arXiv subjects

Pavel Hobza

Publications and source records attributed to Pavel Hobza.

4 recordsLinked to original sources

arXiv2020

Ground State of the Fe(II)-porphyrin Model System Corresponds to the Quintet State: A DFT and DMRG-based Tailored CC Study

Fe(II)-porphyrins (FeP) play an important role in many reactions relevant to material science and biological processes, due to their closely lying spin states. However, this small energetic separation also makes it challenging to establish the correct spin state ordering. Although the prevalent opinion is that these systems posses the triplet ground state, the recent experiment on Fe(II)-phthalocyanine under conditions matching those of an isolated molecule points toward the quintet ground state. We present a thorough study of FeP model by means of the density functional theory and density matrix renormalization group based tailored coupled clusters, in which we address all previously discussed correlation effects. We examine the importance of geometrical parameters, the Fe-N distances in particular, and conclude that the system possesses the quintet ground state, which is in our calculations well-separated from the triplet state.

physics.chem-ph↗

arXiv2017

Statistical Analysis of $σ$-Holes: A Novel Complementary View on Halogen Bonding

To contribute to the understanding of noncovalent binding of halogenated molecules with a biological activity, electrostatic potential (ESP) maps of more than 2,500 compounds were thoroughly analysed. A peculiar region of positive ESP, called $σ$-hole, is a concept of central importance for halogen bonding. We aim at simplifying the view on $σ$-holes and provide general trends in organic drug-like molecules. The results are in fair agreement with crystallographic surveys of small molecules as well as of biomolecular complexes and attempt to improve the intuition of chemists when dealing with halogenated compounds.

physics.chem-ph↗

arXiv2017

Computer Modeling of Halogen Bonds and Other $σ$-Hole Interactions

In the field of noncovalent interactions a new paradigm has recently become popular. It stems from the analysis of molecular electrostatic potentials and introduces a label, which has recently attracted enormous attention. The label is σ-hole, and it was first used in connection with halogens. It initiated a renaissance of interest in halogenated compounds, and later on, when found also on other groups of atoms (chalcogens, pnicogens, tetrels and aerogens), it resulted in a new direction of research of intermolecular interactions. In this review, we summarize advances from about the last 10 years in understanding those interactions related to σ-hole. We pay particular attention to theoretical and computational techniques, which play a crucial role in the field.

physics.chem-ph↗

arXiv2016

Quantum Monte Carlo for Noncovalent Interactions: An Efficient Protocol Attaining Benchmark Accuracy

Reliable theoretical predictions of noncovalent interaction energies, which are important e.g. in drug-design and hydrogen-storage applications, belong to longstanding challenges of contemporary quantum chemistry. In this respect, the fixed-node diffusion Monte Carlo (FN-DMC) is a promising alternative to the commonly used "gold standard" coupled-cluster CCSD(T)/CBS method for its benchmark accuracy and favourable scaling, in contrast to other correlated wave function approaches. This work is focused on the analysis of protocols and possible tradeoffs for FN-DMC estimations of noncovalent interaction energies and proposes an efficient yet accurate computational protocol using simplified explicit correlation terms with a favorable O(N^3) scaling. It achieves an excellent agreement (mean unsigned error ~0.2 kcal/mol) with respect to the CCSD(T)/CBS data on a number of complexes, including benzene/hydrogen,T-shape benzene dimer, stacked adenine-thymine and a set of small noncovalent complexes A24. The high accuracy and reduced computational costs predestinate the reported protocol for practical interaction energy calculations of large noncovalent complexes, where the CCSD(T)/CBS is prohibitively expensive.

physics.chem-ph↗