Mathematical Chemistry! Is It? and If So, What Is It?
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Free and Open Source Software for Computational Chemistry Education
Free and Open Source Software for Computational Chemistry Education Susi Lehtola∗,y and Antti J. Karttunenz yMolecular Sciences Software Institute, Blacksburg, Virginia 24061, United States zDepartment of Chemistry and Materials Science, Aalto University, Espoo, Finland E-mail: [email protected].fi Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. We point out the existence of a variety of free and open source software (FOSS) packages for computational chemistry that offer a wide range of functionality all the way from approximate semiempirical calculations with tight- binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. By their very definition, FOSS packages allow usage for whatever purpose by anyone, meaning they can also be used in industrial applications without limitation. Also, FOSS software has no limitations to redistribution in source or binary form, allowing their easy distribution and installation by third parties. Many FOSS scientific software packages are available as part of popular Linux distributions, and other package managers such as pip and conda. Combined with the remarkable increase in the power of personal devices—which rival that of the fastest supercomputers in the world of the 1990s—a decentralized model for teaching computational chemistry is now possible, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device 1 (BYOD) scheme. In addition to the programs’ use for various applications, open access to the programs’ source code also enables comprehensive teaching strategies, as actual algorithms’ implementations can be used in teaching. -
R. Stephen Berry 1931–2020
R. Stephen Berry 1931–2020 A Biographical Memoir by Stuart A. Rice and Joshua Jortner ©2021 National Academy of Sciences. Any opinions expressed in this memoir are those of the authors and do not necessarily reflect the views of the National Academy of Sciences. RICHARD STEPHEN BERRY April 9, 1931–July 26, 2020 Elected to the NAS, 1980 We have prepared this memoir to bear witness to the life of R. Stephen (Steve) Berry, with emphasis on the view that a memorial is about reminding ourselves and others of more than his many and varied contributions to science; it is also to remind us of his personal warmth and freely offered friendship, of his generous support for all of us in a variety of situations, and of his loyalty to his friends and the institutions he served. The record of an individ- ual’s accomplishment is commonly taken to define his/ her legacy. Using that protocol, creative scientists are fortunate in that their contributions are visible, and those contributions endure, or not, on their own merits. Steve Berry was one of the most broadly ranging and influen- tial scientists in the world. His seminal experimental and By Stuart A. Rice theoretical contributions are distinguished by a keen eye and Joshua Jortner for new concepts and innovative and practical analyses. These contributions, which are remarkable in both scope and significance, have helped to shape our scientific perception. They have had, and continue to have, great influence on the development of chemistry, biophysics materials science, the science and technology related to the use, production, and conservation of energy, the societal applications of science and technology, and national and international science policy. -
Development of Electrochemical Methods for Detection of Pesticides and Biofuel
Development of Electrochemical Methods for Detection of Pesticides and Biofuel Production Asli Sahin Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2012 © 2012 Asli Sahin All Rights Reserved ABSTRACT Development of Electrochemical Methods for Detection of Pesticides and Biofuel Production Asli Sahin Electrochemical methods coupled with biological elements are used in industrial, medical and environmental applications. In this thesis we will discuss two such applications: an electrochemical biosensor for detection of pesticides and biofuel generation using electrochemical methods coupled with microorganisms. Electrochemical biosensors are commonly used as a result of their selectivity, sensitivity, rapid response and portability. A common application for electrochemical biosensors is detection of pesticides and toxins in water samples. In this thesis, we will focus on detection of organosphosphates (OPs), a group of compounds that are commonly used as pesticides and nerve agents. Rapid and sensitive detection of these compounds has been an area of active research due to their high toxicity. Amperometric and potentiometric electrochemical biosensors that use organophosphorus hydrolase (OPH), an enzyme that can hydrolyze a broad class of OPs, have been reported for field detection of OPs. Amperometry is used for detection of electroactive leaving groups and potentiometry is used for detection of pH changes that take place during the hydrolysis reaction. Both these methods have limitations: using amperometric biosensors, very low limits of detection are achieved but this method is limited to the few OPs with electroactive leaving groups, on the other hand potentiometric biosensor can be used for detection of all OPs but they don’t have low enough limits of detection. -
Computational Chemistry
G UEST E DITORS’ I NTRODUCTION COMPUTATIONAL CHEMISTRY omputational chemistry has come of chemical, physical, and biological phenomena. age. With significant strides in com- The Nobel Prize award to John Pople and Wal- puter hardware and software over ter Kohn in 1998 highlighted the importance of the last few decades, computational these advances in computational chemistry. Cchemistry has achieved full partnership with the- With massively parallel computers capable of ory and experiment as a tool for understanding peak performance of several teraflops already on and predicting the behavior of a broad range of the scene and with the development of parallel software for efficient exploitation of these high- end computers, we can anticipate that computa- tional chemistry will continue to change the scientific landscape throughout the coming cen- tury. The impact of these advances will be broad and encompassing, because chemistry is so cen- tral to the myriad of advances we anticipate in areas such as materials design, biological sci- ences, and chemical manufacturing. Application areas Materials design is very broad in scope. It ad- dresses a diverse range of compositions of matter that can better serve structural and functional needs in all walks of life. Catalytic design is one such example that clearly illustrates the promise and challenges of computational chemistry. Al- most all chemical reactions of industrial or bio- chemical significance are catalytic. Yet, catalysis is still more of an art (at best) or an empirical fact than a design science. But this is sure to change. A recent American Chemical Society Sympo- sium volume on transition state modeling in catalysis illustrates its progress.1 This sympo- sium highlighted a significant development in the level of modeling that researchers are em- 1521-9615/00/$10.00 © 2000 IEEE ploying as they focus more and more on the DONALD G. -
Harry H. Wasserman 1920–2013
Harry H. Wasserman 1920–2013 A Biographical Memoir by Jerome A. Berson and Samuel J. Danishefsky ©2015 National Academy of Sciences. Any opinions expressed in this memoir are those of the authors and do not necessarily reflect the views of the National Academy of Sciences. HARRY HERSCHAL WASSERMAN December 1, 1920–December 29, 2013 Elected to the NAS, 1987 Harry Wasserman—a warm, charming, multi-talented man and a keenly creative chemist—served on the faculty of Yale University for more than 50 years. Harry grew up in and around Boston, MA, in a family that often struggled to pay the rent. On weekends, he and his brothers would earn a few dollars sifting sand on nearby Revere Beach for lost coins. He earned high marks at Cambridge & Latin high school and was awarded a Cambridge scholarship to the Massachusetts Institute of Technology, which he entered in 1937 at age 16. He earned a B.S. in chemistry from MIT in 1941. While in college, Harry considered a University. Yale Photography courtesy career as an artist, and he studied with Boston painter and sculptor John Wilson, but science, particularly chemistry, drew him away from a full-time commitment to art. He By Jerome A. Berson continued to follow both muses throughout his life. After and Samuel J. Danishefsky MIT, Harry began graduate studies at Harvard University under the mentorship of the organic chemist Robert Burns Woodward, a future Nobel laureate, Harry interrupted his graduate studies in 1943 to serve in the 503rd Army Air Force in Africa and the Middle East. -
Intuitive Chemical Topology Concepts. / In
1 Intuitive Chemical Topology Concepts Eugene V. Babaev Moscow State University, Moscow 119899, RUSSIA 1. Introduction During last two decades, chemistry underwent a strong influence from nonroutine mathematical methods. Chemical applications of graph theory [1–10], topology [11–18], and related fields of fundamental mathematics [21–27] are growing rapidly. This trend may indicate the birth of a novel interdisciplinary field, mathematical chemistry, imperceptibly flourishing on the border of chemistry and pure mathematics. The term “chemical topology” (the title of this volume) has become frequent in papers, books, and scientific conferences. Similarly, the term molecular topology (differing in its sense from molecular geometry) has become frequently used, although there may exist diverse viewpoints on the meaning of this concept. The key difference between topology and geometry is that in geometry the concepts of distances and angles are important, whereas in topology they are not. Instead, the essential topological properties are connectedness and continuity. Chemical structural formulas are good examples of topological models of molecules: the pattern of connectivity between atoms is essential, whereas the interatomic distances and angles are less important and may be neglected. A colloquial definition of topology is “rubber” geometry. Indeed, one may consider a topological object made of an ideal elastic material, so that any deformation (like stretching or distortion) retains points of this elastic object “close enough” one to another. In contrast, cutting separates previously close points, and any joining of parts makes points “closer” one to another. Such a continuous transformation of an object without cutting and joining any parts is called homeomorphism. (The term should not be confused with homomorphism.) The study of properties that are invariant to homeomorphic transformations is the fundamental goal of topology. -
Outline of Physical Science
Outline of physical science “Physical Science” redirects here. It is not to be confused • Astronomy – study of celestial objects (such as stars, with Physics. galaxies, planets, moons, asteroids, comets and neb- ulae), the physics, chemistry, and evolution of such Physical science is a branch of natural science that stud- objects, and phenomena that originate outside the atmosphere of Earth, including supernovae explo- ies non-living systems, in contrast to life science. It in turn has many branches, each referred to as a “physical sions, gamma ray bursts, and cosmic microwave background radiation. science”, together called the “physical sciences”. How- ever, the term “physical” creates an unintended, some- • Branches of astronomy what arbitrary distinction, since many branches of physi- cal science also study biological phenomena and branches • Chemistry – studies the composition, structure, of chemistry such as organic chemistry. properties and change of matter.[8][9] In this realm, chemistry deals with such topics as the properties of individual atoms, the manner in which atoms form 1 What is physical science? chemical bonds in the formation of compounds, the interactions of substances through intermolecular forces to give matter its general properties, and the Physical science can be described as all of the following: interactions between substances through chemical reactions to form different substances. • A branch of science (a systematic enterprise that builds and organizes knowledge in the form of • Branches of chemistry testable explanations and predictions about the • universe).[1][2][3] Earth science – all-embracing term referring to the fields of science dealing with planet Earth. Earth • A branch of natural science – natural science science is the study of how the natural environ- is a major branch of science that tries to ex- ment (ecosphere or Earth system) works and how it plain and predict nature’s phenomena, based evolved to its current state. -
Metal Complexes of Penicillin and Cephalosporin Antibiotics
I METAL COMPLEXES OF PENICILLIN AND CEPHALOSPORIN ANTIBIOTICS A thesis submitted to THE UNIVERSITY OF CAPE TOWN in fulfilment of the requirement$ forTown the degree of DOCTOR OF PHILOSOPHY Cape of by GRAHAM E. JACKSON University Department of Chernis try, University of Cape Town, Rondebosch, Cape, · South Africa. September 1975. The copyright of th:s the~is is held by the University of C::i~r:: To\vn. Reproduction of i .. c whole or any part \ . may be made for study purposes only, and \; not for publication. The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgementTown of the source. The thesis is to be used for private study or non- commercial research purposes only. Cape Published by the University ofof Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University '· ii ACKNOWLEDGEMENTS I would like to express my sincere thanks to my supervisors: Dr. L.R. Nassimbeni, Dr. P.W. Linder and Dr. G.V. Fazakerley for their invaluable guidance and friendship throughout the course of this work. I would also like to thank my colleagues, Jill Russel, Melanie Wolf and Graham Mortimor for their many useful conrrnents. I am indebted to AE & CI for financial assistance during the course of. this study. iii ABSTRACT The interaction between metal"'.'ions and the penici l)in and cephalosporin antibiotics have been studied in an attempt to determine both the site and mechanism of this interaction. The solution conformation of the Cu(II) and Mn(II) complexes were determined using an n.m.r, line broadening, technique. -
Full Text [PDF]
® The Americas Journal of Plant Science and Biotechnology ©2011 Global Science Books Living in the O-zone: Ozone Formation, Ozone-Plant Interactions and the Impact of Ozone Pollution on Plant Homeostasis Godfrey P. Miles1 • Marcus A. Samuel2* 1 U.S. Department of Agriculture – Agricultural Research Service, 5230 Konnowac Pass Road, Wapato, WA 98951, USA 2 Department of Biological Sciences, University of Calgary, 2500, University Drive, NW, Calgary, AB, T2N 1N4, Canada Corresponding author : * [email protected] ABSTRACT Ozone (O3) is a key constituent of the terrestrial atmosphere. Unlike in the stratosphere, where O3 provides an essential barrier to incoming UV radiation, within the troposphere, it is a major secondary air pollutant that is estimated to cause more damage to plant life than all other air pollutants combined. In the troposphere, O3 is produced by photochemical oxidation of primary precursor emissions of volatile organic compounds (VOCs), carbon monoxide (CO), and sulfur dioxide (SO2) in association with elevated levels of oxides of nitrogen (NOx NO + NO2). Because of its strong oxidizing potential, ozone is damaging to plant life through oxidative damage to proteins, nucleic acids and lipids either directly or as a result of reactive oxygen species (ROS) derived from O3 decomposition. In plants, ROS, directly or indirectly derived from O3 exposure, are routinely scavenged by an array of enzymatic and non-enzymatic antioxidant defense mechanisms. The various ROS generated by O3 have strong influence on the plant’s biochemical -
From Chemical Topology to Molecular Machines Nobel Lecture, December 8, 2016 by Jean-Pierre Sauvage University of Strasbourg, Strasbourg, France
From Chemical Topology to Molecular Machines Nobel Lecture, December 8, 2016 by Jean-Pierre Sauvage University of Strasbourg, Strasbourg, France. o a large extent, the eld of “molecular machines” started aer several groups T were able to prepare reasonably easily interlocking ring compounds (named catenanes for compounds consisting of interlocking rings and rotaxanes for rings threaded by molecular laments or axes). Important families of molecular machines not belonging to the interlocking world were also designed, prepared and studied but, for most of them, their elaboration was more recent than that of catenanes or rotaxanes. Since the creation of interlocking ring molecules is so important in relation to the molecular machinery area, we will start with this aspect of our work. e second part will naturally be devoted to the dynamic properties of such systems and to the compounds for which motions can be directed in a controlled manner from the outside, i.e., molecular machines. We will restrict our discussion to a very limited number of examples which we con- sider particularly representative of the eld. CHEMICAL TOPOLOGY Generally speaking, chemical topology refers to molecules whose graph (i.e., their representation based on atoms and bonds) is non-planar [1–2]. A planar graph cannot be represented in a plane or on a sheet of paper without crossing points. In topology, the object can be distorted as much as one likes but its topo- logical properties are not modied as long as no cleavage occurs [3]. In other 111 112 The Nobel Prizes words, a circle and an ellipse are topologically identical. -
NIST Computational Chemistry Comparison and Benchmark Database
NIST Computational Chemistry Comparison and Benchmark Database A website which compares computed and experimental ideal-gas thermochemical properties http://srdata.nist.gov/cccbdb Russell D. Johnson III Computational Chemistry Group, NIST http://www.nist.gov/compchem How good is that ab initio calculation? For predicting enthalpies. For predicting geometries. For predicting vibrational frequencies. For this molecule. For these molecules. http://srdata.nist.gov/cccbdb CCCBDB Contents • 680 molecules • Enthalpies of formation, Entropies, Geometries, Vibrational frequencies • Experimental values • Computed values • Comparisons • Auxiliary information http://srdata.nist.gov/cccbdb Properties • Energetics – Enthalpies of formation – Atomization enthalpies – Reaction enthalpies – Barriers to Internal Rotation • Entropies – Heat Capacities – Integrated Heat Capacities http://srdata.nist.gov/cccbdb More Properties • Geometries – Bond lengths and angles – Rotational Constants – Moments of Inertia • Vibrational Frequencies – Intensities – Zero point energies http://srdata.nist.gov/cccbdb Even More Properties • Electrostatics – Dipole Moments – Quadrupole Moments – Polarizabilities – Charges • Mulliken •ESP • ChelpG http://srdata.nist.gov/cccbdb Molecules in CCCBDB • Small, gas-phase • Mostly < 7 heavy atoms - hexane • Mostly no atoms with atomic number >17 (chlorine). A dozen Br-containing molecules. • 90 diatomics, 574 polyatomics • 469 organic molecules, – 125 hydrocarbons – 145 CHO species – 16 amides http://srdata.nist.gov/cccbdb Experimental -
UNE Postgraduate Conference 2017
UNE Postgraduate Conference 2017 ‘Intersections of Knowledge’ 17-18 January 2017 Conference Proceedings Postgraduate Conference Conference Proceedings “Intersections of Knowledge” UNE Postgraduate Conference 2017 17th and 18th January 2017 Resource Management Building University of New England Acknowledgement Phillip Thomas – UNE Research Services Co-chair and convenor Postgraduate Conference Organising Committee: – Stuart Fisher (Co-Chair) Eliza Kent, Grace Jeffery, Emma Lockyer, Bezaye Tessema, Kristal Spreadborough, Kerry Gleeson, Marguerite Jones, Anne O’Donnell-Ostini, Rubeca Fancy, Maximillian Obiakor, Jane Michie, John Cook, Sanaz Alian, Julie Orr, Vivek Nemane, Nadiezhda Ramirez Cabral. Back row left to right: Stuart Fisher, Julie Orr, Vivek Nemane, Philip Thomas, Maximillian Obiakor Front row left to right: Emma Lockyer, Bezaye Tessema, Nadiezhda Ramirez Cabral, Kerry Gleeson, Kristal Spreadborough, Rubeca Fancy, Anne O’Donnell-Ostini, Grace Jeffery. Absent: Eliza Kent, Marguerite Jones, John Cook, Jane Michie, UNE Areas: IT Training, Research Services, Audio-Visual Support, Marketing and Public Relations, Corporate Communications, Strategic Projects Group, School of Science and Technology, VC’s Unit, Workforce Strategy, Information Technology Directorate and Development Unit. Sponsor: UNE Life, University of New England Student Association (UNESA) Research creates knowledge and when we share what we have discovered we create rich intersections that self-generate new thinking, ideas and actions within and across networks. With