Regarding SASA

Hello,

I would like to know, is there any way to estimate the site-specific of solvent-accessible area of each atom in a small molecule??

Thanks and regards,

-Nilesh

Molecular Surface Area Plugin can calculate the surface area increments, see http://www.chemaxon.com/marvin/help/calculations/geometrygroup.html#MSA

Zsolt

It was useful..

Zsolt wrote:

Molecular Surface Area Plugin can calculate the surface area increments, see http://www.chemaxon.com/marvin/help/calculations/geometrygroup.html#MSA

Sir, I want to find the molecular surface area of refrigerant R-134a.... I dont know radius of molecule... Please help me for calculating this. Should I be able to find  BET surface area with the value obtained from molecular surface area...

Looking forward your response..... Thank U

Hi,

 

 

I taken the physical properties of the "R-134a"  from this site : http://www.engineeringtoolbox.com/refrigerants-d_902.html

The chemical name of the  "R-134a" is :  Tetrafluoroethane, 

The molecular surface area of tetrafluoroethane calculated with Marvin given on the attached fig. 1.

The calculated Van  der Waals surface area is 107.9 [Ångström]² 

 

The BET equation can be used for calculating surface area of  solid materials.   The value the BET's surface area is macroscopic type ,therefore,  it depends on the morphology of the solid material.For example the "active carbon" and the "mineral carbon"  will have different BET's surface area. 

I think there is no relation beetwen our  Marvin's type surface area and the BET's type surface area.

 

Jozsi

Jozsi wrote:

Hi,     I taken the physical properties of the "R-134a"  from this site : http://www.engineeringtoolbox.com/refrigerants-d_902.html The chemical name of the  "R-134a" is :  Tetrafluoroethane,  The molecular surface area of tetrafluoroethane calculated with Marvin given on the attached fig. 1. The calculated Van  der Waals surface area is 107.9 [Ångström]2    The BET equation can be used for calculating surface area of  solid materials.   The value the BET's surface area is macroscopic type ,therefore,  it depends on the morphology of the solid material.For example the "active carbon" and the "mineral carbon"  will have different BET's surface area.  I think there is no relation beetwen our  Marvin's type surface area and the BET's type surface area.   Jozsi

I know that BET surface area is to find SA of porous substances.. But in that eqn the cross sectional  area of the adsorbate(R-134a) molecule is required. Is their any relation between molecular and cross sectional areas.....Do you have any idea abt this ... Please help..... Waiting for ur reply...

Hi,

 

The crosssectional area  of a molecule can be approximated with the "projection area". 

The calculated minimal/maximal projection area  values are given on the attached figure.

The crossectional area of tetrafluorethane in this range :  (18.27 - 25.34) [Ångström]²

 

Jozsi

Jozsi wrote:

Hi,   The crosssectional area  of a molecule can be approximated with the "projection area".  The calculated minimal/maximal projection area  values are given on the attached figure. The crossectional area of tetrafluorethane in this range :  (18.27 - 25.34) [Ångström]2   Jozsi

Thank U very much Sir....

anastzns wrote:

Jozsi wrote: Hi,   The crosssectional area  of a molecule can be approximated with the "projection area".  The calculated minimal/maximal projection area  values are given on the attached figure. The crossectional area of tetrafluorethane in this range :  (18.27 - 25.34) [Ångström]2   Jozsi Thank U very much Sir....

But I have a question: Is there any reports which supports projection area could be used in place of molecule cross sectional area or is it just an assumption...? Thank U 

Hi,

It is just an assumption.

I'm going to verify projection area  with crosssection areas taken from literature. I go back to you asap.

Jozsi

Hi,

 

I created a linear regression equation for calculating of the BET's cross sectional area from Marvin's projection area. 

Certain experimental data of cross sectional area are given in this reference: http://www.sciencedirect.com/science/article/pii/0095852249900434.

Regression equation attached on Fig.1.

The cross sectional area of tetrafluoroethane  is 34.37  [Ångström]² according to this regresion equation.

 

Jozsi

Jozsi wrote:

Hi,   I created a linear regression equation for calculating of the BET's cross sectional area from Marvin's projection area.  Certain experimental data of cross sectional area are given in this reference: http://www.sciencedirect.com/science/article/pii/0095852249900434. Regression equation attached on Fig.1. The cross sectional area of tetrafluoroethane  is 34.37  [Ångström]2 according to this regresion equation.   Jozsi

Thank U JOZSI sir...

Jozsi wrote:

Hi,   I created a linear regression equation for calculating of the BET's cross sectional area from Marvin's projection area.  Certain experimental data of cross sectional area are given in this reference: http://www.sciencedirect.com/science/article/pii/0095852249900434. Regression equation attached on Fig.1. The cross sectional area of tetrafluoroethane  is 34.37  [Ångström]2 according to this regresion equation.   Jozsi

Sir,

How you made that regression I mean the different values of prohectional area and BET CS area..... Will U let me know how the projection area is obtained from the software..? I have downloaded but dont know how to use...

Looking forward to hear from U... Thank u in advance.....

The "Maximal projection area" values of the molecules were calculated by the Geometry plugin of MarvinSketch.

• After you have downloaded and installed MarvinBeans (https://www.chemaxon.com/download/marvin/for-end-users/), run MarvinSketch application.


• Draw the molecule of which you would like to calculate the "Maximal projection area" value.


• Go to Menu: Calculations > Geometry > Geometry.


• Check option "Maximal projection area (A²)" and click "OK"


• The result will appear in a different window.

Best Regards,

Viktoria

vpalfi wrote:

The "Maximal projection area" values of the molecules were calculated by the Geometry plugin of MarvinSketch. After you have downloaded and installed MarvinBeans (https://www.chemaxon.com/download/marvin/for-end-users/), run MarvinSketch application. Draw the molecule of which you would like to calculate the "Maximal projection area" value. Go to Menu: Calculations > Geometry > Geometry. Check option "Maximal projection area (A2)" and click "OK" The result will appear in a different window. Best Regards, Viktoria

Hi,

Thank U for your willingness to help me. Since I am a beginner I dont even know how to draw tetrafluoroethane. I tried doing it but not succeeded. I dont know how to add fluorine atom to CH3-CH3 so as to get CF3-CH2F or 1,1,1,2- tetrafluoroethane.... Please reply me.. I m looking forward your answer.. thank U...

Anas

If you have succeeded in drawing an ethane, then it's just a small step to draw tetrafluoroethane.

You can find a video about drawing instructions here: https://www.chemaxon.com/library/atom-drawing-and-changing/

BR,

Viktoria

anastzns wrote:

Jozsi wrote: Hi,   I created a linear regression equation for calculating of the BET's cross sectional area from Marvin's projection area.  Certain experimental data of cross sectional area are given in this reference: http://www.sciencedirect.com/science/article/pii/0095852249900434. Regression equation attached on Fig.1. The cross sectional area of tetrafluoroethane  is 34.37  [Ångström]2 according to this regresion equation.   Jozsi Sir, How you made that regression I mean the different values of prohectional area and BET CS area..... Will U let me know how the projection area is obtained from the software..? I have downloaded but dont know how to use... Looking forward to hear from U... Thank u in advance.....

sir,

Please help me to get the different values of BET and projection CS area used in the regression analysis. Please reply with the answer which you used for the regression analysis. I need it so badly.... Thank U in advance....

vpalfi wrote:

If you have succeeded in drawing an ethane, then it's just a small step to draw tetrafluoroethane. You can find a video about drawing instructions here: https://www.chemaxon.com/library/atom-drawing-and-changing/ BR, Viktoria

Hi,

I ethane but dont know how to draw CF3-CH2F. I dont know how to add fluorine atom to CH3-CH3 so as to get CF3-CH2F or 1,1,1,2- tetrafluoroethane....When I am about to add F atom to CH3, it completely replaces the latter. So a I am getting a different structure CH3-F like this. Please help me, I need it so badly

Please reply me.. I m looking forward your answer.. thank U...

Anas

Dear Anas,

You can find the description: "How to draw structures" in MarvinSketch at:
http://www.chemaxon.com/marvin/help/sketch/sketch-basic.html#howto-draw

The short video, sent earlier, also demonstrates structure drawing and the usage of the periodic table tool in MarvinSketch.

https://www.chemaxon.com/library/atom-drawing-and-changing/

BR,

Viktoria