Article
Chemistry, Multidisciplinary
Clemens Mueller, Kevin Scholten, Elric Engelage, Christian Merten
Summary: In this study, the conformational preferences of a series of chiral octaazacryptands were investigated using experimental and computational techniques. The results indicate that these octaazacryptands prefer a collapsed structure in solution.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Multidisciplinary Sciences
Atul Rangadurai, Honglue Shi, Yu Xu, Bei Liu, Hala Abou Assi, John D. Boom, Huiqing Zhou, Isaac J. Kimsey, Hashim M. Al-Hashimi
Summary: Melting experiments provide an easy way to measure thermodynamic preferences for non-native conformations in DNA and RNA. By using chemical modifications, specific minor non-native conformations can be rendered as the major state. This delta-melt approach is faster, simpler, and more cost-effective than NMR, and allows measurement of thermodynamic preferences for low-populated conformations. Through this method, insights into conformational cooperativity and sequence-specific variations in non-native conformations have been obtained.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Yves Auad, Eduardo J. C. Dias, Marcel Tence, Jean-Denis Blazit, Xiaoyan Li, Luiz Fernando Zagonel, Odile Stephan, Luiz H. G. Tizei, F. Javier Garcia de Abajo, Mathieu Kociak
Summary: The authors propose a technique that combines free-space light and electron beams to achieve unmatched spatial and spectral resolution. This approach allows detailed investigation of photonic structures, promising advancements in microscopy and quantum optics.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Inorganic & Nuclear
Monika Kovacevic, Mojca Cakic Semencic, Ivan Kodrin, Suncica Roca, Jana Perica, Jasna Mrvcic, Damir Stanzer, Kresimir Molcanov, Valentina Milasinovic, Lidija Brkljacic, Lidija Barisic
Summary: In this study, the bioactivity and conformational properties of peptidomimetics with heteroannularly functionalized ferrocenes were investigated. The synthesized dipeptide d-2a showed the best antibacterial properties against S. aureus, B. subtilis, and P. aeruginosa. Chirality and the choice of protecting group were found to affect the biological activity. The investigated peptides were highly hydrophobic and chemically stable in both acidic and buffer media.
Article
Multidisciplinary Sciences
Pavel Michal, Jana Hudecova, Radek Celechovsky, Milan Vujtek, Michal Dudka, Josef Kapitan
Summary: This paper describes a methodology for determining enantiomeric excess using Raman optical activity (ROA). The method achieved high accuracy in a short period of time and proposed an algorithm for eliminating systematic errors and the importance of normalization. The results show that ROA spectroscopy has great potential for quantitative analysis of enantiomeric mixtures.
Article
Multidisciplinary Sciences
Luz D. M. Gomez-Pulido, Rafael C. Gonzalez-Cano, Eva Dominguez, Antonio Heredia
Summary: Oleanolic and ursolic acids, terpenoid acids mainly found in plant leaf and fruit cuticles, can be defined as a blend of clusters of different conformers aggregated in dimers and tetramers, stabilized by non-electrostatic interactions.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Review
Spectroscopy
Tucker Carrington
Summary: In this paper, collocation methods for solving the time-independent and the time-dependent Schroedinger equation are reviewed. Compared to traditional variational methods, collocation methods do not require integrals and quadrature, unless the potential does not have a special form. There are established ideas for reducing the size of the basis in a variational calculation, but difficulties with quadrature still arise.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Spectroscopy
K. Dobsikova, D. Spalovska, M. Kuchar, N. Paskanova, V. Setnicka
Summary: An increasing number of products containing synthetic cannabinoids pose a growing crisis to public health worldwide. Recently, a rising number of cases of serious adverse health effects, intoxications, and death cases associated with synthetic cannabinoids were reported. The current study represents the comprehensive structural analysis of three new synthetic cannabinoids (AB-, ADB-and AMB-FUBINACA) in solution investigated by electronic and vibrational circular dichroism together with the conventional methods of infrared and ultraviolet absorption spectroscopy, all supported by the density functional theory (DFT) calculations.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Chemistry, Physical
Kevin Scholten, Christian Merten
Summary: The conformational preferences of peptides are determined by hydrogen bonding interactions, which can be studied using VCD spectroscopy. In chloroform, the peptide's conformational preferences can be described well by assuming implicit solvation effects. In DMSO-d(6), explicit solvation structures are required to match the experimental data. Structures with intramolecular hydrogen bonds contribute to the conformational distribution only when there is no strong interaction with the solvent.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Physics, Multidisciplinary
Michael Yannai, Yuval Adiv, Raphael Dahan, Kangpeng Wang, Alexey Gorlach, Nicholas Rivera, Tal Fishman, Michael Kruger, Ido Kaminer
Summary: The ability to form monoenergetic electron beams is crucial for high-resolution electron spectroscopy and imaging. In this study, a lossless monochromator mechanism for electron energy monochromation is developed, which utilizes the interaction of free-electron pulses with single-cycle THz near fields. The experiment successfully reduces the electron energy spread without compromising the beam flux, demonstrating the robustness and wide tunability of the technique. The findings have direct applications in ultrafast electron microscopy, enabling time- and energy-resolved studies in various areas.
PHYSICAL REVIEW LETTERS
(2023)
Article
Chemistry, Physical
Weslley G. D. P. Silva, Gabrielle Daudet, Sem Perez, Sven Thorwirth, Jennifer van Wijngaarden
Summary: By utilizing rotational spectroscopy and quantum chemical calculations, a rich conformational landscape with 42 energy minima was revealed for diallylamine (DAA). Experimental verification of four low energy conformers in the rotational spectrum showed their energy order. Computational studies indicated that the geometric preferences for the observed conformers are influenced by a combination of subtle attractive interactions and repulsive effects.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
GiBaik Sim, Johannes Knolle, Frank Pollmann
Summary: We study the nonlinear response of nonintegrable 1D spin models using infinite matrix-product state techniques. As a benchmark, we calculate the 2D coherent spectroscopy for the soluble ferromagnetic transverse field Ising model. By introducing a longitudinal field, we observe the emergence of strong nonrephasinglike signals, and use a two-kink approximation to interpret the phenomena.
Article
Chemistry, Physical
Patrick Ober, Sophia H. H. Kolbinger, Ellen H. G. Backus, Mischa Bonn
Summary: The charge and composition of a solid surface are affected by the composition of the aqueous phase due to ion-specific interactions between ions and the surface. This study investigates ion-specific interactions at the fluorite-water interface using surface-sensitive vibrational sum frequency generation spectroscopy and flow experiments. The flow-induced change in dissolved ion concentration at the surface alters chemical equilibria and influences the surface potential, which is probed using the vibrational sum frequency generation intensity in the OH stretch region. The study identifies charge screening and ion-specific effects, including surface adsorption, by analyzing the vibrational sum frequency generation intensity and its flow-induced change for different salts.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Review
Chemistry, Analytical
Riccardo Deidda, Amandine Dispas, Charlotte De Bleye, Philippe Hubert, Eric Ziemons
Summary: Cannabis has attracted scientific attention and numerous studies have focused on its pharmacological potential. However, no globally accepted reference method for cannabinoid determination has been chosen yet. This review identifies recent analytical methods for analyzing phytocannabinoids in cannabis samples and suggests the need for a standardized method. Some techniques are stagnant, while others show promising developments, such as supercritical fluid chromatography and infrared spectroscopy.
ANALYTICA CHIMICA ACTA
(2022)
Article
Food Science & Technology
Na Luo, Xinting Yang, Chuanheng Sun, Bin Xing, Jiawei Han, Chunjiang Zhao
Summary: This study demonstrated the effectiveness of t-SNE in visualizing vibrational spectroscopy data sets, showing better visual discrimination results in 2-dimensional space and higher clustering metric scores compared to PCA and Isomap. The supervised classification models based on the new representations from t-SNE outperformed other methods in terms of accuracy, indicating great potential of t-SNE for recognizing minute spectral differences between classes.
Article
Chemistry, Multidisciplinary
Alen Vizintin, Jan Bitenc, Anja Kopac Lautar, Joze Grdadolnik, Anna Vitanova Vitanova, Klemen Pirnat
Article
Biochemistry & Molecular Biology
Laszlo Petri, Peter Abranyi-Balogh, Imre Timea, Gyula Palfy, Andras Perczel, Damijan Knez, Martina Hrast, Martina Gobec, Izidor Sosic, Kinga Nyiri, Beata G. Vertessy, Niklas Jansch, Charlotte Desczyk, Franz-Josef Meyer-Almes, Iza Ogris, Simona Golic Grdadolnik, Luca Giacinto Iacovino, Claudia Binda, Stanislav Gobec, Gyorgy M. Keseru
Summary: This study presents a toolbox of fragments containing a 3,5-bis(trifluoromethyl)phenyl core equipped with chemically diverse electrophilic warheads, showing a range of reactivities. The library members were characterized for reactivity, aqueous stability, and specificity for nucleophilic amino acids, and were screened against a set of enzymes amenable for covalent inhibition to experimentally assess the accessibility and reactivity of targeted cysteines. Interesting covalent fragment hits were obtained for all investigated cysteine-containing enzymes.
Article
Biochemistry & Molecular Biology
Maria-Eleni Androutsou, Agathi Nteli, Areti Gkika, Maria Avloniti, Anastasia Dagkonaki, Lesley Probert, Theodore Tselios, Simona Golic Grdadolnik
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Iza Ogris, Urska Zelenko, Izidor Sosic, Martina Gobec, Cene Skubic, Marija Ivanov, Marina Sokovic, Darko Kocjan, Damjana Rozman, Simona Golic Grdadolnik
Summary: This study focused on the main drug target for fungal infections, Sterol 14 alpha-demethylase (CYP51), and developed highly selective inhibitors, offering novel directions for the development of anti-fungal drugs.
BIOORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Artem Badasyan, Matjaz Valant, Joze Grdadolnik, Vladimir N. Uversky
Summary: This study investigates the coil to globule transition of the polypeptide chain in relation to the folding of globular proteins and introduces the number of amino acid residues as a parameter. The k(2) measure is found to be related to the degeneracy of the denatured state, while Omega(c) is proportional to the square of the transition interval, allowing for classical size scaling analysis of the coil-globule phase transition.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Spectroscopy
Urban Novak, Joze Grdadolni
Summary: The infrared spectra of long-chain perfluorocarboxylic acid monohydrates show unique features different from other carboxylic acid crystals, indicating the presence of short hydrogen bonds connecting water molecules to carbonyl groups in the structure. The hydrogen bond pattern in the long-chain perfluorocarboxylic acid monohydrates is similar to that found in alpha-oxalic acid dihydrate crystals.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Chemistry, Multidisciplinary
Artem Badasyan, Shushanik Tonoyan, Matjaz Valant, Joze Grdadolnik
Summary: Studies on biopolymer conformations rely on theoretical models and experimental data. The authors have proposed a model with water-polymer interactions to extract H-bonding energies and determine the conditions for cold denaturation.
COMMUNICATIONS CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Urban Novak, Amalija Golobic, Natalija Klancnik, Vlasta Mohacek-Grosev, Jernej Stare, Joze Grdadolnik
Summary: This study provides a detailed analysis of the crystal structure and vibrational spectra of Acetylenedicarboxylic acid dihydrate (ADAD), revealing its neutral structure and polymorphic modifications. Comparison with oxalic acid dihydrate shows interesting details.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Sonia Covaceuszach, Leticia Yamila Peche, Petr Valeryevich Konarev, Joze Grdadolnik, Antonino Cattaneo, Doriano Lamba
Summary: The human genetic variant BDNF (V66M) has a significant impact on psychiatric disorders. The V66M mutation affects the conformation and flexibility of hproBDNF, potentially leading to altered binding and intracellular trafficking, causing cognitive impairment and anxiety. These structural alterations provide insights for drug discovery strategies and personalized medicine for neuropsychiatric disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Barbara ZupanCiC, Nejc Umek, Chiedozie Kenneth Ugwoke, Erika Cvetko, Simon Horvat, Joze Grdadolnik
Summary: Age, obesity, and diabetes mellitus are interconnected factors that significantly contribute to non-communicable diseases. These metabolic conditions lead to structural and functional changes in skeletal muscle, which can be detected through the alterations in macromolecular composition. Fourier transform infrared (FTIR) spectroscopy is an effective method for analyzing the macromolecular composition in muscle tissue.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Francesca Paoletti, Sonia Covaceuszach, Alberto Cassetta, Antonio N. N. Calabrese, Urban Novak, Petr Konarev, Joze Grdadolnik, Doriano Lamba, Simona Golic Grdadolnik
Summary: Nerve growth factor (NGF) and its precursor, proNGF, play different roles in neuronal maintenance and apoptosis. The binding of NGF or proNGF to receptors triggers intracellular signaling pathways, which can be modulated by small-molecule ligands. ATP binds to the pro-peptide of proNGF with a micromolar dissociation constant, and this interaction is modulated by Mg2+. The binding of ATP induces a conformational rearrangement of the flexible pro-peptide domain, suggesting its role as an allosteric modulator of proNGF conformation.
Article
Materials Science, Multidisciplinary
Luigi Giacomazzi, Nikita S. Shcheblanov, Mikhail E. Povarnitsyn, Yanbo Li, Andraz Mavric, Barbara Zupancic, Joze Grdadolnik, Alfredo Pasquarello
Summary: We conducted a comprehensive study combining experimental measurements and first-principles calculations to investigate the infrared properties of amorphous alumina. Our analysis reveals the correlation between the imaginary part of the dielectric function and the motion of threefold-coordinated oxygen atoms. We also provide an alternative interpretation of the vibrational modes, based on the decomposition of the vibrational density of states and the 62(co) spectra.
PHYSICAL REVIEW MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Francesca Paoletti, Franci Merzel, Alberto Cassetta, Iza Ogris, Sonia Covaceuszach, Joze Grdadolnik, Doriano Lamba, Simona Golic Grdadolnik
Summary: NGF plays a crucial role in the maintenance and growth of neuronal populations, with interactions with ATP impacting the binding to specific receptors. The study suggests that ATP may serve as a transient molecular modulator of NGF signaling in health and disease states.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biology
Marija Ivanov, Abhilash Kannan, Dejan Stojkovic, Jasmina Glamoclija, Simona Golic Grdadolnik, Dominique Sanglard, Marina Sokovic