The Periodic Table

user228700

00:54

Hi, everyone :-)

user228700

Can anybody please help me to figure out why, for the process of freezing, the free energy equation is written as follows: $$\Delta G = (H_{liquid} - H_{solid}) -T(S_{liquid}-S_{solid})$$

user228700

Freezing is the phase transition of liquid to solid. Therefore, shouldn't $\Delta H = (H_{solid} - H_{liquid})$ (same for $\Delta S$) instead of the other way around?

Jan

My gut feeling says yes. My ratio says ‘this is thermodynamics; don’t answer!’ ^^'

getafix

01:32

@Kaumudi.H yeah it should be final state - initial state..are you sure gibbs free energy change is for freezing and not for fusion/melting?

also, how do I unfreeze a chatroom?

or have it unfrozen? @orthocresol would you be the person to talk to? ;)

Jan

@getafix I think only mods can, yeah. If they can at all.

Loong

@getafix which room?

getafix

the room with me and penta

wait let me fetch a link

Room for getafix and pentavalentcarbon

I should get back to my training with him..I take my last two mid sem exams this week..

Loong

@getafix done

getafix

@Loong thanks :)

in general, how goes @everyone

haven't been on here as much lately..

Jan

01:42

I can’t see any more Lorem ipsum placeholder abracadabras. Don’t tell me you’re done, @ortho? =D

Loong

16 hours ago, by orthocresol

Little Bobby Tables are done. ;D

Jan

@Loong Now why wasn’t that starred? *fixed it* =D

Well, I’ll leave you guys to it o/

gannex

02:03

I've got a quick question about electron transfer kinetics in proteins. anybody down to help?

user228700

@getafix Yep. Pretty sure.

getafix

@gannex I have done some reading in the general area..a long time ago, just for fun. I don't know if I'll be any help

gannex

OK

getafix

what exactly is the question though?

I'd still like to ponder it/research it if I can..

gannex

I'm trying to estimate a distance between two redox centers in a ternary complex of proteins based on the rate constant of electron transfer, "kET".

My prof gave me this graph

user228700

02:10

Guys, I've a quick question about osmosis. Edema = Puffing up of cells. Presumably, this would be caused by insufficient intake of salt, right? In this case, the cells in our body are surrounded by a hypotonic solution, which causes the water to flow into the cell, resulting in their swelling, yes?

gannex

@getaflix
I have seen the equation kET=ko exp(-beta(R-Ro))

so I figure in the graph they are using ko=10^13

but idk what ko is

user228700

Ah, nvm.

gannex

I know kET, beta, and Ro and I'm trying to solve for R, but idk what ko to plug in

getafix

@gannex hmm I remember something similar

user228700

Wait, no, what?

user228700

02:13

> "Excessive salt in the diet can cause a symptom known as edema."

getafix

so beta is the distance dependance of the ET reaction..

user228700

Wth, how?

getafix

r-r0 is I am guessing the end to end distance between donor and acceptors?

gannex

@getafix

beta is a parameter based on protein structure through which the electron must "travel"

getafix

and..k0 should be the pre exponential factor..or something to that effect..

gannex

02:14

ok

that's what I don't know

getafix

yeah that what I meant when i said distance dependance haha sorry

gannex

in the picture, they used ko=10^13

but that doesn't make any sense because then we'd have ln(kET/10^13)

which will come out negative at any of the rates depicted on the y axis

so I'm wondering what pre-exponential factor to use

getafix

hmm yeah

gannex

if I just lookj at the graph and follow the "typical packed protein" line (beta=1.4), knowing kET=10^3 for my electron transfer, I get approximately 20 angstroms on the x-axis, which is actually very near the real value

but I want to use the equation

getafix

using the equation i got 16.44 A..

hmm

gannex

02:23

using ko=10^13

that is in the ballpark, which is fine

getafix

yup

gannex

ok what am I doing wrong here

getafix

let me check once again, i am notriously bad at putting things into a calculator

gannex

don't you have to go ln(10^3/10^13)?

and end up with a negative value

getafix

yeah but you have a -beta on the other side..

gannex

02:26

so you get -23=-1.4(R-Ro)

oh ok

yeah that works out

getafix

yup 16.447

just chucked it into mathematica to be sure

haha

gannex

and then Ro is 3 angstroms

(VdW close contact distance)

so R= 19.42

getafix

and that gives you 19 something.

so yeah

gannex

real distance is 24 angstroms

kkk

getafix

even from the line I would read 19.. something

gannex

02:27

and it turns out this ko is "maximum coupling when D and A are in the closest (van der Waals contact), 1013 s-1"

makes sense

which makes sense.

idk wtf I was doing

thx @getafix

getafix

no problem haha

gannex

calculator troubles are real...

lol

getafix

yeah haha

anyhoo, I should probably start getting some work done

gannex

enjoy!

getafix

ciao

paracresol

08:03

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08:48

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Q: Is there a least reactive compound?

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physical-chemistry

The least reactive compound will mean its gibbs free energy change has to be positive wrt nearly all known compounds, or have a very high energy barrier wrt nearly all compounds or both. It is unclear whehther there's a theoretical example.

The element example is easy. Neon is the least reactive of all the elements, as it can only form hydride ions under high voltage conditions

Bounty Hunter

15:49

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1,3-feeds

16:29

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pentavalentcarbon

16:56

!!greet/Mystic

Chemobot

Welcome to The Periodic Table Mystic! Here are our chat guidelines and it's recommended that you read them. If you want to turn Mathjax on, follow the instructions in this answer. Happy chatting!

Hexacoordinate-C

18:04

Hello I have a weird question

For the last experiment of the semester we all (160 students) perform a Sonogashira reaction (by group of 12) to make different conditions

All student found on TLC in the same condition with the same revelator Rf=0.16 and the same color with the relevator even my group

All student even my group found the melting point was between 67.5 and 68.3°C

But we are the only one who have not alkyne group in IR spectrum...

Have you some ideas of what happended ?

Hexacoordinate-C

20:12

:(

Melanie Shebel

21:57

Something strange I noticed between the asker's name and the answerer's name on a question. New users.

0

Q: Precipitation problem

We have 5 L of water that contains Ca^+2=1,80*10-3 mol/L in which we put 8,23 g of Na3PO4. We see the fromation of a precipitate. Find the concentration of Ca2+ after precipitation. I know that the precipitate is : Ca3(PO4)2 with Kps = 2,07*10-33 Besides that, I'm stuck. ANy hints?

homework

Loong

@MelanieShebel We will have a look. However, the asker is not so new.

gannex

@Hexacoordinate-C are those IR spectra all from your group, or are those comparison to another group also? I don't see an alkyne band in any of those

maybe the thing that has Rf=0.16 and MP≈68˚C is not the alkyne product. Has anyone ran a column and isolated the fraction corresponding to that TLC spot?
Since TLC is chromatographic and IR just shows the vibrations of everything in the potential mixture, it's possible that everybody's IR spec represents both the alkyne product and an impurity that's seen on TLC. Are other groups getting another spot on TLC that you don't get?

@Hexacoordinate-C The only explanation I can think of would be that your reaction failed for some reason, producing some side product, and that everyone else has a better yield of the desired product than you, but also has the same side product as an impurity.

Hexacoordinate-C

22:28

@gannex yes all from my group just different condition

In our TLC we all got only one product

And our product as the same Rf than other students in the same conditions. We also have the same melting point

gannex

22:43

yes, but did the other students get multiple products on their TLCs?

I mean if you got the Rf=0.16 product and it was not the alkyne, then they must have gotten multiple products

Hexacoordinate-C

Nope

only one each time

gannex

for the groups that DID see an alkyne peak?

that is pretty strange. idk what's going on.

Hexacoordinate-C

Yes only one

That's why I am very confuse

I don't remember, do you see an alkene at 254 nm for a TLC ?

This the reactants we used

gannex

23:04

I have no idea about TLC lights and stuff tbqh.

alkENE?

Hexacoordinate-C

Yes alkene

gannex

hmmm what if you got some Glaser coupling? 1,2-diynes are quite unstable without capping groups (usually phenyl or TMS). If you got glaser coupling, your homocoupling product with OTHP would probably degrade

Hexacoordinate-C

We can see them in TLC but not alkyne right ?

gannex

why do you ask about the alkene?

ok you think you have an alkene but no alkyne?

Hexacoordinate-C

Because we also may formed an alkene

gannex

23:10

hmm

well if you got your desired product it would probably be stable, but the most common side product of these reactions would be unstable with the OTHP group (I think) so maybe it could degrade to an alkene?

Hexacoordinate-C

No impossible to degrade into an alkene

gannex

yeah you're right that doesn't make sense

Hexacoordinate-C

We made a purification by flash chromato

just before and TCL after

So it explain at least why we got only one product

But it was impossible to made an IR for each test tube we all perform between 30 to 70 test tube

So TLC was better to know if our product was in or not

gannex

if it has the exact same MP and Rf as the other peoples purified alkynes then I don't know

maybe you should try to figure out the structure?

Hexacoordinate-C

Well this not my job in the group but I'm am with "broken arms" sorry for the bad translation. I will see :)

gannex

23:24

Do you have any ideas about what it might be?

Room for getafix and pentavalentcarbon

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