| organic nomenclature question |
[Jul. 17th, 2009|04:04 pm] |
This is chapter 6, q.11, Vollhardt's Organic Chemistry 5th. The question asks what the structure of the product is in a double Sn2 reaction of meso-2,4-dibromopentane with cyanide ion. The answer to this is that it's a meso product with the CN atoms on the opposite side of the alkane from the bromine atoms.
But - what is this meso-2,4- compound called? meso-2,4-dicyanopentane?
Thank you! |
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| Comparative bond strength of weak bonds, biochem |
[Jul. 10th, 2009|06:13 pm] |
The question is, "Which is more likely to involve significant loss of free energy: the hybridization of two 100 base-pair stretches of single-stranded DNA to form a double helix, en enzyme binding to its substrate, or an antibody binding to an antigen? Explain."
I think that it would go, in decreasing order of free energy loss:
100 bp DNA strands > antigen/antibody > enzyme substrate
My reasoning is that once the DNA strand is made, it is unlikely to come fully apart again without the input of significant energy. So that bond is the longest-lasting of the three. The antibody bonds to the antigen less long, and the enzyme for an even shorter period of time.
The transitory nature of the bond - how transitory it is - corresponds to how little energy needs to be put in to break it, or, how little is lost when it is made.
Yes/No?
My book puts antibodies into the questions about weak bonds, but has not really discussed them. I can't seem to find web articles that address antibodies' chemical nature - which is why I'm here.
Confirmation/correction/additional insight would be much appreciated. Thanks! |
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| Orbitals |
[Jul. 1st, 2009|10:00 am] |
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What is an empty (atomic or molecular) orbital? Is it an electrical field created by the nucleus and electrons in which a pair of electrons could reside? What dictates the shape of orbitals? |
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| (no subject) |
[Jun. 14th, 2009|09:04 pm] |
| [ | music |
| | Dave Matthews Band - Two Step (1999) | ] |
Hi, I need your help. : )I am a newbie to chemistry. I study psychology and am particulary interested in biopsychology.I think I need to get a good grasp of at least organic chemistry, and I need to find the best textbook in the universe. It has to be in English and preferably not extremely expensive. Can you guys help me?I am pretty familiar with biology, but would specifically like to learn about organic compounds, build-up of them and reactions between them. I want to get down to basic but still understand function. Plus points if the text book focuses on things happening in the body. Other than that, I don't mind learning things outside my "field"!Hoping some of you have ideas for me! |
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| E1 or E2 |
[Jun. 13th, 2009|11:49 am] |
I'm on Bruice Organic Chemistry 5th p422, utterly bedeviled by the nature of the reaction of 1-bromobutane in a high concentration of tert-butoxide ion with tert-butoxide.
Or:
CH3(CH2)3Br + tert-BuO- / tert-BuOH
The product is butene. Is the reaction E1 or E2? How does the mechanism work? If tert-butoxide ion were a strong base, wouldn't it pull a proton off the far carbon on the chain, the one with 3 H's? So, is the reaction E1, with the Bromine coming off first and then the tert-butoxide ion pulling a proton off C2?
Any insight much appreciated! |
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| Aromaticity |
[Jun. 13th, 2009|12:21 am] |
Why is the following compound considered aromatic?
Is it planar? I know that cyclooctatetraene is not. Also, although the three double bonds are conjugated, I'm not sure whether a complete ring current like what we see in benzene is possible since there are two C–C single bonds in a row. Are these taken care of by resonance structures that move the positive charges around the ring? What is this species called, cyclooctatrienyl dication? |
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| Hydrogen peroxide concentration calculations |
[Jun. 1st, 2009|08:08 pm] |
I was making the Christina White bis-sulfoxide ligand based on her latest paper. I think there is a serious error in the procedure for the hydrogen peroxide oxidation of the bis-sulfide (actually, several errors), and I wanted to check to see if I did the calculations right (and am not in error myself).
The procedure is basically dissolving 2 g of bis(phenylthio)ethane (MW = 246.39, 8.12 mmol) in 12.2 mL glacial acetic acid, and adding a solution of 2.11 mL 50 wt% hydrogen peroxide (MW = 34.01, 31.08 mmol, 2 equiv.) in 6.7 mL glacial acetic acid dropwise to the reaction solution.
First, the molar amount of hydrogen peroxide is, according to my calculations, wrong. 2.11 mL of 50 wt% hydrogen peroxide (density of 1.19 g/mL at 20ºC) corresponds to 2.51 g. Half of that is 1.26 g, and hence the amount of hydrogen peroxide is 36.91 mmol. The density on my bottle says 1.2 g/mL at 25ºC, and that corresponds to 37.22 mmol - not that much different, just saying.
Either way, this corresponds to 4.5-4.6 equivalents relative to the thioether, way more than 2 equivalents. The "31.08 mmol" is still 3.8 equivalents. 2 equivalents would correspond to 0.92 mL of 50 wt% hydrogen peroxide.
Doing a similar calculation with 30 wt% hydrogen peroxide (density = 1.11 g/mL) yields 20.66 mmol, but is still not near the reported amount. 2 equivalents would require 1.66 mL.
Are my calculations right, or am I just crazy?
Thanks in advance! |
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| Biochemistry: comparison to o-chem, recommended prep |
[May. 31st, 2009|02:45 pm] |
One week from tomorrow (Monday) I take the ACS test for organic chemistry and bid Markovnikov, Zaitsev, Hückel and the like adieu. I'm taking biochemistry in the fall and I'm wondering what people see as the major differences in how these two courses are taught. Of course there are bound to be differences among schools and professors but I take it that there are some common trends in the way that these courses are taught. To be clear, I think I have a good grasp of the difference between the fields of organic and biochemistry, but I'm interested in pedagogical approaches in particular.
Also, what are the essential concepts from general and organic chemistry that I should review over the summer? I asked a similar question before beginning o-chem and got some really helpful responses. My understanding is that biochem will bring back some of the more quantitative aspects of general chemistry, like equilibrium constants. I'm rusty on a lot of this stuff but am not sure where to start or what to focus on. I still have my books and most of my notes from gen chem and organic, so I should be able to at least do some cursory review before September.
I believe the book we're using is Voet2, which I've heard mixed things about. Any thoughts on this? It appears to be one of the gold standards, and some of the complaints I've encountered are that it's "too chemistry-focused" which seems like sort of an absurd critique. As a biology major, I don't want some watered down treatment of the subject! |
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| Physical chemistry question: |
[May. 28th, 2009|12:08 pm] |
Hello! I'm studying out of Shaum's Outline: Physical Chemistry (2nd Ed), and I'm having trouble with problem (1.7), provided below:
"In 1702, Amonton discovered for a fixed amount of gas under constant volume that the pressure at 0 degrees Celsius increased by the fraction 1/273 for each Celsius degree that the gas was heated. Write the equation for this observation. What does this equation predict at -273 degrees C?"( my work and questions are under the cut )
Thanks!
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| pH of aspirin? |
[May. 27th, 2009|09:28 am] |
What's the pH of aspirin (Acetylsalicylic acid) as a raw ingredient? Is there even *one* answer to that or does it depend on what it's dissolved in? (Is there an answer if it's not dissolved in anything?) I sort of have a science background but I'm embarrassingly rusty.
(This isn't for a class, it's work-related. And while I should probably be able to figure this out on my own, I'm kind of stuck and not able to take the time to re-educate myself right now, sadly, and google isn't giving me clear answers.)
Thanks! |
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| pπ-dπ backbonding |
[May. 25th, 2009|10:34 pm] |
I'm hoping that someone explain pπ-dπ backbonding to me. I know it was mentioned briefly in my first quarter of organic chemistry (lo these many months) but my professor said not to worry about it and we weren't tested on it. It's still not critical to the material I'm learning at the moment, but I want it to mean something. I would like to understand it in general terms, but if it helps to explain it, we are learning about the use of dithiane anions as equivalents to acyl anions in synthesis. My book says:
"The relative ease with which the hydrogen atom of the dithiane can be removed is probably explained best by considering the overlap of orbitals with the dithiane ion. The negative charge is stabilized on carbon by overlap of the p-orbital of carbon with a d-orbital of sulfur. The anion is thus stabilized by this form of pπ-dπ bonding."
And they provide this cute little picture which doesn't help much (yes, my textbook has quaint hand-drawn structures):
I'm curious, is this the sort of thing one learns more about in physical chemistry? |
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| Nomenclature - dicarboxylic acid |
[May. 25th, 2009|12:56 am] |
Another one of these vexing nomenclature questions…
How do you name the conjugate base of a dicarboxylic acid? My understanding is that the species with has lost a proton on both sides is named as the carboxylate salt, but what if just one side is deprotonated? For example, if HOOC-CH2-COOH is malonic acid and -OOC-CH2-COO- or CH2(COO)22- is malonate, then what is HOOC-CH2-COO-? Bimalonate (as in bisulfate, bicarbonate)? Simply hydrogen malonate? |
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| What's the differnce? |
[May. 24th, 2009|09:23 pm] |
What is the difference between 'calcium carbonate natural' and 'calcite'?
A 'mixture' called for a mix of calcium carbonate natural and calcite, but I tried to simplify the formulation by creating mixtures that used entirely calcium carbonate natural or calcite, testing the assumption that they were the same.
The properties of the different mixtures were rather significant. Most noticibly, the high-shear viscosity varies from a low of 1.8 for the entirely calcite mixture to a 2.1 for the entirely calcium carbonate natural with the 'mixture' falling inbetween.
From what I can find,calcite is a naturally forming mineral that contains greater than 90% calcium carbonate (with inevitable impurities). It is the most stable stable polymorph of calcium carbonate with aragonite and vaterite being the other forms of calcium carbonate crystal.
Calcium Carbonate natural seems to be the exact same thing. |
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| Another question, again Sn2 reactions |
[May. 15th, 2009|12:47 pm] |
Basically, I understand that Sn2 reactions proceed more rapidly with reactants that are more easily approached by the nucleophile. So 1-chlorobutane reacts better, in general, than 2-chloro-2-methylpropane.
But where do the cyclic compounds fit in this?
In our experiment, we reacted
Set 1
1-chlorobutane
1-bromobutane
Set 2
bromocyclopentane
bromocyclohexane
Set 3
2-chlorobutane
2-bromobutane
Set 4
2-chloro-2-methylbutane
2-bromo-2-methylbutane
with NaI in acetone.
Set 1 was most reactive, and set 4 was least reactive.
I'm having two problems, though. One is figuring out whether set 2 or 3 was the more reactive. Results were approximately the same, with one of each set giving a solid precipitate after heating. So I'm looking at the structures, and I'm not sure what the effect would be of ring vs. chain.
Does the ring make the molecule more reactive, as alkyl groups are pulled away from the reaction site? Or is that...me making up stories.
Question the Second:
In set 2, bromocyclohexane was more reactive before heating, and bromocyclopentane was more reactive after heating, giving much more precipitate overall. I don't know why this would be, without *really* making up a story. In an Sn1 reaction, I would say that the cyclohexane would hold a positive charge better than cyclopentane, but here...I'm not sure.
Any insight would be much appreciated. |
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| Sn2 reaction question |
[May. 15th, 2009|10:36 am] |
We've done a lab in which 1-chlorobutane and 1-bromobutane were reacted with NaI in the aprotic solvent acetone.
Both reactions produced a small amount of precipitate. My question is, why was any precipitate produced at all? HCl and HBr both have a lower pKa than HI, making them both better bases and more stably attached to the butane than iodine.
Is it just the kinetics, some of the molecules hitting each other with enough energy and in the right way to result in reaction, despite the greater stability of the reactant?
Thanks! |
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| Activity coefiiusion |
[May. 7th, 2009|08:30 pm] |
I turn to you as I have lost my starting point for the following problem:
A 0.1M solution of the weak acid HA was titrated with 0.1M NaOH. The pH measured when Vbase=1/2 Veq.point was 4.62. Using activity coefficients, calculate pKa. fA=0.854, fHA=1.00
I'm confused at to how just act. coeffs can give a pKa. Does the bit about the pH factor in? And in what way does it? Sadly, this is one of those things that derailed me just a bit and then led to a full fledged disaster. I got into the mindset of just using the Debye-Huckel equation but that seems to be making more messes than clean spots. On the plus side, I no longer have excess scrap paper.
Any pointers would REALLY be appreciated |
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| Free structure drawing and online display programs |
[May. 3rd, 2009|10:02 am] |
Dear ![[info]](http://l-stat.livejournal.com/img/community.gif) chemistryhelp folk,
For too long have I suffered through members attempting to draw molecules on MS Paint on here in order to get their questions answered. So I am here to let everyone know about some free and easy-to-use tools that can easily display what you're trying to get help about. Also, the "experts" can use them as tools that will help explain what information they're trying to convey. Both programs are available for Mac and PC. Also, they're free.
The first is MarvinSketch, a very powerful (and free!) chemical structure-drawing program that will let you easily draw organic molecules, reactions, mechanisms, and so on. It will easily allow you to save your structure drawings as picture files, either in 2D or 3D. Downloading the program requires registration through ChemAxon, but MarvinSketch is also available through a java-based web applet that you don't even have to download or register to use. Here's a screenshot of MarvinSketch in use:
( Read more... )
The other, and potentially even more useful, tool is Jing. The Jing project is a free program that lets you take screenshots of your desktop or separate program windows (or selections) and automatically upload them to the Jing Project website. The image of MarvinSketch above was taken and uploaded using Jing. Even more useful is the ability to take videos of your desktop and automatically upload them to the Jing website, or save them as Flash videos for uploading anywhere. Uploading pics requires a free registration to the Jing Project website, but you may also save them to your hard drive for uploading elsewhere.
Everyone on this forum should be using chemistry tools to display their chemistry problems. You don't have to pay a dime to use the two I've mentioned, so I hope everyone will in the future. |
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| NMR doublet of doublets question |
[May. 2nd, 2009|06:11 pm] |
Legend:
blue = Br
yellow = NO2
The above is a benzene ring with a nitrogen dioxide substituent and a bromine substituent.
My textbooks says that proton NMR of this molecule would show 4 signals, 2 doublets and 2 doublets of doublets.
In terms of their numbers, which is which?
I'm slightly confused, because I'd thought that doublets of doublets were caused by non-equivalent hydrogens on the same carbon, but each hydrogen here is the only one on its carbon.
I'm guessing that 1 & 4 are the doublets and 2 & 3 are the doublets of doublets, but why are they d of d and not quartets? |
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| Demetallation in Oxymercuration |
[Apr. 27th, 2009|04:35 pm] |
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Hi everyone.
I was hoping someone could point me in the right direction of the
mechanism for the removal of the mercury moiety after oxymercuration.
I know it's by sodium borohydride, but my textbook says it's by a radical
mechanism but doesn't give it. I can't find it anywhere.
Any help is appreciated :) |
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