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Carnosine (β-alanyl-L-histidine) is a naturally occurring endogenous dipeptide and an over-the-counter food supplement with a well-demonstrated multimodal mechanism of action that includes the detoxification of reactive oxygen and nitrogen species, the down-regulation of the production of pro-inflammatory mediators, the inhibition of aberrant protein formation, and the modulation of cells in the peripheral (macrophages) and brain (microglia) immune systems. Since its discovery more than 100 years ago, a plethora of in vivo preclinical studies have been carried out; however, there is still substantial heterogeneity regarding the route of administration, the dosage, the duration of the treatment, and the animal model selected, underlining the urgent need for "coordinated/aligned" preclinical studies laying the foundations for well-defined future clinical trials. The main aim of the present position paper is to critically and concisely consider these key points and open a discussion on the possible "alignment" for future studies, with the goal of validating the full therapeutic potential of this intriguing molecule. [ABSTRACT FROM AUTHOR]

The article announces the winners of the Molecules Best Paper Award 2013 in the U.S., including Thomas J. Schmidt, Reto Brun, and Holger Trojan.

The suggestion that the paper by Naef and Acree is the first one with the capability to treat "any molecule under the sun" is simply totally incorrect. In Ref. [[7]] (Neaf and Acree), reference to GC methods are only the previous publications by Naef and Acree. 10.3390/molecules25051147 7 Naef R., Acree W.E. Jr. Calculation of the Vapour Pressure of Organic Molecules by Means of a Group-Additivity Method and their Resultant Gibbs Free Energy and Entropy of Vaporization at 298.15 K. References 1 Naef R., Acree W.E. Jr. Revision and Extension of a Generally Applicable Group-Additivity Method for the Calculation of the Standard Heat of Combustion and Formation of Organic Molecules. [Extracted from the article]

The document titled "Advances in Amylases—What's Going on?" provides an overview of the classification and research on amylolytic enzymes, specifically α-amylases. It discusses the classification of α-amylase families within the CAZy database, highlighting GH13 and GH57 as the main families, and mentions the existence of subfamilies within GH13. The document also mentions a special issue of the journal Molecules, titled "Advances in Amylases," which includes thirteen papers covering various aspects of amylolytic enzymes. The papers discuss topics such as enzyme hydrolysis of starch granules, inactivation of α-amylase, protein content in rice flour, and the structure and function of different α-amylase subfamilies. The document concludes by expressing appreciation to the contributors and reviewers of the special issue. This article by Štefan Janeček explores the topic of molecules and their properties, providing an in-depth analysis of various types of molecules, their structures, functions, and interactions. It emphasizes the importance of understanding molecules in fields such as chemistry, biology, and medicine. The article is a valuable resource for library patrons conducting research on molecular science and its applications. [Extracted from the article]

While a country-western song title may seem out of place in a I Molecules i Editorial, the words nevertheless seem most appropriate to define the journal's trajectory since volume 1 was published in 1996, to the occasion we now aim to celebrate with the Special Issue being announced herein. 1 Kulkarni B.A., Chattopadhyay S., Chattopadhyay A., Mamdapur V.R. Synthesis of the demospongic compounds, (6Z,11Z)-octadecadienoic acid and (6Z,11Z)-eicosadienoic acid. [Extracted from the article]

Ferritin (Ft) is a protein with a peculiar three-dimensional architecture. It is characterized by a hollow cage structure and is responsible for iron storage and detoxification in almost all living organisms. It has attracted the interest of the scientific community thanks to its appealing features, such as its nano size, thermal and pH stability, ease of functionalization, and low cost for large-scale production. Together with high storage capacity, these properties qualify Ft as a promising nanocarrier for the development of delivery systems for numerous types of biologically active molecules. In this paper, we introduce the basic structural and functional aspects of the protein, and summarize the methods employed to load bioactive molecules within the ferritin nanocage. [ABSTRACT FROM AUTHOR]

The article discusses a group contribution (GC) method used to calculate the partition coefficients of organic molecules. The GC method assumes that certain aspects of chemical groups are consistent across different molecules. The authors of the article criticize previous publications by Naef and Acree for overlooking relevant research and not providing a rebuttal. They also compare Naef and Acree's results on the octanol-water partition coefficient to previous studies and highlight the limitations of their method. The authors suggest that Naef and Acree's claims of unmatched versatility are not supported by the literature. [Extracted from the article]

This correction notice addresses inaccuracies in an article about two products used in the animal breeding industry in China. The names of the products and a picture were incorrectly used, and the term "impurity" should be replaced with "trace components." The correction provides the accurate names of the products and clarifies their use as safe and effective Chinese veterinary medicine. Additionally, errors in figures and sample preparation information are corrected. The scientific conclusions of the article remain unaffected by these changes. [Extracted from the article]

The piperazine moiety is often found in drugs or in bioactive molecules. This widespread presence is due to different possible roles depending on the position in the molecule and on the therapeutic class, but it also depends on the chemical reactivity of piperazine-based synthons, which facilitate its insertion into the molecule. In this paper, we take into consideration the piperazine-containing drugs approved by the Food and Drug Administration between January 2011 and June 2023, and the synthetic methodologies used to prepare the compounds in the discovery and process chemistry are reviewed. [ABSTRACT FROM AUTHOR]

In the original publication [[1]], there was a mistake in the order of existing authors. The first author should be Xuejiao Wang.The correct authorship of this paper should be:Xuejiao Wang 1, Shuyuan Liu 1, Shu Lin 1, Kezhen Qi 1,*, Ya Yan 1,*, and Yuhua Ma 2,*The authors state that the scientific conclusions are unaffected. This correction was approved by the Academic Editor. The original publication has also been updated.By Xuejiao Wang; Shuyuan Liu; Shu Lin; Kezhen Qi; Ya Yan and Yuhua MaReported by Author; Author; Author; Author; Author; Author [Extracted from the article]

Author Contribution Original: Y.-H.K. and M.-J.C. designed the research; M.-D.W., C.-F.C., H.-S.C. and M.-J.C. performed the research; C.-L.C. and Y.H.K. conducted biological assays, Y.-H.K. and M.-J.C. helped with structure elucidation, M.-J.C. organized the data and wrote the paper. To be replaced with: Y.-H.K. is responsible for the main research framework; Y.-H.K. and M.-J.C. designed the research; C.-F.C. performed the chemical and structure elucidation research; C.-L.C., M.-D.W. and H.-S.C. conducted antifungal assays, Y.-H.K. and M.-J.C. helped with structure elucidation, Y.-H.K. and M.-J.C. organized the data and M.-J.C. wrote the paper. Author List Original: Ming-Jen Cheng SP 1, sp *, Ming-Der Wu SP 1 sp , Chao-Lin Chang SP 2 sp , Hsun-Shuo Chang SP 3 sp , Chiou-Fung Chyu SP 4 sp and Yueh-Hsiung Kuo SP 4,5,6,7 sp 1 Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute (FIRDI), Hsinchu 300, Taiwan; wmd@firdi.org.tw 2 Product & Process Research Center (PPRC), Food Industry Research and Development Institute (FIRDI), Hsinchu 300, Taiwan; ccl@firdi.org.tw 3 School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan; hschang@kmu.edu.tw 4 Department of Chemistry, National Taiwan University, Taipei 106, Taiwan; cmj@firdi.org.tw (C.-F.C.); yhkuo800@gmail.com (Y.-H.K.). [Extracted from the article]

B Author Contribution b Original: Y.-H.K., J.-J.C. and M.-J.C. designed the research; N.K., M.-D.W.,W.-W.L. and M.-J.C. performed the research; N.K. conducted biological assays, J.-J.C., Y.-H.K. and M.-J.C. helped with structure elucidation; M.-J.C. organized the data and wrote the paper. Reference 1 Wu M.-D., Cheng M.-J., Chen J.-J., Khamthong N., Lin W.-W., Kuo Y.-H. To be replaced with: Y.-H.K. is responsible for the main research framework; Y.-H.K. and M.-J.C. designed the research; W.-W.L. performed the chemical research; N.K. and M.-D.W. conducted antimicrobial assays, J.-J.C., Y.-H.K. and M.-J.C. helped with structure elucidation; Y.-H.K. and M.-J.C. organized the data and M.-J.C. wrote the paper. [Extracted from the article]

Reference 1 Chen J.-J., Cheng M.-J., Lee T.-H., Kuo Y.-H., Lu C.-T. Secondary Metabolites with Anti-Inflammatory from the Roots of Cimicifuga taiwanensis. Author Contributions Original: M.-J.C. designed the research; M.-J.C. and C.-T.L. performed the research; J.-J.C. conducted biological assays, T.-H.L., Y.-H.K. and M.-J.C. helped with structure elucidation; M.-J.C. organized the data and wrote the paper. To be replaced with: Y.-H.K. is responsible for the main research framework; Y.-H.K. and M.-J.C. designed the research; C.-T.L. performed the research; J.-J.C. conducted biological assays, T.-H.L., Y.-H.K. and M.-J.C. helped with structure elucidation; Y.-H.K. and M.-J.C. organized the data and wrote the paper. [Extracted from the article]

Regardless of whether the articles they examined were ultimately published, the editors would like to express their appreciation and thank the following reviewers for the time and dedication that they have shown I Molecules i olely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). Thanks to the efforts of our reviewers in 2022, the median time to first decision was 14 days and the median time to publication was 34 days. I Molecules i was able to uphold its high standards for published papers due to the outstanding efforts of our reviewers. [Extracted from the article]

Anderson-type ([XM6O24]n−) polyoxometalates (POMs) are a class of polymetallic-oxygen cluster inorganic compounds with special structures and properties. They have been paid extensive attention by researchers now, due to their chemical modification and designability, which have been widely applied in the fields of materials, catalysis and medicine. In contemporary years, the application of Anderson-type POMs in catalytic organic oxidation reaction has gradually shown great significance for the research of green catalytic process. In this paper, we investigate the application of Anderson-type POMs in organic synthesis reaction, and these works are summarized according to the different structure of POMs. This will provide a new strategy for further investigation of the catalytic application of Anderson-type POMs and the study of green catalysis. [ABSTRACT FROM AUTHOR]

The original funding section in the published paper "The authors extend their appreciation to the Deputyship for Research & Innovation, Ministry of Education, Saudi Arabia, for funding this research work through the project number IFKSURP-59. H.N.M. is thankful for the University Grants Commission-Basic Scientific Research (UGC-BSR) mid-career award grant (No. F.19-223/2018/ (BSR)" is corrected as follows: The authors extend their appreciation to the Deputyship for Research & Innovation, Ministry of Education, Saudi Arabia, for funding this research work through the project number IFKSURP-59. The authors wish to make the following change to the funding section in their paper [[1]]. [Extracted from the article]

Reference 1 Wang J., Shi M., Wang J., Li J., Ji T. Polycyclic Polyprenylated Acylphloroglucinol Derivatives from Hypericum acmosepalum. The manuscript will be updated and the original will remain online on the article webpage. The authors wish to make the following correction to their paper [[1]]. [Extracted from the article]

Reference 1 Boulaka A., Christodoulou P., Vlassopoulou M., Koutrotsios G., Bekiaris G., Zervakis G.I., Mitsou E.K., Saxami G., Kyriacou A., Zervou M. Genoprotective Properties and Metabolites of -Glucan-Rich Edible Mushrooms following Their In Vitro Fermentation by Human Faecal Microbiota. The authors wish to add the following information to the Authors and Affiliation section of our paper published in I Molecules i [[1]]. Genoprotective Properties and Metabolites of -Glucan-Rich Edible Mushrooms Following Their In Vitro Fermentation by Human Faecal Microbiota. [Extracted from the article]

Figures and Tables Graph: Figure 1 Number of submitted manuscripts (blue bars) and published papers (orange bars) in the Medicinal Chemistry section of Molecules in the period 2015-2019. Graph: Figure 3 Total number of special issues launched in the Medicinal Chemistry section of Molecules in 2019. The MDPI journal I Molecules i is organized into 25 sections that cover many different areas of the broad field of chemistry. With regard to the status of the Medicinal Chemistry section of I Molecules i , in 2019: A record of submissions (1197) and published articles (583) was achieved, consolidating a steady increase over previous years (Figure 1). [Extracted from the article]

In the paper, the VCD analysis was performed on the sample (+) B 1 b to determine its absolute configuration and it was found that the AC is ( I R i ). In this note, we report a correction to the published article, I Molecules i B 2020 b , I 25 i , 2272; doi:10.3390/molecules25102272 [[1]], regarding the absolute configuration (AC) of the used catalyst B IV b in the preparation of the sample sent for a VCD analysis. Chiral Phase Transfer Catalysis in the Asymmetric Synthesis of a 3,3-Disubstituted Isoindolinone and Determination of Its Absolute Configuration by VCD Spectroscopy. [Extracted from the article]

Electrochemiluminescence (ECL) detection is widely applied in many fields, including chemical measurement, biological analysis, and clinic tests, due to its high sensitivity. Currently, the fast development of many new electrochemical luminophores is continuously improving the ECL-based detection ability. Besides the enhancement of luminescence emission for a high detection sensitivity, minimizing the effect of co-reactants on ECL detection and achieving multiple analysis in one sample are also the main directions in this field. This review focuses on a summary of recently prepared new luminophores to achieve the three aims mentioned above. Especially, the review is composed by three parts, focusing on the luminophores or materials with high ECL efficiency, self-enhancing properties, and multi-color ECL luminophores. The fabrication of biosensors using these molecules is also reviewed to exhibit the advances in biological applications. [ABSTRACT FROM AUTHOR]

Biological and Spectroscopic Investigations of New Tenoxicam and 1.10-Phenthroline Metal Complexes. The authors of this paper [[1]] have agreed they would like to add Hanem M. Awad as the fourth co-author, as she made a significant contribution to the cytotoxicity tests. Reference 1 Elshafie H.S., Sadeek S.A., Camele I., Awad H.M., Mohamed A.A. Biological and Spectroscopic Investigations of New Tenoxicam and 1.10-Phenthroline Metal Complexes. [Extracted from the article]

Food packaging was not as important in the past as it is now, because the world has more people but fewer food resources. Food packaging will become more prevalent and go from being a nice-to-have to an essential feature of modern life. Food packaging has grown to be an important industry sector in today's world of more people and more food. Food packaging innovation faces significant challenges in extending perishable food products' shelf life and contributing to meeting daily nutrient requirements as people nowadays are searching for foods that offer additional health advantages. Modern food preservation techniques have two objectives: process viability and safe, environmentally friendly end products. Long-term storage techniques can include the use of edible coatings and films. This article gives a succinct overview of the supplies and procedures used to coat food products with conventional packaging films and coatings. The key findings summarizing the biodegradable packaging materials are emphasized for their ability to prolong the freshness and flavor of a wide range of food items; films and edible coatings are highlighted as viable alternatives to traditional packaging methods. We discuss the safety concerns and opportunities presented by applying edible films and coatings, allowing it to be used as quality indicators for time-sensitive foods. [ABSTRACT FROM AUTHOR]

The Lisbon Supramolecular Green Story: Mechanochemistry towards New Forms of Pharmaceuticals. The authors wish to add funding project UIDB/00100/2020 into the Funding section of this paper [[1]]. The corrected funding is provided below: Funding This research was funded by Fundação para a Ciência e a Tecnologia, grant numbers UIDB/00100/2020, PEST-OE/QUI/UI0100/2013 (CQE) and RECI/QEQ-QIN70189/2012 (M.T.D. as PI), V.A. was funded by SFRH/BPD/78854/2011 and CEECIN/02001/2017 post-doctoral grants; S.D. was funded by Research Grant PTDC/CTM-BPC/122447/2010; I.C.B.M. was funded by PhD grant SFRH/BD/93140/2013 and S.Q. by PhD grant SFRH/BD/100024/2014. [Extracted from the article]

Author Contributions Conceptualization, S.R., W.K.K. and B.M.; data curation, S.R.; formal analysis, S.R., N.A. and M.K.O.; funding acquisition, M.K.O.; investigation, S.R.; methodology, S.R.; project administration, B.M.; software, A.K.; supervision, B.M.; validation, I.A.A.; visualization, R.M. and S.A.A., writing - original draft, S.R. and W.K.K.; writing - review and editing, Y.A.A. and B.M. All authors have read and agreed to the published version of the manuscript. The authors of this paper [[1]] have agreed that they would like to add Waqas Khan Kayani as a co-author, as he contributed to the generation of whole plants from transgenic hairy roots of I Ajuga bracteosa i and to the writing the original manuscript. The authors apologize for any inconvenience caused and state that the scientific conclusions are unaffected. [Extracted from the article]

Transition-metal-catalyzed directed C–H functionalization with various carbene precursors has been widely employed for constructing a wide range of complex and diverse active molecules through metal carbene migratory insertion processes. Among various carbene precursors, iodonium ylides serve as a novel and emerging carbene precursor with features including easy accessibility, thermal stability and high activity, which have attracted great attention from organic chemists and have achieved tremendous success in organic transformation. In this review, recent progress on the application of iodonium ylides with multifunctional coupling characteristics in C–H bond activation reactions is summarized, and the potential of iodonium ylides is discussed. [ABSTRACT FROM AUTHOR]

A new series of chiral 4,5-dihydro-1H-[1,2,4]-triazoline molecules, featuring a β-ᴅ-glucopyranoside appendage, were synthesized via a 1,3-dipolar cycloaddition reaction between various hydrazonyl chlorides and carbohydrate Schiff bases. The isolated enantiopure triazolines (8a–j) were identified through high-resolution mass spectrometry (HRMS) and vibrational spectroscopy. Subsequently, their solution structures were elucidated through NMR spectroscopic techniques. Single-crystal X-ray analysis of derivative 8b provided definitive evidence for the 3-D structure of this compound and revealed important intermolecular forces in the crystal lattice. Moreover, it confirmed the (S)-configuration at the newly generated stereo-center. Selected target compounds were investigated for anti-tumor activity in 60 cancer cell lines, with derivative 8c showing the highest potency, particularly against leukemia. Additionally, substituent-dependent anti-fungal and anti-bacterial behavior was observed. [ABSTRACT FROM AUTHOR]

The article delves into the intricate phase transitions of 1-Octadecanol and n-Nonadecane within a binary system, unveiling dynamic structural changes under varying conditions. Through Fourier transform infrared (FTIR) analysis, specific molecular vibrations were identified, shedding light on the molecular composition and interactions. The study highlights the challenges in detecting subtle phase transitions and emphasises the individuality of molecular behaviours in closely related compounds. The findings underscore the complexity of phase transitions in binary systems and advocate for a nuanced approach to studying molecular structures and behaviours. [ABSTRACT FROM AUTHOR]

4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)-based molecules have emerged as interesting materials for optoelectronic applications due to the possibility to easily fine-tune their photophysical and optical properties, dominated by two main absorption bands in the visible range. However, no studies have been reported on the nature of these spectral features. By means of ultrafast spectroscopy, we detect intramolecular energy transfer in a spin-coated film of di-thieno-phenyl BODIPY (DTPBDP) dispersed in a polystyrene matrix after pumping the high-energy absorption band. The same effect is not present upon pumping the lowest-energy band, which instead allows the achievement of efficient amplified spontaneous emission. Density functional calculations indicate the different nature of the two main absorption bands, explaining their different photophysical behavior. [ABSTRACT FROM AUTHOR]

This paper summarizes some of our results on the application of oligothiophenes as fluorescent markers for biological studies. The oligomers of thiophene, widely known for their semiconductor properties in organic electronics, are also fluorescent compounds characterized by chemical and optical stability, high absorbance and quantum yield. Their fluorescent emission can be easily modulated via organic synthesis by changing the number of thiophene rings and the nature of side-chains. This review shows how oligothiophenes can be derivatized with active groups such as phosphoramidite, N-hydroxysuccinimidyl and 4-sulfotetrafluorophenyl esters, isothiocyanate and azide by which the (bio)molecules of interest can be covalently bound. This paper also describes how molecules such as oligonucleotides, proteins and even nanoparticles, tagged with oligothiophenes, can be used in experiments ranging from hybridization studies to imaging of fixed and living cells. Finally, a few multilabeling experiments are described. [ABSTRACT FROM AUTHOR]

Native Collagen II Relieves Bone Impairment through Improving Inflammation and Oxidative Stress in Ageing db/db Mice. The authors would like to correct spelling mistakes (undenatured type II collagen) in the title, as well as in the main manuscript including the tables and figures in the title paper [[1]]. Reference 1 Fan R., Hao Y., Liu X., Kang J., Hu J., Mao R., Liu R., Zhu N., Xu M., Li Y. Native Collagen II Relieves Bone Impairment through Improving Inflammation and Oxidative Stress in Ageing db/db Mice. [Extracted from the article]

To ensure the correctness of the reported results, instead of simply relabeling the old gel image, we have repeated the experiment and run a new gel. Reference 1 Jiao X., Lu X., Chen A.J., Luo Y., Hao J.J., Gao W. Effects of Fusarium solani and F. oxysporum Infection on the Metabolism of Ginsenosides in American Ginseng Roots. Effects of Fusarium solani and F. oxysporum Infection on the Metabolism of Ginsenosides in American Ginseng Roots. [Extracted from the article]

The author reflects on the history of the journal "Molecules" and looks forward as it celebrates the 20th anniversary. Topics mentioned include the creation of Molecular Diversity Preservation International (MPDI) in 1995, the journal "Molecules" become the first electronic chemistry journal in 1996, and the announcing of additional Associate Editors to mark the 20th anniversary.

This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores. [ABSTRACT FROM AUTHOR]

A model potential previously developed for the ammonia molecule is treated in a single-center partial-wave approximation in analogy with a self-consistent field method developed by Moccia. The latter was used in a number of collision studies. The model potential is used to calculate DC Stark resonance parameters, i.e., resonance positions and shifts using the exterior complex scaling method for the radial coordinate. Three molecular valence orbitals are investigated for fields along the three Cartesian coordinates, i.e., along the molecular axis and in two perpendicular directions. The work extends previous work on the planar-geometry water molecule for which non-monotonic shifts were observed. We find such non-monotonic shifts for fields along the molecular axis. For perpendicular fields, we report the splitting of the 1 e orbitals into a fast- and a slow-ionizing orbital. [ABSTRACT FROM AUTHOR]

We report here a series of alkyl group-modified trimesic amide molecules (TAs) with excellent anion transport activities. Among them, TA6, with the highest ion transport activity and excellent selectivity, efficiently transports anions across the membrane in the order of ClO4− > I− > NO3− > Br− > Cl−, with an EC50 value as low as 17.6 nM (0.022 mol% relative to lipid molecules) for ClO4−, which outperforms other anions by 5- to 22-folds and manifests as the best perchlorate transporter ever reported. [ABSTRACT FROM AUTHOR]

Other articles are in the field of medicinal chemistry, they deal with purification of the isotopes and incorporation of the isotopes into molecules of biological interest. It is with great pleasure that I have accepted the challenge of reviewing and summarizing the articles published in Molecules through 2019 and 2020 on radioactive molecules. To reduce further, I have tried to choose papers that support what I have tried to say in my mini-review on radioactive molecules that was published in Molecules in 2019 and 2020, namely that the research area "radioactive molecules" is a very versatile one. [Extracted from the article]

The importance of intermolecular forces in the ionic polymerization process on large clusters of acetylene molecules to form polyaromatic hydrocarbons (PAHs) has been studied by Molina and Stein [[9]]. Furthermore, the calculated SAPT interaction energies had a good correlation with the experimentally measured melting points for these MILs, suggesting that the SAPT interaction energy could be used to predict melting points. Intermolecular forces, determined by the critical balance of interacting components having physical and chemical natures, control most of the static and dynamic properties of matter such as their existence in solid, liquid and gaseous phases, with their relative stability, and their chemical reactivity. [Extracted from the article]

Most of the current docking procedures are focused on fine conformational adjustments of assembled complexes and fail to reproduce large-scale protein motion. In this paper, we test a new modeling approach developed to address this problem. CABS-dock is a versatile and efficient tool for modeling the structure, dynamics and interactions of protein complexes. The docking protocol employs a coarse-grained representation of proteins, a simplified model of interactions and advanced protocols for conformational sampling. CABS-dock is one of the very few tools that allow unrestrained docking with large conformational freedom of the receptor. In an example application we modeled the process of complex assembly between two proteins: Troponin C (TnC) and the N-terminal helix of Troponin I (TnI N-helix), which occurs in vivo during muscle contraction. Docking simulations illustrated how the TnC molecule undergoes significant conformational transition on complex formation, a phenomenon that can be modeled only when protein flexibility is properly accounted for. This way our procedure opens up a new possibility for studying mechanisms of protein complex assembly, which may be a supporting tool for rational drug design. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "Synthesis and Characterization of [Fe(Htrz)2(trz)](BF4)] Nanocubes" published in the journal Molecules in 2022. The correction addresses an error in the references and acknowledges the use of the micelle method described in a previous thesis. The corrected reference clarifies the spin transitions occurring at lower temperatures compared to bulk analogs and other nanoparticles. The document also includes copyright and licensing information. [Extracted from the article]

The main topic of the article is to provide the characteristics of individual intermolecular interactions present between three lantern-like superphanes and the H 2 O, NH 3 , HF, HCN, and MeOH molecules trapped inside them. Despite the large cavity, the freedom of the trapped molecules is significantly limited by the presence of numerous interaction sites on the side chains of the superphane molecule. It is shown that the molecule trapped inside the superphane is stabilized mainly by only one or, less often, two strong hydrogen bonds involving the imino nitrogen atom, but QTAIM calculations also suggest the presence of many other intermolecular interactions, mainly hydrogen bonds involving imino or central hydrogen atoms from the side chains of the superphane molecule. Moreover, it is also shown that the structural simplification of the side chains does not significantly affect both the size of the superphane molecule and the obtained encapsulation energies, which is important in modeling this type of carceplexes. Noticeably, the parent superphane considered here was previously synthesized by the group of Qing He, so the results obtained will help in understanding this type and similar systems. [ABSTRACT FROM AUTHOR]

Consumers in developed and Western European countries are becoming more aware of the impact of food on their health, and they demand clear, transparent, and reliable information from the food industry about the products they consume. They recognise that food safety risks are often due to the unexpected presence of contaminants throughout the food supply chain. Among these, mycotoxins produced by food-infecting fungi, endogenous toxins from certain plants and organisms, pesticides, and other drugs used excessively during farming and food production, which lead to their contamination and accumulation in foodstuffs, are the main causes of concern. In this context, the goals of this review are to provide a comprehensive overview of the presence of toxic molecules reported in foodstuffs since 2020 through the Rapid Alert System for Food and Feed (RASFF) portal and use chromatography to address this challenge. Overall, natural toxins, environmental pollutants, and food-processing contaminants are the most frequently reported toxic molecules, and liquid chromatography and gas chromatography are the most reliable approaches for their control. However, faster, simpler, and more powerful analytical procedures are necessary to cope with the growing pressures on the food chain supply. [ABSTRACT FROM AUTHOR]

In recent years, the application of deep learning in molecular de novo design has gained significant attention. One successful approach involves using SMILES representations of molecules and treating the generation task as a text generation problem, yielding promising results. However, the generation of more effective and novel molecules remains a key research area. Due to the fact that a molecule can have multiple SMILES representations, it is not sufficient to consider only one of them for molecular generation. To make up for this deficiency, and also motivated by the advancements in contrastive learning in natural language processing, we propose a contrastive learning framework called CONSMI to learn more comprehensive SMILES representations. This framework leverages different SMILES representations of the same molecule as positive examples and other SMILES representations as negative examples for contrastive learning. The experimental results of generation tasks demonstrate that CONSMI significantly enhances the novelty of generated molecules while maintaining a high validity. Moreover, the generated molecules have similar chemical properties compared to the original dataset. Additionally, we find that CONSMI can achieve favorable results in classifier tasks, such as the compound–protein interaction task. [ABSTRACT FROM AUTHOR]

Penetration through the blood-brain barrier (BBB) is desirable in the case of potential pharmaceuticals acting on the central nervous system (CNS), but is undesirable in the case of drug candidates acting on the peripheral nervous system because it may cause CNS side effects. Therefore, modeling of the permeability across the blood-brain barrier (i.e., the logarithm of the brain to blood concentration ratio, log BB) of potential pharmaceuticals should be performed as early as possible in the preclinical phase of drug development. Biomimetic chromatography with immobilized artificial membrane (IAM) and the quantitative structure-activity relationship (QSAR) methodology were successful in modeling the blood-brain barrier permeability of 126 drug candidates, whose experimentally-derived lipophilicity indices and computationally-derived molecular descriptors (such as molecular weight (MW), number of rotatable bonds (NRB), number of hydrogen bond donors (HBD), number of hydrogen bond acceptors (HBA), topological polar surface area (TPSA), and polarizability (α)) varied by class. The QSARs model established by multiple linear regression showed a positive effect of the lipophilicity (log kw, IAM) and molecular weight of the compound, and a negative effect of the number of hydrogen bond donors and acceptors, on the log BB values. The model has been cross-validated, and all statistics indicate that it is very good and has high predictive ability. The simplicity of the developed model, and its usefulness in screening studies of novel drug candidates that are able to cross the BBB by passive diffusion, are emphasized. [ABSTRACT FROM AUTHOR]

This document is an editorial review titled "Radioactive Molecules 2021-2022" published in the journal Molecules. The author conducted a search in the journal and identified 172 articles published in 2021-2022 that dealt with radioactive isotopes. The articles were categorized into non-medical applications (23 articles) and medical applications (149 articles), with a focus on diagnostics, therapy, synthesis, and nuclide preparation. The review found an increase in the number of articles on medical uses of radioactive isotopes compared to the previous review in 2019-2020. The document provides tables listing the isotopes mentioned in the articles and their main forms of decay. The article discusses the development of new radiopharmaceuticals for clinical use, focusing on isotopes used in diagnosing and treating specific diseases. It mentions an increase in the number of articles discussing gamma emitters, with isotopes like 99mTc and 125I being mentioned more frequently. The article also highlights the use of theranostics in nuclear medicine, which involves using radiotracers for both diagnosis and treatment. The development process for radiopharmaceuticals is described, including synthesis, ex vivo testing, in vivo animal testing, and human clinical trials. The article categorizes the articles based on the diseases they focus on, such as cancers, brain disorders, inflammation and infection, and other diseases. The number of articles on radioactive isotopes in the journal Molecules has increased [Extracted from the article]

The molecular mechanism of the [3+2] cycloaddition reactions between aryl azides and ethyl propiolate was evaluated in the framework of the Molecular Electron Density Theory. It was found that independently of the nature of the substituent within the azide molecule, the cycloaddition process is realized via a polar but single-step mechanism. All attempts of localization as postulated earlier by Abu-Orabi and coworkers' zwitterionic intermediates were not successful. At the same time, the formation of zwitterions with an "extended" conformation is possible on parallel reaction paths. The ELF analysis shows that the studied cycloaddition reaction leading to the 1,4-triazole proceeds by a two-stage one-step mechanism. It also revealed that both zwitterions are created by the donation of the nitrogen atom's nonbonding electron densities to carbon atoms of ethyl propiolate. [ABSTRACT FROM AUTHOR]

Due to the electronic configuration of the atom and charge of the nucleus, the chlorine in organic molecules can exert a variety of effects. It can depart as a chloride anion in the process of substitution and elimination, facilitates the abstraction of protons and stabilizes generated carbanions, exerts moderate stabilizing effect of carbenes, carbocations and radicals. There are frequent cases where chlorine substituent promotes more than one transformation. These rich effects of chlorine substituent will be illustrated by examples of our work. [ABSTRACT FROM AUTHOR]

Favorable steric and electrostatic fit of a ligand to a receptor is of central interest in theoretical drug design. This paper considers the effects of non-protic solvents, in comparison with the gas phase, on the preferred conformation of the XCYCH3 moiety of simple aliphatic esters and heterocyclic methyl ethers with all combinations of the X and Y atoms as oxygen and sulfur. An IEF-PCM/B97D/aug-cc-pv(t+d)z continuum dielectric solvent study in chloroform and acetonitrile explores the through-space polarization effect of the environment on the conformational preference, not affected by possible solute-solvent hydrogen bond formation. The inherently favored structure for the present molecules is important, since the hypothetical oxygen and sulfur lone-pairs point approximately in opposite directions in the cis conformation of esters, whereas the trans and gauche conformations for the methyl group in ethers define nearly parallel or perpendicular directionality for the lone pairs of the ring heteroatoms and the O or S atoms connecting to the ring. These different preferences for the studied two families of compounds allow for designing formation of hydrogen bonds with a protein in fairly different regions of the latter still within the ligand-binding cavity. For a fine-tuning of these hydrogen bonds, a replacement of an oxygen atom of the ligand by a sulfur atom could be a straightforward possibility. [ABSTRACT FROM AUTHOR]