governed by the electrostatic repulsion between the DyIII ion and the additional charge density found for the phenoxo bridging ligand in 3. This extra charge density was found to be a consequence of the presence of the diamagnetic ZnII ion present in the complex. To explore the influence of diamagnetic ions on the magnetic properties further, previously reported and structurally related Zn-DyIII complexes were analyzed. These structurally analogous complexes unambiguously suggest that the electrostatic repulsion is found to be maximal when the Zn-O-Dy-O dihedral angle is small, which is an ideal condition to maximize the anisotropic barrier in DyIII complexes