Jiří Mareš

Kirkwood–Buff (KB) theory connects measurable thermodynamic properties with radial distribution functions and particle-number fluctuations accessible from molecular dynamics (MD) simulations.

This study uses ²³ Na NMR and quadrupolar relaxation modelling to quantify Na ⁺ partitioning between bulk water, aggregates, and micelles in decanoate solutions, revealing weak binding below the CMC and stronger association at higher concentration.

Advanced NMR relaxation, diffusion, and MD-assisted modeling reveal previously overlooked surfactant aggregation in aqueous sodium decanoate. These aggregates can substantially bias predictions of aerosol hygroscopicity and cloud activation.

We present a molecular restrainer tool capable of energy-minimizing NMR-derived structures using the universal force field (UFF) and NOE-derived distance restraints. The implementation is a part of SAMSON (version 2024 and newer), an integrative molecular design platform. The strength of our tool lies in its ability to swiftly process any molecule and molecular complex without the need to create force field parameters and topology files. We show, using examples, that the quality of these refined structures is significantly improved compared to the starting structures derived by CYANA. Currently, the implementation is targeted toward the postprocessing of structures derived by the software CYANA but can easily be adapted to other molecular restraint formats. This tool enables the generation of publication-ready protein–ligand complex structures for PDB deposition, requiring minimal additional effort beyond the initial NMR structure calculation.

For simple water models, parameters giving the best intermolecular forces cannot provide accurate bulk properties. For AMOEBA model, such parameters can be found.

We exploited ¹²⁹Xe NMR to investigate xenon gas uptake and dynamics in a porous liquid formed by dissolving porous organic cages in a cavity-excluded solvent. Quantitative ¹²⁹Xe NMR shows that when the amount of xenon added to the sample is lower than the amount of cages present (subsaturation), the porous liquid absorbs almost all xenon atoms from the gas phase, with 30% of the cages occupied with a Xe atom. A simple two-site exchange model enables an estimate of the chemical shift of ¹²⁹Xe in the cages, which is in good agreement with the value provided by first-principles modeling. T₂ relaxation times allow the determination of the exchange rate of Xe between the solvent and cage sites as well as the activation energies of the exchange. The ¹²⁹Xe NMR analysis also enables determination of the free energy of confinement, and it shows that Xe binding is predominantly enthalpy-driven.

Having a force field for water providing good bulk properties is paramount for modern studies of most biological systems. Some of the most common three-site force fields are TIP3, SPC/ϵ or OPC3, providing a decent range of bulk properties. That does not mean though, that they have realistic inter- atomic forces. These force fields have been parameterized with a top-down approach, meaning, by fitting the force field parameters to the experimental bulk properties. This approach has been the governing strategy also for many variants of four- and more-site models. We test a bottom- up approach, in which the force field is parameterized by optimizing the non-bonded inter-atomic forces. Our philosophy is that correct inter-atomic forces lead to correct geometrical and dynamical properties. The first system we try to optimize with the accurately system tailored atomic (ASTA) approach is water, but we aim to eventually probe other systems in the future as well. We applied our ASTA strategy to find a good set of parameters providing accurate bulk properties for the simple three-site force field forms, and also for AMOEBA, a more detailed and polarizable force field. Even though our bottom-up approach did not provide satisfactory results for the simple three-site force fields (with fixed charges), for the case of the AMOEBA force field it led to a modification of the original strategy, giving very good intra- and inter-molecular forces, as compared to accurate quantum chemically calculated reference forces. At the same time, important bulk properties, in this study restricted to the density and diffusion, were accurately reproduced with respect to the experimental values.

A shifted phase transition distribution (SIDI) approach enables the determination of NMR cryoporometry and DSC thermoporometry pore size distributions using salty solutions inherently existing in biological porous materials and porous electrolytes.

Developed multi-step computational protocol successfully models the¹³C NMR shielding tensor of carbonate in paramagnetic Mg_2−xNi_xAl-LDH.

The chemical exchange of labile protons of the hydroxyl groups can be exploited in a variety of magnetic resonance experiments to gain information about the groups and their physicochemical environment. The exchangeable –OH protons provide important contributions to the T₂ of water signals thus contributing to the T₂-weighted contrast of MRI images. This exchange can be exploited more specifically and sensitively in chemical exchange saturation transfer (CEST) or longitudinal rotating frame relaxation (T_1,ρ) experiments. Since glucose is omnipresent in living organisms, it may be seen as a rather universal probe. Even though the potential was first recognized many years ago, practical use has remained scarce due to numerous challenges. The major limitation is the rather low glucose concentration in most tissues. The other obstacles are related to multiple dependencies of the exchange parameters, such as temperature, pH, and concentration of various ions that are not known in sufficient detail for glucose. Thus, we embarked on evaluating the exchange parameters of a model that included every relevant chemical site for all –OH protons in both dominant enantiomers of glucose. We have (1) obtained conventional one-dimensional proton NMR spectra of glucose solutions in suitable temperature ranges, (2) we have iterated through several exchange models with various degrees of freedom determined by the number of distinguishable –OH proton sites and compared their performance, (3) we extrapolated the parameters of the best model of physiological temperature and (4) we demonstrated the use of the parameters in virtual experiments. As the main results, (1) we have obtained the temperature dependence of exchange parameters with reliable confidence intervals in three different pH values, with two of them reaching physiological temperature, and (2) we show how the parameters can be used in virtual experiments, helping to develop new applications for glucose as an NMR/MRI probe.