From owner-chemistry ^at^ ccl.net Fri May 5 22:39:00 2023 From: "Kurten, Theo C theo.kurten]=[helsinki.fi" To: CCL Subject: CCL: hydrogen bond Message-Id: <-54912-230505111943-16522-temp07IofarE8vRVDJg3PA..server.ccl.net> X-Original-From: "Kurten, Theo C" Content-Language: en-GB Content-Type: multipart/alternative; boundary="_000_HE1PR07MB327592243A94D6210375267DE7729HE1PR07MB3275eurp_" Date: Fri, 5 May 2023 15:19:28 +0000 MIME-Version: 1.0 Sent to CCL by: "Kurten, Theo C" [theo.kurten=-=helsinki.fi] --_000_HE1PR07MB327592243A94D6210375267DE7729HE1PR07MB3275eurp_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear Partha, are you familiar with the IUPAC definition of a hydrogen bond? E.g. here: http://publications.iupac.org/pac/pdf/2011/pdf/8308x1637.pdf Based on that, it=92s clear that there is indeed a POSSIBILITY of a H-bond,= as you have a potential H-bond donor (N-H) and two possible acceptors (the= N atoms, and the pi-electron system). However, it also seems likely that t= he interaction will be quite weak, to the point of the existence of a H-bon= d being a borderline case, likely depending on the conditions (see the foot= notes in the linked pdf). Some quick-and-dirty calculations on my laptop (using Spartan =9220, wB97xD= and a 6-31+G(d) basis set set - and yes I know there are better basis sets= available but this should be good enough for the present purpose) confirm = this: for the H-bond to the N atom, the distance is pretty large (H=85N is = almost 2.4 =C5), the NHN angle is far from linear (about 129 degrees), the = N-H bond length increase and vibrational redshift (compared to isolated met= hyl amine) are on the order of 0.002 =C5 and a few wavenumbers, respectivel= y, and interaction energy is only about 20 kJ/mol (of which a lot, possibly= even most, is probably just basis set superposition error due to my small = basis set). For the H-bond to the pi-system, the distance (to the center of the ring) i= s even longer (almost 2.6 =C5), the interaction energy is even lower (about= 10 kJ/mol), the N-H bond length is identical (to 0.001 =C5) to isolated me= thyl amine, and the frequencies are actually blueshifted by a few cm-1 (the= latter may just be an artefact though). So this is likely not a H-bond at = all, as per the IUPAC definition Whether or not you want to call the first interaction (from the methyl amin= e NH to the pyrazine N) a H-bond really really depends on what you want to = do with this information. Best regards, Theo Kurt=E9n (University of Helsinki, Finland) > From: owner-chemistry+theo.kurten=3D=3Dhelsinki.fi/a\ccl.net on behalf of Partha Sengupta anapsps= mo=3Dgmail.com Date: Friday, 5. May 2023 at 17.15 To: Kurten, Theo C Subject: CCL: hydrogen bond I am not interested in ChatGpt. I ask the question to be answered from a ch= emical point of view. I repeat the question again" Is there any possibility= between the hydrogen bond formation between pyrazine and methyl amine". If= there is any chance please give me the references. Partha -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --_000_HE1PR07MB327592243A94D6210375267DE7729HE1PR07MB3275eurp_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

Dear Partha,

 

are you familiar with the IUPAC definition of a hydrogen bo= nd? E.g. here: 

 

http://publications.iupac.org/pac/pdf/2011/pdf/8308x1637.pdf<= /a>

 

Based on that, it=92s clear that there is indeed a POSSIBIL= ITY of a H-bond, as you have a potential H-bond donor (N-H) and two possibl= e acceptors (the N atoms, and the pi-electron system). However, it also see= ms likely that the interaction will be quite weak, to the point of the existence of a H-bond being a borderlin= e case, likely depending on the conditions (see the footnotes in the linked= pdf). 

 

Some quick-and-dirty calculations on my laptop (using Spart= an =9220, wB97xD and a 6-31+G(d) basis set set - and yes I know there are b= etter basis sets available but this should be good enough for the presen= t purpose) confirm this: for the H-bond to the N atom, the distance = is pretty large (H=85N is almost 2.4 =C5), the NHN angle is far from linear= (about 129 degrees), the N-H bond length increase and vibrational redshift (compared to isolated methyl amine) are = on the order of 0.002 =C5 and a few wavenumbers= , respectively, and interaction energy is only about 20 kJ/mol (of which a = lot, possibly even most, is probably just basis set superposition error due to my smal= l basis set). =

 

For the H-bond to the pi-system, the distance (to the cente= r of the ring) is even longer (almost 2.6 =C5), the interaction energy is e= ven lower (about 10 kJ/mol), the N-H bond length is identical (to 0.001 =C5) to isolated methyl amine, and th= e frequencies are actually blueshifted by a few= cm-1 (the latter may just be an artefact thoug= h). So this is likely not a H-bond at all, as per the IUPAC definition

 

Whether or not you want to call the first interaction (from= the methyl amine NH to the pyrazine N) a H-bond really really depends on w= hat you want to do with this information.

 

Best regards,

Theo Kurt=E9n

(University of Helsinki, Finland)

 

 

From: owner-chemistry+the= o.kurten=3D=3Dhelsinki.fi/a\ccl.net <owner-chemistry+theo.kurten=3D=3Dhels= inki.fi/a\ccl.net> on behalf of Partha Sengupta anapspsmo=3Dgmail.com <= owner-chemistry/a\ccl.net>
Date: Friday, 5. May 2023 at 17.15
To: Kurten, Theo C <theo.kurten/a\helsinki.fi>
Subject: CCL: hydrogen bond

I am not interested= in ChatGpt. I ask the question to be answered from a chemical point of vie= w. I repeat the question again" Is there any possibility between = the hydrogen bond formation between pyrazine and methyl amine". If there is any chance please give me the references.<= o:p>

Partha

 

 

--

Dr= . Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan

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