Some Chemistry Pages That I Visit

Green Chemistry (last updated 8/08)

People & Labs

• Institute for Green Science (Terry Collins, Carnegie Mellon) - must visit site, course info, web lectures
• Green Chemistry at the U of Oregon (Jim Hutchinson) green organic chemistry lab course, resources, links
• Green Design Initiative (Carnegie-Mellon U) engineering, design, education
• Greening Across the Chemistry Curriculum (Michael Cann, U. Scranton) modules for college chemistry (2/06)

Organizations

• Zero Waste Alliance (Lauren Heine) Portland-based non-profit
• EPA also visit New Chemicals Program
• Green Chemistry Network Royal Society of Chemistry
• Green Chemistry Institute American Chemical Society
• Green Chemistry Education American Chemical Society
• Green Chemistry Resource Exchange American Chemical Society
• Oregon Environmental Council Oregon-based
• Toxics Use Reduction Institute Massachusetts-based
• Crystal Faraday UK-based industry-academe partnership

Journals

• Green Chemistry Royal Society of Chemistry, resources
• Nature (published 11/6/02) Links to free Nature articles on sustainable development

Software

• Tools & Literature build a green process, design a green chemical (EPA)
• ECOSAR predict toxicity of chemicals to aquatic organisms (EPA)

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Chemistry & Education (last updated 12/30/07)

Organic Chemistry

• Virtual Textbook (William Reusch, Mich State U) needs Chime, also O Chem at MSU
• O Chem with JME Molecular Editor (Tom Newton, U South Maine)
• ChemHelper.Com (Arthur Winter, Frostburg State) tutorials, mechanisms, practice exams & more
• O Chem Toolkit (Bob Hanson, St. Olaf) links
• Molecular Modeling for Organic Chemistry (Henry Rzepa, Imperial College) 8 lectures
• O Chem.Com (Thomas Poon, Claremont McKenna & Bradford Mundy, Colby) (busted 12/07)
• NCSA ChemViz (Indiana U) O & G Chem labs for "high school" using Waltz, CSD, & Nanocad
• MIT Open Courseware (MIT) all courses

Chemistry - General, Inorganic, Etc.

• Resources for Chemistry Educators (Steve Lower, Simon Fraser U) K-12 + College, amazing collection of annotated links
• General Chemistry Virtual Textbook (Steve Lower, Simon Fraser U) PDF chapters & tutorials (environ chem too)
• Chem1 Concept Builder (Steve Lower, Simon Fraser U) CAI project, instructional software for introductory chemistry
• Chem1 Problem Proctor (Steve Lower, Simon Fraser U) CAI project, problem booklet + computer-moderated dialog
• Consortium for Technology in Teaching Chemistry (USC Chem Dept) demos, animations, workshops, forums
• ChemCollective (CMU) online tools, virtual labs
• Visionlearning (NSF-supported) free articles, modules, basic chem
• Global Instruction Chemistry (Henry Rzepa, Imperial College) pre-98 links
• Molecular Monte Carlo (Cooper Union) tutorials & software
• Simulations and Animations (Thomas Greenbowe, Iowa State U) electrochemistry and much more
• Electrochemistry Encyclopedia
• World of Chemistry (Annenberg Media, learner.org) free chemistry videos

Learning Styles, Keller Plans, Web Resources & more

• The Learning Curve (ThinkQuest) glossary (busted 12/07)
• Learning Styles Questionaire (Soloman & Felder, NC State) multiple-choice quiz
• Time Capsule on Training & Learning (Don Clark) essays on education (includes Keller, Constructivism)
• Instructional Design & Learning Theory (Brenda Mergel, U Saskatchewan) includes Keller
• Kulik references:
  • Kulik, C. C. & Kulik, J. A., (1987). Mastery testing and student learning: A meta-analysis. J. Educational Technology Systems, 15, 325-345.
  • Kulik, J. A., Kulik, C. C., & Bangert-Drowns, R. L. (1990). Effectiveness of mastery learning programs: A meta-analysis. Review of Educational Research, 60, 265-299.
  • Kulik, J. A., Kulik, C. C., & Cohen, P. A., (1979). A meta-analysis of outcome studies of Keller's personalized system of instruction. American Psychologist, 34, 307-318.
  • Kulik, J. A., Kulik, C., & Carmichael, K. (1974). The Keller Plan in science teaching. Science, 183, 379-383. {U15.01}.
• The Keller Plan: 25 Years of Personal Experience (Paul Herzberg, York University) referenced article in Positive Pedagogy
• Keller Plan () a one-page description
• Keller Plan in Law School (Alan Tyree, formerly U Sydney Law School) colleagues hated it, but law courses based on the Keller Plan and computer-assisted testing worked
• Web Visualization for Teachers (Alistair Fraser) How to make visualizations work

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Portland-Area Libraries (last updated 6/26/06)

• Reed
• Portland State
• OHSU
• Multnomah County

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Databases (last updated 2/07)

• NIST Chemistry WebBook
• NIST Physical Ref Data
• NMR Shifts 2/07
• Synthesis reviews
• Al's Notebook (synthetic procedures, solvent spectra, more, ...)
• SPARC Property predictor (pKa, various properties, simultaneous rate eqns, ...)
• European Pollutant Emission Register (EPER)
• Chemical Entities of Biological Interest
• Hazardous Substances Databank
• DSSTox (EPA Chemical Toxicity Database)
• TOXMAP (Nat Lib Med Environmental Health Maps)
• Toxicology Data Network (NIH)
• IRIS Chemical Tracking Assessment System (EPA)
• ChemSpider (mainly MW, log P estd, surface area) 5/2/07

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Scientists (last updated 7/1/08)

• T. Collins
• L. Pauling & Chemical Bond | L. Pauling & Peace
• M. Banaszak Holl
• P. Hiberty
• N. Epiotis
• S. Shaik
• Ben Eder (1980-2001)

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Random Chemistry Sites

• American Chemical Society (ACS) 6/05
  • Links to ACS Division Home Pages 6/05
  • Chemical Abstracts 6/05
• QSAR & Modeling Society 10/07
• QSAR World 10/07
• Drug-Design Resources 6/05
• WATOC (World Association of Theoretically Oriented Chemists) 6/05
• NIH Guide to Molecular Modeling - modeling resources, 6/05
• Center for Computational Quantum Chemistry - University of Georgia, 9/03
• WWW Chemistry Guide (annotated links, all areas) 6/06
• Not Voodoo - how to get it going with organic chemicals 9/06

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Chemistry Software

(OS codes: L = Linux, W = Windows, M = Mac)

Electronics

• Spartan - Wavefunction, 9/03
• Jaguar - Schrödinger, 9/03
• GAMESS - FREE, L - Mark Gordon, Iowa State U - HF, DFT, post-HF - 5/06
• PCGAMESS - FREE, WL - Alex Granovsky, Moscow State U - 5/06
  • Web GAMESS - FREE - web interface for remote PCGAMESS, 9/03
• more post-HF programs
  • NWChem - FREE, L - 9/03
  • ADF - DFT, 9/03
  • ACES II - Rod Bartlett, U Florida, 9/03
  • Gaussian - 9/03
  • Columbus - FREE - 9/03
  • Dalton - FREE - 9/03
  • AMICA - FREE - 9/03
  • Q-Chem - 9/03
  • Dirac - 5/05
  • Molcas - FREE - Bjorn Roos, U. Lund, Sweden, 9/05
  • Molpro - H-J Werner & P.J. Knowles, 9/03
  • Pyquante - FREE, OpenSource - modules for making your own quantum program - 9/03
  • Crystal03 - L, W("soon") - periodic ab initio for solids - 3/04
  • ORCA - FREE, L, W - F. Neese, Max Planck Inst. - enter "Download Area" or try this link - 1/06
  • DFTB+ - FREE, L - T. Fraunheim, U. Bremen - implements semi-empirical DFTB (SCC & non-SCC) - 3/07
• MOPAC2007 - FREE (to academics), LW - all main group + transition metals (PM6) Stewart Computational Chemistry - 2/07
• Computational Chemistry List (and Archive) - JOIN - 9/03
• Quantum Chemistry Program Exchange - QCPE, Indiana U - 9/03
• EMSL Basis Sets - order form - PNNL, 9/03

Visualization & GUI

• Spartan - Wavefunction, 9/03
• Chime - FREE - MDL (go to Downloads), 9/03
• Molden - FREE - PDB-GAMESS friendly, 7/06
  • Convert Jaguar to Molden - FREE - 7/06
• gOpenMol - FREE, LW - surfaces, maps, animations, 9/03
• Molekel - FREE, LW - surfaces, maps, animations, GAMESS-ADF-NBO friendly, 9/03
• MolSurf - FREE - on-line generation of VRML surfaces, maps from COSMO, VAMP, SMILES, 9/03
• MoCalc - FREE - Anderson Gaudio, U Federal Espírito Santo -interface, visualization, analysis for GAMES, Tinker, Rasmol, Mopac, Babel - 4/06
• WebMO - FREE, L - build, setup, analyze calcs over the Web, GAMESS friendly, 4/04
• PyMOL - FREE, LWM, C/Python-based - basic graphics, animations, superimpose, 4/04
• RasMol - FREE, LWM, famous molecule viewer, also see Protein Explorer and Chime here
• JMV - FREE? LW - Java-based Molecular Viewer, PDB-friendly (active site?), 4/04
• DeepView Swiss PDB Viewer - FREE, LWM - view, superimpose proteins (and more), 4/04
• BioAdviser - W - view/compare small molecules up to big biomolecules, 4/04
• Chimera - FREE, WLM - biomolecules, 4/04
• JMol - FREE - open-source Java-based viewer (like RasMol), GAMESS-Jaguar-PDB-Chime friendly, 4/04
• Gabedit - FREE, LWM - GUI for GAMESS, Gaussian, Molcas, Molpro, MPQC, 5/06
• Facio - FREE, WL - GAMESS, Gaussian-friendly, 2/07
• ChemCraft - W - GAMESS, Gaussian-friendly, 8/07

Electron Density & Orbitals

• Aimpac - FREE - Bader, McMaster U, group and theory pages
• Morphy - FREE (small version only), WL - Popelier PDF book, 4/21/05
• Xaim - FREE, L - Gaussian-ADF friendly
• Aim2000 - FREE (small version only), W 5/05
• AOMix - W - Gorelsky, Stanford, Resolve Spartan or Jaguar wavefns into fragment orbs or do charge decomp analysis, 4/04
• NBO - LW - Weinhold, U Wisconsin, Natural Atomic Orbital analysis of Spartan & Jaguar wavefn, 4/04
• ELF with TopMod - L - instructions, GAMESS, Gaussian-friendly, 8/08

Mechanics

• Spartan - Wavefunction, MMFF
• Macromodel - Schrodinger
• TINKER - FREE - Amber95, Charmm22, , MM3, OPLS
• Ghemical - FREE, L - direct links to MPQC

Dynamics

• GROMACS - FREE - old URL
• GROMOS
• AMBER 4/23/03
• MOIL - FREE?, LW - Amber, 5/03
• TINKER - FREE - Amber95, Charmm22, MM3, OPLS
• CPMD - FREE - DFT-MD (Carr-Parrinello)
• NAMD - FREE - U Illinois, parallel object-oriented scalable, visualize with Visual MD (FREE)
• mdxvu - FREE?, L - MD visualization, Amber-Tinker friendly
• Molecular Monte Carlo - FREE - Cooper Union, tutorials, software, links
• Mol Dynamics Simulations Charmm tutorial - FREE - detailed tutorial, general theory & program
• nMOLDYN - FREE, L/Python - trajectory analysis, neutron scattering simulations, Charm-NAMD-MMTK friendly
• Stark Design - WM - 8/02
• Concord Modeling Workbench - FREE, WL, Java-based - 4/03
• Molecular Modeling Toolkit - FREE, OpenSource - K. Hinsen, (CEA/CNRS, France), Python modules, Amber friendly 5/8/05

Drawing

• Know-It-All - EXCELLENT + FREE (for academics, registration reqd) W - BioRad, suite includes drawing program
• ChemDraw - CambridgeSoft, also ChemOffice, ChemFinder
• Isis/Draw - EXCELLENT + FREE (for academics, registration reqd), WM - MDL, 1/07
• ChemSketch 10.0 - EXCELLENT + FREE, W - ACD Labs, 2/07
• JChemPaint - FREE, Java-based open-source - part of Chemistry Development Kit, Christoph Steinbeck (Cologne U, Germany), 2/07
• MarvinSketch - FREE (for academics), Java-based (draw, copy/paste to other docs, & print from your web browser) - ChemAxon, 2/07

Misc Links

• Mol2Mol - FREE 30d eval, W - file translater + Sterimol calculator, 9/06
• Vigyaan CD - all-in-one-CD modeling kit - 4/06
• Linux 4 Chemistry - FREE, share & commercial, 3/06
• Alchem - FREE, 3/06
• Linux and Chemistry - FREE, share & commercial, 3/06
• SAL (Chemistry, Biology) - FREE, share & commercial, 3/06
• OpenScience Project - FREEware, 3/06
• SourceForge - open source software, 3/06

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