Hydrogen bonding in glassy trehalose-water system: Insights from density functional theory and molecular dynamics simulations.

We report a detailed density functional theory and molecular dynamics study of hydrogen bonding between trehalose and water, with a special emphasis on interactions in the amorphous solid state. For comparison, water-water interactions in water dimers and tetramers are evaluated using quantum calculations. The results show that the hydrogen bonding energy is dependent not only on the geometry (bond length and angle) but also on the local environment of the hydrogen bond.

An embedded cluster CASPT2 study of the Ce:YVO4 spectrum.

Multiconfigurational theory, in combination with the embedded cluster approach, is a precise and ab initio approach to describe the electronic structure of solids. In this work, the spectrum of a Ce(III) dopant in YVO4 has been studied by complete active space perturbation theory of the second order (CASPT2), with the host material represented as a set of ab initio model potentials and point-charges. We assess the sensitivity of the spectrum to the size of both the embedded cluster size as well as the size of the electronic basis set.

The OpenMolcas : 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.

Convergence of Electronic Structure Properties in Ionic Oxides Within a Fragment Approach.

Embedded-cluster models of crystalline solids are important to allow accurate wave function methods to be applicable to solids. The ab-initio model potential method, in which the crystal is divided into three different fragments, one quantum fragment, one ab-initio model potential fragment and one point-charge fragment, has historically been shown to be a viable tool for describing the electronic structure in ionic solids. The optimal size of these regions is, of course, individual for each crystal.

Modern quantum chemistry with [Open]Molcas.

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

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 (E. D.

The ANO-R Basis Set.

In this work, the new ANO-R basis set for all elements of the first six periods is introduced. The ANO-R basis set is an all-electron basis set that was constructed including scalar-relativistic effects of the exact-two component (X2C) Hamiltonian and modeling the atomic nucleus by a Gaussian charge distribution, which makes the basis set suitable for calculations of both light and heavy elements. For high accuracy, it takes advantage of the general contraction scheme and was developed at the CASSCF/CASPT2 level of theory.

OpenMolcas: From Source Code to Insight.

In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform.

Synthesis, spectroscopy and QM/MM simulations of a biomimetic ultrafast light-driven molecular motor.

A molecular motor potentially performing a continuous unidirectional rotation is studied by a multidisciplinary approach including organic synthesis, transient spectroscopy and excited state trajectory calculations. A stereogenic center was introduced in the N-alkylated indanylidene-pyrroline Schiff base framework of a previously investigated light-driven molecular switch in order to achieve the unidirectional C[double bond, length as m-dash]C rotary motion typical of Feringa's motor. Here we report that the specific substitution pattern of the designed chiral molecule must critically determine the unidirectional efficiency of the light-induced rotary motion.

New compact density matrix averaged ANO basis sets for relativistic calculations.

When including relativistic effects in quantum chemical calculations, basis sets optimized for relativistic Hamiltonians such as the atomic natural orbital-relativistic core-correlated (ANO-RCC) basis set have to be used to avoid large errors that appear upon contraction of the basis set. While the large size of the ANO-RCC basis set in terms of primitive basis functions allows for highly accurate calculations, it also hinders its applicability to large sized systems due to the computational costs. To tackle this problem, a new compact relativistic ANO basis set, the ANO-eXtra Small (XS) basis set, is introduced for elements H-Ca.

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.

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.

Potential Energy Surface of the Chromium Dimer Re-re-revisited with Multiconfigurational Perturbation Theory.

The chromium dimer has long been a benchmark molecule to evaluate the performance of different computational methods ranging from density functional theory to wave function methods. Among the latter, multiconfigurational perturbation theory was shown to be able to reproduce the potential energy surface of the chromium dimer accurately. However, for modest active space sizes, it was later shown that different definitions of the zeroth-order Hamiltonian have a large impact on the results.

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm.

The dipeptide conformations of all twenty amino acid types in the context of biosynthesis.

There have been many studies of dipeptide structure at a high level of accuracy using quantum chemical methods. Such calculations are resource-consuming (in terms of memory, CPU and other computational imperatives) which is the reason why most previous studies were restricted to the two simplest amino-acid residue types, glycine and alanine. We improve on this by extending the scope of residue types to include all 20 naturally occurring residue types.

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.

A new module for constrained multi-fragment geometry optimization in internal coordinates implemented in the MOLCAS package.

A parallel procedure for an effective optimization of relative position and orientation between two or more fragments has been implemented in the MOLCAS program package. By design, the procedure does not perturb the electronic structure of a system under the study. The original composite system is divided into frozen fragments and internal coordinates linking those fragments are the only optimized parameters.

The preferred conformation of dipeptides in the context of biosynthesis.

Globular proteins are folded polypeptide structures comprising stretches of secondary structures (helical (α- or 310 helix type), polyproline helix or β-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.

Parallelization of a multiconfigurational perturbation theory.

In this work, we present a parallel approach to complete and restricted active space second-order perturbation theory, (CASPT2/RASPT2). We also make an assessment of the performance characteristics of its particular implementation in the Molcas quantum chemistry programming package. Parallel scaling is limited by memory and I/O bandwidth instead of available cores.

Utilizing high performance computing for chemistry: parallel computational chemistry.

Parallel hardware has become readily available to the computational chemistry research community. This perspective will review the current state of parallel computational chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum chemistry methodologies, algorithms, and software development will also be discussed.

MOLCAS 7: the next generation.

Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets.

Bond length and bond order in one of the shortest Cr-Cr bonds.

Multiconfigurational quantum chemical calculations on the R-diimines dichromium compound confirm that the Cr-Cr bond, 1.80 A, is among the shortest Cr(I)-Cr(I) bonds. However, the bond between the two Cr atoms is only a quadruple bond rather than a quintuple bond.

Not innocent: verdict from ab initio multiconfigurational second-order perturbation theory on the electronic structure of chloroiron corrole.

From a suitably broad perspective, transition metal corroles may be viewed as stable, synthetic analogues of high-valent heme protein intermediates such as compounds I and II. Against this backdrop, the electronic structure of chloroiron corrole has provoked a lively debate in recent years. Thus, whereas NMR spectroscopy and DFT calculations suggest an S = 3/2 Fe(III) corrole (*2-) radical description, certain researchers have favored an Fe(IV) formulation.

New relativistic atomic natural orbital basis sets for lanthanide atoms with applications to the Ce diatom and LuF3.

New basis sets of the atomic natural orbital (ANO) type have been developed for the lanthanide atoms La-Lu. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive ions, and the atom in an electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian.