Chemistry (CHEM) 1
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Chemistry with Biophysical Chemistry Chemistry & Chemical Sciences (CCS)
Chemistry with Biophysical Chemistry Chemistry & Chemical Sciences (CCS) Sample pathway for a degree in Chemistry with Biophysical Chemistry* YEAR 1 ENGAGE WITH THE PRINCIPLES CHEMISTRY MATHEMATICS BIOLOGY Modules include: Modules include: Modules include: 4One Elective 4 4 4 The Basis of Organic and Mathematics for the Cell Biology & Genetics module Biological Chemistry Biological & Chemical 4One 4 The Basis of Physical Sciences Small- Chemistry Group 4 The Molecular World Project YEAR 2 CHOOSE YOUR SUBJECTS A nanoparticle with encapsulated active ingredient is penetrating a cell The subject combinations listed below are illustrative of what a student who graduates in Chemistry with Biophysical Chemistry could choose in Year 2. Further subject combinations are possible depending on the choices in Year 1. Further information is available on page 23. membrane. Image and copyright of Nanobotmodels Company CHEMISTRY WITH BIOPHYSICAL CHEMISTRY ([email protected]). CHEMISTRY Modules include: Modules include: 4Biophysical Chemistry 4Students who choose Chemistry with 4Two n Develop theoretical and 4Physical Chemistry Biophysical Chemistry as their main subject Elective 4Inorganic Chemistry for second year also cover the requirements modules practical skills in exploiting 4 Organic Chemistry for Chemistry. the physical and chemical YEAR principles of the FOCUS ON YOUR CHOSEN SUBJECT 3 biomolecular world in CHEMISTRY WITH BIOPHYSICAL CHEMISTRY – Modules include: modern industrial and 4Instrumental Analysis 4Organometallic & Solid State Chemistry -
Chemistry Courses 2005-2006
Chemistry Courses 2005-2006 Autumn 2005 Chem 11101 General Chemistry I, Variant A Lee Chem 11102 General Chemistry I, Variant B Norris Chem 12200 Honors General Chemistry I Levy Chem 22000 Organic Chemistry I Yu Chem 22300 Intermediate Organic Chemistry Mrksich Chem 26100 Quantum Mechanics Mazziotti Chem 30100 Advanced Inorganic Chemistry Hopkins Chem 30900 Bioinorganic Chemistry He Chem 32100 Physical Organic Chemistry I Ismagilov Chem 32200 Organic Synthesis and Structure Rawal Chem 32600 Protein Fundamentals Piccirilli Chem 36100 Wave Mechanics & Spectroscopy Butler Chem 36400 Chemical Thermodynamics Dinner Winter 2006 Chem 11201 General Chemistry II, Variant A Scherer Chem 11202 General Chemistry II, Variant B Butler Chem 12300 Honors General Chemistry II Dinner Chem 20100 Inorganic Chemistry I Hillhouse Chem 22100 Organic Chemistry II Rawal Chem 23100 Honors Organic Chemistry II Kozmin Chem 26200 Thermodynamics Norris Chem 26700 Experimental Physical Chemistry Levy Chem 30200 Synthesis & Physical Methods in Inorganic Chemistry Jordan Chem 30400 Organometallic Chemistry Bosnich Chem 32300 Tactics of Organic Synthesis Yamamoto Chem 32400 Physical Organic Chemistry II Mrksich Chem 36200 Quantum Mechanics Freed Chem 36300 Statistical Mechanics Mazziotti Chem 38700 Biophysical Chemistry Lee Spring 2006 Chem 11301 General Chemistry III, Variant A Kozmin Chem 11302 General Chemistry III, Variant B Guyot-Sionnest Chem 20200 Inorganic Chemistry II Jordan Chem 22200 Organic Chemistry III Kent Chem 23200 Honors Organic Chemistry III Yamamoto Chem 22700 Advanced Organic / Inorganic Laboratory (8 students) He Chem 26300 Chemical Kinetics and Dynamics Sibner Chem 26800 Computational Chemistry & Biology Freed Chem 30600 Chemistry of the Elements Hillhouse Chem 31100 Supramolecular Chemistry Bosnich Chem 32500 Bioorganic Chemistry Piccirilli Chem 32900 Polymer Chemistry Yu Chem 33000 Complex Systems Ismagilov Chem 36500 Chemical Dynamics Scherer Chem 36800 Advanced Computational Chemistry & Biology Freed . -
Quantum Crystallography†
Chemical Science View Article Online MINIREVIEW View Journal | View Issue Quantum crystallography† Simon Grabowsky,*a Alessandro Genoni*bc and Hans-Beat Burgi*de Cite this: Chem. Sci.,2017,8,4159 ¨ Approximate wavefunctions can be improved by constraining them to reproduce observations derived from diffraction and scattering experiments. Conversely, charge density models, incorporating electron-density distributions, atomic positions and atomic motion, can be improved by supplementing diffraction Received 16th December 2016 experiments with quantum chemically calculated, tailor-made electron densities (form factors). In both Accepted 3rd March 2017 cases quantum chemistry and diffraction/scattering experiments are combined into a single, integrated DOI: 10.1039/c6sc05504d tool. The development of quantum crystallographic research is reviewed. Some results obtained by rsc.li/chemical-science quantum crystallography illustrate the potential and limitations of this field. 1. Introduction today's organic, inorganic and physical chemistry. These tools are usually employed separately. Diffraction and scattering Quantum chemistry methods and crystal structure determina- experiments provide structures at the atomic scale, while the Creative Commons Attribution 3.0 Unported Licence. tion are highly developed research tools, indispensable in techniques of quantum chemistry provide wavefunctions and aUniversitat¨ Bremen, Fachbereich 2 – Biologie/Chemie, Institut fur¨ Anorganische eUniversitat¨ Zurich,¨ Institut fur¨ Chemie, Winterthurerstrasse 190, CH-8057 Zurich,¨ Chemie und Kristallographie, Leobener Str. NW2, 28359 Bremen, Germany. Switzerland E-mail: [email protected] † Dedicated to Prof. Louis J. Massa on the occasion of his 75th birthday and to bCNRS, Laboratoire SRSMC, UMR 7565, Vandoeuvre-l`es-Nancy, F-54506, France Prof. Dylan Jayatilaka on the occasion of his 50th birthday in recognition of their cUniversit´e de Lorraine, Laboratoire SRSMC, UMR 7565, Vandoeuvre-l`es-Nancy, F- pioneering contributions to the eld of X-ray quantum crystallography. -
Entropy and Life
Entropy and life Research concerning the relationship between the thermodynamics textbook, states, after speaking about thermodynamic quantity entropy and the evolution of the laws of the physical world, that “there are none that life began around the turn of the 20th century. In 1910, are established on a firmer basis than the two general American historian Henry Adams printed and distributed propositions of Joule and Carnot; which constitute the to university libraries and history professors the small vol- fundamental laws of our subject.” McCulloch then goes ume A Letter to American Teachers of History proposing on to show that these two laws may be combined in a sin- a theory of history based on the second law of thermo- gle expression as follows: dynamics and on the principle of entropy.[1][2] The 1944 book What is Life? by Nobel-laureate physicist Erwin Schrödinger stimulated research in the field. In his book, Z dQ Schrödinger originally stated that life feeds on negative S = entropy, or negentropy as it is sometimes called, but in a τ later edition corrected himself in response to complaints and stated the true source is free energy. More recent where work has restricted the discussion to Gibbs free energy because biological processes on Earth normally occur at S = entropy a constant temperature and pressure, such as in the atmo- dQ = a differential amount of heat sphere or at the bottom of an ocean, but not across both passed into a thermodynamic sys- over short periods of time for individual organisms. tem τ = absolute temperature 1 Origin McCulloch then declares that the applications of these two laws, i.e. -
Quantum Reform
feature Quantum reform Leonie Mueck Quantum computers potentially offer a faster way to calculate chemical properties, but the exact implications of this speed-up have only become clear over the last year. The first quantum computers are likely to enable calculations that cannot be performed classically, which might reform quantum chemistry — but we should not expect a revolution. t had been an exhausting day at the 2012 International Congress of Quantum IChemistry with countless presentations reporting faster and more accurate methods for calculating chemical information using computers. In the dry July heat of Boulder, Colorado, a bunch of young researchers decided to end the day with a cool beer, but the scientific discussion didn’t fade away. Thoughts on the pros and cons of all the methods — the approximations they involved and the chemical problems that they could solve — bounced across the table, until somebody said “Anyway, in a few years we will have a quantum computer and our approximate methods will be obsolete”. An eerie silence followed. What a frustrating thought! They were devoting their careers to quantum chemistry — working LIBRARY PHOTO RICHARD KAIL/SCIENCE tirelessly on applying the laws of quantum mechanics to treat complex chemical of them offering a different trade-off between cannot do on a ‘classical’ computer, it does problems with a computer. And in one fell accuracy and computational feasibility. not look like all the conventional quantum- swoop, would all of those efforts be wasted Enter the universal quantum computer. chemical methods will become obsolete or as chemists turn to quantum computers and This dream machine would basically work that quantum chemists will be out of their their enormous computing power? like a normal digital computer; it would jobs in the foreseeable future. -
Biophysics 1
Biophysics 1 on interactions between proteins involved in Notch signaling using BIOPHYSICS modern biophysical methods. Thermodynamics of association and allosteric effects are determined by spectroscopic, ultracentrifugation, http://biophysics.jhu.edu/ and calorimetric methods. Atomic structure information is being obtained by NMR spectroscopy. The ultimate goal is to determine the The Department of Biophysics offers programs leading to the B.A., M.A., thermodynamic partition function for a signal transduction system and and Ph.D. degrees. Biophysics is appropriate for students who wish interpret it in terms of atomic structure. to develop and integrate their interests in the physical and biological sciences. NMR Spectroscopy (Dr. Lecomte) Research interests in the Department cover experimental and Many proteins require stable association with an organic compound computational, molecular and cellular structure, function, and biology, for proper functioning. One example of such “cofactor” is the heme membrane biology, and biomolecular energetics. The teaching and group, a versatile iron-containing molecule capable of catalyzing a research activities of the faculty bring its students in contact with broad range of chemical reactions. The reactivity of the heme group biophysical scientists throughout the university. Regardless of their choice is precisely controlled by interactions with contacting amino acids. of research area, students are exposed to a wide range of problems of Structural fluctuations within the protein are also essential to the fine- biological interest. For more information, and for the most up-to-date list tuning of the chemistry. We are studying how the primary structure of of course offerings and requirements, consult the department web page at cytochromes and hemoglobins codes for heme binding and the motions biophysics.jhu.edu (http://biophysics.jhu.edu/). -
Change the Description of CHEM 323, Foundations of Biochemistry; Change Title and Description of CHEM 437, Modern Biochemistry
APC Document RRR (CHEM): Change the description of CHEM 323, Foundations of Biochemistry; Change title and description of CHEM 437, Modern Biochemistry 1. Delete: On page 99, the description for CHEM 323, Foundations of Biochemistry: Designed to approach the fundamentals of biochemistry from a chemical perspective, this course examines the structure and function of biological systems such as proteins, carbohydrates, and lipids; develops an understanding of the kinetics of biological reactions including metabolism and enzyme catalysis. It expands the study of biological equilibria and thermodynamics through the discussion of the properties of aqueous solutions, thermodynamics of enzyme binding and recognition, and oxidation and reduction processes. Prerequisites: CHEM 232, 233. Fall. Add: On page 99, in place of deleted entry: Designed to approach the fundamentals of biochemistry from a chemical perspective, this course examines the structure and function of biological molecules such as nucleic acids, proteins, carbohydrates, and lipids. It introduces the principles of molecular recognition, enzyme catalysis, enzyme kinetics, and metabolism and develops an understanding of biological equilibria, redox, and energy transduction through the discussion of core metabolic pathways and oxidative phosphorylation. Prerequisites: CHEM 232, 233. Fall. Impact: None anticipated. Rationale: The changes are editorial to better reflect the course content. 2. Delete: On page 101, the entry for CHEM 437, Modern Biochemistry: 437 Modern Biochemistry (3) An in depth exploration of reaction kinetics and catalytic mechanisms of enzymes; metabolism; the expression and transmission of genetic information; and biological structural analysis with an emphasis on current research in the field. Prerequisites: CHEM 323, 331. Spring. Add: On page 101, in place of deleted entry: 437 Biophysical Chemistry (3) Takes a deeper look into the dynamic structures and myriad functions of proteins, nucleic acids, and lipids from a quantitative, physical perspective. -
Quantum Chemistry and Spectroscopy – Spring 2018
CHE 336 – Quantum Chemistry and Spectroscopy – Spring 2018 Instructor: Dr. Jessica Sarver Email: [email protected] Office: HSC 364 (email hours: 8 am – 10 pm) Office Hours: 10am-12pm Tuesday, 2-3pm Wednesday, 10:30-11:30am Friday, or by appointment Course Description (from Westminster undergraduate catalog) Quantum chemistry and spectroscopy is the study of the microscopic behavior of matter and its interaction with electromagnetic radiation. Topics include the formulation and application of quantum mechanical models, atomic and molecular structure, and various spectroscopic techniques. Laboratory activities demonstrate the fundamental principles of physical chemistry. Methods that will be used during the laboratory portion include: polarimetry, UV-Vis and fluorescence spectroscopies, electrochemistry, and computational/molecular modeling. Prerequisites: C- grade in CHE 117 and MTH 152 and PHY 152. Course Outcomes The chemistry major outcomes are: • Describe and explain quantum theory and the three quantum mechanical models of motion. • Describe and explain how these theories/models are applied and incorporated to applications of atomic/molecular structure and spectroscopy. • Describe and explain the principles of four major types of spectroscopy and their applications. • Describe and explain the measurable thermodynamic parameters for physical and chemical processes and equilibria. • Describe and explain how chemical kinetics can be used to investigate time-dependent processes. • Solve mathematical problems based on physical chemical principles and connect the numerical results with these principles. Textbook The text for this course is Physical Chemistry, 10th Ed. by Atkins and de Paula. Readings and problem set questions will be assigned from this text. You are strongly urged to get a copy of this textbook and complete all the assigned readings and homework. -
Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Harvard University - DASH Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. Citation Rappoport, Dmitrij, Cooper J. Galvin, Dmitry Zubarev, and Alán Aspuru-Guzik. 2014. “Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.” Journal of Chemical Theory and Computation 10 (3) (March 11): 897–907. Published Version doi:10.1021/ct401004r Accessed February 19, 2015 5:14:37 PM EST Citable Link http://nrs.harvard.edu/urn-3:HUL.InstRepos:12697373 Terms of Use This article was downloaded from Harvard University's DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP (Article begins on next page) Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry Dmitrij Rappoport,∗,† Cooper J Galvin,‡ Dmitry Yu. Zubarev,† and Alán Aspuru-Guzik∗,† Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA, and Pomona College, 333 North College Way, Claremont, CA 91711, USA E-mail: [email protected]; [email protected] Abstract While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for mod- eling complex structures and large-scale chemical systems. Here we present heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in metabolism and prebiotic chemistry. -
BIOPHYSICAL CHEMISTRY an International Journal Devoted to the Physics and Chemistry of Biological Phenomena
BIOPHYSICAL CHEMISTRY An International Journal devoted to the Physics and Chemistry of Biological Phenomena AUTHOR INFORMATION PACK TABLE OF CONTENTS XXX . • Description p.1 • Audience p.1 • Impact Factor p.2 • Abstracting and Indexing p.2 • Editorial Board p.2 • Guide for Authors p.5 ISSN: 0301-4622 DESCRIPTION . Biophysical Chemistry publishes original work and reviews in the areas of chemistry and physics directly impacting biological phenomena. Quantitative analysis of the properties of biological macromolecules, biologically active molecules, macromolecular assemblies and cell components in terms of kinetics, thermodynamics, spatio-temporal organization, NMR and X-ray structural biology, as well as single-molecule detection represent a major focus of the journal. Theoretical and computational treatments of biomacromolecular systems, macromolecular interactions, regulatory control and systems biology are also of interest to the journal. The journal publishes Regular Articles, Reviews, Short Communications (maximum of 4 printed pages) and Feature Articles. Feature Articles are normally by Editor's invitation only, but interested authors can contact the Editors before submission. Author(s) will be asked to focus on her/his recent research contributions, thereby adding a personal perspective to their field of research. These short reviews will include the authors' photo and a brief bio/CV and will have a page limit of 5 printed pages in print. Manuscripts that fall outside the scopes and interests of the journal are returned to the Authors without in-depth review. Relevant manuscripts are reviewed expeditiously with decisions generally made within 3 weeks from receipt. Short Communications are 6 printed pages maximum, reporting results of unusual timeliness and significance. -
Chemical Thermodynamics and Staged Unit Operations
Beginning of Course Memorandum (BOCM) University of Virginia Fall, 2013 CHE 3316 Chemical Thermodynamics and Staged Unit Operations Revised October 22 Instructor: John O'Connell: Office Chemical Engineering 310; Voice (434) 924-3428; E-mail: [email protected] Office Hours: TR1400-1730, Others TBA GTA: Sabra Hanspal: Office CHE 217A; Voice 4-1476; E-mail: [email protected]; Office Hours: MF 12-2 PM Class Meetings: CHE 005, TR 0930-1045, T 1300-1350 Texts: "Lectures in Thermodynamics, Volume 2 (Beta Version)", by J.M. Haile & J.P. O'Connell, 2008 - 12, Electronic copy on CD available from instructor for $15. Total 641 pages. "Separation Process Engineering, 3rd Ed.", by P.C. Wankat, Prentice Hall, 2012. References: “Physical and Chemical Equilibrium for Chemical Engineers, 2nd Ed.” by N. de Nevers, Wiley-Interscience, New York, 2012. "Introduction to Chemical Engineering Thermodynamics, 7th Ed.," by J.M. Smith, H.C. Van Ness, and M.M. Abbott (SVNA). McGraw-Hill, New York, 2005. "Chemical, Biochemical, & Engineering Thermodynamics, 4th Ed.," by S.I. Sandler, John Wiley, 2006. "Schaum's Outline of Thermodynamics with Chemical Applications, 2nd Ed.," by H.C. Van Ness & M.M.Abbott, Schaum's Outlines, McGraw-Hill, 1989. "Lectures in Thermodynamics, Volume 1," by J.M. Haile, Macatea Productions, 2002. “Unit Operations of Chemical Engineering, 7th Ed.”, W. McCabe, J. Smith, & P. Harriott, New York, McGraw-Hill, 2004. “Principles of Chemical Separations with Environmental Applications,” R.D. Noble & P.A. Terry, Cambridge, UK, Cambridge University Press, 2004. “Perry’s Chemical Engineers’ Handbook, 8th Ed.,” D. Green & R. Perry, New York, McGraw-Hill, 2007. -
Introduction to Quantum Chemistry
Chem. 140B Dr. J.A. Mack Introduction to Quantum Chemistry Why as a chemist, do you need to learn this material? 140B Dr. Mack 1 Without Quantum Mechanics, how would you explain: • Periodic trends in properties of the elements • Structure of compounds e.g. Tetrahedral carbon in ethane, planar ethylene, etc. • Bond lengths/strengths • Discrete spectral lines (IR, NMR, Atomic Absorption, etc.) • Electron Microscopy & surface science Without Quantum Mechanics, chemistry would be a purely empirical science. (We would be no better than biologists…) 140B Dr. Mack 2 1 Classical Physics On the basis of experiments, in particular those performed by Galileo, Newton came up with his laws of motion: 1. A body moves with a constant velocity (possibly zero) unless it is acted upon by a force. 2. The “rate of change of motion”, i.e. the rate of change of momentum, is proportional to the impressed force and occurs in the direction of the applied force. 3. To every action there is an equal and opposite reaction. 4. The gravitational force of attraction between two bodies is proportional to the product of their masses and inversely proportional to the square of the distance between them. m m F = G × 1 2 r 2 140B Dr. Mack 3 The Failures of Classical Mechanics 1. Black Body Radiation: The Ultraviolet Catastrophe 2. The Photoelectric Effect: Einstein's belt buckle 3. The de Broglie relationship: Dude you have a wavelength! 4. The double-slit experiment: More wave/particle duality 5. Atomic Line Spectra: The 1st observation of quantum levels 140B Dr. Mack 4 2 Black Body Radiation Light Waves: Electromagnetic Radiation Light is composed of two perpendicular oscillating vectors waves: A magnetic field & an electric field As the light wave passes through a substance, the oscillating fields can stimulate the movement of electrons in a substance.