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09.07.2011 - Chemistry 260 Chemical Principles ...

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Unformatted text preview: Chemistry 260 Chemical Principles Chemistry 261 Introduction to Quantum Mechanics Lecture 1 September 7, 2011 Physical principles that determine the functionality of complex systems ß།From function in biological systems Chem 260/261 - “Chemical Principles” Although chemical phenomena are diverse, a limited and general set of principles can be used to describe and predict. Chemistry links structure and reactivity structure: within atoms and between them reactivity: changes in energy from reactants to products rates at which transformations occur Chemistry links physics and function physics: the properties of and interactions between particles (electrons, nuclei, atoms,…) function: biology, biochemistry, energy storage, energy harvesting, materials, food, medicine, computers … Chem 260/261 - “Chemical Principles” What is Physical Chemistry? Study of the Physics of Chemical Systems: Atoms, molecules, mixtures, solutions, reactions, structures … Study of the theoretical foundation describing chemical reality. http://www.mpibpc.gwdg.de/groups/de_groot/gallery.html To energy harvesting, storage, and use à༎ http://en.wikipedia.org/wiki/File:Twice_Cropped_Zonnecollectoren.JPG ß། To a nanodevice for detection of a biomarker for cancer - prostate- speciIic antigen or PSA A limited number of postulates or assumptions, supported by (or deduced from) experiment, providing a uniIied “Theory of Everything.” 1.  Postulates and consequences of quantum mechanics 2.  Forces of repulsion and attraction 3.  The laws of thermodynamics http://www.nsti.org/news/item.html?id=140 Detection of PSA using the biobarcode assay. Courtesy: Chad Mirkin, Ph.D., Northwestern University Chem 260/261 - “Chemical Principles” Chem 260 – Practical Details Some practical details: Staff YOU Peers Readings Lecturers Kevin Kubarych Barry Dunietz GSIs Christina Franzese John King Josef Dunbar Derek Osborne Texts: Oxtoby et al. Principles of Modern Chemistry. Thomson Brooks/Cole Introduction to Quantum Chemistry (Vol I) Introduction to Thermodynamics and Kinetics (Vol II) Midterm Exam 1 100 points Midterm Exam 2 100 points Final Exam (cumulative) 200 points 11/12 Problem sets 165 points Reading quizzes 70 points Participation (iClicker) 60 points Course Evaluations 5 points Total 700 points Midterm 1 Midterm 2 Final Exam Oct 13 (or 11) Nov, 17 (or 10) Dec, 16 Lowest A Lowest B Lowest C Lowest D 595 points (85%) 490 points (70%) 420 points (60%) 350 points (50%) Grades for 261 follow the same percentages. See syllabus for details. 6:00- 8:00 pm 6:00- 8:00 pm 8:00- 10:00 am 1 Your responsibilities as a student: or how can I get an A Chem 260/261 CTools Site •  Read Syllabus •  Read the textbook and other assigned readings •  CTools: Test Center - for each lecture, reading quizzes are open for credit until 10:00 AM of lecture day (still viewable afterwards) •  Attend Lecture, i>Clicker participation credit •  Attend discussion section •  Weekly problems sets •  OWL exercises are required for the complete HW credit •  Mastery supplements (ctools) •  Additional exercises are available as optional – do until you gain sufIicient conIidence in the material •  Use available resources to prepare for the Exams Syllabus •  course policies •  ofIice hours •  exams/ grading information Lecture & assignment schedule Reading Quizzes (Test Center) Lecture slides Problem sets and solutions (part OWL, part on CTools) Learning objectives and suggested exercises Practice exams and keys Important announcements Tips for Studying •  Read book chapters prior to class. •  Print lecture notes prior to the lecture (4 or 6 slide per page option). –  These will usually be up the evening before class, but will always be available by 8:00 am before lecture. https://ctools.umich.edu Tips for Studying •  Always test your understanding by problem solving. •  Use time with instructors (GSIs, professors, peers) wisely. •  Note- you will have to go over slides and reading material which were not covered during lecture (use book and help if needed). •  Develop a glossary summarizing all the new concepts. Force – something that causes a mass to accelerate. Potential – energy stored in a system due to work done on the system. Trajectory – the path a moving object follows through space as a function of time. Using i>clickers in this class for credit starting on 9/16 þ༏  Purchase your remotes/webclicker subscription at the Computer Showcase in the Michigan Union þ༏  Register your remotes/subscriptions on the course Ctools site (once a year, no matter how many clicker courses you have) þ༏  Web>clicker users: https://webclicker.iclicker.com þ༏  Pull the plastic tab from the back of the remote if there is one; power key is the bottom button. Change your answer if you like; the system records the final answer that is clicked in before polling is stopped. þ༏  Questions? http://bit.ly/studentclickers ConcepTest A practice question... Do you have a birthday today? Reply with: Yes/No What is the probability to have at least one student in our section here today who has a birthday today? (A polling question – there is no right or wrong answer) 2 ConcepTest The probability for NO birthday in a crowd of 200 is: (364/365)200 =0.58 .. (assuming a non leap year) Chance for having no one with a B-D today! è༎ So almost 50/50 chance to have at least one person with a birthday today in the classroom!!! i>clicker Practice Question (ConcepTest) How enthusiastic are you about taking Chemistry 260/261? A. B. C. D. E. Extremely enthused! Chemistry is my life! Looking forward to the class… meh… Is this 50 minutes up yet? Get the crash cart… NOW! Another fun question: i>clicker Practice Question (ConcepTest) iclicker Practice Question I am currently a: A.  freshman. B.  sophomore. C.  junior. D.  senior. E.  none of the above. Choose the option the best describes you: A.  a chemical engineering major B.  a chemistry major C.  majoring in a biological or life science D.  Iilling requirements for medical school E.  I’m tryin’ not to think about my future… Today in Chemistry 260/261 Aquaporin- 1 in action. 200 ps simulation fragment. (1 ps = 1 picosecond = 10- 12 seconds) •  course introduction •  i>clicker •  classical chemistry: forces and potentials This Week in Chemistry 260/261 •  reading: (Fri) Ch. 4.1- 4.4 (Oxtoby) •  remember to take the reading quiz! (try the practice one, too…) •  facing the (quantum) facts Iirst problem set due Mon, September, 12, 2011 by 3:00 pm •  B.L. de Groot and H. Grubmüller: Science 294, 2353- 2357 (2001) http://www.mpibpc.gwdg.de/groups/de_groot/gallery.html 3 HIV- 1 Protease and Inhibitors HIV- 1 protease: cuts up polyprotein into the proteins needed to form the mature HIV virus Timing of the slicing is critical, too soon, not enough time to develop the immature virus Structure of HIV- 1 protease (1989) led to the development of inhibitors This structure shows the drug Indinavir ß།From function in biological systems http://www.mpibpc.gwdg.de/groups/de_groot/gallery.html To energy harvesting, storage, and use à༎ http://en.wikipedia.org/wiki/File:Twice_Cropped_Zonnecollectoren.JPG ß། Novel materials (i.e. graphene) designed based on quantum mechanics Simulate this protein! http://www.rcsb.org/pdb/101/motm.do?momID=6 Protein Databank Structure: 1HSG Follow the Energy! What we mean by “classical” 1.  The “currency” of physical processes is energy 2.  You are most likely to Iind a system in a state where its energy is the lowest 3.  Energy is conserved à༎ you do not create or destroy energy 4.  In an open system then you can’t get more energy out than you put in 5.  If you know the “energy” function (i.e. how to compute it), you also know how the system will evolve in time (!!!) p = mv E= 12 p2 mv + V = +V 2 2m kinetic http://images.iop.org/objects/ntw/news/7/1/28/080128.jpg F = ma = m potential dv d2x dV =m 2 =− dt dt dx 1. MATTER described by the deterministic Laws of Motion Particles of matter travel in a trajectory, a path with a precise position and momentum at each instant. t0 t1 t2 t3 t∞ 2. FIELDS distributions of forces in space described by Field Laws a.  gravity (Isaac Newton) b.  electromagnetism (James Maxwell) In a nutshell: According to classical mechanics, the universe consists of nothing but matter and Iields and we know the laws of both… Go to minimization (force field) Classical Chemistry: Forces and Potentials 1.  Force is something that causes a mass to accelerate F = ma = m dv d2x =m 2 dt dt 2.  Potential is energy stored in a system due to work done on the system a.  Work is energy b.  Change in energy due to a force is: ΔE = F • Δx c.  InIinitesimal change is denoted with a “d” dE = F • dx F= dE dx Fx = − dV dx 4 ...
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