Quantum mechanical (QM) methods are becoming popular in computational drug design and development mainly because high accuracy is required to estimate (relative) binding affinities. For low-to medium-throughput in silico screening, (e.g., scoring and prioritizing a series of inhibitors sharing the same molecular scaffold) efficient approximations have been developed in the past decade, like lin...

Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the asymptotic limit of key energetic and structural properties with respect to increasingly large QM regions. Leveraging recent advances in electronic structure efficiency and accuracy, we investigate catalytic propertie...

Chemical standardization, along with morphological and DNA analysis ensures the authenticity and advances the integrity evaluation of botanical preparations. Achievement of a more comprehensive, metabolomic standardization requires simultaneous quantitation of multiple marker compounds. Employing quantitative 1H NMR (qHNMR), this study determined the total isoflavone content (TIfCo; 34.5-36.5% ...

Accurate precipitation forecasting is challenging, especially on the sub-seasonal to seasonal scale (14–90 days) which mandates bias correction. Quantile mapping (QM) has been employed as a universal method of correction it effective in correcting distribution attributes mean and variance, but neglects correlation between model observation data computing inefficiency large-scale applications. I...

To understand the functional mechanisms of biological macromolecular systems, investigations of both the three-dimensional geometric and electronic structures are important. Accordingly, quantum mechanical (QM) calculations are essential to obtain the properties relevant to the electronic structures of the macromolecular systems. However, because of the high computational costs, only a few hund...

1 2 JIŘ´I SOUČEK Abstract. We present models in which the indeterministic feature of Quantum Mechanics is represented in the form of definite physical mechanisms. Our way is completely different from so-called hidden parameter models, namely, we start from a certain variant of QM – deterministic QM – which has most features similar to QM, but the evolution in this theory is deterministic. Then ...

The old Bohr–Einstein debate about the completeness of quantum mechanics (QM) was held on an ontological ground. The completeness problem becomes more tractable, however, if it is preliminarily discussed from a semantic viewpoint. Indeed every physical theory adopts, explicitly or not, a truth theory for its observative language, in terms of which the notions of semantic objectivity and semanti...

Interpreting Quantum Theories attempts and achieves no less than three different goals. First, it provides an accessible introduction to the conceptual foundations of the algebraic approach to quantum theories—today’s most promising rigorous framework for the formulation of quantum theories that includes those applying to systems with an infinite number of degrees of freedom. Second, it present...

We here suggest and test a new method to obtain stable energies in proteins for charge-neutral reactions by running large quantum mechanical (QM) calculations on structures obtained by combined QM and molecular mechanics (QM/MM) geometry optimization on several snapshots from molecular dynamics simulations. As a test case, we use a proton transfer between a metal-bound cysteine residue and a se...

Lately, there has been great interest in performing free-energy perturbation (FEP) at the combined quantum mechanics and molecular mechanics (QM/MM) level, e.g. for enzyme reactions. Such calculations require extensive sampling of phase space, which typically is prohibitive with density-functional theory or ab initio methods. Therefore, such calculations have mostly been performed with semiempi...