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Item type:Publication, Access status: with files , Thermodynamic mapping of C5-substituent autoxidation pathways in 1,5-dimethylcytosine: a quantum chemical studyThe autoxidation pathways of the methyl substituent at position 5 in 1,5-dimethylcytosine (1,5dmC) were investigated using DFT and DLPNO-CCSD(T) calculations with implicit SMD(H2O) solvation. A radical reaction network was constructed to assess nonenzymatic pathways leading to hydroxymethyl, formyl, and carboxyl oxidation products. The results show that the reactivity of methylated cytosine derivatives is governed not by isolated C-H bond strengths alone, but by the coupled thermodynamics of radical formation, oxygen addition, hydroperoxide formation, and hydroperoxide decomposition. Hydrogen abstraction from the 5-methyl substituent is the most accessible radical-forming step in 1,5dmC, whereas protonation increases BDE(C-H) values and suppresses radical formation. Hydroperoxide intermediates play an important role within the considered propagation network, with O-O cleavage being more accessible than O-H cleavage. The calculated reaction free energies rationalize the possible accumulation of the formyl derivative 1m5fC: this formyl derivative is formed through strongly exergonic pathways, whereas its further conversion to the carboxyl derivative 1m5caC is more thermodynamically constrained. Representative transition-state calculations provide a kinetic consistency check, showing only moderate substrate-dependent variations in H-abstraction barriers within each model-radical class. Overall, the results identify thermodynamically relevant radical intermediates, limiting steps, and product-forming routes within the considered reaction network for the nonenzymatic autoxidation of methylated cytosine derivatives.Publicationtype: Journal Article3 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Unveiling hidden intramolecular non-covalent interactions in a neutral serine, its zwitterion, cluster, and crystal by features of electron densityWe investigate intramolecular non-covalent interactions (NCIs) in neutral serine, its zwitterion, molecular clusters, and crystal using electron density-based approaches, including QTAIM, RDG, IQA, and electronic pressure analysis. In addition to completed NCIs (hydrogen bonds with bond paths), we identify latent interactions—attractive, bond-path-free atomic pair interactions with negative interaction energies. These are classified into dynamic (vibration-induced and transient) and static (secondary, persistent but structurally passive) types. Analysis of the internal pressure in electronic continuum reveals that latent NCIs exhibit distinct signatures in the kinetic and exchange components, which evolve across the molecular, cluster, and crystalline states. Dynamic interactions are characterized by off-axis minima in the exchange part of the pressure, whereas static interactions lack such features. Upon crystallization, intramolecular latent NCIs may disappear due to electron density redistribution and the formation of intermolecular hydrogen bonds. These intermolecular contacts may also spatially constrain atoms, suppressing vibrational flexibility and effectively converting dynamic NCIs into static ones. The kinetic pressure highlights regions of electron localization, while the exchange pressure offers a physical criterion for distinguishing different types of NCIs. Our findings demonstrate the structural and stabilizing roles of latent interactions and establish electronic pressure as a sensitive and informative descriptor for their analysis.Publicationtype: Journal Article54 10 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , The stability of oxygen-centered radicals and its response to hydrogen bonding interactionsThe stability of various alkoxy/aryloxy/peroxy radicals, as well as TEMPO and triplet dioxygen (3O2) has been explored at a variety of theoretical levels. Good correlations between RSEtheor and RSEexp are found for hybrid DFT methods, for compound schemes such as G3B3-D3, and also for DLPNO-CCSD(T) calculations. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have been probed by addition of a single solvating water molecule. While this water molecule always acts as a H-bond donor to the oxygen-centered radical itself, it can act as a H-bond donor or acceptor to the respective closed-shell parent.Publicationtype: Journal Article29 12 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficientsThe importance of membrane-water partition coefficients led to the recent extension of the conductor-like screening model for realistic solvation (COSMO-RS) to micelles and biomembranes termed COSMOmic. Compared to COSMO-RS, this new approach needs structural information to account for the anisotropy of colloidal systems. This information can be obtained from molecular dynamics (MD) simulations. In this work, we show that this combination of molecular methods can efficiently be used to predict partition coefficients with good agreement to experimental data and enables screening studies. However, there is a discrepancy between the amount of data generated by MD simulations and the structural information needed for COSMOmic. Therefore, a new scheme is presented to extract data from MD trajectories for COSMOmic calculations. In particular, we show how to calculate the system structure from MD, the influence of lipid conformers, the relation to the COSMOmic layer size, and the water/lipid ratio impact. For a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer, 66 partition coefficients for various solutes were calculated. Further, 52 partition coefficients for a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer system were calculated. All these calculations were compared to experimental data. © 2013 Wiley Periodicals, Inc.Publicationtype: Journal Article78