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Chemistry Studies and Investigations with Information Technology
Tools under Didactics control.
Aris Kaksis, PhD - doctor. chem..
docent at Medical Biochemistry dep. of Riga Stradins University, Dzirciema Str 16, room A403, Riga, LV-1007,
E-mail: [email protected]
http://aris.gusc.lv/
The universal knowledge about subject of human studies and education is the substance properties and
behaving depending merely on molecular structure and on constituent chemical element compositions in its
conversion destiny. That is universe past, today and future, were humans and life is present, that has the vital
need to be studied, investigated and teach. The mastering of information technology tools are still actual and
should be based on task and goal of education.
The pedagogy task in Chemistry is to teach skills in the use of literacy, reading, speaking, mathematical logic,
and graphical analysis - finally modeling, including newest information technologies.
The pedagogy goal is mastering use of the information (in biochemical sciences) in chemistry about
substances and universe building. The target in chemistry could be completed using skills of new information
technology tools for The Practical Studies and Investigations of Molecular Structure and Dynamics.
During period 1980 - 1990 chemical information technology in biochemical sciences yield profit tools
which are fast adapted in global use and accessible for download on many platforms: Microsoft Windows
PC, Macintosh, Unix, Silicon Graphics. In many cases these applications are completely integrated between
different platforms.
Presentation of class work in chemistry contains seven 1 ÷ 7 chapters schemed to three academic hours per
each:
Class work 1. Valence Electron Shell Pair Formation [7] at  and  bond after hybridization of  valence
orbitals has the task to obtain the working skills with applications
RasWin (RasMol),
ISISDraw [2]
(Integrated Scientific Information System for chemical structural molecular studies, investigation and
presentation), which has the goal its employ for chemical studies and investigation of given molecules.
Coordination number and type of the complex compound central atoms structural hybridization. The 3D
molecular graphics applied
into Chemscape Netscape browser HTML as the plug-in application.
Students can get the knowledge and skills about:
elemental composition and its recognition in the displayed shapes of molecules – wire-frame, stick, stick&ball,
spacefill as well as superimposing the color scheme CPK into symbolic presentation of chemical elements on
the depicted structures of molecules,
bonding geometry (bond – angles, distance, terms of molecular symmetry and antysimmetry)
hybridization types of electron molecular orbitals during bond formation process.
«The Saccharide Viewer » [1] attempt 2. has the task to obtain the working skills with
RasWin
(RasMol),
ISISDraw [2] applications, which has the goal its employ for chemical structural molecular
studies and investigation of given opened chain and cyclic monosaccharide as well as polysaccharide molecules.
Students can get the knowledge and skills about:
elemental (C, O, , N, P, S, Na+, Ca2+) composition and its recognition in the displayed shapes of molecules –
wire-frame, stick, stick&ball, spacefill as well as superimposing the color scheme CPK into symbolic
presentation of chemical elements on the depicted structures of molecules, haw to convert the given opened
chain mono-saccharides from 3D molecular models into Fisher’s projection. Similar relationships between
drawn Haworth’s projections of pyranose and furanose hemiacetal cyclic structures of mono-, di- and oligosaccharides with its presented 3D molecular models.
Optical isomer L or S and D or R recognition using drawn Fisher’s and Haworth’s projections in resemblance
with 3D molecular models.
O-glycoside and N-glycoside links between monosaccharide units on polysaccharide chains.
IUPAC recommendation use for monosaccharide unit designation on polymer chain joined by recommended
nomenclature link description.
3. Drawing the 20 common L-amino [14] acids found in protein as Fisher’s projection at corresponding
biological conditions of water medium pH=7.36 in life systems. That has a task
haw to convert the given molecules from 3D molecular models into Fisher’s projection.
Optical isomer L or S recognition using drawn Fisher’s projections in resemblance with 3D molecular models.
Recognize the 20 amino acids by names, three-letter abbreviation and one letter designation.
4. The constituents of glyco-proteins and proteo glycans [9] has a task to recognize on base of given 3D
molecular models the sequence of given hetero polysaccharides with existing links between units, in order to use
IUPAC mono-saccharide unit abbreviations (for example D-Glucose - Glc) and link designation.
Students can get the knowledge and skills about:
elemental (C, O, , N, P, S, Na+, Ca2+) composition and its recognition in the displayed shapes of molecules –
wire-frame, stick, stick&ball, spacefill as well as superimposing the color scheme CPK into symbolic
presentation of chemical elements on the depicted structures of molecules,
haw to recognize the similarity relationships between drawn Haworth’s projections of pyranose and furanose
hemiacetal cyclic structures of mono-, di- and oligo-saccharides with its presented 3D molecular models.
Optical isomer L or S and D or R recognition using drawn Haworth’s projections in resemblance with 3D
molecular models.
O-glycoside and N-glycoside links between monosaccharide units on polysaccharide chains. IUPAC
recommendation use for monosaccharide unit designation on polymer chain joined by recommended
nomenclature of link description.
5. Using the
KineMage [5] protein science tools and heme structure using the
ISISDraw [2]
(Integrated Scientific Information System for chemical structural molecular studies, investigation and
presentation) application myoglobin [13] and the human hemoglobin investigation has a task to investigate
features and dynamics for O2 adsorption and desorption from heme Fe2+ complex central ion.
The target is to detect coordination number for iron ion Fe2+, into water less heme pocket account related 29
amino acids involved in prevent working of water medium friendly Ox-Red system having high power of
oxidation with well known standard potential Eo = 1.21865 V.
Ox-Red system analyze shows:
O2 + 4 3O+ + 4 epresent absent
present
6 2 O,
absent
absent components: they are four 4 hydrogen ions 3O+ and six 6 water 2O molecules and present
components: they are adsorbed oxygen O2 and electron e- source iron ion Fe2+ as complex maker among delocalized electrons on heme double bond conjugated system.
Students can get the knowledge and skills about:
polypeptide chain sequence order of amino acids beginning from N-terminal first amino acid Val1 which
terminates on C-terminal Gly153 organized as primary 1º polypeptide chain structure.
Secondary 2º structure helices account iron Fe2+ position for O2 oxygen adsorption and its alternative
replacing by Histidine His64 nitrogen after O2 desorption. Conformational changes in myoglobine and heme
structure at adsorption – desorption demonstrated by movie oxydeoxy.avi. Composition of human hemoglobin
by account and name these components Relax R and tense T state of hemoglobin O2 oxygen adsorption and
O2 alternative desorption.
Di-phospho-glycerate induced O2 desorption via hemoglobin cavity causing conformational change.
Hydrophobic – waterless medium investigation for heme pocket of hemoglobin and evolutionary challenge of
hydrophobic spots on hemoglobin surface in sickle cell anemia having fatal hemoglobin deficiency in north
countries leaving peoples and exposing resistance for peoples against malaria in Africa as well equatorial
regions of world too. [13]
6. The mastering DNA fragment [7] in observation has a task obtain the working skills with ISIS Draw
applications
, RasWin (RasMol)
, which has the goal its employ for chemical studies and
Phe
investigation of given DNA and tRNA [10] molecules. Students can get the knowledge and skills about:
elemental (C, O, , N, P+) composition and its recognition in the displayed shapes of molecules – wire-frame,
stick, stick&ball, spacefill as well as superimposing the color scheme CPK into symbolic presentation of
chemical elements on the depicted structures of molecules,
the essential Watson – Crick base pairing A=T and GC between
adenine = timine and guanine  cytosine applied respectively two and three hydrogen bonds per pair.
Hydrogen and hydrophobic bonds supporting primary 1º, secondary 2º, tertiary 3º and quaternary 4º structure
essential stability for single copy of molecule DNA for cell genetic information.
Replication of DNA and drawing the 2D complimentary two strand DNA picture on the student report using A,
U, G and C symbols. Anti-parallelism of DNA strands 5’ and 3’ terminals of strands.
Transcription depicting the 2D complimentary transcript sequences of given DNA as RNA I for first DNA
strand and as RNA II for second DNA strand applying nucleotide symbols A, U, G and C. The Yeast tRNAPhe
features – primary 1º, secondary 2º and tertiary 3º structure and components.
7. The constituent structural features of immunoglobulin IgG1 [11] has a task to recognize on base of given
3D molecular model the two Light chains and two Heavy chains are present in F(ab')2 structure.
Students can get the knowledge and skills about:
elemental (C, O, , N, P, S, Na+, Ca2+) composition and its recognition in the displayed shapes of molecules –
wire-frame, stick, stick&ball, spacefill as well as superimposing the color scheme CPK into symbolic
presentation of chemical elements on the depicted 1°, 2°, 3° and 4° structures of molecule IgG1,
what is the complementarity between epitopes and paratopes with its presented 3D molecular models and Nglycoside links between mono-saccharide units GalNAc on protein Fc units.
Summary
Earlier lecture and laboratory works for students had absence of molecular modeling based on real atomic
coordinates. It created understanding for matter of molecular geometry and composition from elements much
obscure and poorly possible. With new information technologies students can visually touch to the real
molecules and completely limitless investigate those. The application skills for new information technology
support students to have high and correct understanding about building of molecules, structure and bonding the
chemical element atoms into every known molecule at its gas, liquid and solid state as well as for integrated
interphase systems on different phase interfaces.
Kopsavilkums
Agrāk lekcijās un laboratorijas darbos studentiem nebija molekulārās modelēšanas, kas bāzēta uz reālu
atomu koordinātēm. Tas radīja daudz neskaidrāku un niecīgi iespējamu izpratni par vielas molekulārās
ģeometrijas un molekulas sastāvā ietilpstošiem ķīmiskiem elementiem. Ar jaunajām informācijas
tehnoloģijām students var vizuāli sataustīt molekulas un pilnvērtīgi izpētīt tās. Prasme izmantot
programmas jaunajās informācijas tehnoloģijās būtiski paaugstina un precizē studentu izpratnes iespējas par
molekulas uzbūvi, struktūru un ķīmiskajām saitēm visās izpētītās molekulās to gāzveida, šķidrā un cietā
stāvoklī tāpat arī integrētās starpfāzu sistēmās uz dažādu starpfāzu robežvirsmas.
Literature and useful links on Internet
1. Aris Kaksis, «The Saccharide Viewer », RSU “Medical Biochemistry Data Base” © , 2002, >100pp, 21,5 MB
http://aris.gusc.lv/ChemFiles/Saccharides/SSViewer/SSVFrameset.htm.
2. http://www.mdli.com/chemscape/chime/download.html Get the Chime plug-in and
MDL Inc. software download page.
ISIS Draw from the
3. http://www.umass.edu/microbio/rasmol/
The RasMol Home Page maintained by professor Eric Martz,
provides RasMol in versions for several operating systems, with installation instructions, and extensive
supplementary resources.
4. http://home.netscape.com/ These applications all require a frames-enabled browser, such as Netscape
Navigator 4.08 or higher See Netscape's home page for current information. (Microsoft Internet Explorer 5 and
higher has well known limitations on distinct java script engine application may give a crash for your computer).
5. http://www.faseb.org/protein/kinemages/KinemageIndex.html
Protein Society Educational Initiative
have produced in period 1991 – 1995 Protein Science Journal v1 – v5 publications found by address
http://www.faseb.org/protein/kinemages/kinpage.html .
6. Aris Kaksis, « The Practical Studies and Investigations of Molecular Structure and Dynamics in Schools,
Universities and Scientific Communications-Presentations »,
“DU SAULE” Issue of Daugavpils University, International conference, The Chemistry Teaching Methods:
yesterday, to day and tomorrow, EDITED by PhD Michael.Gorskis © , 2003, 4 pp.
7. Eric Martz, Aris Kaksis, «The DNA fragment», RSU“MedicalBiochemistryDataBase”©, 2002,>100pp,≈1MB
http://aris.gusc.lv/ChemFiles/DnaMarzHTM/INDEX.HTM .
8. Aris Kaksis, «The VSEPR Table » , RSU “Medical Biochemistry Data Base” © , 2002, >100pp, ≈2.5 MB.
http://aris.gusc.lv/ChemFiles/ComplexCompounds/PensilvaniaLebanonUniv/PensilvaniaLebanonUniv/VSEPR_
table_C0.html
9. Aris Kaksis, «The Protein Glycans Components»,
http://aris.gusc.lv/ChemFiles/Saccharides/PolySaccharides/HyalurChondroitHeparKeratMucHTM/0GlycoProtei
nComponents.html
RSU “Medical Biochemistry Data Base” © , 2002, >100pp, ≈2.5 MB.
10. Aris Kaksis, «The tRNA_Tour»,
http://aris.gusc.lv/ChemFiles/CarnegieMellonUChem/Programs/Courses/BiochemMols/tRNA_Tour/tRNA_Tou
r.html
RSU “Medical Biochemistry Data Base” © , 2002, >100pp, ≈2.5 MB.
11. Eric Martz, Aris Kaksis, «The Immunoglobulin IgG1» ,
http://aris.gusc.lv/ChemFiles/ChimAntibodyMarz/INDEX.htm
RSU “Medical Biochemistry Data Base” © , 2005, >100pp, ≈1 MB.
12. Eric Martz, Aris Kaksis «The Human Hemoglobin - Hromo-proteins» ,
http://aris.gusc.lv/ChemFiles/hemoglobEricMarzUMas/INDEX.htm
RSU “Medical Biochemistry Data Base” © , 2005, >100pp, ≈1 MB.
13. M.A. Lopez and P.A. Kollman, A. Kaksis, «The Hromo-proteins Myoglobin and Hemoglobin …» ,
http://aris.gusc.lv/ChemFiles/ChromoHem/MyoGlobOxDeoxCoBiliverdin/1MBODeOxyLopez.kin
http://aris.gusc.lv/ChemFiles/ChromoHem/HbOxDeoxCO/2HCOProTour8.kin open with Mage
program after download from RSU “Medical Biochemistry Data Base” © , 2005, >100pp, ≈38 MB.
14. Aris Kaksis, «The Amino Acid Viewer», RSU“Medical Biochemistry Data Base”©, 2002,>100pp, ≈2.5MB
http://aris.gusc.lv/ChemFiles/MCDB108A/tw-amn/aasframes.htm .