Practical Chemist Research Articles

Contrasting Historical and Physical Perspectives in Asymmetric Catalysis: ΔΔG≠ versus Enantiomeric Excess

AbstractWith the rise of machine learning (ML), the modeling of chemical systems has reached a new era and has the potential to revolutionize how we understand and predict chemical reactions. Here, we probe the historic dependence on utilizing enantiomeric excess (ee) as a target variable and discuss the benefits of using relative Gibbs free activation energies (ΔΔG≠), grounded firmly in transition‐state theory, emphasizing practical benefits for chemists. This perspective is intended to discuss best practices that enhance modeling efforts especially for chemists with an experimental background in asymmetric catalysis that wish to explore modelling of their data. We outline the enhanced modeling performance using ΔΔG≠, escaping physical limitations, addressing temperature effects, managing non‐linear error propagation, adjusting for data distributions and how to deal with unphysical predictions,in order to streamline modeling for the practical chemist and provide simple guidelines to strong statistical tools. For this endeavor, we gathered ten datasets from the literature covering very different reaction types. We evaluated the datasets using fingerprint‐, descriptor‐, and graph neural network‐based models. Our results highlight the distinction in performance among varying model complexities with respect to the target representation, emphasizing practical benefits for chemists.

Contrasting Historical and Physical Perspectives in Asymmetric Catalysis: ▵▵G≠ versus Enantiomeric Excess.

With the rise of machine learning (ML), the modeling of chemical systems has reached a new era and has the potential to revolutionize how we understand and predict chemical reactions. Here, we probe the historic dependence on utilizing enantiomeric excess (ee) as a target variable and discuss the benefits of using relative Gibbs free activation energies (ΔΔG≠), grounded firmly in transition-state theory, emphasizing practical benefits for chemists. This perspective is intended to discuss best practices that enhance modeling efforts especially for chemists with an experimental background in asymmetric catalysis that wish to explore modelling of their data. We outline the enhanced modeling performance using ΔΔG≠, escaping physical limitations, addressing temperature effects, managing non-linear error propagation, adjusting for data distributions and how to deal with unphysical predictions,in order to streamline modeling for the practical chemist and provide simple guidelines to strong statistical tools. For this endeavor, we gathered ten datasets from the literature covering very different reaction types. We evaluated the datasets using fingerprint-, descriptor-, and graph neural network-based models. Our results highlight the distinction in performance among varying model complexities with respect to the target representation, emphasizing practical benefits for chemists.

Molecular discovery by optimal sequential search

In the development of a new compound in chemistry and molecular biology, especially a new medicine in pharmaceutical industry, we often need to find candidate(s), a molecule or molecules, with the best desired property (e.g., binding affinity in medicine) from a large set of molecules with the same scaffold but m distinct functional substitutes at each of its n different sites. The total number $$N_{\mathrm{lib}}$$ of molecules in this library is $$m^n$$ . In some cases, $$N_{\mathrm{lib}}$$ can be a very large number (e.g., millions). This is a challenging task because it is costly and often infeasible to synthesize and test all of these molecules. A new algorithm referred to as optimal sequential search is developed to overcome this difficulty. Especially, this algorithm is chemically intuitive which only uses the information of molecule composition, and accessible to practical chemists. The algorithm can be applied to small, medium and large size molecule libraries. With syntheses and property measurements for a limited number of molecules, the top best candidate molecules can be effectively captured from the whole library. Three examples with library size 64, 160,000 and 1,048,576, respectively, are used for illustration. For the first small library, syntheses and property measurements of 17 molecules are sufficient to capture the top 7 best candidate molecules; for the two medium and large libraries, syntheses and property measurements of about one thousand molecules can capture most or a large part of the top 500, especially the top 100 best candidate molecules. However, the algorithm needs to perform multiple (e.g., hundreds of) iterative syntheses and property measurements. The time cost may not be acceptable if the algorithm is performed manually. To make the algorithm practical, automation of the sequential searching process is the following task.

Computational study of the thermodynamic stabilities of hydrogen-bonded complexes in solution

Understanding of the multiple H-bonding arrays of heterocyclic compounds is essential to design effective building blocks of supramolecular polymers. We have carried out a comprehensive computational study on the thermodynamic stabilities of thirty-six H-bonded complexes with all possible H-bonding arrays in the gas phase and chloroform solvent by using M06-2X, SMD calculations and cc-pVDZ basis set. The multiple H-bonding arrays include donor acceptor–acceptor donor (DA–AD), DD–AA for the doubly H-bonded pairs, and DAD–ADA, DDA–AAD and DDD–AAA for the triply H-bonded pairs. The computational results have provided insights into the geometrical, energetic and solvation effects on the stabilities of these H-bonded complexes. The calculated free energies of association for the DD–AA (8–9) and the DDD–AAA (33–35, 36–35) H-bonded complexes are found to be inconsistent with the experimental measurements and observations that these complexes are the most strongly doubly and triply H-bonded pairs in solution, respectively, while the calculated binding free energies for all other H-bonding arrays are in good agreement with experimental values. The computational protocol can be used by practical chemists and undergraduate researchers as an efficient and state-of-the-art tool to study H-bonding interactions in supramolecular chemistry.

Acolytes of Nature: Defining Natural Science in Germany, 1770–1850 by Denise Phillips (review)

Reviewed by: Acolytes of Nature: Defining Natural Science in Germany, 1770–1850 by Denise Phillips David Cahan Acolytes of Nature: Defining Natural Science in Germany, 1770–1850. By Denise Phillips. Chicago: The University of Chicago Press, 2012. Pp. viii + 356. Cloth $45.00. ISBN 978-0226667379. Intellectual and cultural developments in the German lands of the late eighteenth and early nineteenth centuries have long constituted a contentious and confusing area of historical analysis, not least when they involved the interaction of the history of science, philosophy, and intellectual history more generally. The era is associated of course with systematic but idiosyncratic thinkers like Immanuel Kant, Georg Wilhelm Friedrich Hegel, Johann Gottlieb Fichte, Friedrich Wilhelm Joseph Schelling, Alexander von Humboldt, and Johann Wolfgang von Goethe, as well by their eponymous systems of thought; and by the vague but all-pervasive presence of Naturphilosophie and Romanticism and their supposed influences on science and culture. This intellectually and culturally perplexing era has left historians of science and culture with complementary as well as conflicting interpretations of how German men of learning, natural philosophers, natural historians, and others moved from the Enlightenment’s “learned estate” and “republic of letters” to an intellectual and academic life that, by 1850, was largely dominated by university-based disciplinary specialists. Denise Phillips’s stimulating book offers a fresh approach to this historiographic question by purposely ignoring the great German philosophers and scientists of the era. It instead presents a straightforward philological and sociological study of the term and category of Naturwissenschaft in the German-speaking lands from the late Enlightenment to the mid-nineteenth century. It systematically traces, on the one hand, the emergence, evolution, and multiple meanings of the term Naturwissenschaft (e.g., as natural history, as natural philosophy, or even as physical objects and processes) until the term’s meaning settled on “science.” On the other hand, it studies the sociological history of how various individuals, as well as local societies and their journals, gradually created a modern meaning for the term and category within the broader context of expanding urban life and developing school and university systems. Following the evolution of the term and category, Phillips skillfully depicts the once porous boundaries between academic scientists and amateurs in the late eighteenth and early nineteenth centuries, as well as the gradual hardening of those same boundaries after around 1800, as academics slowly appropriated the category of Naturwissenschaft for themselves alone. Making good use of unpublished archival sources, as well as dictionaries, journals, and other published primary sources, Phillips devotes much of her study to local natural research societies, such as those in Dresden and Halle, and to the little-known individuals associated with them who embodied “low” (or popular) scientific culture and thus stood apart from what came to be regarded as “high” academic science. The category of “natural science,” Phillips shows, was originally “the border zone [End Page 165] where learned natural researchers met the broader public” (28). But that zone, and the associated relationships between “learned experts” and laymen, evolved—and to a good extent dissolved—into two different worlds. Along the way, Phillips notes, women were simultaneously excluded from academic science. Phillips also argues that the period witnessed the gradual separation (not conversion, as some have held) of science and practice, that high (elite) science increasingly found its home in universities and sometimes even the new polytechnics, and that popular science became largely relegated to local societies. In contrast to the practices and goals of the Enlightenment, German Naturwissenschaftler gradually distanced themselves from the local utilitarian societies, increasingly composed of apothecaries, gardeners, botanical specimen collectors, medical men, schoolteachers, practical chemists, public lecturers of all sorts, and other amateurs—even as these societies were often presided over by local university professors. In the early nineteenth century, these societies—which had once, like the Enlightenment itself, aimed at national and even international audiences—became increasingly local, losing their broader appeal throughout the German lands. Science and “practice,” and their associated practical and economic societies, now went in different directions. This development helped further define Naturwissenschaft by making it more separate from practical matters. “By 1830,” Phillips writes, “two previously interwoven projects—general Naturforschung (natural research...

Neither Physics nor Chemistry: A History of Quantum Chemistry, by Kostas Gavroglu and Ana Simões

Neither Physics nor Chemistry: A History of Quantum Chemistry, by Kostas Gavroglu and Ana Simoes. Transformation: Studies in the History of Science and Technology. Cambridge, Massachusetts, MIT Press, 2012. xiv, 351 pp. $40.00 US (cloth). Kostas Gavroglu and Ana Simoes have presented a tour de force in their work on the history of quantum chemistry. Neither Physics nor Chemistry is not, however, for the casual reader. The authors assume that the reader will be familiar with valence bonds, Planck's constant, orbitals, and why X-ray crystallography can elucidate the internal structure or a molecule. If you are more intrigued than put off by the technical material, the book will reward you with a lucid investigation of the development of modern physical chemistry. Physical chemistry is to general chemistry as theoretical physics is to general physics. Physical chemistry is the study of the underlying principles of chemical behaviour and, like theoretical physics, has become over time more mathematical and esoteric. When the discovery of radioactivity in the nineteenth century opened the door to new areas of physics and led to the idea that energy carne in packets (the quanta), physical chemistry had to adapt to the new quantum universe. Underlying the story of quantum chemistry are two concerns. The first is a simple pragmatic question: How much physics do chemists need to know to do their jobs? The second issue is more transcendental: What is the relationship between forces and the structure of the material world? On the issue of the first question, the physicist Hans Hellmann, who fled Nazi Germany to Russia only to be killed in the purges of 1938, neatly summarized this problem by saying ... organic and inorganic chemistry are engaged in organic and inorganic substances, which substances are the topic of theoretical chemistry? Purely theoretical substances? Does quantum theory have any useful role in chemistry at all? (p. 33). For anyone who has assembled molecules out of sticks and plastic balls in a high school chemistry class, the answer seems to be a resounding no. Certainly in the first half of the twentieth century, the majority of chemists would also have answered that complex mathematics and the ghostly world of quantum physics added nothing to the chemists' toolbox. There was a cultural divide between the practical chemists and the physicist who looked at transcendental questions about the underlying principles of nature. Even amongst those who looked at the material world (such as Neils Bohr's work with Ernest Rutherford on the planetary model of the atom) tended to regard chemistry as at best a secondary topic; a by-product of physics. Physicists were looking at the majestic and eternal forces of nature, while chemistry was concerned with the crude world of dyes, chemical warfare and baby soap. There was a serious argument made by some physicists that the material world was just an illusion and the real world was created by fields of force. …

Let there be light! Sir Joseph Swan and the incandescent light bulb

Joseph Swan was an outstanding British practical chemist and electrical engineer who produced a series of major innovations, covered extensively by patents, in both fields in the late Victorian period. In particular he produced the first cost-effective incandescent electric lamp in 1878 which was a major domestic benefit and greatly stimulated the growth of a modern electric power industry.

One-electron properties of several small molecules calculated using the local density approximation within density functional theory

Density functional theory (DFT) is a field enjoying a tremendous recent surge in popularity among theoretical and practical chemists alike because of its ability to more easily handle larger molecular systems than conventional ab initio methods. Until recently, however, assessment of the quality of the properties predicted (and therefore the charge density) from DFT had been limited mainly to dipole moments and their nuclear coordinate and electric field derivatives. This paper presents the calculated results for some of the one-electron properties of the eight small molecules (NH3, PH3, H2O, H2S, HF, HCl, CO, and N2). The properties chosen weight different regions of the charge density, from either very close in or at the nucleus (e.g., δ, the electron density at the nucleus) to regions farther out from the nucleus (e.g., the diamagnetic susceptibility 〈r2〉). It is found that properties which depend on an accurate knowledge of the electron density near to the nucleus are predicted poorly by the local density approximation (LDA), while others more dependent on the charge density farther out from the nucleus are predicted much more accurately, possibly due to cancellation of errors. Use of the LDA is therefore not recommended for ‘‘tight’’ properties; use of a functional employing gradient corrections would be more suitable for this purpose.

The EDISFAR Programs. Rational Drug Series Design

AbstractThe computer package EDISFAR is described. The programs can manage physico‐chemical information from a database (MONOBASE) of the fragment parameters classically used in drug design, providing assistance in the use of the techniques related with the Hansch‐Fujita analysis. The user can make design of exploring series of bioactive compounds, using a great variety of techniques, and once a QSAR model has been obtained, can calculate optimum derivatives using the parameters of the MONOBASE. The program has been designed emphasizing its flexibility, accessibility by the practical chemist, and compatibility with other statistics programs or computers.

Chemistry and Cannon: J.-L. Proust and Gunpowder Analysis

Chemistry and Cannon: J.-L. Proust and Gunpowder Analysis SEYMOUR H. MAUSKOPF D’un instrument de guerre à un instrument de labo­ ratoire, les affinités ne changent certainement pas. [J.-L. Proust, “Cinquième mémoire sur la poudre à canon,” Journal de physique, de chimie et d’histoire na­ turelle 73 (novembre 1811): 390] This is the story of an attempt by a major chemist of the late 18th century to develop “useful knowledge” for industry under govern­ ment patronage. The chemist was Joseph-Louis Proust (1754—1826; known as Luis José Proust in Spain); the industry was munitions; the government was Spanish. It is not a success story in any simple sense; Proust’s research did not bring about any change in the manufacture of gunpowder (although Proust rather passionately argued for some reforms based on his experiments) and his work on gunpowder has been all but forgotten. Yet, on closer scrutiny of Proust’s career, I came to realize the significance of the gunpowder research for it. Although Proust is best known for his work in analytical chemistry (the enunciation of the law of definite proportions, a basic principle of chemical stoichiometry), he carried out research and taught on a wide range of chemical topics, many of them practical. Indeed, it was primarily through his practical chemistry that Proust was enabled to spend his mature and most creative years in Spain in the employ of the Spanish government. Of central importance were his activities as researcher, consultant, and teacher concerning munitions, carried on when he was professor of chemistry at the Royal Artillery School in Segovia (1785—98). Proust Dr. Mauskopf is professor of history at Duke University and, in 1988—89, was Edelstein International Fellow in the History of Chemical Sciences and Technologies at the Beckman Center for the History of Chemistry and the Edelstein Center, Hebrew University of Jerusalem. He is currently researching scientific involvement in explo­ sives and munitions from the late 18th century through World War I. He thanks the secretarial staffs of the Duke Department of History and of the Beckman Center for their expert services; and Alex Roland, Joe Burchfield, and the Beckman Center “brown bag seminar” for their helpful, frank readings of various drafts of the article.© 1990 by the Society for the History of Technology. All rights reserved. 0040-165X/90/3103-0003$01.00 398 Chemistry and Cannon: J -L. Proust and Gunpowder Analysis 399 certainly did not regard his practical chemistry as any less important than his “pure” chemical analysis; as we shall see, he placed high value on his gunpowder research. In fact, this research was probably the most comprehensive and systematic study of gunpowder chemistry of its day. Moreover, it was part of a scientific research tradition devoted to the elucidation of the physics and chemistry of gunpowder that spanned the 18th century.1 Therefore, one of the objectives of this study is to present and analyze Proust’s scientific research on gunpowder for its intrinsic scientific interest and significance. That this work has been neglected is only partly due to its limited application to the munitions industry in its own day; it is also a part of the general neglect that the history of modern scientific investigations of munitions has suffered. The classical study by J. R. Partington has for its focus the medieval and early modern eras and is very sketchy about the history of gunpowder after 1700.2 To discover information about the later period, one is forced to turn to state-of-the-art treatises of the 19th century, with their inevitable “textbook” orientation to the history of science.3 This study and its companion in Osiris are intended to provide partial redress for the shortcomings in the history of the scientific study of munitions. There is also a second objective related to the state patronage of Proust as practical chemist: the examination of Proust’s gunpowder research as a species of the “useful knowledge” so prized by 18thcentury reformers, bureaucrats, and entrepreneurs. There has devel­ oped a vast literature on the issue of the relationship between science and industry encapsulated by this phrase. Much of it has focused on 'Seymour H...

Practical exploratory experimental designs

Abstract Morgan, E., Burton, K.W. and Church, P.A., 1989. Practical exploratory experimental designs. Chemometrics and Intelligent Laboratory Systems , 5: 283–302. Depending upon the particular aims of an experiment, different experimental designs may be adopted by the practical chemist. This article initially discusses the possible objectives that an experiment can take. Following this a discussion of mechanistic and empirical models leads into sections explaining some of the methods used in the analysis of experimental results. The technique of analysis of variance is explored by means of a worked example in which the effects of variables, blocks and interactions are discussed. When more than one variable is potentially important, factorial and fractional factorial designs are useful designs for quantifying their effects and possible interactions between them. Here again a worked example is presented. However, when it is desired to graph the response as a function of explanatory variables, such as when it is desired to find an optimum response, specific response surface designs can often prove more useful. These are presented by means of a matrix approach.

Lost & Found: 28. Isaiah Deck (fl 1826-1827)

In GCG p. 455 we recorded an annotated copy of Wm. Babington's book *A New System of Minerology 1799' which has now been acquired by the City of 488 Plymouth Museum. We quoted the annotation and gave the name of the annotation as A. or H. Deck. Both John Thackray and Peter Embrey have written to say the initial letter of Deck's name was most likely a florid capital I and that the annotator is thus I(saiah) Deck who describes himself as 'Practical Chemist and Mineralogist of Trumpington Street, Cambridge' in his publications. These include an undated 12,page Catalogue of Geological Series according to Werner (Thackray collection) and two...

Solvation of ions in pure and mixed solvents

Abstract

Reaction rates for the practical chemist

Reaction rates for the practical chemist

Chemistry at the Older Universities of Britain during the Eighteenth Century

IN 1814 Sir John Sinclair, president of the Board of Agriculture, wrote: "At present there are a greater number of intelligent practical chemists in Scotland, in proportion to the population, than perhaps in any other country in the world"(J. Sinclair, "General Report", App. 2, p. 307).

Robert Warington, F. R. S. (1838–1907)

ON August 22 occurs the centenary of the birth of the English agricultural chemist, Robert Warington, who for many years worked at Rothamsted, Harpenden, Herts, and, like his contemporaries. Sir John Lawes and Sir Joseph Gilbert, is buried at Harpenden. Warington was the son of Robert Warington (1807-67) the practical chemist who convened the meeting at the Royal Society of Arts on February 23, 1841, which led to the formation of the Chemical Society. At this time, Warington's parents were living at the Apothecaries Hall, in the City of London, and as a boy he learned chemistry from his father and from the lectures of Faraday, Brande and Hofmann. When twenty years of age, he worked under Lawes at Rothamsted as an unpaid assistant ; but a year later he returned to London as assistant to Frankland at South Kensington, whence he went to the Royal Agricultural College, Cirencester. It was here that he commenced lecturing on the Rothamsted experiments. Leaving Cirencester in 1867, he became chemist to Lawes's manure and acid factory at Millwall, but in 1876 returned to Harpenden, where he remained until 1891, publishing many memoirs on the nitrification of the soil. Leaving the Rothamsted laboratory, he lectured in America, and after his return home was examiner in agriculture to the Science and Art Department and Sibthorpian professor of rural economy at Oxford, a post he held for three years. He died at Harpenden on March 20, 1907. His most successful Work was his “Chemistry of the Farm”, which was translated into several foreign languages and reached its nineteenth edition while he was still alive.

Priestley as a Practical Chemist

NOT enough attention has been paid, in studying the work of Priestley in chemistry, to his admission that he was “not a practical chemist”. He made that admission again and again—and amplified it—in scientific memoirs, in the memoirs of his life and in letters. The following list of references to the point should be of use to those who study Priestley: (1) “Philosophical Empiricism”, etc., 1775, pp. 24, 26; (2) “Experiments and Observations”, etc., 1775, p. 1 (reproduced in “Experiments and Observations”, etc., 1790, 2, p. 295); (3) “Experiments and Observations”, etc., 1779, p. 134 (cf. “The Collected Papers of Carl Wilhelm Scheele”, trans. by Dobbin, p. 302); (4) Bolton, “Correspondence of Priestley”, p. 124 (a letter, dated 12. 1. 1792, sent to Keir); (5) Thorpe, “Humphry Davy, Poet and Philosopher”, p. 39 (a letter, dated 31. 10. 1801, sent to Davy); (6) “Memoirs of Dr. Joseph Priestley written by himself”, Centenary edition, 1904, p. 40, par. 101. I suppose that other references to the same point are to be found.

Priestley as a Practical Chemist

WITHOUT wishing to be captious, may I say that the statement by Prof. Meldrum at the Chemical Society on April 6 (NATUBE, April 15, page 555) that Priestley had confessed himself “not a practical chemist”, seems to me to convey rather a wrong impression, because I fancy that by the term practical chemist, Priestley meant something a little different from what we nowadays would mean by the expression.

SUCCESS IN TEACHING MATERIA MEDICA

MATERIA Medica is undoubtedly the most difficult subject in a nurse's curriculum, and one which is not always successfully mastered. One finds commonly that about all that the average nurse knows of it at the end of her course is what she has learned in her practical work in the hospital wards. This is hardly an ideal state of affairs, and it can be remedied, to some extent at least, by improved methods in teaching. First, who shall teach it? Preferably the chief nurse, though it may be done by a doctor, providing he makes it a class, and not a lecture. Materia Medica has rarely been successfully taught by the lecture method; the lecturer almost invariably presupposes knowledge which the nurses do not possess, or tries to cover too much ground in one evening, thereby confusing and discouraging his hearers. The supervising nurse of a large hospital observed recently that a doctor touched on seventy-five drugs in one lecture; it is to be doubted whether the class gained much from the time spent. Therefore, let the teacher be someone who is willing to do a plentiful amount of iteration and reiteration, and who is not in too great haste for results. Materia Medica should be a first-year study. This, one would think to be self-evident; but a number of hospitals leave it until the second or third year. Meantime, nurses are giving medicines of which they know practically nothing, and are handling poisons, recklessly perhaps, because they do not know that they are poisons. Nurses who did not study Materia Medica until their second year have told me that their first impression of the study was fright over the mistakes which they might have made during their first year. There should be preliminary lessons on weights and measures, both apothecaries' and metric, with a certain amount of committing to memory of names and definitions. Next, four or five letters on the elements of chemistry should be given by a doctor or practical chemist; simple experiments should accompany these lectures. The hospital druggist might be pressed into service for this part of the work. A little skilful inquiry among nurses will prove how absolutely essential these lectures are. Many nurses have failed to grasp the meaning of Materia

Problems of Applied Chemistry

THE science and art of the engineer are intimately interlaced with those of the practical chemist. The practical, as distinguished from the scientific, chemist possesses sufficient knowledge and experience to see to the working of machines and to minor repairs without calling in an engineer, save in difficult or complicated cases. In former times the chemical manufacturer learned his trade, both on the chemical and the engineering side, as far as it was indispensable, but he learned it simply “by rote,” as the saying goes. To be sure, this never took place without large sums of money being thrown away, either in the form of misshapen or faulty apparatus and machinery, or of spoilt chemicals, and so on. And this happened to the unstudied “practical man,” who, through family connections or by mere chance, had stumbled into chemical manufacturing, as well as to men who had studied the science of chemistry, and who desired to apply the knowledge thus gained to the execution of some well-known process, or to the working of some laboratory invention on a large scale. Those men who possessed a scientific foundation were, in their turn, compelled to learn the technical side of their profession by dint of practice, just as the tailor has to learn the art of making clothes and the barber the art of shaving. A man of scientific attainments had certainly, even in the olden times, a clear advantage over the mere practical man.”