From an earlier question I was grateful to learn about the two step process for the movement of a double bond from a Schiff base (-N=C) down the backbone of a glucose molecule to form C=C. This involved 1) the protonation of the nitrogen, then 2) the removal of a hydrogen from the further carbon involved in the eventual C=C.
If I start from my schiff base, should the protonation of the nitrogen be considered as an intermediate step with OR without a transition state? For example, I cannot optimise a starting structure with H3O, it converges to be a protonated schiff base plus H2O. Equally I can't optimise the protonated intermediate having first used H2O (the intermediate N+ .... OH-, always reverts back to N .... H2O).
As a protonation is simply the acceptance of a proton from the environment, is there a transition step for it? Or is it just a further intermediate step before the transition step which would be the removal of the hydrogen from the carbon chain with the shift of -HN+=C-C to -HN-C=C?
Many thanks
Anthony
Mr. Nash,
First of all can you provide info about which systems Schiff-base/H3O+ you have obtained "protonated Schiff base plus H2O" and how much is the energy. Because of optimization yields not to NH+/H2O, but rather to a NH-C(H)+/H2O state (Form I, page 7, attachment). For this reason a proposed hydrolysis has involved interaction with centre C+/OH- and formation of -NH-CH(OH)- (Form II, page 7).
But to study this type of reaction, there is not suitable to use self-protolysis of H2O as model of interaction, meaning 2H2O = H3O+ + OH-, accounting only for base/H3O- interaction, because of if you have focused attention on the data in page 7, the energies of the initial state and form "I" are comparable. Moreover you should compare with base/OH-, too, because of if you have used 2H2O = H3O+ + OH-, both interaction types are equally probable. The ions are at ratio 1:1 in the solution and base/H3O+ system is more stable about D(E) = 0.11 kcal.mol-1 than base/OH- one.
Even if you have used a model base/H3O-/OH- to form II (page 7), the next intramolecular H-transfer process, in order to obtain -N+H2-C(H)O(-)- (yielding to amine/aldehyde as final products), is a less favourable one as well. Given that, you can include, for example, metal ion (M), but the attack to N-should be via OH-, not H+. A N-M bond formation is expected. In this case your model system should be base/Mn+/OH-.
In the context of the last paragraph please take into consideration that some of MS data (attachment) are in CH3CN/HCOOH mixture. The MS/MS data have shown different fragmentation pathways for different dyes, which are not associated with cutting of C-N bond, too. This should be taken into consideration within the frame of a gas-phase/continuum/solution theoretical analysis. Or even in the presence of those acidic conditions (we have also tested presence HSO4- ions), there is not hydrolysis. Thus the usage of base/H3O+ cannot express the real picture of mechanism. In other words the formation of hydrogen bonds between the species is more favourable in those cases.
In other words, C=N to C=C shifting is a less probably process, generally, if you have not suitable molecular structural factors allowing to stabilize, for example, a quinolide like form like this one shown in page 4 (attachment). But in this form the deprotonation is associated with -OH+ group, not with CH-fragment.
Set of such possible processes we have taken into consideration studying Schiff's bases (Ref. [1]) as ligands for metal-organic NLOs. However experimentally we have found that they are often less probable ones. Minimum for the shown set of derivatives (Ref. [1a]). Please see the theoretical and experimental UV-VIS spectra for neutral and protonated forms in page 3 as well.
On the other hand protonation of N(H)+=C causes for a charge redistribution, rather than to shifting to a quinolide like form (Example of a structure in page 5). Those data are supported by NBO analysis to all neutral and possible polyprotonated forms for the shown dyes. Or tautomerism C=N to C=C is a less expectable process.
Furthermore, depending on the type of substituents in the molecular scaffold there is not strict rule that nitrogen in C=N atom is the most preferred centre for protonation. So that you cannot expect that for any Schiff's base the first protonation step is associated with NH+=C formation. Have you any theoretical data about the proton accepting ability of your base? Please pay attention to a set of substances, where theoretical data have shown different proton accepting centres with a greater affinity for stabilization of mono - and polycations (Ref. [1a]). Even simple substitution of -N(CH3)2 (dye, page 1) with -N(CH2CH3)2 in causes to a change of the proton accepting centre from N=C to N(CH2CH3)2. So that you have stabilized not NH+=C but -NH+(CH2CH3)2 cations (Ref. [1a]).
Moreover, depending again on the type of substituents, such as for example dye-molecule shown in pages 1 and 2, C=NH+ protonated form is less stable and within the frame of a zwitterionic structure equilibrium is shifted to the neutral COOH/N=C-fragments.
On this view are you sure that the mentioned "removal of a hydrogen from the further carbon involved in the eventual C=C" is associated only with H2O and/or most probably acidic catalysed reaction, and it is not a result for an organometallic catalysing process, for example? Are there theoretical quantum chemical data about the thermodynamic stability of your system(s); any experimental ones; which are the structures of the proposed intermediates (if there are shown such as ones)?
Because of we have examples of similar products of interactions, but they are catalysed by ZnII- and AgI-ions, via organometallic intermediates? Or the mechanism is more complicated.
[Ref. 1] (a)J. Incl. Phenom. Macrocycl. Chem. 2013, 75, 211-221, Optical and nonlinear optical properties of new Schiff’s bases: experimental versus theoretical study of inclusion interactions, B. Ivanova , M. Spiteller; (b)Linear and nonlinear optical Zn(II)-metal-organic materials. Correlation between molecular structure, crystal structure and chemical-physical properties, B. Ivanova, M. Spiteller, 2015, pp. 1-353; ISBN 978-3-668-11137-0, GRIN Verlag, Muenchen.
Dear Anthony,
Generally, all reactions have transition states; it can be a stable transition state with low activation energy or unstable with high activation energy. All proton transfer reactions have transition states; In your case the protonoted imminum entity is an intermediate and its transition state is achieved when the hydrogen is placed almost in the middle of the distance between the nitrogen of the imine and the oxygen of a H3o+. What happened in your calculations is that you did not place H3O+ far from the imine; the closest distance between the reactants atoms (imine and H3O+) should be at least 4 angstrom; placing them in such away prevents the hydrogen of H3O+ to jump onto the imine. After getting the minimzed structure of the reactants (in one input file) you run a reaction coordinate for the proton transfer by approaching the proton of H3O+ to the nitrogen of the imine.
Hoping this will help you to start your calculations,
Rafik
As much as 4 Angstroms, that is quite a fair distance. Many thanks for that, I will give this a try.
Thanks again, Rafik.
Mr. Nash,
First of all can you provide info about which systems Schiff-base/H3O+ you have obtained "protonated Schiff base plus H2O" and how much is the energy. Because of optimization yields not to NH+/H2O, but rather to a NH-C(H)+/H2O state (Form I, page 7, attachment). For this reason a proposed hydrolysis has involved interaction with centre C+/OH- and formation of -NH-CH(OH)- (Form II, page 7).
But to study this type of reaction, there is not suitable to use self-protolysis of H2O as model of interaction, meaning 2H2O = H3O+ + OH-, accounting only for base/H3O- interaction, because of if you have focused attention on the data in page 7, the energies of the initial state and form "I" are comparable. Moreover you should compare with base/OH-, too, because of if you have used 2H2O = H3O+ + OH-, both interaction types are equally probable. The ions are at ratio 1:1 in the solution and base/H3O+ system is more stable about D(E) = 0.11 kcal.mol-1 than base/OH- one.
Even if you have used a model base/H3O-/OH- to form II (page 7), the next intramolecular H-transfer process, in order to obtain -N+H2-C(H)O(-)- (yielding to amine/aldehyde as final products), is a less favourable one as well. Given that, you can include, for example, metal ion (M), but the attack to N-should be via OH-, not H+. A N-M bond formation is expected. In this case your model system should be base/Mn+/OH-.
In the context of the last paragraph please take into consideration that some of MS data (attachment) are in CH3CN/HCOOH mixture. The MS/MS data have shown different fragmentation pathways for different dyes, which are not associated with cutting of C-N bond, too. This should be taken into consideration within the frame of a gas-phase/continuum/solution theoretical analysis. Or even in the presence of those acidic conditions (we have also tested presence HSO4- ions), there is not hydrolysis. Thus the usage of base/H3O+ cannot express the real picture of mechanism. In other words the formation of hydrogen bonds between the species is more favourable in those cases.
In other words, C=N to C=C shifting is a less probably process, generally, if you have not suitable molecular structural factors allowing to stabilize, for example, a quinolide like form like this one shown in page 4 (attachment). But in this form the deprotonation is associated with -OH+ group, not with CH-fragment.
Set of such possible processes we have taken into consideration studying Schiff's bases (Ref. [1]) as ligands for metal-organic NLOs. However experimentally we have found that they are often less probable ones. Minimum for the shown set of derivatives (Ref. [1a]). Please see the theoretical and experimental UV-VIS spectra for neutral and protonated forms in page 3 as well.
On the other hand protonation of N(H)+=C causes for a charge redistribution, rather than to shifting to a quinolide like form (Example of a structure in page 5). Those data are supported by NBO analysis to all neutral and possible polyprotonated forms for the shown dyes. Or tautomerism C=N to C=C is a less expectable process.
Furthermore, depending on the type of substituents in the molecular scaffold there is not strict rule that nitrogen in C=N atom is the most preferred centre for protonation. So that you cannot expect that for any Schiff's base the first protonation step is associated with NH+=C formation. Have you any theoretical data about the proton accepting ability of your base? Please pay attention to a set of substances, where theoretical data have shown different proton accepting centres with a greater affinity for stabilization of mono - and polycations (Ref. [1a]). Even simple substitution of -N(CH3)2 (dye, page 1) with -N(CH2CH3)2 in causes to a change of the proton accepting centre from N=C to N(CH2CH3)2. So that you have stabilized not NH+=C but -NH+(CH2CH3)2 cations (Ref. [1a]).
Moreover, depending again on the type of substituents, such as for example dye-molecule shown in pages 1 and 2, C=NH+ protonated form is less stable and within the frame of a zwitterionic structure equilibrium is shifted to the neutral COOH/N=C-fragments.
On this view are you sure that the mentioned "removal of a hydrogen from the further carbon involved in the eventual C=C" is associated only with H2O and/or most probably acidic catalysed reaction, and it is not a result for an organometallic catalysing process, for example? Are there theoretical quantum chemical data about the thermodynamic stability of your system(s); any experimental ones; which are the structures of the proposed intermediates (if there are shown such as ones)?
Because of we have examples of similar products of interactions, but they are catalysed by ZnII- and AgI-ions, via organometallic intermediates? Or the mechanism is more complicated.
[Ref. 1] (a)J. Incl. Phenom. Macrocycl. Chem. 2013, 75, 211-221, Optical and nonlinear optical properties of new Schiff’s bases: experimental versus theoretical study of inclusion interactions, B. Ivanova , M. Spiteller; (b)Linear and nonlinear optical Zn(II)-metal-organic materials. Correlation between molecular structure, crystal structure and chemical-physical properties, B. Ivanova, M. Spiteller, 2015, pp. 1-353; ISBN 978-3-668-11137-0, GRIN Verlag, Muenchen.
Hi Bojidarka,
Many thanks for the response. That is a lot of information. I am currently reading through the attachment and going through your reference.
With regards to you final question, this is not a process of organometallic intermediates. This is a compound which we have isolated in the lab in a solution of lysine, arginine and glucose. The product is glucosepane. I am currently working on defining the possible reaction pathway. Unfortunately, there is no quantum mechanical data to use.
Thanks again for the material.
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