Scientists from the IOCB Prague, the Institute of Physics of the Czech Academy of Sciences, and Palacký University Olomouc, have once again successfully uncovered the mysteries of the world of molecules and atoms. They have experimentally confirmed the correctness of a decades-old theory that assumed a non-uniform distribution of electron density in aromatic molecules. This phenomenon significantly affects the physicochemical properties of molecules and their interactions. This research expands the possibilities for designing new nanomaterials and is the theme of a paper that has just been published in Nature Communications.
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Scientists_continue_to_push_the_boundaries_of_imaging_techniques_and_reveal_the_mysterious_world_of_molecules_Experimental_measurements_35db678a3f.jpg" alt="IOCB Prague: Scientists continue to push the boundaries of imaging techniques and reveal the mysterious world of molecules. Experimental measurements confirmed the theoretical predictions of the existence of the π-hole. From left to right: Chemical structure of the investigated molecule, calculated electrostatic potential map of the molecule, experimental Kelvin probe force microscopy (KPFM) image, and simulated KPFM image."/>
The same team of authors in its previous groundbreaking study published in Science described the non-uniform distribution of electrons in an atom, the so-called σ-hole. Now the researchers have confirmed the existence of the so-called π-hole. In aromatic hydrocarbons, we find electrons in clouds above and below the plane of carbon atoms. If we replace the peripheral hydrogens with more electronegative atoms or groups of atoms that pull electrons away, the originally negatively charged clouds turn into positively charged electron holes.
Scientists have taken the advanced method of scanning electron microscopy and pushed its capabilities further. The method works at subatomic resolution and can therefore image not only atoms in molecules but also the structure of the electron shell of an atom. As one of the researchers involved, Bruno de la Torre from the Czech Advanced Technology and Research Institute (CATRIN) of Palacký University Olomouc, points out, the success of the experiment described here is mainly due to the excellent facilities at his home institution and the participation of excellent Ph.D. students.
&quot;Thanks to our previous experience with the Kelvin Probe Force Microscopy (KPFM) technique, we have been able to refine our measurements and acquire very complete data sets that have helped us to deepen our understanding not only of how the charge is distributed in the molecules but also of what observables are obtained with the technique,&quot; says Bruno de la Torre.
Modern force microscopy has long been the domain of researchers at the Institute of Physics. Not only in the case of molecular structures have they used the unprecedented spatial resolution to the full. Some time ago they confirmed the existence of a non-uniform distribution of electron density around halogen atoms, the so-called σ-holes. This achievement was published in 2021 by Science. The former as well as current research was significantly contributed to by one of the most cited Czech scientists of today, Prof. <a href="https://hobza.group.uochb.cz/en">Pavel Hobza</a> from the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague).
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Scientists_continue_to_push_the_boundaries_of_imaging_techniques_and_reveal_the_mysterious_world_of_molecules_Prof_Pavel_Hobza_1119814488.jpg" alt="IOCB Prague / Tomáš Belloň: Scientists continue to push the boundaries of imaging techniques and reveal the mysterious world of molecules. Prof. Pavel Hobza, Distinguished Chair &amp; head of the Non-Covalent Interactions group at IOCB Prague."/>
&quot;The confirmation of the existence of the π-hole, as well as the σ-hole before it, fully demonstrates the quality of the theoretical predictions of quantum chemistry, which have accounted for both phenomena for decades. It shows that they can be relied upon even in the absence of available experiments,&quot; says Pavel Hobza.
The results of Czech scientists’ research at the subatomic and submolecular levels can be compared to the discovery of cosmic black holes. They had also been theorized for decades before their existence was confirmed by experiments.
A better knowledge of the distribution of the electron charge will help the scientific community to understand many chemical and biological processes in the first place. On a practical level, it will translate into the ability to build new supramolecules and subsequently into the development of advanced nanomaterials with improved properties.

Scientists continue to push the boundaries of imaging techniques and reveal the mysterious world of molecules

CHAMPAIGN, Ill. — Scientists tested nine fish species from four northern Illinois rivers for contamination with per- or polyfluoroalkyl substances, synthetic chemicals found in numerous industrial and commercial products and known to be harmful to human health. They found fish contaminated with PFAS in every one of their 15 test sites. Elevated levels of PFOS, one type of PFAS compound, were found in nearly all fish tested.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/University_of_Illinois_Urbana_Champaign_Fred_Zwicky_U_of_I_bioengineering_professor_Joseph_Irudayaraj_and_his_colleagues_found_PFAS_contaminated_fish_in_every_one_of_the_15_sites_they_853f56f1d8.jpg" alt="University of Illinois Urbana-Champaign / Fred Zwicky: Joseph Irudayaraj in the lab U. of I. bioengineering professor Joseph Irudayaraj and his colleagues found PFAS-contaminated fish in every one of the 15 sites they tested along four northern Illinois rivers." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_University_of_Illinois_Urbana_Champaign_Fred_Zwicky_U_of_I_bioengineering_professor_Joseph_Irudayaraj_and_his_colleagues_found_PFAS_contaminated_fish_in_every_one_of_the_15_sites_they_853f56f1d8.jpg 234w," sizes="100vw" width="1200" height="800">The findings are reported in the journal Science of the Total Environment.The qualities that make PFAS desirable for industrial uses — their durability and stability under stresses such as high heat or exposure to water, for example — also make these chemicals particularly problematic in the environment and hazardous to human and animal health, said&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://bioengineering.illinois.edu/people/jirudaya">Joseph Irudayaraj</a>, a professor of&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://bioengineering.illinois.edu/">bioengineering</a> at the University of Illinois Urbana-Champaign who led the new study. &nbsp;“PFAS contain multiple carbon-fluorine bonds, one of the strongest bonds in organic chemistry,” Irudayaraj said. “Because of this, they are also very hard to break down. They persist for a long time because they are very, very stable.”&nbsp;There are nearly 15,000 PFAS chemicals, according to the U.S. Environmental Protection Agency. These are classified either as short-chain PFAS, which have less than six carbon-fluorine bonds, and long-chain PFAS, with six or more of these bonds, Irudayaraj said.Long-chain PFAS were widely used before awareness grew about the hazards of these chemicals. More recently, many industries switched to using short-chain PFAS.“It was thought that the short-chain PFAS were less toxic, and that they could more easily degrade,” he said. “But surprisingly, that was not the case.”&nbsp;Now, both types of PFAS are found in groundwater, soil and human tissues.“About 99% of people living in the U.S. have PFAS in their system,” Irudayaraj said.&nbsp;Despite a voluntary phasing out of some PFAS in industry in the U.S. and efforts to reduce PFAS pollution, these chemicals are still found in drinking water, household products, food packaging and agricultural products, he said.&nbsp;The researchers focused on fish in northern Illinois rivers because they are close to urban and industrial areas. Industrial emissions and urban rainwater runoff may further contaminate local waterways with PFAS. Sport fishing is also popular across the state, including in areas inside and near Chicago. More than 666,000 fishing licenses were issued across the state of Illinois in 2020.The researchers focused on fish in the Pecatonica River, Rock River, Sugar River and Yellow Creek from 2021-22. The team collected dozens of samples from nine species of fish, including bluegill, channel catfish, common carp, northern pike, smallmouth bass and walleye. The fish represented different levels of the food chain, from those that feed only on plants, like bluegill, to those eating other fish, such as channel catfish and northern pike.&nbsp;Back in the lab, the scientists analyzed fish tissues for 17 PFAS chemicals. They found PFAS-contaminated fish in every river they tested and in every one of their 15 sampling sites. Fish from the Rock River had the highest concentrations of PFAS in their tissues. Contamination levels were highest in channel catfish, at the top of the food chain, and lowest in the plant eaters.&nbsp;<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/University_of_Illinois_Urbana_Champaign_Eric_Engbretson_USFWS_U_of_I_Channel_catfish_had_the_highest_accumulation_of_PFAS_in_their_tissues_the_researchers_found_00231c2241.jpg" alt="University of Illinois Urbana-Champaign / Eric Engbretson / USFWS: Channel catfish had the highest accumulation of PFAS in their tissues, the researchers found. " srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_University_of_Illinois_Urbana_Champaign_Eric_Engbretson_USFWS_U_of_I_Channel_catfish_had_the_highest_accumulation_of_PFAS_in_their_tissues_the_researchers_found_00231c2241.jpg 234w," sizes="100vw" width="1200" height="800">Four chemicals known as perfluorooctanesulfonic acids or PFOS were detected in fish from every site tested.&nbsp;“These are long-chain PFAS that have been in use over the past few decades,” Irudayaraj said. “They were found in all the sites, along with a few short-chain PFAS.”&nbsp;Because fish are mobile, it is problematic to tie their contamination levels to the locale where they were sampled, he said. But the finding is worrisome for people who are exposed to the water or eating the fish from these sites.&nbsp;“Further studies are warranted to comprehensively evaluate the occurrence and sources of PFAS throughout the state of Illinois,” the researchers wrote. “Such information is crucial to better understand the distribution and potential risks of these compounds to the environment.”Bioengineering is a department in the&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://grainger.illinois.edu/">The Grainger College of Engineering</a> at Illinois. Irudayaraj also is a professor in the&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://beckman.illinois.edu/">Beckman Institute for Advanced Science and Technology</a> and an affiliate of the&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.igb.illinois.edu/">Carl R. Woese Institute for Genomic Biology</a> and the&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://medicine.illinois.edu/">Carle Illinois College of Medicine</a> at the U. of I.

PFAS found in nearly all fish tested from four northern Illinois rivers

A research team at IOCB Prague led by Jiří Kaleta has described a new concept for light-driven molecular motors that remain fully functional even after being anchored to a metal surface, where they continue to perform controlled rotary motion. The scientists have thus overcome one of the main obstacles on the road to fully controllable molecular machines – a development expected to have a major impact on the creation of intelligent materials, among other applications. The study provides deeper insight into the control of motion at the nanoscale. The paper was published in the journal Angewandte Chemie International Edition.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Tomas_Bellon_UOCHB_Dr_Jiri_Kaleta_vedouci_vedecke_skupiny_Molekularni_stroje_UOCHB_4585ced86b.jpg" alt="Tomáš Belloň / IOCB Prague: Dr. Jiří Kaleta, head of the Molecular Devices group at IOCB Prague" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Tomas_Bellon_UOCHB_Dr_Jiri_Kaleta_vedouci_vedecke_skupiny_Molekularni_stroje_UOCHB_4585ced86b.jpg 234w," sizes="100vw" width="1600" height="1068">The study of molecular motors is among the most fascinating areas of contemporary chemistry and nanotechnology. Comprising only a few dozen atoms, these machines can move or rotate in a precisely defined direction when exposed to an external stimulus, such as light. The team at IOCB has developed two types of so-called four-legged motors attached to a rigid triptycene base. Triptycene is a three-dimensional structure that holds the stationary part of the motor slightly above the surface, allowing the rotor to move freely and in a precisely controlled manner. Upon exposure to light, the rotor first makes a partial turn and then completes the rotation through the influence of heat, resulting in a full, controlled 360° rotation. Kateřina Bezděková, the first author of the study and a member of <a target="_blank" rel="noopener noreferrer" href="https://kaleta.group.uochb.cz/en">Kaleta’s research group</a>, explains: „Our motors are designed like building blocks, making them easy to adjust for different applications. We show that controlled motion at the molecular level can not only be achieved but also modified.”Jiří Kaleta’s team succeeded in overcoming one of the major technical challenges: molecules attached to solid surfaces often lose their ability to move due to excessively tight contact with the substrate. Thanks to the innovative design, the motors remain mobile under all conditions. “By using a rigid triptycene base, we managed to solve several problems,” explains Jiří Kaleta. “Among other things, we effectively decoupled the photoactive part of the motor from the surface. As a result, it retains its mobility and can be easily controlled by light.”The results from IOCB Prague pave the way for the practical use of molecular machines, for example in the development of intelligent materials, photoactive switches, or surface sensors. “Every step that improves our ability to control motion at the atomic level brings us closer to the time when molecular machines will perform precisely defined tasks – just like the machines we know from the macroscopic world, only a billion times smaller,” adds Jiří Kaleta.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/IOCB_Prague_Molecular_motors_aa40e38cb0.jpg" alt="IOCB Prague: Two tetrapodal triptycene-based light-driven molecular motors with precisely oriented rotation axes—parallel or perpendicular to a gold surface—achieve full 360° rotation in both solution and as monolayers. The design minimizes surface quenching, enabling functional integration into surface-mounted nanomachines." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_IOCB_Prague_Molecular_motors_aa40e38cb0.jpg 209w," sizes="100vw" width="667" height="498"><blockquote><h4>The original article</h4><h4><a target="_blank" rel="noopener noreferrer" href="https://onlinelibrary.wiley.com/doi/10.1002/anie.202513922">Surface-Decoupled Altitudinal and Azimuthal Triptycene-Fused Tetrapodal Molecular Motors</a></h4>Kateřina Bezděková, Lukáš Severa, Eva Kaletová, Katarina Majerová Varga, Milan Mašát, Liang-Ting Wu, Jyh-Chiang Jiang, Ivana Císařová, Jiří KaletaAngew. Chem., Int. Ed. 2025.<a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1002/anie.202513922">https://doi.org/10.1002/anie.202513922</a><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a></h6></blockquote><h4>Abstract</h4>Two light-driven molecular motors, fused to a triptycene-based tetrapodal platform, with rotational axes oriented either parallel or perpendicular to the surface, were successfully designed and synthesized. Both systems demonstrated complete 360° rotation cycles, efficient photoswitching at 385 ± 5 nm (reaching ∼90% at the photostationary state), and quantitative thermal helix inversion with half-lives of ∼7 min at 20 °C. When assembled as monolayers on gold surfaces, the motors retained their full rotational functionality, demonstrating the ability of the tetrapodal platform to minimize surface interactions. These findings highlight the potential of these systems for applications in surface-integrated molecular devices and machines.

IOCB researchers take a key step toward fully controllable molecular machines

A team of researchers at IOCB Prague headed by Dr. Tomáš Slanina has developed a new method for labeling molecules with fluorescent dyes that surpasses existing approaches in both precision and stability. The new fluorescent label remains covalently bonded to its target molecule and does not fall apart even under demanding conditions inside living cells. This allows scientists to track labeled molecules over long periods with high reliability – an advantage for research in biology, chemistry, and medicine. The study was published in Angewandte Chemie International Edition.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Tomas_Bellon_UOCHB_Dr_Tomas_Slanina_vedouci_vedecke_skupiny_Redoxni_fotochemie_a_Lucie_Salkova_doktorandka_UOCHB_36ca9e4598.jpg" alt="Tomáš Belloň / IOCB Prague: Dr. Tomáš Slanina, head of the Redox Photochemistry research group, and Lucie Šálková, PhD student, IOCB Prague" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Tomas_Bellon_UOCHB_Dr_Tomas_Slanina_vedouci_vedecke_skupiny_Redoxni_fotochemie_a_Lucie_Salkova_doktorandka_UOCHB_36ca9e4598.jpg 234w," sizes="100vw" width="1600" height="1068">Fluorescent labeling of proteins and peptides enables scientists to determine where a molecule is located in a cell and how its behavior changes over time. Current methods, however, have clear limitations. The label often attaches to an unintended site on the molecule, potentially disrupting its structure and, in extreme cases, even its biological function. Moreover, molecules labeled in this way tend to be unstable and can easily unlabel in the cellular environment.“In our work, we applied a highly precise peptide-labeling approach that uses a two-step chemical reaction triggered by light. This allows us to create exceptionally stable fluorescently labeled molecules,” says Tomáš Slanina.The new method from IOCB Prague combines the best features of existing strategies – namely, precision and outstanding molecular stability.Fluorescent labeling proceeds in two steps. First, the dye attaches to the molecule at a precisely defined position. Then, upon exposure to light, the attached label is “glued” in place, converting a temporary bond into a permanent, chemically robust one.“We call the method Stick and Glue!" explains Lucie Šálková, the study’s first author and a PhD student. “Imagine someone dancing with a glow stick. If the stick isn’t activated, you can’t see it and they disappear into the crowd – they might even drop it. But once they snap it and fasten it to their wrist, they won’t lose it, and you can easily spot where they are. Our method works similarly. First, we attach the fluorescent dye, and only after illuminating it with light do we stabilize it – we glue it to the target molecule. From then on, the molecule can be tracked easily without the dye falling off. Unlike other methods, our glow sticks don’t end up scattered on the floor at the end of the night,” she adds.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Banka_s_fluorescencne_znacenym_glutathionem_242a93510b.jpg" alt="IOCB: The photo shows a flask containing fluorescently labeled glutathione. Glutathione is a small tripeptide and one of the most important antioxidants in cells – it helps neutralize free radicals and protects cells from oxidative stress. In our research, it served as a model molecule to test a new labeling method. While glutathione consists of three amino acids, by the end of the project, we were able to label a protein containing 583 amino acids. This sample, therefore, represents an important milestone of the project – the moment we confirmed that our method truly works. The image captures the lyophilization step, during which the peptide is being dried after conjugation. The visible transition from yellow to red color is related to changes in the fluorophore’s environment as the sample dries." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_UOCHB_Banka_s_fluorescencne_znacenym_glutathionem_242a93510b.jpg 117w," sizes="100vw" width="1600" height="2133">The innovative labeling method developed at IOCB Prague offers a universal, precise, gentle, and permanent way of attaching fluorescent dyes – suitable for small molecules as well as large peptides and proteins. These highly stable labels allow scientists to monitor the movement of selected biomolecules in cells and study their interactions with their environment. The technology expands the possibilities for research in biology, chemistry, and materials science and may contribute to the development of new diagnostic and therapeutic tools.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Angew_Chem_Int_Ed_Engl_2025_Nov_2e15338_figure_1_36885ae230.jpg" alt="Angew Chem Int Ed Engl. 2025 Nov 2:e15338: Figure 1 - Comparison of different labeling methods: a) iodoacetamide, b) maleimide, and c) MTS and our approach." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Angew_Chem_Int_Ed_Engl_2025_Nov_2e15338_figure_1_36885ae230.jpg 245w," sizes="100vw" width="1344" height="375"><blockquote><h4>The original article</h4><h4><a target="_blank" rel="noopener noreferrer" href="https://onlinelibrary.wiley.com/doi/10.1002/anie.202515338">Thiosulfonate-Derived BODIPY “Stick and Glue” Strategy for Fluorescent Thiol Labeling</a></h4>Lucie Šálková, David Dunlop, B. Buse Tütüncü, Dr. Zdeněk Knejzlík, Dr. Tomáš SlaninaAngew Chem Int Ed Engl. 2025 Nov 2:e15338.&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1002/anie.202515338">https://doi.org/10.1002/anie.202515338</a><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a></h6></blockquote>

Stick and Glue! Tomáš Slanina and his team introduce a new biomolecule-labeling method for more precise observation of cellular processes

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The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague) is a leading scientific institution in the Czech Republic, recognized internationally. Its primary mission is basic research in the fields of chemical biology and medicinal chemistry, organic and material oriented chemistry, chemistry of natural compounds, biochemistry and molecular biology, physical chemistry, theoretical chemistry, and analytical chemistry. 

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

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Stick and Glue! Tomáš Slanina and his team introduce a new biomolecule-labeling method for more precise observation of cellular processes

IOCB researchers take a key step toward fully controllable molecular machines

PFAS found in nearly all fish tested from four northern Illinois rivers

Scientists continue to push the boundaries of imaging techniques and reveal the mysterious world of molecules

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