A5040252070- Advanced Chemical Physics Studies
- Spectroscopy and Quantum Chemical Studies
- Crystallography and molecular interactions
- Protein Structure and Dynamics
- Computational Drug Discovery Methods
- Ionic liquids properties and applications
- Molecular Junctions and Nanostructures
- Molecular Sensors and Ion Detection
- Molecular spectroscopy and chirality
- Chemical Synthesis and Analysis
- Porphyrin and Phthalocyanine Chemistry
- Surface Chemistry and Catalysis
- Supramolecular Chemistry and Complexes
- Graphene research and applications
- Click Chemistry and Applications
- Photochemistry and Electron Transfer Studies
- Chemical Thermodynamics and Molecular Structure
- Force Microscopy Techniques and Applications
- Organometallic Complex Synthesis and Catalysis
- Trace Elements in Health
- Monoclonal and Polyclonal Antibodies Research
- Metal-Catalyzed Oxygenation Mechanisms
- Synthesis and Catalytic Reactions
- Organic Chemistry Cycloaddition Reactions
- Thermal and Kinetic Analysis
Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
2017-2025
Czech Academy of Sciences
2024
Regional Centre of Advanced Technologies and Materials
2019-2023
Palacký University Olomouc
2019-2023
University of Johannesburg
2014-2017
Pohang University of Science and Technology
2014
Indian Institute of Technology Indore
2009
Indian Institute of Technology Kanpur
2009
We have analyzed the description of non‐covalent interactions in multiple variants self‐consistent charges density functional tight binding (SCC‐DFTB) method. While London dispersion can be easily improved by empirical correction, hydrogen bonding poses a much more difficult problem. implemented an interaction energy decomposition scheme that allowed us to quantify error at level first‐order electrostatic and polarization terms. Both are underestimated because monopole approximation used...
Cationic cyclophanes with bridging and spacer groups possess well-organized semirigid cavities are able to encapsulate stabilize anionic species through diverse molecular interactions. We highlight the precise tuning of functionalized toward selective recognition AMP, GTP, pyrophosphate (PPi) using fluorescence, NMR spectroscopy, density functional theory (DFT).
Abstract It is generally expected that a solvent has only marginal effect on the stability of covalent bond. In this work, we present combined computational and experimental study showing surprising stabilization covalent/dative bond in Me 3 NBH complex with increasing polarity. The results show for given complex, its correlates strength Notably, trends calculated changes binding (free) energies, observed polarity, match differences solvation energies (Δ E solv ) isolated fragments....
This study provides a comprehensive investigation of the structural and vibrational properties protonated cytosine monomers dimers. Experimental IRPD spectroscopy, combined with theoretical calculations, revealed distinct behaviors for monomers...
Semiempirical quantum mechanical (QM) methods with corrections for noncovalent interactions provide a favorable combination of accuracy and computational efficiency that makes them useful tool study large molecular systems. It was, however, noted the these deteriorates at intermolecular distances shorter than equilibrium. In this work, we explore issue systematically using newly developed data set benchmark interaction energies named R160×6. This maps repulsive contacts in organic molecules,...
Abstract The generally observed decrease of the electrostatic energy in complex with increasing solvent polarity has led to assumption that stability complexes ion‐pair hydrogen bonds decreases polarity. Besides, smaller solvent‐accessible surface area (SASA) comparison isolated subsystems results a solvation latter, leading destabilization compared gas phase. In our study, which combines Nuclear Magnetic Resonance, Infrared Spectroscopy experiments, quantum chemical calculations, and...
The compliance constants, the inverse of force constant matrix elements offer advantage that any one them could be calculated directly without need to calculate full Hessian. Here we show such a direct calculation produces accurate results. Since diagonal G and (G(ii),C(ii)) give unique values are independent other internal coordinates, an frequency (nu) is defined which effectively used study related molecules. conventional coordinates for benzene cubane some differ from obtained by method...
Although group (IV–VII) nonmetallic elements do not favor interacting with anionic species, there are counterexamples including the halogen bond. Such binding is known to be related charge deficiency because of adjacent atom's electron withdrawing effect, which creates σ/π-holes at bond-ends. However, a completely opposite behavior exhibited by N2 and O2, have electrostatically positive/negative character around cylindrical-bond-surface/bond-ends. Inspired this, here we elucidate unusual...
In general, the stability of neutral complexes with dative bonds increases as polarity solvent increases. This is based on fact that dipole moment complex charge transferred from donor to acceptor As a result, solvation energy becomes greater than subsystems, causing an increase in stabilization increasing polarity. Our research confirms this assumption, but only when transfer sufficiently large. If it below certain threshold, complex's insufficient result higher subsystems. Thus, magnitude...
Abstract The DFT‐level computational investigations into Gibbs free energies (Δ G ) demonstrate that as the dielectric constant of solvent increases, stabilities [M(NH 3 n ] 2+/3+ ( = 4, 6; M selected 3d transition metals) complexes decrease. However, there is no observed correlation between stability complex and donor number. Analysis charge transfer Wiberg bond indices indicates a dative‐bond character in all complexes. effect assessed through solvation energy determined by change...
Abstract Invited for this month's cover is the group of Prof. Pavel Hobza, Czech Academy Sciences, Prague. The picture shows a powerful automated quantum mechanics based SQM/COSMO approach to protein–ligand scoring. It comprises thorough preparation ligand structures, extensive generation binding complexes, fast geometry relaxation and reliable affinity prediction. Read full text Minireview at 10.1002/cplu.202000120 .
It is generally assumed that hydrogen-bonded complexes are less stable in solvents than the gas phase and their stability decreases with increasing solvent polarity. This assumption based on size of area available to solvent, which always smaller complex compared subsystems, thereby reducing solvation energy. reduction prevails over amplification electrostatic hydrogen bond by polar solvent. In this work, we show, using experimental IR spectroscopy DFT calculations, there whose becomes...
Fluorescent imaging probes have revolutionised cell biology by monitoring cellular objects. However, the lack of fluorescent with high selectivity for RNA has been a drawback. Thus, selective binding sensors is essential. Here, we report fluorescence enhancement upon addition RNA. By exploiting recognition small tetra-cationic probe 1 RNA, also explain possible mode As membrane-permeant probe, provides not only in human neuroblastoma tumour SH-SY5Y line used Parkinson's disease but...
Using computational calculations, we have revisited the potential energy surface (PES) of reaction between OH and SO 2 , which is believed as rate-limiting step in atmospheric formation H 4 . In this work, report for first time presence a pre-reaction hydrogen-bonded complex PES. Based on finding, it has been shown that can be considered two-step process second transformation to product. It was observed due well PES, barrier height got increased by around two-fold step. observation, proposed...
Hemochromatosis (iron overload) encompasses a group of diseases that are characterized by toxic hyperaccumulation iron in parenchymal organs. Currently, only few treatments for this disease have been approved; however, all these possess severe side effects. In study, paradigm hemochromatosis maintenance/preventive therapy is investigated: polymers with negligible systemic biological availability form stable complexes ions the gastrointestinal tract, which reduces iron. Macroporous polymer...
Graphene and its derivatives are useful building blocks for the bottom-up assembly of advanced functional materials. Noncovalently functionalized graphene networks offer a wide range applications. We investigated formation sandwich-like three-layered nanostructures with graphene. Novel architectures have been generated by stacking selected suitable organic molecules based on their characterized donor acceptor strengths vertically surface. This paper describes adsorption electron-acceptor...
Abstract The generally observed decrease of the electrostatic energy in complex with increasing solvent polarity has led to assumption that stability complexes ion‐pair hydrogen bonds decreases polarity. Besides, smaller solvent‐accessible surface area (SASA) comparison isolated subsystems results a solvation latter, leading destabilization compared gas phase. In our study, which combines Nuclear Magnetic Resonance, Infrared Spectroscopy experiments, quantum chemical calculations, and...
Rhomboid proteases play a variety of physiological roles, but rhomboid protease inhibitors have been mostly developed for the E. coli model GlpG. In this work, we screened different electrophilic scaffolds against human mitochondrial PARL and found 4-oxo-β-lactams as submicromolar inhibitors. Multifaceted computations suggest explanations activity at molecular scale provide models covalently bound complexes. Together with straightforward synthesis 4-oxo-β-lactam scaffold, may pave way toward...
Insulin is a key hormone involved in the regulation of overall energetic homeostasis organism. The dimeric character receptor for insulin evokes ideas about its activation or inhibition with peptide dimers that could either trigger block structural transition receptor, leading to activation. Herewith, we present chemical engineering and biological characterization several series specific peptides should be able bind receptors growth factor 1. hormones were interconnected different linkers,...