Bromine and hydrogen play unusual roles as mobile atom and dissociation dynamics moderator, respectively, during roaming in the 3-bromo-4H-1,2,4-triazole anion. The present study of the reactivity of 3-bromo-1H-1,2,4-triazole and 3-bromo-4H-1,2,4-triazole with low-energy electrons reveals the effect of the hydrogen position on the reaction dynamics. We report energy-dependent ion yields for both molecules showing significant differences. Quantum chemical calculations reveal that heavy Br atom migration is energetically more favored than H atom migration in the case of the H atom adjacent to Br. This is enabled by the energetically favorable formation of a noncovalent complex of Br- around the triazole ring. Recently, such complexes have been reported for several other biologically relevant molecules. In the present work, we demonstrate that the position of hydrogen on the ring influences the character of the lowest resonant state and, consequently, the Br- roaming and dissociation dynamics, particularly the neutral release of hydrogen bromide.

• Publikační typ
• časopisecké články MeSH

A series of 12-phenyl-closo-thiaboranes (12-(4-X-C6H4)-closo-1-SB11H10, where X = OMe (2), X = SMe (3), X = Ph (4), and X = NMe2 (5)) has been prepared. Except for 2, all compounds exhibit a chalcogen bond of thiaborane to the phenyl ring or the neighboring molecule as major supramolecular structural motif. 5, having the strongest (-12.47 kcal/mol) structure-making intermolecular interaction via noncovalent S···π(phenyl) chalcogen bond, was crystallized from different solvents in the form of various solvatopolymorphs. n-Hexane and diethyl ether can be removed from 5 easily upon the formation of a porous material with large cavities (up to 20.5% of the unit cell). This first stable and useful noncovalently bound organic framework material with an ultramicroporous structure exhibits a molecular sieve effect. The selective and repeatable adsorption of CO2 to the material crystallized from n-hexane was explained on the basis of cooperative and consecutive machine-like molecular interactions of quadrupolar CO2 molecule with B-H and amino groups inside rectangular cavities.

• Publikační typ
• časopisecké články MeSH

The binding free energy of hydrogen-bonded complexes is generally inversely proportional to the solvent dielectric constant. This occurs because the solvent-accessible surface area of the complex is always smaller than that of the individual subsystems, leading to a reduction in solvation energy. The present study explores the potential for stabilizing hydrogen-bonded complexes in a solvent with higher polarity. Contrary to the established understanding, we have demonstrated that the hydrogen-bonded complex (CH3CH2COOH⋅⋅⋅2,4,6-trimethylpyridine) can be better stabilized in a solvent with higher polarity. In this case, a significant charge transfer between the subsystems results in an increased dipole moment of the complex, leading to its stabilization in a more polar solvent. The expected inverse relationship between binding free energy and solvent dielectric constant is observed when the charge transfer between the subsystems is low. Thus, the magnitude of the charge transfer between subsystems is possibly the key factor in determining the stabilization or destabilization of H-bonded complexes in different solvents. Here, we present a comprehensive study that combines experimental and theoretical approaches, including nuclear magnetic resonance (NMR), infrared (IR) spectroscopies and quantum chemical calculations to validate the findings.

• Klíčová slova
• Hydrogen bonding, IR, Metadynamics, Micro-solvation, NMR, ONIOM, Solvent effect,
• Publikační typ
• časopisecké články MeSH

Machine learning (ML) methods offer a promising route to the construction of universal molecular potentials with high accuracy and low computational cost. It is becoming evident that integrating physical principles into these models, or utilizing them in a Δ-ML scheme, significantly enhances their robustness and transferability. This paper introduces PM6-ML, a Δ-ML method that synergizes the semiempirical quantum-mechanical (SQM) method PM6 with a state-of-the-art ML potential applied as a universal correction. The method demonstrates superior performance over standalone SQM and ML approaches and covers a broader chemical space than its predecessors. It is scalable to systems with thousands of atoms, which makes it applicable to large biomolecular systems. Extensive benchmarking confirms PM6-ML's accuracy and robustness. Its practical application is facilitated by a direct interface to MOPAC. The code and parameters are available at https://github.com/Honza-R/mopac-ml.

• Publikační typ
• časopisecké články MeSH

Two chiral bambusurils, which are diastereomers to each other, show remarkable differences in their binding affinity and selectivity toward inorganic anions as determined by isothermal titration calorimetry. These differences are explained by quantum-chemical calculations.

• Publikační typ
• časopisecké články MeSH

Despite recent tremendous progress in the synthesis of nonplanar chiral aromatics, and helicenes in particular, their conversion to half-sandwich or sandwich transition metal complexes still lags behind, although they represent an attractive family of modular and underexplored chiral architectures with a potential catalytic use. In this work, starting from various chiral helicene-indene proligands, we prepared the enantio- and diastereopure oxa[6]- and oxa[7]helicene-indenido half-sandwich RhI and RhIII complexes and oxa[7]helicene-bisindenido ansa-metallocene FeII complex. To document their use, oxahelicene-indenido half-sandwich RhIII complexes were employed as chiral catalysts in enantioselective C-H arylation of benzo[h]quinolines with 1-diazonaphthoquinones to afford a series of axially chiral biaryls in mostly good to high yields and in up to 96 : 4 er. Thus, we developed stereocontrolled synthesis of chiral helicene-indenido ansa- and half-sandwich metal complexes, successfully demonstrated the first use of such helicene Cp-related metal complexes in enantioselective catalysis, and described an unusual sequence of efficient central-to-helical-to-planar-to-axial chirality transfer.

• Klíčová slova
• C−H activation, ansa-metallocene, enantioselective catalysis, half-sandwich complexes, helicenes,
• Publikační typ
• časopisecké články MeSH

Previously studied complexes with protonic and hydridic hydrogen bonds exhibit significant similarities. The present study provides a detailed investigation of the structure, stabilization, electronic properties, and spectral characteristics of protonic and hydridic hydrogen bonds using low-temperature infrared (IR) spectroscopy and computational methods. Complexes of pentafluorobenzene with ammonia (C₆F₅H⋯NH₃) and triethylgermane with trifluoroiodomethane (Et₃GeH⋯ICF₃) were analyzed using both experimental and computational tools. Additionally, 30 complexes with protonic hydrogen bonds and 30 complexes with hydridic hydrogen bonds were studied computationally. Our findings reveal that, despite the opposite atomic charges on the hydrogens in these hydrogen bonds, and consequently the opposite directions of electron transfer in protonic and hydridic hydrogen bonds, their spectral manifestations - specifically, the red shifts in the X-H stretching frequency and the increase in intensity - are remarkably similar. The study also discusses the limitations of the current IUPAC definition of hydrogen bonding in covering both types of H-bonds and suggests a way to overcome these limitations.

• Publikační typ
• časopisecké články MeSH

The ISWI family protein SMARCA5 contains the ATP-binding pocket that coordinates the catalytic Mg2+ ion and water molecules for ATP hydrolysis. In this study, we demonstrate that SMARCA5 can also possess an alternative metal-binding ability. First, we isolated SMARCA5 on the cobalt column (IMAC) to near homogeneity. Examination of the interactions of SMARCA5 with metal-chelating supports showed that, apart from Co2+, it binds to Cu2+, Zn2+ and Ni2+. The efficiency of the binding to the last-listed metal was influenced by the chelating ligand, resulting in a strong preference for Ni-NTA over the Ni-CM-Asp equivalent. To gain insight in the preferential affinity for the Ni-NTA ligand, QM calculations were performed on model systems and metal-ligand complexes with a limited protein fragment of SMARCA5 containing the double-histidine (dHis) motif. The calculations correlated the observed affinity with the relative stability of the d-block metals to tetradentate ligand coordination over tridentate, as well as their overall octahedral coordination capacity. Likewise, binding free energies derived from model imidazole complexes mirrored the observed Ni-NTA/Ni-CM-Asp preferential affinity. Finally, similar calculations on complexes with a SMARCA5 peptide fragment derived from the AlphaFold structural prediction, captured almost accurately the expected relative stability of the TM complexes, and produced a large energetic separation (~10 kcal∙mol-1) between Ni-NTA and Ni-CM-Asp in favour of the former.

• MeSH
• adenosintrifosfatasy MeSH
• chromozomální proteiny, nehistonové metabolismus   chemie   MeSH
• kovy chemie   metabolismus   MeSH
• kvantová teorie MeSH
• lidé MeSH
• ligandy MeSH
• molekulární modely MeSH
• restrukturace chromatinu MeSH
• vazba proteinů * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• adenosintrifosfatasy MeSH
• chromozomální proteiny, nehistonové MeSH
• kovy MeSH
• ligandy MeSH
• SMARCA5 protein, human MeSH Prohlížeč

Knowledge of reliable geometries and associated intermolecular interaction energy (ΔE) values at key fragments of the potential energy surface (PES) in the gas phase is indispensable for the modeling of various properties of the pyrene dimer (PYD) and other important aggregate systems of a comparatively large size (ca. 50 atoms). The performance of the domain-based local pair natural orbital (DLPNO) variant of the coupled-cluster theory with singles, doubles and perturbative triples in the complete basis set limit [CCSD(T)/CBS] method for highly accurate predictions of the ΔE at a variety of regions of the PES was established for a representative set of pi-stacked dimers, which also includes the PYD. For geometries with the distance between stacked monomers close to a value of such a distance in the ΔE minimum structure, an excellent agreement between the canonical CCSD(T)/CBS results and their DLPNO counterparts was found. This finding enabled us to accurately characterize the lowest-lying configurations of the PYD, and the physical origin of their stabilization was thoroughly analyzed. The proposed DLPNO-CCSD(T)/CBS procedure should be applied with the aim of safely locating a global minimum of the PES and firmly establishing the pertaining ΔE of even larger dimers in studies of packing motifs of organic electronic devices and other novel materials.

• Klíčová slova
• CCSD(T), DLPNO, intermolecular interactions, potential energy surfaces, pyrene dimer,
• MeSH
• dimerizace * MeSH
• molekulární modely MeSH
• pyreny * chemie   MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• pyrene MeSH Prohlížeč
• pyreny * MeSH

N-Acetyllactosamine is a common saccharide motif found in various biologically active glycans. This motif usually works as a backbone for additional modifications and thus significantly influences glycan conformational behavior and biological activity. In this work, we have investigated the type-2 N-acetyllactosamine scaffold using the complete series of its monodeoxyfluorinated analogs. These glycomimetics have been studied by molecular mechanics, quantum mechanics, X-ray crystallography, and various NMR techniques, which have provided a comprehensive and complete insight into the role of individual hydroxyl groups in the conformational behavior and lipophilicity of N-acetyllactosamine.

• MeSH
• aminocukry * chemie   MeSH
• halogenace MeSH
• krystalografie rentgenová MeSH
• kvantová teorie MeSH
• magnetická rezonanční spektroskopie MeSH
• molekulární konformace MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• aminocukry * MeSH
• N-acetyllactosamine MeSH Prohlížeč