Israel Journal of Chemistry最新文献

{"title":"Cover Picture: (Isr. J. Chem. 10-11/2024)","authors":"","doi":"10.1002/ijch.202481001","DOIUrl":"https://doi.org/10.1002/ijch.202481001","url":null,"abstract":"<p>The cover image shows the logo of the 15th International Conference on Quasicrystals, held at Tel Aviv University in June 2023. The logo depicts the hexagonal Star of David. The background depicts a hexagonal quasiperiodic tiling, whose construction and characterization are the focus of the Review by Coates et al. in this volume. Such aperiodic yet perfectly ordered trigonal and hexagonal tilings served to study various experimental systems, such as the 3-fold surfaces of icosahedral quasicrystals and 6-fold bilayer graphene.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202481001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142861809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Topological Quantum Numbers in Quasicrystals","authors":"Johannes Kellendonk","doi":"10.1002/ijch.202400027","DOIUrl":"https://doi.org/10.1002/ijch.202400027","url":null,"abstract":"<p>We provide an overview on the theory of topological quantum numbers from the point of view of non-commutative topology. Topological phases are described by <i>K</i>-groups of <i>C</i>*-algebras. The algebras are constructed from the set of positions of the nuclei of the materials we want to study. Topological quantum numbers are Chern numbers of <i>K</i>-group elements. Maps between <i>K</i>-groups which are of algebraic topological origin provide the means to obtain relations between different topological quantum numbers as, for instance, in the bulk edge correspondence. We present simple aperiodic examples related to quasicrystals to illustrate the theory.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142860946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent Advances in Quasicrystal Research","authors":"Ron Lifshitz","doi":"10.1002/ijch.202412000","DOIUrl":"https://doi.org/10.1002/ijch.202412000","url":null,"abstract":"<p>The study of quasicrystals – materials that are characterized by their aperiodic yet long-range ordered structures<span>^1-5</span> – continues to evolve, offering new challenges and opportunities in understanding complex-ordered systems that transcend traditional crystallography. They have emerged as a rich interdisciplinary field, encompassing mathematics, physics, chemistry, and materials science. This introduces the additional challenge of bridging varied research communities, each with its distinct language and culture. Central to the investigation of quasicrystals are mathematical tools that describe their intricate geometric and topological properties, physical models that capture their unique electronic and other physical properties, as well as innovative experimental methods that can be employed to analyze their unique and complex nature. This special issue of the <i>Israel Journal of Chemistry</i> is dedicated to the latest advancements in quasicrystal research, presented at ICQ15 – the <i>15th International Conference on Quasicrystals</i> – held on the campus of Tel Aviv University in June 2023 (see Fig. 1 for a group photo). It offers a valuable snapshot of the current state of quasicrystal research, highlighting the progress made in recent years and the challenges that lie ahead. The collection of Reviews and Research Articles, included here, spans a broad spectrum of topics, reflecting the diverse and interdisciplinary nature of quasicrystal research, providing a good entry point, as well as some deep insight, into the theoretical, experimental and practical underpinnings of aperiodic long-range order.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202412000","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142860520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Substitutions and their Generalisations","authors":"Neil Mañibo","doi":"10.1002/ijch.202300159","DOIUrl":"https://doi.org/10.1002/ijch.202300159","url":null,"abstract":"<p>Tilings and point sets arising from substitutions are classical mathematical models of quasicrystals. Their hierarchical structure allows one to obtain concrete answers regarding spectral questions tied to the underlying measures and potentials. In this review, we present some generalisations of substitutions, with a focus on substitutions on compact alphabets, and with an outlook towards their spectral theory. Guided by two main examples, we will illustrate what changes when one moves from finite to compact (infinite) alphabets, and discuss under which assumptions do we recover the usual geometric and statistical properties which make them viable models of materials with almost periodic order. We also present a planar example (which is a two-dimensional generalisation of the Thue−Morse substitution), whose diffraction is purely singular continuous.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pure Point Diffraction and Almost Periodicity","authors":"Daniel Lenz,&nbsp;Timo Spindeler,&nbsp;Nicolae Strungaru","doi":"10.1002/ijch.202300158","DOIUrl":"https://doi.org/10.1002/ijch.202300158","url":null,"abstract":"<p>This article deals with pure point diffraction and its connection to various notions of almost periodicity. We explain why the Fibonacci chain does not fit into the classical concept of Bohr almost periodicity and how it fits into the classes of mean, Besicovitch and Weyl almost periodic point sets. We report on recent results which characterize pure point diffraction as mean almost periodicity of the underlying structure, and discuss how the complex amplitudes fit into this picture.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300158","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142861216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling Disorder in Aperiodic Crystals – Diffuse Scattering and Atomic Resolution Holography","authors":"J. R. Stellhorn,&nbsp;E. G. Meekel,&nbsp;A. Minelli","doi":"10.1002/ijch.202300154","DOIUrl":"https://doi.org/10.1002/ijch.202300154","url":null,"abstract":"<p>The atomic-scale disorder of aperiodic crystals, and quasicrystals in particular, is inherently difficult to explore by experimental methods due to their complex atomic arrangements. Two advanced characterization techniques, a revived and an emerging one, offer direct experimental access even to such complex atomic structures: Diffuse Scattering and Atomic Resolution Holography. In this overview, we introduce their specific application to aperiodic crystals and discuss their merits and difficulties.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142861731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cover Picture: (Isr. J. Chem. 8-9/2024)","authors":"","doi":"10.1002/ijch.202480801","DOIUrl":"https://doi.org/10.1002/ijch.202480801","url":null,"abstract":"<p>The cover art depicts the RNA catalyst ‘flexizyme’ based on its three-dimensional structure. It attaches a yellow sphere representing a non-canonical amino acid onto a tRNA, which is shown as a classical two-dimensional ‘cloverleaf’ representation. The catalyst is aided by two structural magnesium ions represented by small, darker red circles. Surrounding the flexizyme is a pool of acylated tRNA molecules and numerous macrocyclic peptides incorporating the non-canonical amino acids shown as colored circles.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202480801","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142328480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Special Issue on RNA-Based Catalysts that Revolutionized the Discovery of Bioactive Peptides","authors":"Assoc. Prof. Seino A. K. Jongkees,&nbsp;Assoc. Prof. Joseph M. Rogers,&nbsp;Dr. Louise J. Walport","doi":"10.1002/ijch.202400064","DOIUrl":"https://doi.org/10.1002/ijch.202400064","url":null,"abstract":"&lt;p&gt;This special issue of the &lt;i&gt;Israel Journal of Chemistry&lt;/i&gt; is in celebration of the Wolf Prize awarded to Hiroaki Suga in 2023 &lt;i&gt;“for pioneering discoveries that illuminate the functions and pathological dysfunctions of RNA and proteins and for creating strategies to harness the capabilities of these biopolymers in new ways to ameliorate human diseases”&lt;/i&gt;. In this issue we collect contributions from former trainees, collaborators, and beyond to profile how his work has impacted the fields of bioorganic chemistry, synthetic biology, and drug discovery. Focusing on his development of RNA-based aminoacylation catalysts, his share of the prize &lt;i&gt;“For developing RNA-based catalysts that revolutionized the discovery of bioactive peptides&lt;/i&gt;” is emphasised here in a collection of nine review articles and one research article that span aspects of oligonucleotide acylation catalysis, reprogramming of the genetic code, and applications of this in peptide drug discovery.&lt;/p&gt;&lt;p&gt;The RNA-based catalysts developed by Suga are called flexizymes. These were initially developed using the oligonucleotide selection platform ‘SELEX’ (systematic evolution of ligands by exponential enrichment). The &lt;i&gt;in vitro&lt;/i&gt; selection scheme was designed to select for self-acylating activity by evolving a 5’ extension on tRNA, mimicking a key step in a potential transition between RNA-based life and modern protein-dominant life. RNA molecules that were able to attach a biotinylated amino acid to their own 3’ end were enriched by streptavidin pull-down, connecting survival to catalytic activity. After several more selection campaigns aiming to improve the level of activity and scope of the 5’ extension to independently aminoacylate added tRNA in &lt;i&gt;trans&lt;/i&gt;, the modern flexizymes eFx, dFx, and aFx were born (discussed in detail in several reviews elsewhere).&lt;span&gt;&lt;sup&gt;1, 2&lt;/sup&gt;&lt;/span&gt; While this work began in fundamental biochemistry, the practical applications of a catalyst that is largely agnostic about which amino acid it attaches to which tRNA soon became apparent. However, as outlined in the contribution by &lt;b&gt;Cho, Lee, and coworkers&lt;/b&gt;,&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; an understanding of the precise working of flexizymes at the molecular level is still lacking. While a crystal structure of the oligonucleotide has been available for some time,&lt;span&gt;&lt;sup&gt;4&lt;/sup&gt;&lt;/span&gt; the amino acid component is poorly resolved and so this leaves open questions about the positioning of the substrate ester and contributions of nucleotides in the catalytic pocket. They describe attempts to profile the rules for design of good flexizyme substrates, and how this has expanded research into novel bio-based polymers. One consequence of having relatively easy access to tRNA acylated with amino acid-like non-canonical building blocks is the ease with which translational space could be explored, and this fed back into further fundamental insights into the translation process itself.&lt;/p&gt;&lt;p&gt;Flexizy","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142328457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hexagonal and Trigonal Quasiperiodic Tilings","authors":"Sam Coates,&nbsp;Akihisa Koga,&nbsp;Toranosuke Matsubara,&nbsp;Ryuji Tamura,&nbsp;Hem Raj Sharma,&nbsp;Ronan McGrath,&nbsp;Ron Lifshitz","doi":"10.1002/ijch.202300100","DOIUrl":"10.1002/ijch.202300100","url":null,"abstract":"<p>Exploring nonminimal-rank quasicrystals, which have symmetries that can be found in both periodic and aperiodic crystals, often provides new insight into the physical nature of aperiodic long-range order in models that are easier to treat. Motivated by the prevalence of experimental systems exhibiting aperiodic long-range order with hexagonal and trigonal symmetry, we introduce a generic two-parameter family of 2-dimensional quasiperiodic tilings with such symmetries. We focus on the special case of trigonal and hexagonal Fibonacci, or golden-mean, tilings, analogous to the well studied square Fibonacci tiling. We first generate the tilings using a generalized version of de Bruijn's dual grid method. We then discuss their interpretation in terms of projections of a hypercubic lattice from six dimensional superspace. We conclude by concentrating on two of the hexagonal members of the family, and examining a few of their properties more closely, while providing a set of substitution rules for their generation.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300100","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Breaking the Degeneracy of Sense Codons – How Far Can We Go?","authors":"Clark A. Jones,&nbsp;Matthew C. T. Hartman","doi":"10.1002/ijch.202400026","DOIUrl":"10.1002/ijch.202400026","url":null,"abstract":"<p>Genetic code expansion aims to incorporate non-canonical amino acids (ncAAs) into biological systems, enhancing protein functionality or enabling the <i>in vitro</i> selection of peptides from diverse mRNA displayed libraries. Typically, genetic code expansion has involved reassignment of stop codons to ncAAs through orthogonal translation systems. This review instead focuses on efforts to expand the genetic code by breaking the redundancy of sense codons <i>in vitro</i> and <i>in vivo. In vivo</i>, orthogonal aminoacyl-tRNA synthetase (AARS)/tRNA/AA systems are able to compete with endogenous machinery, enabling partial to full codon reassignment. Recent approaches, like genome recoding, offer potential solutions to reduce competition. <i>In vitro</i> studies utilize cell extract-based or reconstituted translation systems, allowing precise control of codon usage via gene design and tRNA addition, making breaking of sense degeneracy easier. In these systems several unsplit codon boxes have been successfully reassigned multiple to ncAAs. These efforts showcase both the successes and challenges in achieving orthogonality and selective codon decoding and point towards a future where the 64 codons can encode more than 30 monomers, enabling new advances in synthetic biology and drug discovery.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141939715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}