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. This is seen in quantum calculations of complexes in vacuum as well as in amorphous solid states with periodic boundary conditions. The temperature-induced glass transition in the trehalose-water system was studied using molecular dynamics simulations with varying cooling and heating rates. The obtained parameters of the glass transition are in good agreement with the experiments. Moreover, the dehydration of trehalose in the glassy state was investigated through a gradual dehydration with multiple small steps under isothermal conditions. From these simulations, the values of water sorption energy at different temperatures were obtained. The partial molar enthalpy of mixing of water value of -18 kJ/mol found in calorimetric experiments was accurately reproduced in these simulations. These findings are discussed in light of the hydrogen bonding data in the system. We conclude that the observed exothermic effect is due to different responses of liquid and glassy matrices to perturbations associated with the addition or removal of water molecules.

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. A comparison of our best computational model with experimental results shows that the embedding approach is robust and can accurately model the spectrum of low-concentration dopants in complex host materials.

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. In this study we analyzed the convergence of the electronic structure properties with respect to an increase of the size of the quantum part and the layer of potentials. MgO crystal and Ni: MgO were used for this purpose as examples of an ideal crystal and a crystal with a point defect. We demonstrated that with an increase of the cluster size, the electron density in the inner part of the cluster becomes very similar to the electron density in the periodic model. Clusters, embedded into a layer of model potential and electrostatic field, are a good alternative to periodic description.

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. Hedegård and U. Ryde, Chem. Sci., 2018, 9, 3866-3880). In this mechanism, intermediates 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).

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. The distinguishing feature of the ANO-R basis set is its compactness in terms of both primitive and contracted basis functions, thus containing no superfluous functions for a given quality. An optimum number of primitive basis functions was selected based on studying the convergence toward the complete basis set limit for each element individually. The primitive basis sets were then contracted using the density-averaged atomic-natural-orbital (ANO) scheme, and suitable contraction levels were determined solely based on the natural orbital occupation numbers that describe the contribution of each natural orbital to the one-particle density matrix. Rather than following the common "split-valence n-tuple zeta plus polarization functions" structure, the resulting basis sets ANO-R0 to ANO-R3 possess a unique composition for each element, ensuring that no unnecessary functions are included while the basis sets are still balanced across the first six periods (H-Rn).

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. More specifically, we find that a stereogenic center containing a methyl group and a hydrogen atom as substituents does not create a differential steric effect large enough to fully direct the motion in either the clockwise or counterclockwise direction especially along the E→Z coordinate. However, due to the documented ultrafast character and electronic circular dichroism activity of the investigated system, we find that it provides the basis for development of a novel generation of rotary motors with a biomimetic framework and operating on a picosecond time scale.

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. The number of primitive basis functions in ANO-XS is about half that of the ANO-RCC basis set. This greatly reduces the computational costs in the integral calculations especially when used in combination with Cholesky decomposition. At the same time, the ANO-XS basis set is able to predict molecular properties such as bond lengths and excitation energies with reasonable errors compared to the larger ANO-RCC basis set. The main intention for the ANO-XS basis set is to be used in conjunction with the ANO-RCC basis set for large systems that can be divided with regions demanding different qualities of basis sets. This is exemplified in CASPT2 calculations for an Ir(C3H4N)3 complex, where substituting the larger ANO-RCC for the compact ANO-XS basis set at the ligand atoms yields only minor differences for a large number of excited states compared to calculations employing the ANO-RCC basis set on all atoms. Thus, accurate calculations including relativistic effects for large systems become more affordable with the new ANO-XS basis set.

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.

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.

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. In this work, we revisit the system for the third time with multiconfigurational perturbation theory, now in order to increase the active space of the reference wave function. This reduces the impact of the choice of zeroth-order Hamiltonian and improves the shape of the potential energy surface significantly. We conclude by comparing our results of the dissocation energy and vibrational spectrum to those obtained from several highly accurate multiconfigurational methods and experiment. For a meaningful comparison, we used the extrapolation to the complete basis set for all methods involved.

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. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

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. Our results reveal differences in secondary structure preferences for the all residue types. There are in most cases very deep energy troughs corresponding either to the polyproline II (collagen) helix and the α-helix or both. The ß-strand was not strongly favoured energetically although the extent of this depression in the energy surface is, while not "deeper" (energetically), has a wider extent than the other two types of secondary structure. There is currently great interest in the question of cotranslational folding, the extent to which the nascent polypeptide begins to fold prior to emerging from the ribosome exit tunnel. Accordingly, while most previous quantum studies of dipeptides were carried out in the (simulated) gas or aqueous phase, we wished to consider the first step in polypeptide biosynthesis on the ribosome where neither gas nor aqueous conditions apply. We used a dielectric constant that would be compatible with the water-poor macromolecular (ribosome) environment.

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. Graphical AbstractScreenshot of luscus program showing molecular orbital.

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 procedure is capable to handle fully independent (no border atoms) fragments as well as fragments connected by covalent bonds. In the framework of the procedure, the optimization of relative position and orientation of the fragments are carried out in the internal "Z-matrix" coordinates using numerical derivatives. The total number of required single points energy evaluations scales with the number of fragments rather than with the total number of atoms in the system. The accuracy and the performance of the procedure have been studied by test calculations for a representative set of two- and three-fragment molecules with artificially distorted structures. The developed approach exhibits robust and smooth convergence to the reference optimal structures. As only a few internal coordinates are varied during the procedure, the proposed constrained fragment geometry optimization can be afforded even for high level ab initio methods like CCSD(T) and CASPT2. This capability has been demonstrated by applying the method to two larger cases, CCSD(T) and CASPT2 calculations on a positively charged benzene lithium complex and on the oxygen molecule interacting to iron porphyrin molecule, respectively.

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 ß-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.

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. Significant time savings for calculations on large and complex systems can be achieved by increasing the number of processes on a single machine, as long as memory bandwidth allows, or by using multiple nodes with a fast, low-latency interconnect. We found that parallel efficiency drops below 50% when using 8-16 cores on the shared-memory architecture, or 16-32 nodes on the distributed-memory architecture, depending on the calculation. This limits the scalability of the implementation to a moderate amount of processes. Nonetheless, calculations that took more than 3 days on a serial machine could be performed in less than 5 h on an InfiniBand cluster, where the individual nodes were not even capable of running the calculation because of memory and I/O requirements. This ensures the continuing study of larger molecular systems by means of CASPT2/RASPT2 through the use of the aggregated computational resources offered by distributed computing systems.

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. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies.