the other day i decided to make a poster for my room of a molecule of DNA and a protein (to be announced). the DNA is a sort of test to see how
difficult it is before i go crazy trying to make a protein, which is much more difficult considering folding, etc.
when i draw these molecules i want it to be perfectly accurate; ie, i want to write in the bond lengths, bond angles and bond energies. needless to
say, this is quite a challenge.
i've had a bit of success thus far but i am not sure of one factor, that is the bond angles in a phosphate. i figured that phosphorus was SP^3
hybridized. i figured also that the bond angle would be 109.5 degrees (like the angles in methane) if the covalent radii of the phosphorus with
respect to each of the oxygen atoms were equal. of course, the doubly bonded oxygen is closer, so consequentially i believe the angle between the
doubly bonded oxygen and the singly bonded oxygen is greater than 109.5 degrees. the covalent radius of phosphorus is 164nm when singly bonded to an
oxygen atom and 145nm when doubly bonded to an oxygen atom. is there a directly proportional relationship between the difference in bond lengths and
the bond angles in this case?chemoleo - 22-12-2004 at 13:13
You realise you can actually download structure files of DNA, proteins, and whatever? There is then software that allows you to calculate bond angles.
Or is that too easy?budullewraagh - 22-12-2004 at 14:34
it is too easyneutrino - 22-12-2004 at 17:11
Quote:
Originally posted by budullewraagh
of course, the doubly bonded oxygen is closer, so consequentially i believe the angle between the doubly bonded oxygen and the singly bonded oxygen is
greater than 109.5 degrees.
Maybe I’m missing something here, but doesn’t resonance ensure that all of the bonds are identical? As for protein folding… you quite frankly
don’t stand a snowball’s chance in hell. It takes ultra-fast supercomputers a very long time to calculate even several microseconds worth of
protein folding.budullewraagh - 22-12-2004 at 17:33
Quote:
Maybe I’m missing something here, but doesn’t resonance ensure that all of the bonds are identical?
when the bond lengths are different, the angles are changed. the doubly bonded oxygen repels the other oxygen atoms.
as for protein folding, it depends on the size of the protein actually. large ones take a great deal of time, of course, but small ones aren't
necessarily too time consuming.Darkfire - 22-12-2004 at 17:57
I there is no double bonded oxygen,budullewraagh - 22-12-2004 at 18:02
in a phosphate?? are you kidding me?
PO4-3
__O
__|
O=P-O
__|
__ODarkfire - 22-12-2004 at 22:55
Its a resonance structure, theres 1.3333333 bonds between each P and O, put more correctly, it has a bond order of four thirds between P and O. All
bond distances are equal.budullewraagh - 26-12-2004 at 09:28
does anyone here know of any sources i can look to for information on advanced orbital hybridiation? (im talking about things that explain more than
SP, SP^2, SP^3, DSP^3 and D^2SP^3)JohnWW - 26-12-2004 at 11:48
For a start, look it up in Linus Pauling's The Nature Of The Chemical Bond.budullewraagh - 26-12-2004 at 12:09
it's out of print:\neutrino - 26-12-2004 at 13:01
Out of print doesn’t necessarily mean impossible to find. Many can still be found at used book stores, libraries, scanned in on the internet,
Amazon, eBay, etc.
