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DR.S.ARAVAMUDHAN
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the_gamess



This WebPage was published to the INTERNET by Dr. Aravamudhan, for the first time at SHILLONG on Wednesday, October 29, 2008.
This page Last updated: Shillong, the Friday, October 31, 2008 at 6:50 PM

The date TODAY:- 

This webpage is linked to the page:   http://ugc-inno-nehu.com/ToxicHE.html


The following are the List of internet files uploaded for building the contents of this WebPage

http://ugc-inno-nehu.com/THE_cmpchm/0_2W_optimz_clustr.JPG
http://ugc-inno-nehu.com/THE_cmpchm/1_optimization_evolves_for2H2O.JPG
http://ugc-inno-nehu.com/THE_cmpchm/2_06W_10W_Sphr_Lguess_Uoptmzd.JPG
http://ugc-inno-nehu.com/THE_cmpchm/3_6W_Ca_Lguess_Uoptmzd.JPG
http://ugc-inno-nehu.com/THE_cmpchm/4_06W_10W_Sphr_Lguess_Uoptmzd.JPG
http://ugc-inno-nehu.com/THE_cmpchm/5_10WCa_Li_Na_Ca_OptimizationSequnce.JPG
http://ugc-inno-nehu.com/THE_cmpchm/6_CLin6Water.JPG
http://ugc-inno-nehu.com/THE_cmpchm/Clin6W_allruns_1_through_to_10.JPG
http://ugc-inno-nehu.com/THE_cmpchm/Hexgnl_Structre_water.JPG
http://ugc-inno-nehu.com/THE_cmpchm/SampleInput_file1.JPG
http://ugc-inno-nehu.com/THE_cmpchm/SampleInput_file2.JPG
http://ugc-inno-nehu.com/THE_cmpchm/SampleInput_file3.JPG
http://ugc-inno-nehu.com/THE_cmpchm/SampleInputs_PCGamess.txt
http://ugc-inno-nehu.com/THE_cmpchm/Water_Linewidth_purity.JPG
http://ugc-inno-nehu.com/THE_cmpchm/Water_NMRLwidth_purity.JPG

The contents of this WebPage arose when the contents of website http://www.frequencyrising.com/water_VitalizerPlus.htm indicated that certain ions in water had structure making properties and a few others had structure breaking properties.

CLICK on this image to display  the original site for this info

The ions which are structure making in its interaction characteristics, could result such hexagonal close packed structures which prevented toxins from approaching and complexing with the water molecules. The commercial product which resulted from this phenomena had been documented as Water VITALIZER Plus retrieved by internet Google search. Because of the regularity of structures which resulted the treatment of water with Vitalizer Plus resulted in water clusters of smaller sizes than the cluster sizes with Toxins. Hence thsi cluster size was evident by the significant difference in the Proton NMR line widths (smaller width) of treated water as compared to that of untreated water (larger NMR width)



CLICK on this image to display the original site for this info

It seemed a good exercise to use a Quantum Chemical Computational Package by name "PC GAMESS", to investigate the ways by which water structure can be affected by associations in presence of elements like, Ca(+2),Na(+1),Li(+1),Cl(-1) etc. For this purpose a study was made on the possibilities of a "Structure Optimization" for not single water molecules but 'N' number of water molecules within interacting reaches due to their intermolecular proximity

It was envisaged that, the quantum computational packages, essentially, treat input molecule structure as a cluster of atoms placed at secific posistion coordinates. What is required is that the atoms must all be within such reaches (interatomic distances), that the various of integrals required during excution can all be calculated, as per the capabilities built in for the programme. Once the Energy of such a set of atoms can be calculated, optimization can proceed as per the preferred algorithm to result in a set of coordinates (in place of the input set) which would correspond to the minimum energy structure. If the quantum chemical programme is well standardized for the chemical nature of molecules, the reulting structure would be a structure with bonding between atoms as per what the conventional chemists look for.

Thus, instead of a single water molecule represented by an "INPUT" of one Oxygen atom and two Hydrogen atoms, a set of N water molecules can be fed in as INPUT with N Oxygen atoms and 2N Hydrogen atoms. As per the chemical intuition, a regular (unoptimized) structure for this set of N water molecules can be chosen with reasonable intermolecular distances. This set of 3N hetero atoms can be subjected to an "structure optimization" by the PC Gamess, to know what can be the out come.

More Iluustrations and Approaches with Quantum Mechanical Calculations using available softwares can be found at :
URL1:  http://www.ugc-inno-nehu.com/events_2012.html
URL2:  http://www.ugc-inno-nehu.com/crsi_13nsc_nmrs2011.html


The picture below depicts the results of such programme implementation with TWO molecules placed at well separated unoptimized distances:

CLICK on this image to display an image with more details

CLICK on the image above to display an image with more details on two water-molecule cluster optimization

As has been pointed out for the two-molecule water cluster, the tendency for water molecules to get arranged in such a way the "O-H" protons tend to get aligned collinear with the nearest Oxygen atom of the neighbor molecule. This tendency can be discerned in almost all cases of the cluster optimizations with water molecules even with increasing number of molecules in the cluster

After the result on water molecule disposition after optimization, a similar exercise could be adapted for 6Water molecules and 10water molecules with initial guess dispositions for the water molecules in these cases. The results are dispalyed below as images of structures constructed on the basis of the optimized out puts for every corresponding input guess structures.

Logistics

THE LOGISTICS FOR THE CHOICE OF THE INPUT (Guess) STRUCTURES FOR
THE 6-Molecules and 10-Molecules WATER CLUSTERS

The original announcement as above for the Vitalizer action was depicted by the 6 Water molecular Hexagonal Clusters and hence all the 6 Molecules are to be in the same plane with the Hexagonal disposition. The simplest choice as per the structure editor is to draw the hexagonally placed 6 molecules in the XY Plane with Oxygen towards the Center and the Hydrogens placed outwards from the ring. Thus all the 18 atoms had the Z-cordinate zero. When the Optimization proceeded all iterations yielded intermediate structures where the z-cordinate value for all 18 atoms were zero. The even if the value of the z-coordinate was not exctly zero, but all the nonzero z-values for the 18 atoms are kept the same (confined to a plane), then the z-value did not change during the iterations or at the optimized structure. But when the 6 water molecules were placed in a three dimensional geometry, an Octahedral disposition (CLICK HERE    and view the structure in the Flash embedded video below) then the optimized strycture did not become a set of 6 molecuules in any single plane. Then the question arose if the molecules are distributed in two perpendicular planes, the XY-plane and the YZ-plane then would the molecules confine themselves strictly along the original corresponding plane through out the iteration and finally in the optimized structure? To find an answer to this question,a 10 Molecule cluster with the original 6 Molecules at the Hexagonal palcement in XY Plane, and 4 Molecules in the YZ plane were chosen and as depicted in the image picture below the consequence was obviuosly no specific palne was preferrred. It is the next step to find if 10 molecules are placed symmetrically in the XY plane would the palnarity be retained as for the 6 molecule case? Such studies are on the considertaions to pusrsue. The planarity of 6 Molecules is evidenced in the Image displayable by clicking on the image below.

The item above on Logistics added on November 2, 2008


CLICK on image to display 6 water molecule cluster with the table of coordiantes for input and optimized structures: Note all Z-values are zero


Then for the effect of inserting cations and anions in the guess structure was considered and the previously used guess structures for 6Water molecules and 10 Water molecules were used now with the corresponding ions placed at the center of the guess structures.The results from PCGamess output file are dispalyed below as images for illustrations

Image-1   6 Water molecules with Ca(+2) cation at the centre
Case of 10 water molecules: in Image-3 below

Image-2   6 Water molecules with Cl(-1) cation at the centre.    
CLICK on this image below to display a picture for intersting details of this aspect.


CLICK on this image for the details of how water molecules reorient as the iterations proceed


Image-3   10 Water molecules cluster exclusively and then with Ca(+2) cation at the centre

Image-4   10 Water molecules cluster exclusively and then with Ca(+2),Li(+1) and Na(+1) cation at the centre



Embedded Flash Video   Go TO 'LOGISTICS' above



This video can be dispalyed by clicking at this URL:   http://in.youtube.com/watch?v=zMlykFKQc1E

At the home page of YOUTUBE   in the "search" box type-in "aram1121944" and select for "Videos" and click on "Search"; this would result in the display of the list of all videos uploaded by Dr.S.Aravamudhan and would be available for view on click

This video file above has the same contents as the video file on the Left column. For the video on the left column the original movie file made with windows movie maker ( ".wmv")was uploaded at  http://www.youtube.com . And, on display at "youtube" the embedding html scripts were copied and pasted ion this webpage.

For the video flash embedded file above the original ".wmv" file was converted to flash ".flv" file using the software "Falsh Video MX Pro" with the setting to embed the file as shock wave flash file resulting in a ".swf" file which generated a ".html" file copying to the webpage. This ".swf" file was uploaded to the website (domain: "ugc-inno-nehu.com") and also the ".html" file into the same directory and thus the embedded video flash is displayable above.
Video feature added on October 31,2008
CLICK HERE for a Video display for the consideration of results obtained with PCGAMESS on Biphenyl and Benzene cluster (in adifferent context). This is a Video .wmv file of about 57MB size. Download and save to your computer with a High Speed Interent Connection. The saved file can be palyed with Windows Media Player.
Link provided on 10-11-2009 at NEHU campus,Shillong
Image-5  A typical PCGamess input file reproduced below

Links to two more sample files:-
  Link-1     Link-2




CLICK HERE to down load the corresponding "txt" files of the above sampleinputs to PCGamess