Weekly Report (2015.7.6—2015.7.12)
Jingjing Wu
Results summary: This week I have collected the project of BN-Clar structure and
then calculated the other project. Here I am going to summarize the project of halogen
bond. Firstly, I have selected the substrate using different functional level M06-2X and
B97-1. The results have been shown in Figure 1.
Figure 1. Explore the best substrate based on furan.
Then fixed pyridine, all these structures are optimized at M06-2X level, cc-pVTZ basis
set for C, H, O, S, N,P… expect for I atom, the aug-cc-pVTZ-pp basis set is used for I
atom. Because the complexes can’t be optimized at M062X/aug-cc-pVTZ level
sussfully. These calculated zero-point-energy and Gibbs free energy are summarized in
Table 1.
Table 1. All these geometries are calculated at M06-2X/cc-pVTZ level.
X
ZPE (G)
/kcal mol-1
Bond length (BL)/Å
NICS(0)/NICS(1)/NICS(1)zz
ppm (RE)
CH+
-19.6 (-9.6)
2.510
32.3/14.1/76.9
SiH+
-18.0 (-8.4)
2.589
11.6/11.8/44.6
GeH+
-17.2 (-8.9)
2.604
11.2/11.2/43.3
NH2+
-18.4 (-10.8)
2.545
-8.4/-3.4/-3.0
PH2+
-17.9 (-8.1)
2.563
-4.6/-1.2/6.4
AsH2
-17.2 (-7.2)
2.572
-5.1/-1.4/6.9
BH
-5.8 (2.6)
2.975
14.1/11.5/42.2
AlH
-5.1 (3.0)
2.998
1.9/3.5/18.6
CH2
-5.5 (2.7)
2.980
-7.9/-3.2/-3.3
SiH2
-5.5 (2.7)
2.976
-3.7/-0.9/6.2
O
-6.3 (2.0)
2.934
-15.2/-7.3/-17.7
+
NH
-5.4 (2.7)
2.981
-18.2/-8.5/-21.9
Figure 2. Their connection between NICS(1)zz and relative Gibbs free enegy.
As the Gibbs free energy values are not negative in some cases. And according to others
report, the weak interaction of halogen or hydrogen bond should have a correction for
the inherent BSSE (basis-set superposition error) using the counterpoise method.
Therefore, the next calculations about halogen bond all using BSSE energy. In addition,
the B971 function has been used1 and the diffuse basis set 6-31+G(d,p) could be used
in these systems. Hence, all the next calculated at B97-1/6-31+G(d,p) level, and the
aug-cc-pVTZ-pp basis set is used for I atom.
(1) Fixed the substrate pyridine at singlet and triplet state,respectively.
Table 1. Singlet state. When X =N-,P-,As-,Se,SiH-,GeH-,B- all failed.
X
EBSSE
(kcal/mol)
NBO
Charge
RE (I)
Wiberg bond
index (PR:I-N)
NBO Charge
(PR：I/N)
CH+
-22.57
0.556
0.1862
0.557/-0.530
2.576
31.7/24.0/79.2
SiH+
-20.75
0.516
0.1856
0.502/-0.521
2.584
14.0/13.8/51.6
GeH+
-20.02
0.497
0.1825
0.485/-0.519
2.590
14.1/13.5/51.2
+
-21.59
0.415
0.2139
0.361/-0.510
2.538
-8.7/-3.8/-2.7
+
-20.72
0.430
0.2046
0.386/-0.511
2.555
-4.9/-1.6/6.5
AsH2
-20.15
0.415
0.2036
0.374/-0.509
2.557
-5.1/-1.7/7.1
BH
-5.76
0.264
0.0651
0.287/-0.488
2.914
13.6/11.7/44.1
AlH
-4.83
0.219
0.0608
0.248/-0.482
2.948
1.3/3.3/18.9
CH2
-5.28
0.233
0.0634
0.252/-0.484
2.929
-8.7/-3.9/-3.1
SiH2
-5.39
0.231
0.0659
0.255/-0.484
2.919
-4.4/-1.3/6.4
O
-6.32
0.253
0.0746
0.262/-0.487
2.879
-15.6/-7.5/-16.4
NH
-5.09
0.231
0.0637
0.245/-0.483
2.929
-18.4/-8.7/-20.3
S 虚频
-10.12
0.243
作图未考虑
2.602
-15.6/-8.1/-15.2
AsH
-5.48
0.229
0.251/-0.484
2.913
-7.9/-3.5/-0.6
NH2
PH2
+
0.0676
Bond
(BL)/Å
length
NICS(0)/NICS(1)/NICS(1)zz
ppm (RE)
PH
-5.64
0.234
0.0686
0.255/-0.485
2.907
-8.8/-3.9/-3.8
Figure 3. Their connections.
Table 2. Triplet. When X = B-, S, N-,P-,NH,As-,Se,SiH,GeH,AsH failed
X
EBSSE
(kacl/mol)
Bond length (BL)/Å
NICS(0)/NICS(1)/NICS(1)zz/ppm
(RE)
CH+
-119.92
SiH+
2.575
-5.2/-6.6/-11.8
-117.70
0.0464
GeH+
0.495/-0.521
2.578
-4.3/-5.7/-8.9
-117.94
+
0.0486
0.493/-0.521
2.571
-3.0/-5.3/-7.8
+
-117.47
0.0494
0.424/-0.515
2.565
Broken(作图未考虑)
-116.81
0.0461
0.445/-0.516
2.577
-7.4/-5.1/-4.7
-116.18
0.0480
0.435/-0.514
2.584
0.3/1.9/16.8
BH
-104.41
0.0162
0.304/-0.490
2.909
-6.4/-7.2/-13.8
AlH
-103.55
0.0163
0.275/-0.485
2.933
-5.5/-5.6/-9.6
CH2
-103.48
0.0153
0.273/-0.485
2.943
-5.7/-3.0/-0.2
SiH2
-103.78
0.0157
0.280/-0.486
2.921
-5.2/-3.8/-2.5
O(C-I)
-102.99
0.1470
0.143/-0.411
2.731
-6.7/-4.6/-5.5
NH2
PH2
AsH2
+
NH
S 虚频
PH
Wiberg bond
index (PR:I-N)
0.0474
NBO Charges
(PR：I/N)
0.597/-0.533
Figure 4. Their connections at triplet state.
Next I fixed phenylacetonitrile, similarly, I change the X atom and calculated these
structures at T1 and S0 state. The results shown in Table 3 and Table 4.
Table 3. S0 state.
X
EBSSE
(kacl/mol)
NBO Charges
RE (I)
Wiberg bond
index(PR:I-N)
NBO Charges
(PR：I/N)
Bondlength (BL)/Å
Bond angle
(CNI)/°
NICS(0)/NICS(1)/
NICS(1)zz/ppm (RE)
CH+
-18.94
0.556
0.1078
0.632/-0.457
2.700/177.9
31.7/24.0/79.2
SiH+
-16.70
0.516
0.1012
0.575/-0.447
2.725/179.8
14.0/13.8/51.6
GeH+
-16.08
0.497
0.0985
0.557/-0.443
2.734/178.5
14.1/13.5/51.2
+
-16.00
0.415
0.1151
0.429/-0.436
2.694/179.8
-8.7/-3.8/-2.7
+
-15.57
0.430
0.1077
0.457/-0.436
2.714/179.6
-4.9/-1.6/6.5
-15.02
0.415
0.1057
0.443/-0.432
2.722/179.4
-5.1/-1.7/7.1
BH
-3.82
0.264
0.0290
0.307/-0.356
3.102/179.6
13.6/11.7/44.1
AlH
-2.84
0.219
0.0263
0.264/-0.346
3.141/179.3
1.3/3.3/18.9
CH2
-3.26
0.233
0.0286
0.269/-0.350
3.112/178.2
-8.7/-3.9/-3.1
SiH2
-3.29
0.231
0.0289
0.273/-0.350
3.110/179.5
-4.4/-1.3/6.4
O
-4.02
0.253
0.0346
0.283/-0.356
3.005/179.8
-15.6/-7.5/-16.4
NH
-3.01
0.231
0.0289
0.262/-0.347
3.112/177.8
-18.4/-8.7/-20.3
NH2
PH2
AsH2
+
S 虚频多
未作图
0.243
AsH
-3.34
0.229
0.0298
0.270/-0.351
3.102/175.8
-7.9/-3.5/-0.6
PH
-3.48
0.234
0.0303
0.274/-0.352
3.096/177.7
-8.8/-3.9/-3.8
-15.6/-8.1/-15.2
-
N
(nonlinear)
CH-
0.072
Figure 5. Their connections at singlet state.
At last, the substrate is replaced by four-membered ring, six-membered ring and
pentalene as shown in Figure 5. It has marked the NICS values of substrate, BSSE
correction, bond length of N-I atoms, NBO charge on I and N atoms and I (reaction).
1 Substituent Effects on the Cooperativity of Halogen Bonding.