Physical Organic Research Articles

Chemistry of Bridged Lactams: Recent Developments.

Bridged lactams represent the most effective and wide-ranging method of constraining the amide bond in a non-planar conformation. A previous comprehensive review on this topic was published in 2013 (Chem. Rev. 2013, 113, 5701–5765). In the present review, which is published as a part of the Special Issue on Amide Bond Activation, we present an overview of the recent developments in the field of bridged lactams that have taken place in the last five years and present a critical assessment of the current status of bridged lactams in synthetic and physical organic chemistry. This review covers the period from 2014 until the end of 2018 and is intended as an update to Chem. Rev. 2013, 113, 5701–5765. In addition to bridged lactams, the review covers recent advances in the chemistry of bridged sultams, bridged enamines and related non-planar structures.

Near-IR Photochemistry for Biology: Exploiting the Optical Window of Tissue.

Photoactive molecules enable much of modern biology and biochemistry-a vast library of fluorescent chromophores is used to track and label cellular structures and macromolecules. However, photochemistry is better known to the synthetic or physical organic chemist as a "light switch" that turns on unusual excited-state reactivity, isomerization, or dynamic adjustment of structure. This review details a rapidly growing approach to biophotochemistry that uses low-energy near-IR wavelengths not only for imaging, but also for close spatial control over chemical switching events in biosystems. Emphasis is placed on topics of biomedical interest: release of gaseous biological messengers, uncaging of drugs, nano-therapeutics, and modification of biomaterials.

The logic of translating chemical knowledge into machine-processable forms: a modern playground for physical-organic chemistry

With renewed interest and significant progress in computer-assisted synthetic planning, it is essential to codify the logic that should be followed when translating organic synthetic knowledge into reaction rules understandable to the machine.

Alternating catalytic reactions

The application of alternating current is advantageous in energy transfer over long distances. It is a well-known fact now, but subject of long conflict in the era of pioneering works in electric power production. There are also some processes in physical chemistry, organic and inorganic chemistry, in biochemistry and related sciences, which take place in opposite directions, with consecutive alternations in time. However, the very existence of alternate reactions, now known as the oscillatory or oscillating reactions, has long been disputed because it was thought that it is contrary to the basic principles of thermodynamics. Nevertheless, according to our knowledge, there are no oscillatory reactions without catalytic loop as the essential part of a mechanism. There could be a fundamental rule that catalysis is necessary to generate oscillations in concentrations and reaction rates. Particularly, homogeneous oscillatory reactions are often subject of research as relatively simple systems with good chance to clearly define feedbacks responsible for instability phenomena. However, oscillations can at least equally often be found in heterogeneous catalytic reactions. Recently, changes in product selectivity was proved when Pd catalyzed carbonylation of phenylacetylene was moved to the oscillatory dynamic state. With this simple result, the doors are now open for wide spectrum of research projects and applications.

From Active Sites to Machines: A Challenge for Enzyme Chemists.

As researchers who study enzyme chemistry embrace increasingly complex systems, especially biological machines, our attention is also shifting from steps involving covalent bond formation or cleavage to those that exclusively involve changes in non-covalent bonding. Assembly line polyketide synthases are an example of this growing challenge. By now, the chemical reactions underpinning polyketide biosynthesis can be unequivocally mapped to well-defined active sites and are, for the most part, readily explicable in the language of physical organic chemistry. Yet, all of these insights merely serve as a backdrop to the real problem of explaining how the catalytic functions of dozens of active sites are synchronized in order to allow these remarkable machines to turn over with remarkable specificity. Notwithstanding the fact that the time-honored language of physical organic chemistry can teach us a lot, it is often insufficient to describe many of these events, and must therefore evolve.

Cluster Preface: Atropisomerism

Jay S. Siegel received his Ph.D. from Princeton (1985), was a Swiss Universities Fellow at ETH Zurich (1983-4), and NSF–CNRS postdoctoral fellow at the University of Louis Pasteur in Strasbourg (1985-6). He began as Assistant Professor of Chemistry (1986) at UCSD, was promoted to Associate Professor (1992) and Full Professor (1996). In 2003, he was appointed as Professor and co-director of the Organic chemistry institute of the University of Zurich (UZH) and Director of its laboratory for process chemistry research (LPF). He served as Dean of Studies and Head of the Research Council for the Faculty of Sciences at UZH. He moved to Tianjin University in 2013 as dean and joined the Schools of Pharmaceutical and Life Sciences into a new Health Science Platform. His research is in the area of Stereochemistry and Physical Organic Chemistry.

Prologue: Atropisomerism

Jay S. Siegel received his Ph.D. from Princeton (1985), was a Swiss Universities Fellow at ETH Zurich (1983-4), and NSF–CNRS postdoctoral fellow at the University of Louis Pasteur in Strasbourg (1985-6). He began as Assistant Professor of Chemistry (1986) at UCSD, was promoted to Associate Professor (1992) and Full Professor (1996). In 2003, he was appointed as Professor and co-director of the Organic chemistry institute of the University of Zurich (UZH) and Director of its laboratory for process chemistry research (LPF). He served as Dean of Studies and Head of the Research Council for the Faculty of Sciences at UZH. He moved to Tianjin University in 2013 as dean, and joined the Schools of Pharmaceutical and Life Sciences into a new Health Science Platform. His research is in the area of Stereochemistry and Physical Organic Chemistry.

Frank Henry Westheimer. 15 January 1912—14 April 2007

Frank H. Westheimer integrated physical and organic chemistry to become an important contributor to the field that came to be called ‘physical organic chemistry’. He then went on to apply physical organic chemistry to the study of biological transformations. He identified fundamental classes of chemical reactions, studied in detail how they occurred in a relevant non-biological format and then investigated corresponding enzymatic reactions. These included oxidation–reduction, decarboxylation and phosphate transfer reactions. In the process, he made fundamental observations in the field of bio-organic chemistry he had helped to create. This line of research led to conceptual advances relevant to the ability of enzymes to distinguish enantiotopic and diastereotopic centres in their substrates, the perturbation of p K a values in enzymatic active sites as a source of catalytic power, and the broad range of transition state structures available for reactions at electrophilic phosphorus. These studies prompted similar work across many classes of enzymatic reactions. These experiments also benefitted from Westheimer's guidance in the application of kinetic isotope effects to probe reaction transition states, his invention of molecular mechanics to understand molecular dynamics, his widely cast studies on how organic reactivity depends on the molecular environment and his demonstration that photochemistry could be used to probe structure in complex biological systems.

Two Laboratory Deaths, and Keeping Organic Solvents Dry.

The historic evolution of the use of molecular sieves for drying organic solvents, as most likely pioneered by Saul Winstein, is discussed in relation to laboratory safety and the emergence of physical organic chemistry.

The history and triumph of physical organic chemistry

AbstractThe beginnings of physical organic chemistry can be traced back to the early 19th Century in the work of Michael Faraday, and this area of study gained great prominence with the discovery by Moses Gomberg of the triphenylmethyl radical in 1900. From that time, the field has continually grown in its capabilities and now is widely used for the understanding of organic and bioorganic chemistry, using both experimental and theoretical approaches. Some of the history of this development is described.

Christoph Rüchardt (1929–2018)

Rüchardt addressed a multitude of questions in physical-organic chemistry, putting strong emphasis on a deep and accumulated understanding of reactivity, stability, mechanisms, and intermediates. His first independent projects were dedicated to radical and sextet rearrangements, before he started extensive research on the formation of radicals, in particular emerging from azo compounds, peroxides, and highly substituted alkanes. The last compound class determined his work over nearly thirty years, leading to the systematic evaluation of the stability of the carbon–carbon bond from different angles, with a particular emphasis on steric effects. The creation of a complete reaction coordinate required not only kinetic data, but also the careful execution of thermochemical measurements in order to quantify polar, steric, anomeric, and captodative effects on radical stability. Accordingly, the arsenal of methods was extended by modern combustion calorimetry and the respective contemporary computational methods, the accuracy of the latter being challenged by experimental heats of combustion and transition-state energies. With the determination of the heat of combustion of C60 , Rüchardt created a quantitative basis for the understanding of σ-strain and stability–reactivity relationships regarding the most prominent fullerene. In addition, his great knowledge of radical mechanisms allowed extension of the synthetic use of noncatalyzed transfer hydrogenation and transfer hydrogenolysis. With his many studies, in particular those on the effect of steric strain on the carbon–carbon bond, conformational analysis of complex hydrocarbons and stability, structure and reactivity of carbon radicals, did he not only enrich organic chemistry textbooks, but also gave important insights into the refinement of technically useful radical initiators, for cracking procedures based on thermal decomposition, and for coal hydrogenation. The scientific merits of Rüchardt were widely recognized with many awards, an honorary doctorate, and memberships of scientific academies. In addition to his scientific activities, Rüchardt was highly committed to social and educational issues. As Rector of the University of Freiburg (1987–1991), he initiated the foundation of, among others, the Faculty of Engineering. In 1996, he was awarded the Officer's Cross of the Order of Merit of the Federal Republic of Germany. Rüchardt was a great role model for his students, acting with integrity and correctness, and was well-organized in thought and action. He was also archetype, motivator, and guiding spirit for his co-workers through organization, discipline, and unselfish commitment. With his generosity and systematic support for young academics, he set up excellent working conditions for his approximately 90 PhD students and 4 habilitation candidates (Giese, Langhals, Lüning, Schmittel). Almost 300 publications, 94 of them together with his assiduous and congenial companion Dr. Beckhaus, illustrate his work and contribution to science. Rüchardt was married to his wife Käte for over 60 years and they had three children. His family gave him strength and unconditional support for his far-reaching scientific, university, political, and social activities. As a result, his life and work will not only remain unforgotten in the scientific community but also at the University of Freiburg.

Immanuel J. Wilk

Immanuel J. Wilk, 97, died on Aug. 14, 2017, in Menlo Park, Calif. “A refugee from Nazi Germany, Immanuel Wilk came to the U.S. at age 19. After graduating from college, Wilk enlisted in the U.S. Army, moving with his unit through Europe. Afterward, he spent several years teaching and working in industry, including California Polytechnic, Stanford University, Abbott Laboratories, and Aerojet, and in 1963, he founded Science Services. A longtime member of the American Chemical Society, he was a charter member of the Division of Chemical Health & Safety. His interest in wine quality led him to investigate the effect of oxygen on aging in wines.”—Karen Wilk Klein, cousin Most recent title: founder, Science Services Education: B.S., chemistry, North Dakota State University, 1942; M.A., organic chemistry, Northwestern University, 1948; Ph.D., physical-organic chemistry, University of California, Los Angeles, 1954 Survivors: many cousins and beloved friends To recognize your late loved

Call for papers: MWRM 2018

Abstract submissions are being accepted for the 2018 Midwest Regional Meeting, which will take place Oct. 21–23 at the Iowa State Center Scheman Building in Ames, Iowa. Symposia will highlight advances in all areas of chemical research, education, industry, and their intersections with diverse scientific and technological domains. In addition to 16 technical symposia and a poster session, the meeting will feature a plenary lecture, the Midwest Award Lecture, an award symposium, an undergraduate program, workshops, and an instrument exhibition. The symposium sessions include “Biological Applications of Mass Spectrometry,” “Bioanalysis: Sensing, Separations & Spectroscopy,” “Carbon Capture, Utilization & Storage,” “Physical Organic Chemistry,” “Catalysts for Organic Synthesis,” “Inorganic Chemistry for All,” “Materials for Energy,” “Materials for Biomedicine,” “Materials for Optical, Magnetic & Electronic Devices,” “Materials & Interfaces,” “Inorganic Materials Synthesis,” “Solid-State NMR Spectroscopy: Mat...

Coconut agro-industrial waste in the production of catalyst containing palladium: The report of a mini-project for teaching of sustainable Suzuki-Miyaura reaction

A four-week mini-project for teaching is described for an experimental physical chemistry or organic chemistry course. The activities included synthesis of a Pd catalyst, PdCl2 supported on calcined coconut shell fiber, and its use in the preparation of 4-methylbiphenyl via Suzuki-Miyaura cross-coupling reaction. The technical skills and concepts that are typically presented in practical chemistry courses were covered, including notions of surface chemistry – development of new catalysts, modern organic synthesis, gas chromatography techniques, separation of mixtures, and stoichiometric calculations.

Using Physical Organic Chemistry To Shape the Course of Electrochemical Reactions.

While organic electrochemistry can look quite different to a chemist not familiar with the technique, the reactions are at their core organic reactions. As such, they are developed and optimized using the same physical organic chemistry principles employed during the development of any other organic reaction. Certainly, the electron transfer that triggers the reactions can require a consideration of new "wrinkles" to those principles, but those considerations are typically minimal relative to the more traditional approaches needed to manipulate the pathways available to the reactive intermediates formed downstream of that electron transfer. In this review, three very different synthetic challenges-the generation and trapping of radical cations, the development of site-selective reactions on microelectrode arrays, and the optimization of current in a paired electrolysis-are used to illustrate this point.

John D. Roberts, his beginnings at UCLA, his transformation of physical organic chemistry, and his impact on science

AbstractThis is a short account of the life and accomplishments of John D. Roberts on the occasion of his 100th birthday. Jack Roberts' education at the University of California, Los Angeles, his extraordinary career, and chemical discoveries contributed to the development of physical organic chemistry as a pervasive force on science.

Stephen F. Nelsen

Stephen F. Nelsen, 77, died on Sept. 23, 2017, in Madison, Wis. “Steve joined the chemistry faculty at the University of Wisconsin, Madison, in 1965, immediately after receiving his Ph.D. at Harvard with P. D. Bartlett. Steve maintained an international reputation as a physical organic chemist, studying radicals, radical ions, and electron transfer. Steve was a marvelous mentor to his students, striking just the right blend of enthusiasm, encouragement, and sage advice for students to satisfy his high standards. Steve also possessed a deep knowledge of history and was a scholar of the mushrooms native to Wisconsin. He was appointed emeritus professor upon his retirement in 2012. His sarcasm and crusty surface hid a heart of gold.”—Robert McMahon, friend and colleague Most recent title: professor emeritus of chemistry, University of Wisconsin, Madison Education: B.S., chemistry, University of Michigan, Ann Arbor, 1962; Ph.D., chemistry, Harvard University, 1965 Survivors: wife, Adrienne; daughter,

The ‘<i>Yard Stick</i>’ to Interpret the Entropy of Activation in Chemical Kinetics: A Physical-Organic Chemistry Exercise

No physical or physical-organic chemistry laboratory goes without a single instrument. To measure conductance we use conductometer, pH meter for measuring pH, colorimeter for absorbance, viscometer for viscosity, potentiometer for emf, polarimeter for angle of rotation, and several other instruments for different physical properties. But when it comes to the turn of thermodynamic or activation parameters, we don’t have any meters. The only way to evaluate all the thermodynamic or activation parameters is the use of some empirical equations available in many physical chemistry text books. Most often it is very easy to interpret the enthalpy change and free energy change in thermodynamics and the corresponding activation parameters in chemical kinetics. When it comes to interpretation of change of entropy or change of entropy of activation, more often it frightens than enlightens a new teacher while teaching and the students while learning. The classical thermodynamic entropy change is well explained by Atkins in terms of a sneeze in a busy street generates less additional disorder than the same sneeze in a quiet library (Figure 1) . The two environments are analogues of high and low temperatures, respectively. In this article making use of Eyring equation a factor usually called ‘universal factor’ is derived and made use as a ‘yard stick’ to interpreting the change in entropy of activation for physical or physical-organic chemistry senior undergraduate and graduate students’ class-room.

A Conversation with Natia Frank

The physical organic chemist is developing next-generation materials for low-power computer memory.

James Flack Norris Award in Physical Organic Chemistry: Cynthia J. Burrows

James Flack Norris Award in Physical Organic Chemistry: Cynthia J. Burrows