To my understanding the nucleophilic attack of H2C=O is a two step process:
1) The slight positive charge on the carbon is open to attack by a nucleophile. The C=O loses its pi bond and reduces down to a sigma bond.
2) This enables the large negative charge on the pi orbital of O to attract a proton from its environment.
How would one best model the reaction pathway of this mechanism in Gaussian? I am working on a larger reaction pathway which includes a couple of these reactions. Should I attempt to search for a transition state of both steps happening simultaneously, or as two transition states with NuHC-(O-) as an intermediate? My nucleophile is lysine and the carbonyl molecule is linear glucose.
Very new to Gaussian, I would appreciate as much detail as possible.
Hi Xie,
I am currently modelling the nucleophilic attack. I wonder whether the TS would be the carbonyl carbon bound to five atoms rather than four. In either case of I performing a modred scan geometry by elongating the C=O bond, and the nucleophilic C-Nu bond just to see roughly where the higher energy structure is.
Thanks
Please consider the possibility of having a one step addition consisting of 3 simultaneous concerted electronic motions. Carbon never forms 5 bonds but during the reaction there is bond formation & bond breaking at the same time.
Don't hesitate to correct me if I am wrong.
Thanks for the attachment. I understand the mechanism, I just don't know how Gaussian would go about modelling the transition state of Nu attacking the carbon? Would I be correct in saying that it would be both a bond formation Nu:C and an adjustment to the C=O bond? And then the second TS would be the high energy state of C-O--HOH2 ?
Thanks
I think that you are right. The O was partially negative & transformed into fully negative & then attacked the H+ (in a slow picture which depicts the motions). When O has full negative charge attacking the proton then it is a high energy state.
My regards.
Hi Nick,
Thanks for the information, I'm out for the rest of today but just from a moment's glance this looks perfect.
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