Article
Chemistry, Multidisciplinary
Yeting Guo, Jianxi Ying, Dongru Sun, Yumeng Zhang, Minyang Zheng, Ruiwen Ding, Yan Liu, Yufen Zhao
Summary: The yields of DKPs were found to be influenced by the sequence of linear dipeptides and the presence of trimetaphosphate in the reaction, suggesting that DKPs may play a key role in the origin of life.
FRONTIERS IN CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Charlene Elizabeth Ogilvie, Clarissa Melo Czekster
Summary: Research on the human microbiome has shown that its constituents play a role in various non-communicable diseases. Microbes communicate and coordinate their behavior through the secretion of small molecules, such as cyclic dipeptides (CDPs). CDPs are widespread signaling molecules with diverse biological activities, particularly relevant to human health as potential modulators of the microbiome.
BIOORGANIC & MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Yinglu Wang, Qian Zheng, Li Li, Lile Pan, Hu Zhu
Summary: Quorum sensing (QS) plays an important role in regulating the pathogenicity of bacteria, and cyclo (L-Trp-L-Ser) and its derivatives have been found to exhibit anti-QS activity, making them potential candidates for developing anti-virulence agents.
Article
Engineering, Chemical
Jens Abildskov, Sten Bay Jorgensen
Summary: This study investigates the influence of finite drainage time on separation performance in periodic separation. The results show that draining periods should be minimized regardless of the operating mode. Simultaneous draining is more efficient for columns with a few stages, while sequential draining becomes superior for higher numbers of stages, partly due to enabling mass transfer during draining.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Fokrul Alom Mazarbhuiya, Mohamed Shenify
Summary: Finding real-time anomalies in network systems is challenging, but crucial for information security. This paper proposes a clustering-based approach that utilizes rough set theory and a dynamic k-means clustering algorithm to detect anomalies in real-time data. Experimental results show that this method outperforms existing algorithms and has a cubic time complexity.
APPLIED SCIENCES-BASEL
(2023)
Article
Chemistry, Physical
Ireneusz Buganski, Janusz Wolny
Summary: This study investigates the atomic structure of an icosahedral quasicrystal and finds that Tsai and Bergman clusters can be used interchangeably to describe the structure. By studying different crystal structures, it is discovered that both types of clusters play equivalent roles in structure formation. The difference between Tsai and Bergman structures lies in the irregular positioning of the shell structure and the formation of vacancies. Understanding the conditions for their stabilization can provide insights into the formation of these two structures.
JOURNAL OF ALLOYS AND COMPOUNDS
(2023)
Article
Chemistry, Physical
Oinam Romesh Meitei, Troy Van Voorhis
Summary: Bootstrap embedding (BE) is a successful electronic structure method for electron correlation in molecules. In this study, BE is extended to surfaces and solids, allowing for the representation of wave functions in periodic boundary conditions using reciprocal space sums. The resulting fragment Hamiltonians have no explicit dependence on the reciprocal space sums, enabling the application of traditional nonperiodic electronic structure codes to the fragments. The use of BE has shown promising results in recovering the electron correlation energy and can be applied to complex systems such as donor-acceptor polymers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Computer Science, Artificial Intelligence
Jun-Yi Li, Yang-Cheng Huang, Hong-Xia Rao, Yong Xu, Renquan Lu
Summary: This paper addresses the finite-time cluster synchronization problem for complex dynamical networks (CDNs) with cluster characteristics under false data injection (FDI) attacks. A new periodic secure control (PSC) strategy is proposed to improve the synchronization effect while reducing the control cost. The gains of the periodic secure controller are derived to ensure desired cluster synchronization performance in the presence of external disturbances and false control signals.
Article
Biochemistry & Molecular Biology
Margareta Sohora, Irena Sovic, Zlatan Spahic, Darko Kontrec, Mladenka Jurin
Summary: A series of dipeptides with a phthalimide group at the N-site and different amino acids at the C-site were synthesized. Photodecarboxylation of these dipeptides under acetone-sensitized conditions resulted in the formation of simple decarboxylation products, decarboxylation-induced cyclization products, as well as some secondary products formed by elimination of H2O or ring enlargement. The investigation is important as it provides a comprehensive understanding of dipeptide cyclizations activated by phthalimides.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Joanna Bojarska, Adam Mieczkowski, Zyta M. Ziora, Mariusz Skwarczynski, Istvan Toth, Ahmed O. Shalash, Keykavous Parang, Shaima A. El-Mowafi, Eman H. M. Mohammed, Sherif Elnagdy, Maha AlKhazindar, Wojciech M. Wolf
Summary: Cyclic dipeptides, especially those containing proline, have emerged as biologically pre-validated platforms for drug discovery with enormous potential in developing next-generation theranostics, smart delivery systems, and biomaterials. Recent advances in supramolecular structuring and synthons based on proline-based DKP scaffolds show promise in the design of compound libraries for ideal ligands, self-assembled nanomaterials, and bio-functional architectures.
Article
Biochemistry & Molecular Biology
Shingo Kasamatsu, Somei Komae, Kana Matsukura, Yuki Kakihana, Koji Uchida, Hideshi Ihara
Summary: The study found that the 2-oxo-IDPs derived from IDPs play a crucial role in antioxidant functions, demonstrating a higher antioxidant capacity compared to traditional IDPs. This suggests that the conversion of IDPs to 2-oxo-IDPs may be a critical step in antioxidant functions.
Article
Computer Science, Artificial Intelligence
Guisheng Chen, Zhanshan Li
Summary: Periodic pattern mining is becoming increasingly important in the data mining field due to the common occurrence of periodic events. However, there is currently no uniform definition for periodic patterns, making it difficult to discover seasonally prevalent events. This paper introduces a new definition for periodic events based on the coefficient of variation and proposes an efficient algorithm, PCPM, to mine periodic cluster patterns in event sequence datasets. The application of periodic cluster patterns is demonstrated through the development of PCPP, a method for periodic cluster pattern prediction in next basket recommendation. Experimental results show the effectiveness of PCPM in mining periodic cluster patterns, while PCPP performs similarly to baseline methods in real-world transaction datasets. The authors also suggest that periodic cluster patterns have wider applications in domains such as time series prediction and meteorological forecasting.
APPLIED INTELLIGENCE
(2022)
Article
Chemistry, Physical
Christina Kjaer, Emil Vogt, Jeppe Langeland, Nanna Falk Christensen, Thomas Toft Lindkvist, Henrik G. Kjaergaard, Steen Brondsted Nielsen
Summary: Recent developments in fluorescence spectroscopy allow for the measurement of absorption and dispersed fluorescence spectra of isolated molecular ions at low temperatures. Lower temperatures provide narrower spectra and better information on vibronic features. Experiments were conducted on oxazine dyes cooled to around 100 K, and the results showed small Stokes shifts and broader spectra for the darrow-red cations compared to other ionic dyes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Christina Kjaer, Jeppe Langeland, Steen Brondsted Nielsen
Summary: Fireflies, click beetles, and railroad worms are bioluminescent insects that emit light in the dark. The color of their light is determined by the electronically excited oxyluciferin formed by the luciferase enzyme. This study presents emission spectra of oxyluciferin monoanions recorded at room temperature and at 100 K. The results provide important references for understanding the color tuning mechanism and the influence of the protein microenvironment on the emission wavelength.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Engineering, Electrical & Electronic
Ravinder Singh Sawhney, Gaurav Sikri
Summary: The electron transport properties of two different dipeptides have been investigated, revealing one with exceptionally high rectification ratio and the other with significant negative differential resistance characteristics. The density functional theory method used in this study shows good agreement with experimental results, highlighting the importance of these dipeptides in future molecular electronic devices.
JOURNAL OF ELECTRONIC MATERIALS
(2023)
Article
Chemistry, Organic
Jaroslav Jacko, Monika Stasprime, Lubomir Rulisek, Ivana Cisarova, Martin Kotora
Summary: We have demonstrated that C-C bond activation in biphenylenes catalyzed by iridium, followed by reaction with tribenzocyclyne, is a suitable method for synthesizing strained and unknown monoadducts. By modifying the reaction conditions, [12]annulene products with cis and/or trans double bonds formed by hydrogen transfer can also be obtained. In addition, a [9]annulene side product was formed during the reaction.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Lea Girard, Niels Geudens, Brent Pauwels, Monica Hofte, Jose C. Martins, Rene De Mot
Summary: Pseudomonas lipopeptides are secondary metabolites with diverse ecological functions and biotechnological applications, and a reliable transporter gene-guided approach allows for the detection and classification of lipopeptide producers among Pseudomonas strains, providing a valuable tool for strain prioritization.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Martin Jakubec, Ivana Cisarova, Jindrich Karban, Jan Sykora
Summary: This study investigated the effect of substitution on intermolecular interactions in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. It was found that the substitution of hydroxy group by hydrogen or fluorine weakens the intermolecular interaction by approximately 4 kcal/mol. The strength of the interactions follows the descending order of hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine, and weak electrostatic interactions. Fluorine interactions were weak and often supported by other weak interactions.
Article
Chemistry, Multidisciplinary
Eva Kaletova, Carina Santos Hurtado, Ivana Cisarova, Simon J. Teat, Jiri Kaleta
Summary: In this study, a fully modular synthesis approach was used to obtain three representative rigid molecular rods. These rods can form sturdy monolayers on various surfaces. The compounds were characterized using X-ray diffraction and capillary electrophoresis, revealing their crystal structure and acidity. Langmuir-Blodgett monolayers were successfully formed, and atomic force microscopy was used to visualize the structure of one of the films. These geometrically unique molecules have great potential in the field of supramolecular architecture.
Article
Chemistry, Inorganic & Nuclear
Jiri Schulz, Jakub Antala, Ivana Cisarova, Petr Stepnicka
Summary: Compared to phosphine counterparts, little attention has been paid to the study of ferrocene stibines. This paper describes the synthesis of ferrocene stibine derivatives and their reactivity and coordination behavior. The compounds were characterized through various spectroscopic techniques and crystallography. The research findings reveal important insights into the structural parameters and electrochemical properties of the ferrocene stibines, but their catalytic efficiency needs to be further improved in Suzuki-Miyaura biaryl coupling reactions.
DALTON TRANSACTIONS
(2023)
Article
Chemistry, Inorganic & Nuclear
Zuzana Kotkova, Filip Koucky, Jan Kotek, Ivana Cisarova, David Parker, Petr Hermann
Summary: A series of Cu(II) complexes with cyclam-based ligands containing two N-(2,2,2-trifluoroethyl)-aminoalkyl pendant arms were studied for their potential use as F-19 MRI contrast agents. Structural analysis and NMR measurements revealed the formation of isomeric complex species in solution. The Cu(II) ion showed significant relaxation enhancement and can be considered as a highly suitable metal ion for efficient F-19 MRI contrast agents.
DALTON TRANSACTIONS
(2023)
Article
Chemistry, Organic
Adela Krizkova, Guillaume Bastien, Igor Roncevic, Ivana Cisarova, Jiri Rybacek, Vaclav Kasicka, Jiri Kaleta
Summary: In this study, a radical chlorination reaction of cubane-1,4-dicarboxylic acid was reported, resulting in the preferential formation of a monochlorinated derivative (approximately 70%) along with four dichlorinated derivatives (approximately 20% in total). The positions of the chlorine atoms were confirmed by X-ray diffraction analysis. The acidity constants of the different chlorinated cubane dicarboxylates were determined, and their thermal stability was evaluated using differential scanning calorimetry. The reaction pathways and strain energies of the derivatives were investigated through computational calculations.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Organic
Andrea Vopalenska, Vojtech Docekal, Simona Petrzelova, Ivana Cisarova, Jan Vesely
Summary: The present study reports an asymmetric organocascade reaction that efficiently catalyzes the reaction between oxindole-derived alkenes and 3-bromo-1-nitropropane using a bifunctional catalyst. The reaction produces spirooxindole-fused cyclopentanes in moderate-to-good isolated yields (15-69%) with excellent stereochemical outcomes. The synthetic utility of the protocol is demonstrated through additional transformations of the resulting spirooxindole compounds.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Organic
Ladislav Loska, Vojtech Docekal, Ivana Cisarova, Jan Vesely
Summary: The study presents an asymmetric NHC-catalyzed formal [4 + 2] cycloaddition of heterocyclic alkenes with an azolium-dienolate intermediate. The reaction is achieved without external oxidation of the Breslow intermediate. Good yields (typically about 90%) and stereochemical outcomes (in most cases, dr > 20/1, and ee = 70-99%) were obtained for heterocyclic cyclohexenones. The synthetic utility of the protocol was demonstrated by the scope of heterocyclic alkenes.
Article
Microbiology
Catherine Cesa-Luna, Niels Geudens, Lea Girard, Vic De Roo, Hassan R. Maklad, Jose C. Martins, Monica Hofte, Rene De Mot
Summary: By mining the genomes of Pseudomonas species, we have mapped the global Pseudomonas lipopeptidome and found its impressive diversity to be linked to taxonomy of the producers. The synthesis of lipopeptides is facilitated by nonribosomal peptide synthetases (NRPSs), which assemble siderophores and lipopeptides. Our analysis also revealed that lipopeptide production is confined to the Pseudomonas fluorescens lineage and shows a correlation between NRPS and taxonomic affiliation.
Article
Chemistry, Multidisciplinary
Kevin Van Holsbeeck, Baptiste Fischer, Simon Gonzalez, Charlene Gadais, Wim Versees, Jose C. Martins, Charlotte Martin, Alexandre Wohlkoenig, Jan Steyaert, Steven Ballet
Summary: RAS proteins play a crucial role in regulating intracellular signaling networks and mutations that stabilize their active state are associated with cancer development. The study investigated the potential of developing peptide mimetics to modulate RAS signaling by mimicking the complementarity-determining region 3 (CDR3) of the regulatory guanine nucleotide exchange factor (GEF) son of sevenless 1 (SOS1). Through optimization and conformational rigidification, CDR3 mimetics with half of the maximal activation potential of Nanobody14 (Nb14) were obtained, demonstrating the feasibility of modulating protein-protein interactions through structural mimicry of a paratope.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Inorganic & Nuclear
Michal Navratil, Ivana Cisarova, Petr Stepnicka
Summary: This study describes the synthesis of two functional phosphines and their coordination behavior with palladium. The results show that the two compounds form different complexes with palladium.
DALTON TRANSACTIONS
(2022)
Article
Chemistry, Multidisciplinary
Viraj A. Bhosale, Ivana Cisarova, Martin Kamlar, Jan Vesely
Summary: This study presents a novel chiral phosphoric acid (CPA)-catalyzed reaction, allowing for the asymmetric addition of alpha-fluoro(phenylsulfonyl)methane (FSM) derivatives to in situ generated cyclic N-acyliminium. The process demonstrates high stereoselectivity, leading to the formation of biorelevant isoindolinones containing sulfone and fluorine substituents with excellent stereoselectivities.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Organic
Jan Choutka, Michal Kratochvil, Ivana Cisarova, Radek Pohl, Jakub Kaminsky, Kamil Parkan
Summary: This manuscript presents an early investigation on the synthesis, structure, and conformational behavior of a novel type of glycomimetics called (1 -> 1)-Si-disaccharides. The study shows that these glycomimetics have good stability and flexibility in conformation, which differs from natural carbohydrates.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Article
Chemistry, Inorganic & Nuclear
Jiri Schulz, Ivana Cisarova, Robert Gyepes, Petr Stepnicka
Summary: The reactions of a gold(I) metalloligand with bare or ligand-stabilised group 11 metal ions lead to the formation of diverse oligometallic clusters stabilized by different types of interactions. The unique properties of the bridging ferrocene groups enable the accommodation of capping moieties and supporting ligands, resulting in the formation of structurally unique products. The strength of the metallophilic interaction between gold and the other metal ions determines the behavior of the capping reactions.
DALTON TRANSACTIONS
(2022)