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

Computational Study of Nonadiabatic Spin-Forbidden Processes in Metal-Sulfur Proteins

We investigate the role of nonadiabatic spin-forbidden transitions in the catalytic and electron transfer processes in the active sites of metal-sulfur proteins. We focus on two biologically important metal-sulfur proteins, namely the [NiFe]-hydrogenase enzyme capable of catalytic H2 oxidation and proton reduction, and the electron transfer protein rubredoxin. The synthetic analogs of [NiFe]-hydrogenase are the promising inexpensive alternative to platinum-based catalysts. Our studies indicate that nonadiabatic transitions between the electronic states with different spin multiplicities could be important for the catalytic activity of [NiFe]-hydrogenase. These transitions are mediated by spin-orbit coupling between the quasidegenerate singlet and triplet states of the Ni(II) center. As for rubredoxin, its ability to transfer electrons makes this small protein a promising starting model for the development of future self-sufficient biosensors and the novel catalysts. The presence of multiple low-lying electronic states with different spin multiplicities in the active site of rubredoxin indicates a possibility of nonadiabatic transitions during the electron transfer processes. The probabilities and the rates of nonadiabatic spin-forbidden transitions in the metal-sulfur proteins predicted using the nonadiabatic transition state theory (NA-TST). The NA-TST calculations require the knowledge of molecular properties at a minimum energy crossing point (MECP), an analog of transition state in the traditional transition state theory. Therefore, part of the work was dedicated to implementation of the MECP search algorithm for the fragment molecular orbital (FMO) method that can be applied to systems with thousands of atoms, including large models of metal-sulfur proteins. The last part of the dissertation is dedicated to the design and manufacture of the 3D-printed models of potential energy surfaces for different chemical reactions. These models proved to be valuable for the chemical dynamics and kinetics demonstrations in graduate and undergraduate chemistry classes

Effect of H₂ Binding on the Nonadiabatic Transition Probability between Singlet and Triplet States of the [NiFe]-Hydrogenase Active Site

We investigate the effect of H₂ binding on the spin-forbidden nonadiabatic transition probability between the lowest energy singlet and triplet electronic states of [NiFe]-hydrogenase active site model, using a velocity averaged Landau–Zener theory. Density functional and multireference perturbation theories were used to provide parameters for the Landau–Zener calculations. It was found that variation of the torsion angle between the terminal thiolate ligands around the Ni center induces an intersystem crossing between the lowest energy singlet and triplet electronic states in the bare active site and in the active site with bound H₂. Potential energy curves between the singlet and triplet minima along the torsion angle and H₂ binding energies to the two spin states were calculated. Upon H₂ binding to the active site, there is a decrease in the torsion angle at the minimum energy crossing point between the singlet and triplet states. The probability of nonadiabatic transitions at temperatures between 270 and 370 K ranges from 35% to 32% for the active site with bound H₂ and from 42% to 38% for the bare active site, thus indicating the importance of spin-forbidden nonadiabatic pathways for H₂ binding on the [NiFe]-hydrogenase active site

Effect of H₂ Binding on the Nonadiabatic Transition Probability between Singlet and Triplet States of the [NiFe]-Hydrogenase Active Site

We investigate the effect of H₂ binding on the spin-forbidden nonadiabatic transition probability between the lowest energy singlet and triplet electronic states of [NiFe]-hydrogenase active site model, using a velocity averaged Landau–Zener theory. Density functional and multireference perturbation theories were used to provide parameters for the Landau–Zener calculations. It was found that variation of the torsion angle between the terminal thiolate ligands around the Ni center induces an intersystem crossing between the lowest energy singlet and triplet electronic states in the bare active site and in the active site with bound H₂. Potential energy curves between the singlet and triplet minima along the torsion angle and H₂ binding energies to the two spin states were calculated. Upon H₂ binding to the active site, there is a decrease in the torsion angle at the minimum energy crossing point between the singlet and triplet states. The probability of nonadiabatic transitions at temperatures between 270 and 370 K ranges from 35% to 32% for the active site with bound H₂ and from 42% to 38% for the bare active site, thus indicating the importance of spin-forbidden nonadiabatic pathways for H₂ binding on the [NiFe]-hydrogenase active site

Quantum-Chemical Study of the Sorption and Migration of Carbon Atom on the Surface of Graphene and Bigraphene

With using of quantum-chemical calculations the binding energies of adatom on graphene and bigraphene in different positions, as well as the binding energies between layers in AA and AB type bigraphene were investigated. The values of energy barriers of transitions in graphene and bigraphene were calculated. It was shown that values of energy barriers of transitions in bigraphene is less than value of energy barrier of transition in graphene, because of weak dispersive interaction of the adatom with the second layer.С помощью квантово-химических расчетов исследованы энергии взаимодействия адатома углерода с поверхностью графена и биграфена в различных положениях, а также энергии взаимодействия плоскостей биграфена AA и AB типа. Рассчитаны величины энергетических барьеров переходов в графене и биграфене. Показано, что величины энергетических барьеров переходов в биграфене меньше, чем величина энергетического барьера перехода в графене вследствие слабого дисперсионного взаимодействия адатома со вторым слоем

Quantum-Chemical Study of the Sorption and Migration of Carbon Atom on the Surface of Graphene and Bigraphene

With using of quantum-chemical calculations the binding energies of adatom on graphene and bigraphene in different positions, as well as the binding energies between layers in AA and AB type bigraphene were investigated. The values of energy barriers of transitions in graphene and bigraphene were calculated. It was shown that values of energy barriers of transitions in bigraphene is less than value of energy barrier of transition in graphene, because of weak dispersive interaction of the adatom with the second layer.С помощью квантово-химических расчетов исследованы энергии взаимодействия адатома углерода с поверхностью графена и биграфена в различных положениях, а также энергии взаимодействия плоскостей биграфена AA и AB типа. Рассчитаны величины энергетических барьеров переходов в графене и биграфене. Показано, что величины энергетических барьеров переходов в биграфене меньше, чем величина энергетического барьера перехода в графене вследствие слабого дисперсионного взаимодействия адатома со вторым слоем

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.</p

The OpenMolcas <i>Web</i>: A Community-Driven Approach to Advancing Computational Chemistry

The developments of the open-source Open-Molcas 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

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