NRT analysis 5-membered ring

NRT analysis 5-membered ring

Postby Tobias Kraemer » Thu Mar 14, 2019 11:15 am

Dear all,

I am wondering if you could give me some advise on how to generate reasonable results from NRT analysis. The system I am studying contains a 5-membered ring, and represents the product of CO insertion into a phosphaborete. I have attached a structure. The presence of double bonds and lone pairs in the parent structure suggests that multiple Lewis resonance forms may be important in the overall description of the bonding. In the original structure there are substituted aromatic rings attached to the molecule, which I had to truncate to overcome memory issues in NBO. When specifying that only the atoms of the ring structure (carbonyl, B, N, P, C=C) are contained in the NRT analysis, the situation is relatively clearcut (see below). There is one leading Lewis structure, and other reasonable resonances are being formed from the reference, with weights between 1-9%.

Code: Select all
         Resonance
    RS   Weight(%)                  Added(Removed)
 ---------------------------------------------------------------------------
    1*     74.09
    2       8.59   ( N  9- B 45), ( C 11- C 13),  C 11- B 45,  N  9
    3       7.25    P  7- C 13, ( C 11- C 13), ( P  7),  C 11
    4       6.39   ( P  7- C 10),  O  8- C 10,  P  7, ( O  8)
    5       2.50    P  7- C 10, ( O  8- C 10), ( P  7),  O  8
    6       1.19    O  8- C 10, ( C 10- B 45), ( O  8),  B 45
 ---------------------------------------------------------------------------
          100.00   * Total *                [* = reference structure]


When I include all atoms, the result changes as expected (shown is a truncated version of the output):

Code: Select all
        Resonance
    RS   Weight(%)                  Added(Removed)
 ---------------------------------------------------------------------------
    1*     15.30
    2*     12.99   ( C  2- C  3),  C  2- C 43,  C  3- C  5, ( C  5- C 40),
                    C 29- C 30, ( C 29- C 36), ( C 30- C 31),  C 31- C 33,
                   ( C 33- C 34),  C 34- C 36,  C 40- C 41, ( C 41- C 43)
    3*     10.85   ( C  2- C  3),  C  2- C 43,  C  3- C  5, ( C  5- C 40),
                    C 40- C 41, ( C 41- C 43)
    4*     10.01    C 29- C 30, ( C 29- C 36), ( C 30- C 31),  C 31- C 33,
                   ( C 33- C 34),  C 34- C 36
    5       3.14   ( N  9- B 45), ( C 11- C 13),  C 11- B 45,  C 29- C 30,
                   ( C 29- C 36), ( C 30- C 31),  C 31- C 33, ( C 33- C 34),
                    C 34- C 36,  N  9
    6       2.32   ( C  2- C  3),  C  2- C 43,  C  3- C  5, ( C  5- C 40),
                   ( N  9- B 45), ( C 11- C 13),  C 11- B 45,  C 40- C 41,
                   ( C 41- C 43),  N  9
    7       2.32   ( P  7- C 10),  O  8- C 10,  C 29- C 30, ( C 29- C 36),
                   ( C 30- C 31),  C 31- C 33, ( C 33- C 34),  C 34- C 36,
                    P  7, ( O  8)
    8       2.31   ( C  2- C  3),  C  2- C 43,  C  3- C  5, ( C  5- C 40),
                   ( N  9- B 45), ( C 11- C 13),  C 11- B 45,  C 29- C 30,
                   ( C 29- C 36), ( C 30- C 31),  C 31- C 33, ( C 33- C 34),
                    C 34- C 36,  C 40- C 41, ( C 41- C 43),  N  9
    9       2.04   ( C  5- C 40), ( C 11- C 13),  C 13- C 40,  C 29- C 30,
                   ( C 29- C 36), ( C 30- C 31),  C 31- C 33, ( C 33- C 34),
                    C 34- C 36,  C 11
   10       1.88    P  7- C 10, ( O  8- C 10),  C 29- C 30, ( C 29- C 36),
                   ( C 30- C 31),  C 31- C 33, ( C 33- C 34),  C 34- C 36,
                   ( P  7),  O  8
   11       1.72   ( C  2- C  3),  C  2- C 43,  C  3- C  5, ( C  5- C 40),
                   ( P  7- C 10),  O  8- C 10,  C 40- C 41, ( C 41- C 43),
                    P  7, ( O  8)
   12       1.70   ( C  2- C  3),  C  2- C 43,  C  3- C  5, ( C  5- C 40),
                   ( P  7- C 10),  O  8- C 10,  C 29- C 30, ( C 29- C 36),
                   ( C 30- C 31),  C 31- C 33, ( C 33- C 34),  C 34- C 36,
                    C 40- C 41, ( C 41- C 43),  P  7, ( O  8)
   13       1.57   ( C  2- C  3),  C  2- C 43,  C  3- C  5, ( C  5- C 40),
                   ( C 11- C 13),  C 13- C 40,  C 29- C 30, ( C 29- C 36),
                   ( C 30- C 31),  C 31- C 33, ( C 33- C 34),  C 34- C 36,
                   ( C 41- C 43),  C 11
   14       1.56   ( C  2- C  3),  C  2- C 43,  C  3- C  5, ( C  5- C 40),
                   ( C 11- C 13),  C 13- C 40, ( C 41- C 43),  C 11
   15       1.50   ( C  2- C  3),  C  3- C  5, ( C  5- C 40),  C 29- C 30,
                   ( C 29- C 36), ( C 30- C 31),  C 31- C 33, ( C 33- C 34),
                    C 34- C 36,  C 40


Naturally, there are many more resonance structures now, for one because the aromatic resonances of the phenyl rings contribute now as well. Overall, the weights have dramatically changed, and the leading reference has a weight of only 15%. From inspection, I can identify those Lewis structures that were also found when restricting the number of atoms, but their contribution is now reduced significantly. My question here is, would it be meaningful to just focus on selected atoms of the ring (I tend to think so), which then confines the NRT analysis to the region of interest. To which extend are these resonance structures important, when their weight is 1-10%? Also, when running the calculation on the full system, I seem to get a lot of reference structures, which can not be handled due to memory reasons, unless I keep NRTREF=50.

Any comments on how to deal with this system and obtain meaningful results would be appreciated. I have included my input for the restricted NRT analysis below.

Thanks for your comments,

Tobias

Code: Select all
#P b3lyp/def2svp pop=(full,nbo6read) gfinput gfprint int=ultrafine

5-membered ring test

0 1
H        5.204132000      3.971356000      0.246056000
C        4.350365000      3.297002000      0.164043000
C        4.416781000      2.176077000     -0.661602000
H        5.320165000      1.971718000     -1.238431000
C        3.330733000      1.309432000     -0.759588000
H        3.402818000      0.435679000     -1.410409000
P        1.153928000     -1.026193000     -0.873728000
O       -0.895227000     -2.715247000     -0.283818000
N       -2.782476000      0.006281000      0.030045000
C       -0.557218000     -1.560390000     -0.245844000
C       -0.302324000      0.979247000      0.116644000
H       -0.514958000      2.016022000      0.390675000
C        0.989349000      0.635029000     -0.142696000
C       -3.692326000     -1.082572000      0.522647000
C       -4.989454000     -0.464850000      1.071231000
H       -4.725309000      0.135085000      1.954682000
H       -5.614181000     -1.290089000      1.442817000
C       -5.765979000      0.380782000      0.063378000
H       -6.506369000     -0.235528000     -0.467426000
H       -6.340095000      1.150533000      0.600163000
C       -4.825877000      1.024616000     -0.955451000
H       -4.735820000      0.389929000     -1.849193000
H       -5.236072000      1.983567000     -1.304383000
C       -3.402044000      1.291706000     -0.436495000
H       -3.921970820     -1.807833666     -0.270485884
H       -3.228931599     -1.598382980      1.375293270
H       -2.852592481      1.695994387     -1.298153243
H       -3.428287376      2.042337236      0.365792375
C        2.633497000     -1.819847000     -0.076088000
C        3.089993000     -1.528778000      1.240862000
C        4.471463000     -1.461233000      1.448905000
H        4.829268000     -1.146796000      2.430304000
C        5.412092000     -1.790476000      0.476755000
C        4.924630000     -2.321173000     -0.717124000
H        5.632848000     -2.695432000     -1.450227000
C        3.558537000     -2.360351000     -1.018439000
H        2.488589000     -1.251238000      2.109049000
H        6.477529000     -1.729746000      0.708313000
H        3.267816000     -2.770365000     -1.987889000
C        2.149107000      1.551175000     -0.040535000
C        2.096887000      2.687624000      0.783649000
H        1.198662000      2.883222000      1.372246000
C        3.183630000      3.549446000      0.887286000
H        3.122773000      4.420557000      1.541399000
B       -1.379623000     -0.146244000      0.038900000

$NBO NRT <7 8 9 10 11 13 45> NRTTHR=5 NRTREF=50 NRTRES=1000 $END
Attachments
ring.png
ring.png (35.38 KiB) Viewed 7515 times
Tobias Kraemer
 
Posts: 4
Joined: Wed May 02, 2018 12:12 pm

Re: NRT analysis 5-membered ring

Postby ericg » Tue Apr 02, 2019 12:18 pm

Tobias,

You're correct that including the phenyl substituents in the calculation will lead to many more structures in your resonance hybrid, and that the weights will therefore, on average, decrease. So it is problematic to compare the resonance weights of the heterocycle with and without the phenyl groups.

The principal NRT deliverable, however, is the bond orders, which can be compared from one molecule to the next, despite their differing sizes. I think that it would be interesting here to compare the bond lengths in the heterocycle with the NRT bond orders, with and without the substituents, to determine what influence phenyl might have on the ring.

I would recommend that you consider upgrading to NBO7, which has a vastly improved NRT implementation. I ran your molecule, with phenyl groups, through the new NRT and got the following results:

Code: Select all
 NATURAL RESONANCE THEORY ANALYSIS:

    Parent structure threshold:  50% of leading weight
 Delocalization list threshold:  1 kcal/mol
         Maximum search cycles:  3

 C1 symmetry, 1 symmetry operator(s), 1 unique atom permutation(s)
 4 initial TOPO matrices: NLS = 1; NBI = 3; SYM = 0

  cycle  structures    D(w)     kmax  CHOOSE   ION    E2   SYM   dbmax   dbrms
 ------------------------------------------------------------------------------
    1       8/8     0.07471453     8       8     0   804     0   2.000   1.199
    2      71/1392  0.07091190    87    2008   -64   704     0   0.511   0.083
    3     240/800   0.06981351   245     964 -1296   748     0   0.305   0.048

 QPNRT(240/800): D(0)=0.09278578; D(w)=0.06981351; dbmax=0.305; dbrms=0.048
 Timing(sec): search=709.86; Gram matrix=542.40; minimize=11.57; other=20.15


NRT completed in under 1300 seconds, reporting a resonance expansion of 240 structures (from 800 candidate structures). The leading structures are shown in the following image. No structure has weight higher than 5.5%, so the molecule is highly delocalized.

tobias.png
16 leading structures of the NRT expansion
tobias.png (103.04 KiB) Viewed 7512 times


Perhaps somewhat concerning is that the two leading structures (totaling about 10.5%) reveal no P-CO bond. But P-CO bond length is rather large (1.899 Angstroms), and the rest of the structures in the hybrid do exhibit at least one P-CO bond. The P-CO bond order (0.904) is considerably less than one, which isn't surprising for such a long bond.

The resonance hybrid can then be used to determine the origin of the long P-CO bond. The missing bond in the two leading structures appears to be associated with triply-bonded CO character, arising from delocalization of an in-plane O p-type lone pair into the vicinal C-P sigma* antibond. This delocalization acts to shorten the CO bond and lengthen the C-P bond.

Eric
ericg
 
Posts: 317
Joined: Sat Dec 29, 2012 9:31 am


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