From owner-chemistry@ccl.net Tue Sep 22 20:59:01 2015 From: "Nico Green nicogreen6!^!gmail.com" To: CCL Subject: CCL: The use of NMR spectra computations for verification of computational method Message-Id: <-51771-150922204516-25994-pRTZMq1A7JzSbNsBeTwp0A!^!server.ccl.net> X-Original-From: Nico Green Content-Type: multipart/alternative; boundary=001a113a723244598505205f6dd9 Date: Wed, 23 Sep 2015 00:45:01 +0000 MIME-Version: 1.0 Sent to CCL by: Nico Green [nicogreen6~!~gmail.com] --001a113a723244598505205f6dd9 Content-Type: text/plain; charset=UTF-8 Dear Grigoriy The values you obtain seems to reproduce correctly the experimental chemical shifts. However, may I suggest you try using the MSTD? Here are the references: for 13C: The Journal of Organic Chemistry 2009; 74(19):7254-60. for 1H: The Journal of Organic Chemistry 2012; 77(14):6059-65. On the other hand, in my humble experience mPW1PW91 is the best cost/accuracy basis set, depending on your structure the functional you'll need to use, but as a start a 6-31G(d) or 6-31G(d,p) should work fine. In GIAO NMR is very common to use one level for the optimization step and another for the NMR calculation. So you may use your geometries and just perform a single point NMR calculation with mPW1PW91/6-31G(d) and check. Hope this helps On Mon, Sep 21, 2015 at 6:28 PM Grigoriy Zhurko reg_zhurko^chemcraftprog.com wrote: > > Sent to CCL by: Grigoriy Zhurko [reg_zhurko^chemcraftprog.com] > I have been computing NMR spectra of several organic compounds, comparing > them with the experiment. Usually these computations show big systematic > errors, but correlate well with the experiment (for C13 spectra of organic > molecules, I got the correlation coefficient R about 0.9995 with > B3LYP/6-311G(D,P) method). > Now I have computed some NMR spectra of bilirubin molecule with different > DFT functionals, and I found that the correlation coefficient is not a good > criteria of computation accuracy in my case. This molecule has internal > hydrogen bonds, and different functionals (in particular, B3LYP and PBE) > give quite different O..H distance (the difference is about 0.1 A), while > other bond lengths in this molecule do not differ significantly (the > difference is 0.012 A or less). The PMR spectrum with B3LYP correlates with > the experimental one with R=0.997, and with PBE ? R=0.995. These values do > not differ very much. But the coefficient B in the equation Y=A+B*X (for > the linear approximation of experiment vs theory graph) is 1.02 for B3LYP, > and 1.14 for PBE. So, with PBE it is far less from 1. Does that mean that > PBE is much less appropriate method for this task? > I suppose, that the systematic error of absolute values of the NMR > chemical shifts is caused by unclear physical meaning of these chemical > shifts and shieldings (maybe the solvent gives some additional shielding in > experiment). So, my question is, whether the B coefficient in correlation > must be always equal 1. If yes, then instead of correlation coefficients R > I should use another criteria of computation accuracy ? the RMS of MAE > difference between the computed and experimental chemical shifts, if the > shielding of the standard (TMS) simply fitted for best agreement (not > computed quantum-chemically). Is that correct? In my case, these MAE > difference must be much bigger for PBE functional, than for the B3LYP > functional. > > Grigoriy Zhurko.> > > --001a113a723244598505205f6dd9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Grigoriy
=
The values you obtain seems to reproduce correctly the exper= imental chemical shifts.
However,= may I suggest you try using the MSTD?
Here are the re= ferences:
for 13C: The Journal of Organic Chemistry 2009; 74(19):7254-= 60.
for 1H:=C2=A0The Journal of= Organic Chemistry 2012; 77(14):6059-65.=C2=A0<= /span>

On the other hand, in my humble = experience=C2=A0mPW1PW91 is the best cost/accuracy basi= s set, depending on your structure the functional you'll need to use, b= ut as a start a 6-31G(d) or 6-31G(d,p) should work fine.
<= span style=3D"line-height:17px;font-family:arial,helvetica,clean,sans-serif= ;color:rgb(0,0,0)">
In GIAO NMR is= very common to use one level for the optimization step and another for the= NMR calculation. So you may use your geometries and just perform a single = point NMR calculation with=C2=A0mPW1PW91/6-31G(d) and c= heck.

<= /span>
Hope this h= elps

=C2=A0


<= /span>

=

On Mon, Sep 21, 2015 = at 6:28 PM Grigoriy Zhurko reg_zhurko^chemcraftprog.com <owner-chemistry() ccl.net> wrote:

Sent to CCL by: Grigoriy Zhurko [reg_zhurko^chemcraftprog.com]
I have been computing NMR spectra of several organic compounds, comparing t= hem with the experiment. Usually these computations show big systematic err= ors, but correlate well with the experiment (for=C2=A0 C13 spectra of organ= ic molecules, I got the correlation coefficient R about 0.9995 with B3LYP/6= -311G(D,P) method).
Now I have computed some NMR spectra of bilirubin molecule with different D= FT functionals, and I found that the correlation coefficient is not a good = criteria of computation accuracy in my case. This molecule has internal hyd= rogen bonds, and different functionals (in particular, B3LYP and PBE) give = quite different O..H distance (the difference is about 0.1 A), while other = bond lengths in this molecule do not differ significantly (the difference i= s 0.012 A or less). The PMR spectrum with B3LYP correlates with the experim= ental one with R=3D0.997, and with PBE ? R=3D0.995. These values do not dif= fer very much. But the coefficient B in the equation Y=3DA+B*X (for the lin= ear approximation of experiment vs theory graph) is 1.02 for B3LYP, and 1.1= 4 for PBE. So, with PBE it is far less from 1. Does that mean that PBE is m= uch less appropriate method for this task?
I suppose, that the systematic error of absolute values of the NMR chemical= shifts is caused by unclear physical meaning of these chemical shifts and = shieldings (maybe the solvent gives some additional shielding in experiment= ). So, my question is, whether the B coefficient in correlation must be alw= ays equal 1. If yes, then instead of correlation coefficients R I should us= e another criteria of computation accuracy ? the RMS of MAE difference betw= een the computed and experimental chemical shifts, if the shielding of the = standard (TMS) simply fitted for best agreement (not computed quantum-chemi= cally). Is that correct? In my case, these MAE difference must be much bigg= er for PBE functional, than for the B3LYP functional.

Grigoriy Zhurko.



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY() ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST() ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/


--001a113a723244598505205f6dd9--