Examining and Supporting Mechanistic Explanations Across Chemistry and Biology Courses.

Causal mechanistic reasoning is a thinking strategy that can help students explain complex phenomena using core ideas commonly emphasized in separate undergraduate courses, as it requires students to identify underlying entities, unpack their relevant properties and interactions, and link them to construct mechanistic explanations. As a crossdisciplinary group of biologists, chemists, and teacher educators, we designed a scaffolded set of tasks that require content knowledge from biology and chemistry to construct nested hierarchical mechanistic explanations that span three scales (molecular, macromolecular, and cellular). We examined student explanations across seven introductory and upper-level biology and chemistry courses to determine how the construction of mechanistic explanations varied across courses and the relationship between the construction of mechanistic explanations at different scales. We found non-, partial, and complete mechanistic explanations in all courses and at each scale. Complete mechanistic explanation construction was lowest in introductory chemistry, about the same across biology and organic chemistry, and highest in biochemistry. Across tasks, the construction of a mechanistic explanation at a smaller scale was associated with constructing a mechanistic explanation for larger scales; however, the use of molecular scale disciplinary resources was only associated with complete mechanistic explanations at the macromolecular, not cellular scale.

Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives.

More than a half century ago it became feasible to simulate, using classical-mechanical equations of motion, the dynamics of molecular systems on a computer. Since then classical-physical molecular simulation has become an integral part of chemical research. It is widely applied in a variety of branches of chemistry and has significantly contributed to the development of chemical knowledge. It offers understanding and interpretation of experimental results, semiquantitative predictions for measurable and nonmeasurable properties of substances, and allows the calculation of properties of molecular systems under conditions that are experimentally inaccessible. Yet, molecular simulation is built on a number of assumptions, approximations, and simplifications which limit its range of applicability and its accuracy. These concern the potential-energy function used, adequate sampling of the vast statistical-mechanical configurational space of a molecular system and the methods used to compute particular properties of chemical systems from statistical-mechanical ensembles. During the past half century various methodological ideas to improve the efficiency and accuracy of classical-physical molecular simulation have been proposed, investigated, evaluated, implemented in general simulation software or were abandoned. The latter because of fundamental flaws or, while being physically sound, computational inefficiency. Some of these methodological ideas are briefly reviewed and the most effective methods are highlighted. Limitations of classical-physical simulation are discussed and perspectives are sketched.

Reflections from Nobel laureates in chemistry.

Since the first award in 1901, the Nobel Prize has come to signify the pinnacle of scientific achievement. In this Voices piece in the August special issue of Cell Chemical Biology entitled "Bridging chemistry and biology," we ask Nobel laureates to reflect on the impact the prize had on them. We learn how it affected their life or work, their outlook on science, the lessons learned, and their advice for the next generation of scientists.

Towards a Sustainable Future: Challenges and Opportunities for Early-Career Chemists.

The concepts of sustainability and sustainable chemistry have attracted increasing attention in recent years, being of great importance to the younger generation. In this Viewpoint Article, we share how early-career chemists can contribute to the sustainable transformation of their discipline. We identify ways in which they can engage to catalyse action for change. This article does not attempt to answer questions about the most promising or pressing areas driving research and chemical innovation in the context of sustainability. Instead, we want to inspire and engage early-career chemists in pursuing sustainable actions by showcasing opportunities in education, outreach and policymaking, research culture and publishing, while highlighting existing challenges and the complexity of the topic. We want to empower early-career chemists by providing resources and ideas for engagement for a sustainable future globally. While the article focuses on students and early-career chemists, it provides insights to further stimulate the engagement of scientists from diverse backgrounds.

Editorial of Special Issue "Current Trends in Chemistry Towards Biology".

One of the definitions of chemical biology is that it is a scientific discipline spanning the fields of chemistry, biology, and physics; it primarily involves the application of chemical techniques, tools, analyses, and often compounds (also known as chemical probes), which are produced through synthetic chemistry, in order to study and manipulate biological systems [...].

The culinary chemist: Out of the lab and into the tent.

In this Stories piece, Josh Smalley, a postdoctoral research associate at the University of Leicester and finalist of The Great British Bake Off, discusses the parallels between chemistry and baking, revealing how he successfully combines the two.

Lavoisier and the History of Chemistry.

During the eighteenth century, authors of chemical treatises and courses on chemistry often introduced their work with a chapter devoted to the history of chemistry. While there may have been different reasons for the use of history, its importance was never seriously questioned. However, when Antoine Laurent Lavoisier (1743-1794) took a professional interest in chemistry in the early 1770s, he progressively became uneasy with this literary tradition. In this essay, I intend to explore the ways in which Lavoisier looked at the history of chemistry and to show how, from the 1780s onwards, he began to adopt a hostile attitude towards historical erudition. This vision, which culminated in the publication of the Traité élémentaire de chimie (Paris, 1789), was not only the result of a stylistic preference but constituted a direct attack on a way of doing chemistry from which Lavoisier intended to distance himself.

Voices: Challenges and opportunities for bioorthogonal chemistry.

Bioorthogonal chemistry was deservedly recognized with the 2022 Nobel Prize in Chemistry, having transformed the way chemists and biologists interrogate biological systems in the past twenty years. This Voices piece asks researchers from a range of backgrounds: what are some major challenges and opportunities facing the field in coming years?

Mendeleev's discovery of the periodic table and the first European Academy of Sciences to honour him.

The chemical science community will commemorate the 155th anniversary of Mendeleev's groundbreaking discovery of the periodic table of elements in 2024. This paper aims to underscore the significance of Mendeleev's honorary membership in the Academy of Sciences in Zagreb, Croatia, which occurred in 1882, making it the first scientific academy in Europe to extend this recognition. Additionally, we seek to explore the contextual circumstances that contributed to this noteworthy event within the broader European context. To provide insight into the specificities and variations in the influence and reception of the periodic table of elements within the educational process of select European countries (Russia, Germany, Czech Lands, Serbia), we conducted a comprehensive review, drawing comparisons to Croatia. Notably, upon its initial publication in 1869, the discovery of the periodic table did not gain immediate acceptance in Croatia, largely attributed to the absence of a well-established presence of chemical science within the country. About fifteen years passed from Mendeleev's discovery of the periodic law to its reception and dissemination throughout Croatia. Despite an initial delay, Croatian chemical science followed the development of the periodic table through secondary and university education, while actively partaking it in.

Opening New Avenues in Bioorganic Chemistry: Prof. Chuan He Receives the Tetrahedron Prize.

Prof. Chuan He was awarded the Tetrahedron Prize this year, one of the world's most prestigious prizes in organic chemistry. This In Focus briefly delves into the remarkable work of Prof. Chuan He and explores how his recent accolades underscore his impact on the world of science. His seminal contributions have paved the way for new directions at the interface of organic chemistry and life sciences.

The Archaeology of Alchemy and Chemistry: Past, Present, and Ideas for the Future.

The materials and practices of chymical procedures have become key sources of information among science historians, opening up channels for cross-disciplinary dialogue. This is especially true with regard to material culture-based disciplines such as archaeology whose bottom-up approach offers significant contributions to the new historiography of science. Parallel to this trend, some archaeological scientists who specialise in reconstructing past technologies have begun to address questions concerning the production and circulation of scientific knowledge, and have focused as well on the contributions of artists/artisans to the development of natural philosophical theories. This essay charts the history of this archaeology of alchemy and chemistry and its development as a sub-discipline of archaeological science. By mapping this history, from an initial period with a focus on metallurgy to current trends, it demonstrates how the archaeology of alchemy and chemistry both mirrors and, at the same time, feeds the broadening scope of the historiography of science. After surveying the most relevant works and highlighting the key contributions that archaeologists have brought to a discourse related to the creation of scientific knowledge, the essay also offers a series of ideas related to materials awaiting comprehensive study that will further strengthen methodological synergies across disciplines.

Non-Hydrolysable Analogues of Cyclic and Branched Condensed Phosphates: Chemistry and Chemical Proteomics.

Studies into the biology of condensed phosphates almost exclusively cover linear polyphosphates. However, there is evidence for the presence of cyclic polyphosphates (metaphosphates) in organisms and for enzymatic digestion of branched phosphates (ultraphosphates) with alkaline phosphatase. Further research of non-linear condensed phosphates in biology would profit from interactome data of such molecules, however, their stability in biological media is limited. Here we present syntheses of modified, non-hydrolysable analogues of cyclic and branched condensed phosphates, called meta- and ultraphosphonates, and their application in a chemical proteomics approach using yeast cell extracts. We identify putative interactors with overlapping hits for structurally related capture compounds underlining the quality of our results. The datasets serve as starting point to study the biological relevance and functions of meta- and ultraphosphates. In addition, we examine the reactivity of meta- and ultraphosphonates with implications for their "hydrolysable" analogues: Efforts to increase the ring-sizes of meta- or cyclic ultraphosphonates revealed a strong preference to form trimetaphosphate-analogue structures by cyclization and/or ring-contraction. Using carbodiimides for condensation, the so far inaccessible dianhydro product of ultraphosphonate, corresponding to P4 O11 2- , was selectively obtained and then ring-opened by different nucleophiles yielding modified cyclic ultraphosphonates.

Wolf Prize in Chemistry 2023: A Celebration for Chemical Biology.

On February 7th, 2023, the Wolf Foundation (www.wolffund.org.il/) announced that the Wolf Prize in Chemistry was awarded to three distinguished scholars, Prof. Chuan He from The University of Chicago, Prof. Hiroaki Suga from The University of Tokyo, and Prof. Jeffery W. Kelly from The Scripps Research Institute, "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." Their pioneering research works have made a huge impact on contemporary chemical biology and deserve celebration by the whole community.