A postgraduation course in the 1st semester of 2003, QP-399:
Special Topics in Physical Chemistry IX:
“Relationships Between Structure and Property/Reactivity/Biological Activity”
by Prof. Dr. Márcia M. C. Ferreira and Dr. Rudolf Kiralj,
Institute of Chemistry, UNICAMP. Schedules: Tuesday and Thursday, from 7 to 9 PM.
Contact: marcia@iqm.unicamp.br, rudolf@iqm.unicamp.br

CONTENTS

Multivariate Analysis

Introduction.
Exploratory data analysis:
PCA - principal component analysis.
HCA - hierarchical cluster analysis.
Building the regression models:
PCR - principal component regression.
PLS - partial least squares regression.
Building the models for classification (pattern recognition):
KNN.
SIMCA.

Structural and Theoretical Chemistry

Introduction.
Structural parameters of atoms, small molecules and macromolecules.
Structural conformational analysis.
Molecular symmetry and stereochemistry.
Hydrogen bonds.
Intra- and intermolecular interactions.
Molecular complexes.
Crystal symmetry.
Crystal packing.
Crystallographic data bases.
Brief overview on theories used in theoretical, computational and structural chemistry.
Introduction to graph theory.
Use of structural data in theoretical chemistry.
Computational conformational analysis.
Geometry optimization of molecular complexes.

QSAR/QSPR

Introduction.
Quantitites in (Q)SAR/(Q)SPR.
Global and local molecular descriptors.
Descriptors of  molecular complexes and crystal packing.
Reactivity and magnetic property descriptors.
Methodology of (Q)SAR/(Q)SPR.
QSAR-3D.
Visualization techniques for molecules, molecular complexes, electron density and crystal packing.
Molecular graphics at qualitative and quantitative level.
Basic principles of molecular modeling.
Docking.
Pharmacophores.

BESIDES THEORETICAL LECTURES, THE COURSE INCLUDES PRACTISE, EXERCISES, PRESENTATION OF WORKS FROM LITERATURE AND OWN PROJECTS.

Course material to download

Lecture Notes 4, 16-28 are available im small .pdf format (2 original pages in only one) on the portuguese link, and big .pdf format (1 original page in one pdf page) on the english link. Choose the better option for you!

The Lecture Notes, Exercises and the Supplements are the property of the Laboratory of Theoretical and Applied Chemometrics, Institute of Chemistry, The State University of Campinas, Campinas, SP, and so they can be used only for teaching and didactive/education purposes (learning) with adequate citation! It is prohibited to use this material or represented ideas to make any kind of work, to write texts or make any other stuff where the content is modified and/or the authorship named differently than in these original documents!

NEW!
ANNOUNCEMENT: After the official date of the end of the semester, the course material (the Lecture Notes, Exercises and Supplements) are not more available for download. Who wants some material, please contact Profa. Márcia or Rudolf.
 

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–CONTENTS (in portugese)

–Lecture No. 1 (18 February 2003): Introduction to the Course (in portugese)

–Lecture No. 2 (20 February 2003): Introduction to Multivariate Analysis. Data Preprocessing (in portugese)

–Lectures No. 3, 5, 6 and 7 (25 February, 11, 13 and 18 March 2003): Exploratory Analysis, parts I, II, III and IV (in portugese)

–Lecture No. 4 (27 February 2003): Introduction to Structural Chemistry. Atomic Properties (in english)

–Lectures No. 8, 9, 10 and 11 (20, 25 and 27 March, and 1 April 2003): Regression Models, parts I, II, III and IV (in portugese)
–Exercises I:List of Exercises I (in portugese)Data I

–Lecture No. 12 (3 April 2003): Interpretation of literature works, by free choice, from the area of applied chemometrics - 6 presentations by students (in portugues)

–Lectures No. 13, 14 e 15 (8, 10 e 15 April 2003): Classification Models (Pattern Recognition), parts I, II, III and IV (in portugese); Interpretation of literature works, by free choice, from the area of applied chemometrics - 3 presentations by students (8 April 2003; in portugues)
–Exercises II:List of Exercises II (in portugese)Data II

–Lecture No. 16 (22 April 2003): Chemical Bond. Bond Length and Angle, Torsion Angle (in english)

–Lectures No. 17 and 18 (24 and 29 April 2003): Other Structural (Geometrical) Parameters of Small Molecules. Structural Conformational Analysis (in english)

–Lecture No. 19 (6 May 2003): Other Structural (Geometrical) Parameters of Macromolecules. Isomerism and Absolute Configurationand Conformation (in english)

–Lecture No. 20 (8 May 2003): Point Groups and Symmetry. Molecular Symmetry (in english)

–Lecture No. 21 (13 May 2003): Hydrogen Bonds and Other Intra- and Intermolecular Interactions. Molecular Complexes (in english)

–Lecture No. 22 (15 May 2003): Crystal Systems. Crystal Symmetry and Space Groups. Crystal Packing I (in english) - [A Xerox copy of the Supplement is neccessary to get at the beginning of the lecture]

–Lecture No. 23 (20 May 2003): Crystal Packing II. Crystallographic Data Bases and Other Useful Data Bases (in english)
-Lecture on Cambridge Structural Database

–Lecture No. 24 (22 May 2003): Special Topics in Theoretical, Computational e Structural Chemistry I, (in english)
A very short manual and an output example for program PLATON
–Exercises III:List of Exercises III (in portugese)
This list of exercises has to be done and given at most at the end of the first week of JULY! The list can be done using the DEMO version of Pirouette.
–Exercises IV:List of Exercises IV (in english)Data III
This list of exercises has to be done and given up to 10th of July! After this date will not be possible to hand over the list. The list can be done by using programs PLATON with Raswin, and Pirouette.

–Lecture No. 25 (3 June 2003): Special Topics in Theoretical, Computational e Structural Chemistry II (in english)
- [It is recommended to download the Supplements A, B, C, D and E before the beginning of the lecture]

–Lecture No. 26 (5 June 2003): Introduction to Medicinal Chemistry. Molecular Descriptors (in english) - [It is recommended to download the following Lecture Notes on QSAR by H. Kubinyi before the beginning of the lecture: Ligand-Receptor Interactions, QSAR Parameters and Hansch and Free-Wilson Analyses.]
The deadline for giving the List of Exercises IV is prolonged up to 12th of July. Visit this site to see if there are more changes of the deadline!

–Lecture No. 27 (10 June 2003): Molecular Desriptors II. Chemical Similarity and Biological Activity. Introduction to Medicinal Chemistry II. (in english) - [It is recommended to download the following Lecture Notes on QSAR by H. Kubinyi before the beginning of the lecture: Chemical Similarity and Biological Activity, Drug Discovery and Non-Linear QSAR.]
The deadline for giving the List of Exercises IV is prolonged once more up to 17th of July!

–Lecture No. 28 (12 June 2003): QSAR/QSPR Methodology. Examples of QSAR and QSPR. 3D QSAR (in english) - [It is recommended to download the following Lecture Notes on QSAR by H. Kubinyi before the beginning of the lecture: 3D QSAR, Pharmacophore Analysis e Virtual Screening. Also download small suplements: pharmacophore analysis by Catalyst, QSAR with COMFA, advanced COMFA and virtual screening.] Examples of QSAR/QSPR: HIV-1 protease inhibitors, physico-chemical properties of PAHs, derivatives of omeprazole and logP of PCBs.

–Lecture No. 29 (17 June 2003): Molecular Graphics. Molecular Modeling. Drug Design. (in english)  - [It is recommended to download the following Lecture Notes on QSAR by H. Kubinyi before the beginning of the lecture: Structure-Based Drug Design, Computer-Aided Drug Design and Combinatorial Drug Design.] Handing the List of Exercises IV.
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-Lecture No. 30 (26 June 2003): Presentation of the Projects I

-Lecture No. 31 (3 July 2003): Presentation of the Projects II. Comments on the Lists of Exercises.

More than one practical lecture was given by Profa. Márcia out of the official time, to teach the students how to make chemometric analysis on some concrete data. With that, the total number of the lectures is greater than 31.
 
 

ANNOUNCEMENT: Who wants to participate the minicourse on the use of the Cambridge Structural Database in August or September, please send an e-mail with the complete name and e-mail to Profa. Márcia or Rudolf, so we can contact you right at the time!

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Didactic Materials Related to the Course
 

Links to the publications of Prof. Márcia M. C. Ferreira

Theoretical and Applied Chemometrics:
Publicações No. / Publications No.    14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 31, 32, 34, 39, 43, 44, 45, 46, 49, 55, 56, 59, 61, 62

SAR/QSAR, SPR/QSPR, SSR/QSSR:
Publicações No. / Publications No.     16, 30, 33, 35, 36, 37, 38, 40, 41, 42, 47, 48, 50, 51, 52, 53, 54, 57, 58, 60

Molecular Graphics and Modeling:
Publicações No. / Publications No.     13, 18, 35, 36, 38, 51, 52, 53, 57
 
 

External links (internet)
 

Molecular Descriptors and QSAR Web News, Chemometrics Web News: http://www.disat.unimib.it/chm/WebMagazine.htm, http://www.disat.unimib.it/chm/Chemometrics.htm  -  University of Milan, Italy

Computational Chemistry List (CCL): http://server.ccl.net/  - USA

The QSAR and Modelling Society - Resources: http://www.ndsu.nodak.edu/qsar_soc/resource.htm  - USA

Homepage of Chemometrics: http://www.acc.umu.se/~tnkjtg/chemometrics/  - Umeå University, Sweden
Tutorials on Chemometrics: http://www.acc.umu.se/%7Etnkjtg/chemometrics/tutorials.html

Chemometrics World - Spectroscopynow.com: http://www.spectroscopynow.com/Spy/basehtml/SpyH/1,1657,2-0-0-0-0-home-0-0,00.html

Commission on Crystallographic Teaching Teaching Pamphlets : http://www.iucr.org/--> Teaching Pamphlets   or http://www.iucr.ac.uk--> Teaching Pamphlets   - International Union for Crystallography
Recommended articles to download:
1. A non-mathematical introduction to X-ray diffraction by C. A. Taylor
2. An introduction to the scope, potential and applications of X-ray analysis by M. Laing
6. Pourquoi les groupes de Symétrie en Cristallographie by D. Weigel
9. Rotation Matrices and Translation Vectors in Crystallography by S. Hovmöller
10. Metric Tensor and Symmetry Operations in Crystallography by G. Rigault
11. The Stereographic Projection by E. J. W. Whittaker
13. Symmetry by L. S. Dent Glasser
14. Space Group Patterns by W. M. Meier
15. Elementary X-Ray Diffraction for Biologists by Jenny P. Glusker
21. Crystal Packing by Angelo Gavezzotti (download here! - www download does not work)
22. Matrices, Mappings and Crystallographic Symmetry by Hans Wondratschek

Lecture Notes on QSAR by H. Kubinyi: http://home.t-online.de/home/kubinyi/
 

Especial materials to download
 

Conformation of alkanes and cycloalkanes: Chapter 3 from F. A. Carey: Organic Chemistry, 4th ed., McGraw-Hill Co., NY, 2000.
 

If using any program or database, it (the program or database) should be cited.
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Sofware for visualization of molecular / crystallographics structures (molecular graphics):
 

Raswin for Windows or Rasmol for other systems:
http://www.rcsb.org/pdb/help-graphics.html --> Rasmol  or directly   http://www.bernstein-plus-sons.com/software/rasmol/
 


Mercury for Windows or other systems: http://www.ccdc.cam.ac.uk/prods/mercury/index.html --> Mercury Download --> etc.
Download: http://www.ccdc.cam.ac.uk/prods/mercury/1_1_2/mercury_download_js.html
Documentation (manual): http://www.ccdc.cam.ac.uk/prods/mercury/docs/mercurydocn.pdf
 


DS ViewerPro 5.0, demo (30 days trial), Accelrys Inc.: http://www.accelrys.com/dstudio/ds_viewer/
Informação básica / Basic information
 


VMD - Visual Molecular Dynamics, University of Illinois at Urbana-Champaign, IL, USA: http://www.ks.uiuc.edu/Research/vmd/

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Sofware for analysis of molecular / crystallographics structures (structural analysis):
 


PLATON for Windown v. 2000, download:    files1    e / and   files2
Detailed instructions, University of Utrecht, The Netherlands: http://www.cryst.chem.uu.nl/platon/

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Software for calculation of moleculare properties
 

Dragon Web 3.0, University of Milan, Italy: http://www.disat.unimib.it/chm/Dragon.htm
Input in SMILES and some other formats.
The compressed document contains representation of Dragon as ppt.
 List of molecular descriptors: list

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LogP calculations using SMILES format of molecules:
 

ALOGPS 2.1, Virtual Computational Chemistry Laboratory: http://146.107.217.178/lab/alogps/--> start the program
 


Molinspiration, SMILES builder: http://www.molinspiration.com/services/logp.html

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Sofware for similarity search:
 


Molinspiration, SMILES builder: http://www.molinspiration.com/services/index.html --> Substructure, similarity and pharmacophore similarity searches

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Sofware for molecular geometry optimization (quantum-chemical methods):

Hückel MO, MOPAC, Gaussian, Gamess, University of Tasmania, Australia: http://www.chem.utas.edu.au/staff/yatesb/honours/modules/faces.html  -->
--> Hückel interfaces
--> MOPAC interfaces
--> Gaussian interfaces
--> Gamess interfaces
An input and output example for MOPAC: http://www.chem.utas.edu.au/staff/yatesb/honours/modules/mod3/m_input.shtml
 

MOPAC 6.0 for Windows:   program    e / and    manual
Input only with internal coordinates

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Software for chemometric analysis
 


The QSAR server, The University of North Carline, Chapel Hill, USA: http://mmlin1.pha.unc.edu/~jin/QSAR/


The Nucleic Acid Database, The Rutgers University, New Jersey, USA: http://ndbserver.rutgers.edu/NDB/index.html
 


The Protein Data Bank, The Rutgers University, New Jersey, USA: http://www.rcsb.org/pdb/
Mirror site, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brasil: http://www.pdb.ufmg.br/pdb/
There are various tools for analysis/visualization of biomacromolecules and links for other data banks.
 


The Cambridge Structural Database at NCSA Chem Viz, Univ. Urbana-Champaign, Illinois, USA: http://chemviz.ncsa.uiuc.edu/content/homenew.html  -->  Tools  --> CSD
or directly http://chemviz.ncsa.uiuc.edu/content/run-csd.html
It is neccessary to obtain first  login  and password: http://chemviz.ncsa.uiuc.edu/content/request_account.html
Basic information about this database on the page of the CCDC, Cambridge Crystallographic Data Centre, University of Cambridge, UK: http://www.ccdc.cam.ac.uk/
If using this database, it (the database) and its owner (NCSA) should be cited.
 


NIST Chemistry WebBook at NIST, USA: http://webbook.nist.gov/chemistry/ --> Search Options  or directly http://webbook.nist.gov/chemistry/#Search
 


Polycyclic Aromatic Hydrocarbons (PAHs) Database, Toyohashi University of Technology, Japan: http://chrom.tutms.tut.ac.jp/JINNO/DATABASE/00database.html
 


Polycyclic Aromatic Hydrocarbon Structure Index, NIST, USA: http://ois.nist.gov/pah/
Introdução / Introduction
 


WebElements.com at University of Sheffield, UK: http://www.webelements.com
 


3D Molecular Modeling Home Page, Tokyo University of Pharmacy and Life Science: http://triton.ps.toyaku.ac.jp/~dobashi/database/indexe.html
 


The IMB Jena Image Library of Biological Macromolecules, University of Jena, Germany: http://www.imb-jena.de/IMAGE.html
There are various tools for analysis/visualization of biomacromolecules and links for other data banks.
 


The Metalloprotein Database and Browser, the Scripps Research Institute, La Jolla, CA, USA: http://metallo.scripps.edu/
 


PROLYSIS - a protease and protease inhibitor Web server, University of Tours, France: http://delphi.phys.univ-tours.fr/Prolysis/
 


Database for Anti-HIV Compounds, NIAID-NIST, USA: http://www.niaid.nih.gov/daids/dtpdb/protinh.htm
 


Proteinase Inhibitor Database, the University of York, UK : http://www.ysbl.york.ac.uk/~proteinase/
 


HIV Protein Database, National Cancer Institute, USA: http://mcl1.ncifcrf.gov/hivdb/index.html
 
 
 

Links for various structural databases:
http://xray.bmc.uu.se/embo/structdb/links.html
http://www.bio.unizh.ch/db/
http://www.xtal.iqfr.csic.es/ing/assistance.html
http://www.kisac.ki.se/education/courses/kth03/strdbs.html
http://www.life.uiuc.edu/z-huang/structldbs.html
http://swarna.ncsa.uiuc.edu/structdbs.html
http://www.rcsb.org/databases.html
http://www3.oup.co.uk/nar/database/cat/11
http://www.biochem.ucl.ac.uk/~robert/bioinf/lecture2/
etc.

Organic Chemistry Database, Colby College, Waterville, Maine, USA : http://www.colby.edu/chemistry/cmp/cmp.html
 

Klotho - Biochemical Compounds Declarative Database: http://www.biocheminfo.org/klotho/
 

Development Therapeutics Program, NCI-NIH, USA: http://dtp.nci.nih.gov/
Bancos de dados com atividades biológicas / Databases with biological activities
 

Integrated Spectral Data Base System for Organic Compounds, AIST, Japan: http://www.aist.go.jp/RIODB/SDBS/sdbs/owa/sdbs_sea.cre_frame_sea

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