Thymine


 





 





 





 














 








Nitrogen


Nuclear Quadrupole Coupling Constants

in Thymine


 








 








 








14N nqcc's in thymine were determined by López et al. [1].   A semi-experimental equilibrium structure (reSE) was derived by Vogt et al. [2].


 








Calculation of the nqcc's was made here on the reSE structure.  These calculated nqcc's are compared with the experimental values in Tables 1 and 2.  Structure parameters are given in Z-matrix format in Table 3.












Calculation was made with both B3PW91/6-311+G(df,pd) and B3PW91/6-311+G(d,p) models.











In Tables 1 and 2, subscripts a,b,c refer to the principal axes of the inertia tensor, subscripts x,y,z to the principal axes of the nqcc tensor.  The z-principal axis of the nqcc tensor is perpendicular to the symmetry plane of the molecule.  ETA = (Xxx - Xyy)/Xzz.

RMS is the root mean square difference between calculated and experimental nqcc's (percentage of average experimental nqcc).  RSD is the residual standard deviation of calibration of the model used for calculation of the efg's/nqcc's.


 








 








   








Table 1.  14N(1) (see figure below) nqcc's Thymine (MHz).  Calculation was made on the reSE structure with (1) B3PW91/6-311+G(df,pd) and (2) B3PW91/6-311+G(d,p) models.
   










Calc (1)
Calc (2)

Expt. [1]
   








Xaa
1.845
1.931
1.954(11)

Xbb
1.782
1.860
1.850(12)

Xcc - 3.627 - 3.791 - 3.804(12)

|Xab|
0.147
0.169



 







RMS
0.126 (4.5 %)
0.016 (0.62 %)



RSD
0.030 (1.3 %)
0.086 (3.8 %)



 







Xxx
1.964
2.069



Xyy
1.663
1.722



Xzz - 3.627 - 3.791 - 3.804(12)

ETA - 0.0830 - 0.0914



 







   








 








   








Table 2.  14N(3) (see figure below) nqcc's Thymine (MHz).  Calculation was made on the reSE structure with (1) B3PW91/6-311+G(df,pd) and (2) B3PW91/6-311+G(d,p) models.
   










Calc (1)
Calc (2)

Expt. [1]
   








Xaa
1.713
1.807
1.768(13)

Xbb
1.627
1.687
1.652(14)

Xcc - 3.340 - 3.494 - 3.420(14)

|Xab|
0.213
0.230



 







RMS
0.058 (2.5 %)
0.052 (2.5 %)



RSD
0.030 (1.3 %)
0.086 (3.8 %)



 







Xxx
1.888
1.984



Xyy
1.452
1.510



Xzz - 3.340 - 3.494 - 3.420(14)

ETA - 0.130 - 0.136



 








 








 












Table 3.  Thymine.  Molecular structure parameters, reSE (Å and degrees).  Z-matrix for reSE structure was derived here from coordinates given in Table 5 of Ref. [2].
   


N
C,1,B1
N,2,B2,1,A1
C,3,B3,2,A2,1,D1,0
C,4,B4,3,A3,2,D2,0
C,5,B5,4,A4,3,D3,0
C,5,B6,4,A5,3,D4,0
H,1,B7,6,A6,5,D5,0
H,3,B8,2,A7,1,D6,0
O,2,B9,1,A8,6,D7,0
O,4,B10,3,A9,2,D8,0
H,6,B11,5,A10,4,D9,0
H,7,B12,5,A11,4,D10,0
H,7,B13,5,A12,4,D11,0
H,7,B14,5,A13,4,D12,0






B1=1.37817543
B2=1.37968081
B3=1.39319951
B4=1.46349869
B5=1.34570239
B6=1.49301575
B7=1.00386099
B8=1.00868418
B9=1.20948554
B10=1.21532214
B11=1.08039770
B12=1.08835754
B13=1.08929505
B14=1.08929505
A1=112.77075237
A2=127.96721549
A3=114.80580484
A4=117.87768474
A5=117.83616603
A6=120.94781756
A7=115.56872554
A8=123.38751815
A9=120.42085926
A10=122.16444720
A11=110.77063946
A12=110.56536854
A13=110.56536854
D1=0.
D2=0.
D3=0.
D4=180.
D5=180.
D6=180.
D7=180.
D8=180.
D9=180.
D10=180.
D11=59.19638655
D12=-59.19638655







 








 








[1] J.C.López, M.I.Peña, M.E.Sanz, and J.L.Alonso, J.Chem.Phys. 126,191103(2007).

[2] N.Vogt, J.Demaison, D.N.Ksenafontov, and H.D.Rudolph, J.Mol.Struct. 1076,483(2014).


 









 









Uracil
2-Pyridone






 








Table of Contents




Molecules/Nitrogen




 








 













thymine.html






Last Modified 1 July 2015