Glycosaminoglycan Monosaccharide Blocks Analysis by Quantum Mechanics, Molecular Dynamics, and Nuclear Magnetic Resonance
Table 1
B3LYP6311ppdd//B3LYP/6-31+G(d) relative energies for ring and gg/gt/tg conformations of GlcNAc and GalNAc derivatives.
Molecule/conformation
(), kcal/mol
(, kcal/mol
(, kcal/mol
Saccharides
gg
gt
tg
gg
gt
tg
gg
gt
tg
GlcNAc
2.02
1.77
0
10.17
6.85
10.31
2.81
4.28
11.66
M-GlcNAc
3.40
2.72
1.09
5.67
2.01
6.04
1.67
0
7.40
GlcNAcPCM
0.39
0.28
0
7.83
6.39
8.29
4.04
4.25
9.65
M-GlcNAcPCM
4.02
2.55
0
3.11
4.28
6.97
4.81
3.02
8.22
GlcNAc(4S)
7.77
8.30
0
19.19
14.61
14.70
7.00
15.05
4.77
M-GlcNAc(4S)
16.46
13.76
0
19.37
15.11
15.10
1.71
15.94
8.22
GlcNAc(4S)PCM
3.31
3.31
0
10.04
9.15
8.38
3.98
7.33
4.38
M-GlcNAc(4S)PCM
5.26
2.83
0
8.61
6.61
6.44
4.59
5.65
6.28
GlcNAc(6S)
0.22
0
10.14
8.98
16.84
19.47
22.93
14.08
14.49
M-GlcNAc(6S)
6.94
3.45
0
1.30
12.49
11.76
15.04
11.53
16.06
GlcNAc(6S)PCM
0.27
0
1.52
7.18
5.28
6.83
8.51
4.62
6.06
M-GlcNAc(6S)PCM
0
0.35
2.46
2.67
2.66
2.56
≥
4.1
5.79
GlcNAc(46S)
0
6.13
1.89
44.14
29.03
21.05
17.59
37.31
14.50
M-GlcNAc(46S)
11.96
7.90
0
23.16
24.90
12.29
≥
28.70
0.49
GlcNAc(46S)PCM
1.61
3.78
0
12.45
9.27
8.28
9.44
11.52
10.78
M-GlcNAc(46S)PCM
3.71
4.65
0
8.86
8.89
4.56
7.33
8.32
1.75
GalNAc
0
2.03
3.67
9.29
8.88
12.10
0.78
6.98
10.95
M-GalNAc
0
2.07
2.81
3.99
3.60
5.95
3.43
4.51
4.09
GalNAcPCM
0
1.04
2.40
8.55
8.40
8.68
3.78
6.64
9.39
M-GalNAcPCM
0
1.99
3.70
5.74
5.50
6.11
7.36
6.77
6.98
GalNAc(4S)
7.77
8.30
0
19.19
14.61
14.70
7.00
15.05
4.77
M-GalNAc(4S)
4.99
0.80
0
10.43
26.57
15.24
7.22
24.22
7.79
GalNAc(4S)PCM
0
2.96
2.09
9.57
12.48
9.28
3.90
11.29
5.00
M-GalNAc(4S)PCM
0
0.31
3.09
7.25
11.13
8.31
6.21
8.59
4.45
GalNAc(6S)
0
4.69
15.80
10.42
20.96
20.91
23.99
20.26
21.75
M-GalNAc(6S)
3.14
0
5.86
11.79
11.01
5.44
12.10
10.36
10.23
GalNAc(6S)PCM
0
0.81
0.20
6.09
5.13
5.44
12.88
7.71
7.42
M-GalNAc(6S)PCM
0.82
3.13
0
4.04
4.39
5.44
9.48
5.42
3.09
GalNAc(46S)
0
6.15
6.43
5.60
29.94
25.15
3.48
19.74
3.13
M-GalNAc(46S)
3.14
8.75
0
5.11
22.36
13.03
4.59
12.43
15.29
GalNAc(46S)PCM
1.50
2.09
0
6.94
9.19
16.43
4.55
13.68
4.90
M-GalNAc(46S)PCM
0
2.35
2.74
5.13
6.53
10.39
11.72
6.32
2.99
Relative energies were calculated using the energy of the most stable conformation for the same molecule as a reference for in vacuo and PCM solvent model (marked with PCM subscript).
4C1: The ring conformation changed to 4C1 during geometry optimization.
