Physical Organic Research Articles

Exceptions, Paradoxes, and Their Resolutions in Chemical Reactivity.

Progress in chemistry has primarily been framed through inductive processes, leading to the frequent emergence of exceptions and unexpected reactivities. These anomalies─ranging from surprising reactivity trends and paradoxical understandings to unanticipated parameter influences and unexpected successes or failures in synthetic methods─offer valuable insights that can drive scientific discovery. While it is commonly accepted that such exceptions can drive progress, many have been passively accepted without being explored for opportunities. Although numerous chemists have addressed exceptions and refined chemical models and theories, employing a systematic framework for actively exploring and understanding the underlying causes of exceptions could resolve paradoxes in broader contexts and create a greater impact than treating anomalies as isolated occurrences. This perspective demonstrates a proactive epistemic approach to uncovering the opportunities presented by exceptions and promotes deliberate, thoughtful engagement with paradoxes and anomalies. While the examples primarily focus on physical organic chemistry, the concepts are broadly applicable across various fields in chemical science. The thinking framework presented here is neither exhaustive nor prescriptive, but it outlines one of many potentially possible ways to inspire further development in how these anomalies could be harnessed for advancement.

Machine learning-guided prediction of hydroformylation.

A holistic model for predicting yield and linear selectivity for the hydroformylation of 1-octene was developed by machine learning using the experimental data collected from literatures. Physical organic chemistry (POC) parameter-based descriptors were adopted to represent pre-catalyst molecular features. Machine learning models trained respectively by Random Forests (RF) and Extreme Gradient Boost (XGBoost) algorithm showed remarkable performance on predicting linear selectivity. The method can also comprehensively map the correlation between reaction conditions and the results. The accuracy of the prediction results was verified by experimental data.

Pnictogen-Assisted Self-Assembly as a Means to Study Mediated Thiol/Disulfide Exchange in Supramolecular Dynamic Covalent Assemblies.

Thiol-disulfide interchange has been a large field of study for both biochemists and physical organic chemists alike due to its prevalence within biological systems and fundamentally interesting dynamic nature. More recently, efforts have been made to harness the power of this reversible reaction to make self-assembling systems of macrocyclic molecules. However, less effort has focused on the fundamental work of isolating these assemblies and studying the factors that control the assembly and sorting of these emerging cyclic systems. A more complete fundamental understanding of factors controlling such self-assembly could also improve understanding of the complex systems biology of thiol exchange while also aiding in the design of dynamic thiol assembly to enable applications ranging from drug delivery and biosensing to new materials synthesis. We have shown previously that pnictogen-assisted self-assembly enables formation of discrete disulfide macrocycles and cages without competition from polymer formation for a wide variety of alkyl thiols. In this study, we report the expansion of pnictogen-assisted self-assembly methods to form disulfide bearing macrocycles from aryl thiol containing ligands, allowing access to previously unreported molecules. These studies complement classical physical organic and chemical biology studies on the rates and products of aryl thiol oxidation to disulfides, and we show that this self-assembly method revises some prevailing wisdom from these key classical studies by providing new product distributions and new isolable products in cyclic disulfide formation.

John I. Brauman (1937–2024)

Groundbreaking physical organic chemist

In Memoriam: The Life and Scientific Accomplishments of Frank A. L. Anet (1926–2024)

ABSTRACTA memorial tribute detailing the life and scientific accomplishments of Frank A. L. Anet, a pioneer of nuclear magnetic resonance (NMR) spectroscopy who discovered bedrock principles in organic chemistry and magnetic resonance. He was the first to show that nuclear Overhauser effects could provide structural information, significantly impacting future NMR applications. In the 1960s and 1970s, he built entire multinuclear NMR spectrometers operating as high as 396 MHz for protons, detecting nuclei inaccessible to commercial instruments, and operating at very low temperatures for studying molecular structure and dynamics. A titan of physical organic chemistry, Frank made important contributions in the areas of conformational analysis, stereochemistry, isotope effects, NMR relaxation theory, and chemical origins of life.

Molecular Ball Joints: Mechanochemical Perturbation of Bullvalene Hardy-Cope Rearrangements in Polymer Networks.

The solution-state fluxional behavior of bullvalene has fascinated physical organic and supramolecular chemists alike. Little effort, however, has been put into investigating bullvalene applications in bulk, partially due to difficulties in characterizing such dynamic systems. To address this knowledge gap, we herein probe whether bullvalene Hardy-Cope rearrangements can be mechanically perturbed in bulk polymer networks. We use dynamic mechanical analysis to demonstrate that the activation barrier to the glass transition process is significantly elevated for bullvalene-containing materials relative to "static" control networks. Furthermore, bullvalene rearrangements can be mechanically perturbed at low temperatures in the glassy region; such behavior facilitates energy dissipation (i.e., increased hysteresis energy) and polymer chain alignment to stiffen the material (i.e., increased Young's modulus) under load. Computational simulations corroborate our work that showcases bullvalene as a reversible "low-force" covalent mechanophore in the modulation of viscoelastic behavior.

A life in light - in honor of David Mauzerall on his 95th birthday.

David Mauzerall was born on July 22, 1929 to a working-class family in the small, inland textile town of Sanford, Maine. Those humble origins instilled a lifelong frugality and an innovative spirit. After earning his PhD degree in 1954 in physical organic chemistry with Frank Westheimer at the University of Chicago, he joined The Rockefeller Institute for Medical Research (now University) as a postdoctoral fellow that summer, rose to the rank of professor, and remained there for the rest of his career. His work over more than 60 years encompassed porphyrin biosynthesis, photoinduced electron-transfer reactions in diverse architectures (solutions, bilayer lipid membranes, reaction centers, chromatophores, and intact leaves), the light-saturation curve of photosynthesis, statistical treatments of photoreactions, and "all-things porphyrins." His research culminated in studies he poetically referred to as "listening to leaves" through the use of pulsed photoacoustic spectroscopy to probe the course and thermodynamics of photosynthesis in its native state. His research group was always small; indeed, of 185 total publications, 39 were singly authored. In brief, David Mauzerall has blended a deep knowledge of distinct disciplines of physical organic chemistry, photochemistry, spectroscopy and biophysics with ingenious experimental methods, incisive mathematical analysis, pristine personal integrity, and unyielding love of science to deepen our understanding of photosynthesis in its broadest context. He thought creatively - and always independently. His work helped systematize the fields of photosynthesis and the origin of life and made them more quantitative. The present article highlights a number of salient scientific discoveries and includes comments from members of his family, friends, and collaborators (Gary Brudvig, Greg Edens, Paul Falkowski, Alzatta Fogg, G. Govindjee, Nancy Greenbaum, Marilyn Gunner, Harvey Hou, Denise and Michele Mauzerall, Thomas Moore, and William Parson) as part of a celebration of his 95th birthday.

Recent Developments in the Ruthenium‐Catalyzed Azide Alkyne Cycloaddition (RuAAC) Reaction

AbstractThe ruthenium‐catalyzed azide‐alkyne cycloaddition (RuAAC) gives access to 1,5‐disubstitued triazoles in a single atom‐economical step and offers advantages compared to its copper‐catalyzed counterpart in that both terminal and internal alkynes can be employed. This review summarizes recent findings in this field during the last eight years, covering mechanistic investigations, synthetic developments, as well as applications in medicinal chemistry, polymer synthesis and physical organic chemistry.

Towards to some published misconceptions about TNT and ɛ-CL20

The literature widely reported information about apparent high impact sensitivities of both the pure 2,4,6-trinitrotoluene (TNT; i.e. of 14–16 J) and ɛ-2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (ɛ-CL20; i.e. of 2–4.4 J), which mostly correspond to the BAM method of determination. This brief overview discusses the reasons of these error data. The physical organic chemistry approach to this problem has confirmed the Beijing Inst. of Technology value of 13.2 J for ɛ-CL20 and the LANL value of 39.2 J for TNT. The morphological instability of ɛ-CL20, when in contact with polar binders or plasticizers, might not have much influence on its application in propellants. The stabilization of ɛ- to β-CL20 upon its entry into a cocrystal with a coformer having the character of a polynitro compound (especially with nitramines) could be of practical importance. The high impact sensitivity of TNT and ɛ-CL20 is important for handling and processing safety when related to the specific practical samples. However, they cannot be used for molecular-structural analyses and predictions or as a comparative standard, which is currently widespread in the literature.

Accurate Protein pKa Prediction with Physical Organic Chemistry Guided 3D Protein Representation.

Protein pKa is a fundamental physicochemical parameter that dictates protein structure and function. However, accurately determining protein site-pKa values remains a substantial challenge, both experimentally and theoretically. In this study, we introduce a physical organic approach, leveraging a protein structural and physical-organic-parameter-based representation (P-SPOC), to develop a rapid and intuitive model for protein pKa prediction. Our P-SPOC model achieves state-of-the-art predictive accuracy, with a mean absolute error (MAE) of 0.33 pKa units. Furthermore, we have incorporated advanced protein structure prediction models, like AlphaFold2, to approximate structures for proteins lacking three-dimensional representations, which enhances the applicability of our model in the context of structure-undetermined protein research. To promote broader accessibility within the research community, an online prediction interface was also established at isyn.luoszgroup.com.

A detailed overview of quercetin: implications for cell death and liver fibrosis mechanisms

BackgroundQuercetin, a widespread polyphenolic flavonoid, is known for its extensive health benefits and is commonly found in the plant kingdom. The natural occurrence and extraction methods of quercetin are crucial due to its bioactive potential.PurposeThis review aims to comprehensively cover the natural sources of quercetin, its extraction methods, bioavailability, pharmacokinetics, and its role in various cell death pathways and liver fibrosis.MethodsA comprehensive literature search was performed across several electronic databases, including PubMed, Embase, CNKI, Wanfang database, and ClinicalTrials.gov, up to 10 February 2024. The search terms employed were “quercetin”, “natural sources of quercetin”, “quercetin extraction methods”, “bioavailability of quercetin”, “pharmacokinetics of quercetin”, “cell death pathways”, “apoptosis”, “autophagy”, “pyroptosis”, “necroptosis”, “ferroptosis”, “cuproptosis”, “liver fibrosis”, and “hepatic stellate cells”. These keywords were interconnected using AND/OR as necessary. The search focused on studies that detailed the bioavailability and pharmacokinetics of quercetin, its role in different cell death pathways, and its effects on liver fibrosis.ResultsThis review details quercetin’s involvement in various cell death pathways, including apoptosis, autophagy, pyroptosis, necroptosis, ferroptosis, and cuproptosis, with particular attention to its regulatory influence on apoptosis and autophagy. It dissects the mechanisms through which quercetin affects these pathways across different cell types and dosages. Moreover, the paper delves into quercetin’s effects on liver fibrosis, its interactions with hepatic stellate cells, and its modulation of pertinent signaling cascades. Additionally, it articulates from a physical organic chemistry standpoint the uniqueness of quercetin’s structure and its potential for specific actions in the liver.ConclusionThe paper provides a detailed analysis of quercetin, suggesting its significant role in modulating cell death mechanisms and mitigating liver fibrosis, underscoring its therapeutic potential.

Raney Nickel‐Catalyzed Deuterium Labeling of Nitrogen‐Containing Heterocycles and Pharmaceuticals under Continuous Flow Conditions

Deuterium‐labeled compounds play a pivotal role in physical organic chemistry, life sciences, and materials science. This has resulted in a surge of interest in deuterium‐labeled active pharmaceutical ingredients in recent years. In this study, we present a continuous flow Raney nickel‐catalyzed hydrogen isotope exchange process that boasts compatibility with a wide spectrum of nitrogen‐containing heterocycles and pharmaceutical compounds. The broad applicability of the developed method was demonstrated through successful labeling of various purine bases, imidazoles, pyridines, and active pharmaceutical ingredients, including complex structures like abacavir and remdesivir. Control experiments revealed Raney nickel's crucial role in the exchange process, showcasing the superiority of the continuous flow approach over batch reactions. Furthermore, a scaled‐up experiment demonstrated the robustness of the catalyst.

Methanetriol─Formation of an Impossible Molecule.

Orthocarboxylic acids─organic molecules carrying three hydroxyl groups at the same carbon atom─have been distinguished as vital reactive intermediates by the atmospheric science and physical (organic) chemistry communities as transients in the atmospheric aerosol cycle. Predicted short lifetimes and their tendency to dehydrate to a carboxylic acid, free orthocarboxylic acids, signify one of the most elusive classes of organic reactive intermediates, with even the simplest representative methanetriol (CH(OH)3)─historically known as orthoformic acid─not previously been detected experimentally. Here, we report the first synthesis of the previously elusive methanetriol molecule in low-temperature mixed methanol (CH3OH) and molecular oxygen (O2) ices subjected to energetic irradiation. Supported by electronic structure calculations, methanetriol was identified in the gas phase upon sublimation via isomer-selective photoionization reflectron time-of-flight mass spectrometry combined with isotopic substitution studies and the detection of photoionization fragments. The first synthesis and detection of methanetriol (CH(OH)3) reveals its gas-phase stability as supported by a significant barrier hindering unimolecular decomposition. These findings progress our fundamental understanding of the chemistry and chemical bonding of methanetriol, hydroxyperoxymethane (CH3OOOH), and hydroxyperoxymethanol (CH2(OH)OOH), which are all prototype molecules in the oxidation chemistry of the atmosphere.

An Organic Chemist's Guide to Fluorophores – Understanding Common and Newer Non‐Planar Fluorescent Molecules for Biological Applications

AbstractLabeling and detection of biomolecules in vitro and in vivo is essential to many areas of biomedical science. Fluorophores stand as indispensable tools within chemical biology, underscoring the importance of fine‐tuning their optical properties. This review focuses on methods for optimizing emission wavelength, quantum yield and photostability. We focus not just on the trends, but the fundamental physical organic chemistry concepts that inform the connection between molecular structure and fluorescent properties. This approach offers an essential understanding of fluorescence, enabling readers to develop a systematic analytical framework for thinking about fluorescence. Furthermore, an evaluation of newer non‐planar fluorophores shines light on the bright future of fluorescent molecules.

A Continuing Career in Physical Organic Chemistry: Donna G. Blackmond

A Continuing Career in Physical Organic Chemistry: Donna G. Blackmond

Looking inside: Analysis of keto‐enol equilibrium using agent‐based models

AbstractThe subject of keto‐enol equilibrium has a long history and well‐established position within physical organic chemistry. Nonetheless, one still finds numerous reports of confusing findings and questions of accuracy when dealing with its practical application. In this report, some apparently anomalous recent observations are reviewed and then reexamined using density functional theory computations and agent‐based (cellular automata) models of the keto‐enol‐anion equilibrium system. It becomes apparent that a resolution of many of the results can be achieved by taking into account the fact that although the ketone form is often present in overwhelmingly greater concentration, the enol can still contribute significantly to formation of the anion through its much greater acidity. Thus, in these cases, dissociation data assigned solely to the ketone form should in fact be recognized as representing a mixture of contributions from both the keto and the (neglected) enol form.

Electrophilic Reactivity of Sulfated Alcohols in the Context of Skin Sensitization.

The surfactant sodium lauryl sulfate (SLS), although consistently positive in the murine local lymph node assay (LLNA) for skin sensitization, shows no evidence of being a human sensitizer and is often described as a false positive, lacking structural alerts for sensitization. However, there is evidence of the cinnamyl sulfate anion being the metabolite responsible for the sensitization potential of cinnamyl alcohol to humans and in animal tests. Here, manufacturing chemistry data and physical organic chemistry principles are applied to confirm that SLS is not reactive enough to sensitize, whereas sensitization to cinnamyl alcohol via cinnamyl sulfate is plausible. Sensitization data for several other primary alcohols, including geraniol, farnesol, and possibly hydrocortisone, are also consistent with this mechanism. It seems possible that biosulfation may play a wider role than has previously been recognized in skin sensitization.

Computational prediction of complex cationic rearrangement outcomes.

Recent years have seen revived interest in computer-assisted organic synthesis1,2. The use of reaction- and neural-network algorithms that can plan multistep synthetic pathways have revolutionized this field1,3-7, including examples leading to advanced natural products6,7. Such methods typically operate on full, literature-derived 'substrate(s)-to-product' reaction rules and cannot be easily extended to the analysis of reaction mechanisms. Here we show that computers equipped with a comprehensive knowledge-base of mechanistic steps augmented by physical-organic chemistry rules, as well as quantum mechanical and kinetic calculations, can use a reaction-network approach to analyse the mechanisms of some of the most complex organic transformations: namely, cationic rearrangements. Such rearrangements are a cornerstone of organic chemistry textbooks and entail notable changes in the molecule's carbon skeleton8-12. The algorithm we describe and deploy at https://HopCat.allchemy.net/ generates, within minutes, networks of possible mechanistic steps, traces plausible step sequences and calculates expected product distributions. We validate this algorithm by three sets of experiments whose analysis would probably prove challenging even to highly trained chemists: (1) predicting the outcomes of tail-to-head terpene (THT) cyclizations in which substantially different outcomes are encoded in modular precursors differing in minute structural details; (2) comparing the outcome of THT cyclizations in solution or in a supramolecular capsule; and (3) analysing complex reaction mixtures. Our results support a vision in which computers no longer just manipulate known reaction types1-7 but will help rationalize and discover new, mechanistically complex transformations.

Gordon Research Conference on Physical Organic Chemistry

AbstractEnde Juni fand die Gordon Research Conference on Physical Organic Chemistry nach einer vierjährigen pandemiebedingten Pause nun erneut in der Holderness School in New Hampshire in den USA statt. Organisiert wurde die fünftägige Tagung von Burkhard König (Universität Regensburg) und Cornelia Bohne (University of Victoria); etwa 160 Teilnehmer aus aller Welt trafen sich und tauschten sich aus. Die GDCh unterstützte mit einem Reisestipendium drei Promovierende, die hier über die Konferenz berichten.

Cold Plasma for Green Advanced Reduction/Oxidation Processes (AROPs) of Organic Pollutants in Water.

Cold plasma is gaining increasing attention as a novel tool to activate energy demanding chemical processes, including advanced reduction/oxidation processes (AROPs) of organic pollutants in water. The very complex milieu generated by discharges at the water/plasma interface comprises photons, strong oxidants and strong reductants which can be exploited for achieving the degradation of most any kind of pollutants. Despite the complexity of these systems, the powerful arsenal of mechanistic tools and chemical probes of physical organic chemists can be usefully applied to understand and develop plasma chemistry. Specifically, the added value of air plasma generated by in situ discharge with respect to ozonation (ex situ discharge) is demonstrated using phenol and various phenol derivatives and mechanistic evidence for the prevailing role of hydroxyl radicals in the initial attack is presented. On the reduction front, the impressive performance of cold plasma in inducing the degradation of recalcitrant perfluoroalkyl substances, which do not react with OH radicals but are attacked by electrons, is reported and discussed. The widely different reactivities of perfluorooctanoic acid (PFOA) and of perfluorobutanoic acid (PFBA) underline the crucial role played in these processes by the interface between plasma and solution and the surfactant properties of the treated pollutants.