The Periodic Table

@1,3-feeds clever username indeed

11:22 AM

I don't have to justify why I downvote something. I have the right to vote any way I like. You want to upvote something that I don't like? Fine. I downvote something you like? Fine.

One downvote is not supposed to be a problem, such that people start asking "why did I get one downvote". WHY? Because more people are supposed to exercise their votes

and eventually the question reaches a positive score if most people like it. And a negative score if most people don't like it. And, by the way, I am not even the one who downvoted it.

=^.^=

Hullo, humans, molecules and seals!

hullo @Wildcat

bye @Wildcat

off for dinner haha

De novo peptide sequencing

In mass spectrometry, de novo peptide sequencing is the method in which a peptide amino acid sequence is determined from tandem mass spectrometry. Knowing the amino acid sequence of peptides from a protein digest is essential to study the biological function of the protein. In the old days, this was accomplished by the Edman degradation procedure. Today, analysis by a tandem mass spectrometer is a more common method to solve the sequencing of peptides. Generally, there are two approaches: database search and de novo sequencing. Database search is a simple version as the mass spectra data of the...

> When the backbone bonds cleave, six different types of sequence ions are formed as shown in Fig. 1. The N-terminal charged fragment ions are classed as a, b or c, while the C-terminal charged ones are classed as x, y or z.

I don't get this. Why only 6? What if the amino acid is large?

@CowperKettle backbone bonds cleave

there are only 3 types of backbone bonds

Calpha-C; Calpha-N; N-C

@orthocresol Thank you! Good afternoon!

11:30 AM

Actually, I don't know why the side chain bonds don't get cleaved either.

That, you'll probably have to ask somebody who knows more about proteomics.

I'll try to find what "backbone bonds" are first

@orthocresol :(

@Wildcat Seals need to eat too you know ;)

@CowperKettle lectures.molgen.mpg.de/ProteinStructure/Intro

@orthocresol Bon appetite! ;)

@orthocresol Thank you!

11:33 AM

TO myself: vote more, you forgetful animal! XD

Why could not I vote more? What prevents me from doing so?

:|

-1

Q: Hybridisation of Orbitals

I was reading about Hybridisation, but I couldn't get the topic. How does it occur and Why? Any help would be appreciated.

quantum-chemistry

I was thinking about closing it as a dupe, but do we have a canonical answer on what the heck hybridization is and is not? :O

user116211

I HATE cross-posting ;(

@MAFIA36790 we all hate it. :|

user116211

@Wildcat We should better have it if it is not; we get tons of hybrid posts day in and day out ;P

@MAFIA36790 but did you know that it is mutual, i.e. that cross-posting HATES you? XD

2

user116211

@Wildcat This noon, I mentioned a poster that his query is better suited at Chem.SE; he simply cross-posted it ;P

user116211

11:37 AM

Don't know what happened to it now; edited that very bad formatted post; seems to be deleted now.

user116211

Man, yesterday I learnt Lagrange's undetermined $\lambda$ Method; it's insanely amazing ;))

user116211

@Rubisco, I'm show-offing ;P

@MAFIA36790 I think you can derive Boltzmann distribution with that.

@MAFIA36790 yea, it is used (among many other things) in the derivation of the Hartree-Fock equations, which are essentially the basis of the general chemistry. :O

user116211

._.

user116211

11:41 AM

@orthocresol temperature is Lagrange's multiplier.

user116211

I am studying Calculus of Variations; read it in Lanczos' The Variational Principles of Mechanics.

@orthocresol I understood it. No matter where it cleaves in the protein, if it cleaves, say, between C alpha and C, and if the fragment contains the N-terminus, then it is an "a-ion"

user116211

The method increases the degrees of freedom from $n-m$ to $n+m$ where $m$ is the number of auxiliary conditions and $n$ is the dimension of the configuration space.

user116211

It preserves the symmetries of the virtual variations without eliminating any of them.

nods

user116211

11:53 AM

@Wildcat Googled that; but I have no idea on it; it's still beyond my scope now.

@MAFIA36790 well, just another example of a constrained optimization problem solved by the method of Lagrange multipliers.

We want to minimize the energy of a Slater determinant keeping spin orbitals orhonormal.

We should have a reason "closed as hybrid"

user116211

@Wildcat somewhat got the point.

Q: Why can't al N atoms of arginine accept a H atom at low pH

0

I was wondering why arganine isn't able to accept hydrogen atoms on all the N atoms in the side chain (because they all have a free electron pare). The structure of arginine: Maybe it has something to do with resonance because of the presence of the double bond, but I'm not sure. p.s. for th...

ph amino-acids

Can anyone tell me what this guy is asking?

12:11 PM

@DHMO no idea :D

@Wildcat facepalm

Q: Concise description of primary organic reaction types mechanisms

12:32 PM

@MAFIA36790 @Wildcat Hehe sorry, but you guys have lost me :D

I don't know all this stuff

Bounty Hunter

4

Long story short, I'm mostly doing calculations in the past 5 years of my scientific carrier and every year I get less and less confident in my knowledge of organic chemistry which besides was never perfect. Yeah, I still remember pretty well some trivial things like nomenclature, classes of comp...

organic-chemistry reference-request

@BountyHunter Wow... That is a tough ask.

:D

Q: Why can't al N atoms of arginine accept a H atom at low pH

Now the question is better

and it might be quite interesting

2

I was wondering why arganine isn't able to accept hydrogen ions (at pH = 0) on all the N atoms in the side chain (because they all have a free electron pare). The structure of arginine: Maybe it has something to do with resonance because of the presence of the double bond, but I'm not sure. ...

ph amino-acids

12:48 PM

Oh well, here comes another argument that I downvote because I am insecure.

Loong

@DHMO it's essentially about the guanidinium cation

@Loong so it's a dup?

Sheesh, I don't even want to respond anymore

user116211

@orthocresol Which troll did it; name me; I'm sending my MAFIAs to get his job done!!

Anyway, wrt guanidinium, double protonation puts two positive charges close to each other. But on top of that, after one is protonated, the other lone pairs on the nitrogen atoms are delocalised into C=N pi* orbital.

12:54 PM

@orthocresol make that an answer instead of answering in chat?

You can go ahead and do it. I'm lazy.

19 hours ago, by pentavalentcarbon

@DHMO Why not try answering? It's fine to start somewhere. I see too many "answers" in the comment sections.

"not answering" to a whole 'nother level

I can't answer every qn on the site

@orthocresol TRY! :D

@Wildcat This mechanism is very interesting! For more information I would like to refer you to our website www.orthocreseal.com

user116211

1:02 PM

Serious fact of the day: A ring cannot be empty.

@MAFIA36790 it's the newest post on meta

@orthocresol This site can’t be reached :|

:D

user116211

@orthocresol checking; preparing the Tommy Guns and Molotov Cocktails...

I actually responded quite nicely.

user116211

1:15 PM

@orthocresol I'm only seeing your comments; did OP delete his?

@MAFIA36790 meta.chemistry.stackexchange.com/a/3345/16683 Nah, nothing was deleted.

The accusation is in the main text.

user116211

@orthocresol oh lord; I thought he made comments ;P

user116211

Misusing.... can't deny, okay. reading...

The implication is: people here downvote because 1) they are insecure 2) kneejerk reaction 3) they are upset IRL and take out their anger on questions. 4) think they are too intelligent to answer trivial question

@orthocresol ?

user116211

1:18 PM

@orthocresol okay, that's it; he is himself insecure.

I think I was probably overly grumpy in the post itself.

Meh. I'll try to rewrite it.

user116211

So, he is just ranting about as he got downvotes and he couldn't go with it, as I suspected.

user116211

While I encourage to mention explicit reasons for downvotes; it shouldn't be mandatory, IMO.

Oops I accidentally flagged NAA, intended VLQ...

user116211

1:33 PM

@orthocresol Could you read the post? Was it in English or other language?

Loong

@orthocresol You know that you can retract flags on questions and answers? (since August)

user116211

If you can read it; the language is English; then it shouldn't be flagged as VLQ.

user116211

If it is plain wrong; then downvote it.

Ah, thanks Loong

Sorry to interrupt, but does anyone know of a userscript or extension that would show if you've voted on a question when looking at the question list?

user116211

1:39 PM

@pentavalentcarbon Unless you refreshed the cache, the post you looked into should appear in somewhat conspicuous color, distinct from the others you haven't visited. But I've no idea how to check the votings.

Hm. I'm going to search then, because not having that makes voting difficult IMO.

Maybe this is what we need. stackapps.com/questions/3802/punch-a-user-button

2:34 PM

hi everyone

Somehow the 2s orbital must be involved, right

Also, in methane, what is the experimental charge on carbon?

Did you just post same pic twice?

@Wildcat yes

@DHMO involved in the bonding MO you mean?

@Wildcat yes

@DHMO might be. All these general chemistry picture are oversimplified models. In reality AOs mix way more awkwardly than it is depicted in such nice simple diagrams.

Q: Why a higher s character increases a carbon atom's electronegativity?

2:40 PM

@Wildcat by the way, can you help me with the comments here?

0

To make us understand certain phenomenon like the higher acidity of alkynes than alkanes and alkenes, our teacher told us to learn this as a general rule: Higher s character leads to a more electronegative carbon atom. Note: By s character I mean the percentage of s in the hybridisation of ...

molecular-orbital-theory orbitals electronegativity

I don't know how to respond

Still, I would not expect a huge income from the 2s AO into the sigma MO.

This guy has put me into a bottomless pit

an unsolvable dilemma

an everlasting self-doubt

user116211

@pentavalentcarbon Why do you want to punch ;P

@MAFIA36790 I don't, but others might. Also, look who wrote the script.

@DHMO Hmmm... Looks like it is 100% related to the other question about the s character popped up today.

2:44 PM

@Wildcat please help me

user116211

@pentavalentcarbon Manish ;P

Q: Bond energy and s-character

0

While studying the basics of chemical bonding, I've often come across the following statements: 1. The bond energy increases with the increase in the s-character in a hybrid orbital, i.e sp3 sp2-sp2, and so on. I can't seem to correlate the two. If a hybrid has a higher bond energy, shouldn't it...

bond orbitals hybridization

@Wildcat Please help me in the comments. I don't know the answer.

So, the more s character C hybrid orbitals have, the lower will be the molecular orbitals.

Lower MOs -> stronger bonds.

I think we are not using MO theory

and this is not about bonds

this is about electronegativity

2:46 PM

@DHMO and what's electronegativity?

@Wildcat the tendency to have electron

user116211

@DHMO No.

@MAFIA36790 the tendency to attract electron

@DHMO read the IUPAC definition.

> Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons.

2:51 PM

Not this part.

"more frequently a relative scale due to Pauling is used where dimensionless relative electronegativity differences are defined on the basis of bond dissociation energies"

@Wildcat but the question is, since H has 100% s character, why doesn't it attract more?

and this is the question I failed to answer

I honestly speaking don't want to waste my time looking for any rationalization of pretty crappy general chemistry views.

but that's a real question

@Wildcat like, doesn't H has a lower potential energy

@DHMO No, it is not.

??

i thought 1s of H has lower energy than 2sp3 of C

@Wildcat at least that's what this says?

2:58 PM

@DHMO did you read the question? "So, how would one explain this using the concept of orbitals or molecular orbital theory?" Even OP mentioned MOT. ;)

@Wildcat .... i automatically excluded MO upon seeing the word "hybridized"

had no idea they can co-exist

@DHMO I don't quite following you. What this diagram is supposed to tell me?

@Wildcat that 1s has lower energy than 2sp3?

or are we talking about relative electron affinity

@DHMO although orbital hybridization originally appeared in VBT, in can be (an often is) introduced into MOT with ease.

@Wildcat alright

3:00 PM

@DHMO electronegativity is not electron affinity

@Wildcat yes, the tendency to attract bonding pair of electrons

@DHMO closer to the truth

actually, why is C more electronegative than H?

@DHMO may be due to a much bigger positive charge of its nucleus? ;)

See

@Wildcat come on

3:04 PM

electronegativity is effected not only by the distance between electrons and a nucleus but also by the charge of the nucleus

Electronegativity

Electronegativity, symbol χ, is a chemical property that describes the tendency of an atom or a functional group to attract electrons (or electron density) towards itself. An atom's electronegativity is affected by both its atomic number and the distance at which its valence electrons reside from the charged nucleus. The higher the associated electronegativity number, the more an element or compound attracts electrons towards it. The term "electronegativity" was introduced by Jöns Jacob Berzelius in 1811, though the concept was known even before that and was studied by many chemists includi...

Second sentence of Wiki article, really. :D

Then why is B less electronegative than H?

Because, electronegative is a complete useless crap.

Forget about it.

...

Don't waste your time.

So, if I would like to combine hybridization and MO...

I would need to hybridize the two theories?

Like, I make 4 sp3 orbitals, and then draw bonding MOs?

3:07 PM

Good evening all.

@Wildcat Does H1s have more energy or C2sp3?

I wonder what "free sulfhydryl group" is

> A sulfhydryl is a functional group consisting of a sulfur bonded to a hydrogen atom.

Electronegativity

Electronegativity, symbol χ, is a chemical property that describes the tendency of an atom or a functional group to attract electrons (or electron density) towards itself. An atom's electronegativity is affected by both its atomic number and the distance at which its valence electrons reside from the charged nucleus. The higher the associated electronegativity number, the more an element or compound attracts electrons towards it. The term "electronegativity" was introduced by Jöns Jacob Berzelius in 1811, though the concept was known even before that and was studied by many chemists includi...

@Wildcat what

3:08 PM

Read it carefully.

@DHMO Yes, but what is a "free" sulfhydryl group? Just a sulfur bonded to two hydrogens?

Stupid chat engine does not show that I linked to a particular section of wiki article.

Read about Pauling electronegativity.

Oh, common...

> In order to determine the quantity of disulfide bonds and free sulfhydryl groups, we used spectrophotometry and the Ellman's reagent, which yields a colored product upon reaction. (Why are they "free"? What's that?)

The difference in electronegativity between atoms A and B is given by:
$$\chi _{\rm {A}}-\chi _{\rm {B}}=({\rm {eV}})^{-1/2}{\sqrt {E_{\rm {d}}({\rm {AB}})-[E_{\rm {d}}({\rm {AA}})+E_{\rm {d}}({\rm {BB}})]/2}}$$
where the dissociation energies, Ed, of the A–B, A–A and B–B bonds are expressed in electronvolts, the factor (eV)−½ being included to ensure a dimensionless result. Hence, the difference in Pauling electronegativity between hydrogen and bromine is 0.73 (dissociation energies: H–Br, 3.79 eV; H–H, 4.52 eV; Br–Br 2.00 eV)

@Wildcat I don't care how you define electronegativity; why does C attract more electron than H?

3:12 PM

@DHMO it is not me, it was Pauling who defined it.

@Wildcat come on

@DHMO first, who told you that C attracts more electron than H?

@Wildcat electronegativity?

@DHMO I mean, how do you know that?

@Wildcat because of electronegativity?

3:13 PM

@DHMO you've just said you don't care what electronegativity is, so don't say anything about it.

@Wildcat I know it because my teacher told me that a larger (smaller) electronegativity means more electrons but I do not understand the reason behind.

@DHMO what you actually want to say here is that "because electronegativity of H is less than that of C"

Would it be a good question to ask on main site about "free" sulfhydryl groups?

@DHMO ask you teacher than, I didn't tell you this shit, it was him/her :D

@CowperKettle the only context I can find is about proteins, where its opposite is "masked sulfhydryl group"... maybe it means sulfhydrl groups that did not take part in dilsulfide bonding (tertiary folding)

@Wildcat please

3:16 PM

@DHMO Meaning, it sticks out and is available for reaction? That may be it.

@DHMO lets start from the scratch them.

@CowperKettle next time give us the context

What do you want to be explained?

@Wildcat sure

@DHMO Thank you!

3:17 PM

@Wildcat why C attracts more electron than H

5 mins ago, by CowperKettle

> In order to determine the quantity of disulfide bonds and free sulfhydryl groups, we used spectrophotometry and the Ellman's reagent, which yields a colored product upon reaction. (Why are they "free"? What's that?)

Context (0:

@DHMO I repeat my question then: how do you know that?

@CowperKettle not even a mention of "protein"

@Wildcat ...

@DHMO can disulfide bonds be not on a protein?

@Wildcat why the formula of electronegativity can tell us which atom attracts more electron

3:18 PM

@DHMO it can not

Disulfide

In chemistry and biology a disulfide refers to a functional group with the general structure R–S–S–R'. The linkage is also called an SS-bond or a disulfide bridge and is usually derived by the coupling of two thiol groups. In formal terms, the connection is a persulfide, in analogy to its congener, peroxide (R–O–O–R'), but this terminology is rarely used, except in reference to hydrodisulfides (R–S–S–H or H–S–S–H compounds). In inorganic chemistry disulfide usually refers to the corresponding anion S2− 2 (−S–S−), for example in disulfur dichloride. == Organic disulfides == === Properties === The...

Thanks, it's already opened in my Chrome

@Wildcat but electronegativity means that?

I meant "bonding pair of electrons" if you insist

@DHMO there is no electronegativity

it is a word invented by Pauling

@Wildcat basically, how that formula works

3:20 PM

Pretty simple.

You put dissociation energies in formula

and get relative elecrtonegatives out of it.

@Wildcat by "how" I mean "why".

English.

@DHMO it somehow follows from VBT, IIRC.

@Wildcat how?

But I have no clue how exactly. XD

Sorry.

@Wildcat thanks

3:22 PM

dx.doi.org/10.1021%2Fja01348a011

try to read the original Pauling article

@Wildcat heh, i'm too noob

Well, I myself don't care about VBT in general and about electronegativity in particular to do so.

But that can be a pretty good question.

Just ask the community to explain the Pauling definition for not an expert in VBT.

ASK THE QUESTION!

@Wildcat It is already in teh main?

That is Q&A site, isn't it? :D

Q: Why a higher s character increases a carbon atom's electronegativity?

0

To make us understand certain phenomenon like the higher acidity of alkynes than alkanes and alkenes, our teacher told us to learn this as a general rule: Higher s character leads to a more electronegative carbon atom. Note: By s character I mean the percentage of s in the hybridisation of ...

molecular-orbital-theory orbitals electronegativity

3:25 PM

Yeah, but it looks that to answer that you need to understand the very definition of electronegativity.

exactly

OK

I skimmed through it.

That is pretty simple definition to some extent.

So, look.

alright

We first define the electronegativity as the tendency of an atom to attract electrons.

Now, If two atoms A and B have exact same tendency to attract electrons (i.e. same electronegativity)

than it should be as difficult to break the A-B bond as it is to break A-A and B-B bonds at average

$E(\ce{A-B}) = 1/2 \left( E(\ce{A-A}) + E(\ce{B-B}) \right)$

Pauling has a very simple quantum chemical argument in favour of this idea.

I mean, it is VBT based, but still relatively clear. XD

Although, he takes it as a postulate anyway. :D

So...?

3:41 PM

So, it A and B have different electronegativity that there will be a difference.

That is it, essentially.

Now, since electornegativity is not an observable, but rather tendency

but why does the sign point that way?

Pauling was free to define it anyway he liked

and he did it in some particular way

@Wildcat but it can be verified by charge density...

@DHMO what can be verified? that electrons stay closer to C in C-H bond?

Sure, they do.

@Wildcat yes

3:43 PM

And what then?

That is the way nature works.

@Wildcat so you can't define it anyway you like

@Wildcat and there's a reason behind why electrons stay closer to C in C-H bond

electronegatuivity don't even need to be defined

The fact that electrons stay closer to C than to H can be explained by studying the electronic structure of a molecule with C-H bond.

@Wildcat how?

> DTT can also be used as an oxidizing agent. Its principal advantage is that effectively no mixed-disulfide species are populated, in contrast to other agents such as glutathione. (What is "no mixed disulfide species are populated"?)

Everything is dictated by quantum mechanics, not by all these electronegativities.

Q: Should Blast furnace reactions to be considered as solid state reaction

3:45 PM

@Wildcat yes, but how?

@CowperKettle context?

paper link?

user116211

0

Are reactions in blast furnace while extraction of iron to be considered as solid state reactions.?

solid-state-physics

user116211

^^Do you think, comrades, the question is explicitly clear in tis content and query? Is it competent at Chemistry?

@DHMO pretty simple, in fact :)

@Wildcat but how?

Dithiothreitol

Dithiothreitol (DTT) is the common name for a small-molecule redox reagent also known as Cleland's reagent. DTT's formula is C4H10O2S2 and the chemical structure of one of its enantiomers in its reduced form is shown on the right; its oxidized form is a disulfide bonded 6-membered ring (shown below). The reagent is commonly used in its racemic form, as both enantiomers are reactive. Its name derives from the four-carbon sugar, threose. DTT has an epimeric ('sister') compound, dithioerythritol (DTE). == Reducing agent == DTT is a reducing agent; once oxidized, it forms a stable six-membered ring...

3:47 PM

@DHMO that what solution of SE tells us: electrons will be closer to C since it is energetically favourable.

@Wildcat you didn't solve the SE of that thing

@DHMO many times

Well, not me, but a computer. :D

> The reduction usually does not stop at the mixed-disulfide species because the second thiol of DTT has a high propensity to close the ring, forming oxidized DTT and leaving behind a reduced disulfide bond.

Now, from this text, deduce what a mixed-disulfide species is

@Wildcat no explanation?

user116211

@Rubisco o/

Yo

3:50 PM

@DHMO that is the only explanation.

Everything else is rationalization.

@Wildcat does electronegativity always align with SE?

@Wildcat that's an evil statement

@DHMO You can't tell why someone voted, so don't make assumptions

@DHMO Pauling's one should definitely agree with what QM predicts since it has a pretty straightforward definition. :)

@Rubisco how on this round planet earth did you seek that message out?

3:51 PM

@pentavalentcarbon well, simple, in some sense :D

@Wildcat can you rationalize?

user116211

@DHMO trascripts

@Wildcat I know, I know...just so sneaky sometimes

@MAFIA36790 like, how does he even see that message? Does he go through every message?

@DHMO I guess I can, but I'm not interested in it.

user116211

3:52 PM

@DHMO chat.stackexchange.com/transcript/3229

@pentavalentcarbon Sorry, I don't remember any.

user116211

@DHMO Can't he?

@DHMO I loaded to my last message, then came down.

@Rubisco so you do go through every message.

@DHMO Ah, it means that no mixed disulfide species (i.e. a species where the protein is connected to the DTT) arise in the solution

3:53 PM

@MAFIA36790 Nah, that's for when I'm bored. And there's drama. And I have ice cream.

@CowperKettle bingo

@Rubisco If I knew JS I would write a hack myself but it isn't worth the time investment

user116211

@Rubisco ohh ;P

@DHMO How hard is it to skim?

@pentavalentcarbon btw, could you please tell me what is so wrong with using M06-2X for TD-DFT? I asked you in comments section. :) chemistry.stackexchange.com/questions/59054/…

3:54 PM

"Populated" disoriented me.

@Rubisco it isn't about the difficulty.

@Wildcat I know, I haven't read the review yet.

@CowperKettle You know, the wonders of English.

OK, at least you noticed my comment. :)

@DHMO But about?

3:55 PM

@Rubisco but about why would anyone do that

user116211

Okay, I'm asking again; could any of you provide insight on this post whether it is competent to be posted here at Chem:

Q: Should Blast furnace reactions to be considered as solid state reaction

@Wildcat Oh, definitely, I ignore nothing. Especially when I make potentially baseless accusations. It's always just a matter of time...

user116211

9 mins ago, by MAFIA36790

0

Are reactions in blast furnace while extraction of iron to be considered as solid state reactions.?

solid-state-physics

user116211

?

@DHMO Because their name would be Rubi.

3:55 PM

@Rubisco ...

user116211

I need to complete the review ._.

user116211

What is solid state reactions? I have no idea.

Solid-state reaction route

The solid-state reaction route is the most widely used method for the preparation of polycrystalline solids from a mixture of solid starting materials. Solids do not react together at room temperature over normal time scales and it is necessary to heat them to much higher temperatures, often to 1000 to 1500 °C in order for the reaction to occur at an appreciable rate. The factors on which the feasibility and rate of a solid state reaction depend include, reaction conditions, structural properties of the reactants, surface area of the solids, their reactivity and the thermodynamic free energy change...

user116211

@DHMO NOO!

@MAFIA36790 closed as unclear

user116211

3:57 PM

This is not what I'm telling; what I'm saying is that it is not related with solid-state-physics.

user116211

@DHMO What do you mean by closed? There is no CV till now.