Journal of Chemistry

Volume 2013 (2013), Article ID 124659, 13 pages

http://dx.doi.org/10.1155/2013/124659

Research Article

Vibrational Spectroscopy Investigation Using Ab Initio and Density Functional Theory Analysis on the Structure of tert-Butyl 3a-Chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate

Hakan Arslan,¹ Aydin Demircan,² Gun Binzet,³ and Ilhan Ozer Ilhan⁴

¹Department of Chemistry, Faculty of Arts and Science, Mersin University, 33343 Mersin, Turkey

²Department of Chemistry, Faculty of Arts and Science, University of Nigde, 51100 Nigde, Turkey

³Department of Chemistry, Faculty of Education, Mersin University, 33343 Mersin, Turkey

⁴Department of Chemistry, Faculty of Science, Erciyes University, 38100 Kayseri, Turkey

Received 26 May 2012; Revised 17 June 2012; Accepted 21 June 2012

Academic Editor: Cherumuttathu H. Suresh

Copyright © 2013 Hakan Arslan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract.

The molecular structure, vibrational frequencies, and infrared intensities of the tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate were calculated by the HF and DFT (BLYP and B3LYP) methods using 6-31G(d) and 6-31G(d,p) basis sets. The FT infrared spectrum of the solid sample was measured under standard condition. We obtained two stable conformers for the title compound; however Conformer 1 is approximately 0.2 kcal/mol more stable than the Conformer 2. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of Conformer 2. Comparison of the observed fundamental vibrational frequencies of the title molecule and calculated results by HF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. The harmonic vibrations computed by the B3LYP/6-31G(d,p) method are in a good agreement with the observed IR spectral data. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using VEDA 4 program.

1. Introduction

Epoxides are used as an important intermediate tool in organic synthesis of fine chemicals and pharmaceuticals [1]. Intramolecular Diels-Alder (IMDA) reactions and epoxidation of its cycloadduct have also been of great interest in synthetic pathway of natural products, like conduritols [2], z-isomeric insect sex pheromone components [3], dihydrophenanthroline derivatives [4], vitamin D total synthesis [5], and so on. We have previously prepared a variety of key precursors to the intramolecular Diels-Alder reaction of furan (IMDAF) diene via facile alkylation of furan compounds and its protection. Subsequently IMDAF reaction carried out under thermal condition provided five- and six-membered heterocycles fused to an easily cleavable oxabicycloheptene moiety [6–9].

In this study, tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate, 3, was prepared from 5-chloro-10-oxa-3-aza-tricyclo[5.2.1.01,5]dec-8-en-3-carboxylic acid tert-butyl ester, 1, using meta-chloroperbenzoic acid, 2, in dry dichloromethane which was previously recrystallized in dry diethyl ether at 0°C. The product 3 was analyzed by X-ray diffractometer [10], ¹H and ¹³C NMR, IR, mass spectrometer, and elemental analysis. The goal of this project is to transferring chloro-cycloadduct, 3, to highly substituted tetrahydroisoindole derivative, 4. We are currently researching this stage by opening epoxy bridges on compound 3 (Scheme 1).

Scheme 1: Synthesis of the tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate.

The crystal structure of tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate (TBCEIC) has been determined by X-ray diffraction [10], however so far no ab initio studies have been made on the conformation and vibrational spectra of the title compound in the gas phase. In the present study, we have synthesized and calculated the vibrational frequencies and geometric parameters of TBCEIC in the ground state to distinguish the fundamentals from the experimental vibrational frequencies and geometric parameters, by using the Hartree-Fock [11] and density functional using B3LYP [12, 13] and Becke’s exchange functional in combination with the Lee, Yang, and Parr correlation functional methods [13, 14] (BLYP) with the standard 6-31G(d) and 6-31G(d,p) basis sets. In continuation of our theoretical studies, in the present work, we checked the relative performance of B3LYP and BLYP methods, as well as of HF for comparison, at the 6-31G(d) and 6-31G(d,p) levels taking as a test compound tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate.

2. Results and Discussion

2.1. Conformational Stability

We performed full geometry optimization of the title compound. To establish the most stable conformation as the initial point for further calculations, the molecule was submitted to a rigorous conformation analysis around all bonds having free rotation. This study was performed with the software Spartan 06 [15, 16]. The structure of the title compound has two conformations which are shown in Figure 1. For comparison, the total energy and the relative energies of both conformer of the title compound are given in Table 1. Energetics show that Conformer 1 is the most stable. But comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of Conformer 2. Therefore, we will focus on this particular form (Conformer 2) of the title compound in this paper.

Table 1: Energies B3LYP/6-31G(d,p) of the different conformations of the title compound.

Conformer
(au)
Δ (kcal/mol)
Dipole (debye)

Conformer 1
−1322.05349
0.0
1.5

Conformer 2
−1322.05323
0.2
3.9

(a)

(b)

Figure 1: Two stable conformers of the title compound calculated at B3LYP/6-31G(d,p) level. The torsion angles, C22–N13–C15=O11, for Conformer 1 and 2 are −4.74° and 175.65°, respectively.

2.2. Molecular Geometry

The optimized structure parameters of the title compound calculated by ab initio and DFT method listed in Table 2 are in accordance with atom numbering scheme given in Figure 2(a). The crystal and molecular structure of the title compound have been reported previously [10]. The geometric structure is monoclinic, the space group P2₁/c, with the cell dimensions: Å, Å, Å, , and  Å³ (Figure 2(b)). The structure parameters obtained by X-ray single-crystal diffraction method are given in Table 2. Also, Table 2 compares the calculated geometric parameters with the experimental data.

Table 2: Optimized and experimental geometries of the title compound in the ground state.

Parametersa,b
Experimentalc
Calculated

6-31G(d)
6-31G(d,p)
6-31G(d)
6-31G(d,p)
6-31G(d)
6-31G(d,p)

Bond lengths (Å)

    R (10,16)
1.800 (2)
1.806
1.807
1.865
1.865
1.834
1.834

    R (11,15)
1.210 (3)
1.199
1.200
1.235
1.235
1.222
1.223

    R (12,19)
1.446 (3)
1.411
1.410
1.459
1.459
1.438
1.439

    R (12,21)
1.432 (2)
1.409
1.409
1.457
1.458
1.436
1.437

    R (13,15)
1.339 (3)
1.351
1.349
1.378
1.379
1.364
1.365

    R (13,18)
1.459 (3)
1.456
1.458
1.479
1.481
1.467
1.466

    R (13,22)
1.453 (3)
1.454
1.455
1.476
1.477
1.462
1.463

    R (14,20)
1.442 (3)
1.401
1.401
1.453
1.454
1.433
1.432

    R (14,25)
1.440 (3)
1.401
1.401
1.452
1.452
1.431
1.431

    R (15,17)
1.342 (3)
1.325
1.325
1.378
1.378
1.357
1.356

    R (16,21)
1.548 (3)
1.549
1.550
1.580
1.579
1.566
1.566

    R (16,22)
1.514 (3)
1.532
1.530
1.547
1.547
1.536
1.535

    R (16,24)
1.538 (3)
1.550
1.549
1.566
1.566
1.553
1.554

    R (17,23)
1.463 (3)
1.448
1.449
1.495
1.496
1.472
1.472

    R (18,21)
1.501 (3)
1.512
1.512
1.525
1.526
1.516
1.517

    R (19,24)
1.536 (4)
1.547
1.547
1.567
1.568
1.556
1.556

    R (19,25)
1.509 (4)
1.527
1.526
1.547
1.548
1.535
1.536

    R (20,21)
1.516 (3)
1.526
1.524
1.545
1.545
1.533
1.532

    R (20,25)
1.450 (3)
1.449
1.449
1.480
1.480
1.467
1.468

    R (23,26)
1.508 (4)
1.526
1.525
1.543
1.541
1.531
1.531

    R (23,30)
1.502 (4)
1.527
1.526
1.543
1.543
1.531
1.531

    R (23,34)
1.502 (4)
1.527
1.527
1.544
1.542
1.532
1.532

0.9868
0.9871
0.9961
0.9962
0.9951
0.9950

Bond angles (°)

    A (19,12,21)
96.88 (15)
99.0
99.0
97.6
97.6
98.0
98.0

    A (15,13,18)
120.21 (17)
120.1
120.1
120.0
119.7
120.0
119.9

    A (15,13,22)
127.19 (17)
125.5
125.6
126.1
126.3
126.0
126.3

    A (18,13,22)
112.59 (16)
114.1
114.0
113.8
113.3
113.8
113.6

    A (11,15,13)
123.6 (2)
122.9
122.9
123.0
122.9
123.1
122.9

    A (11,15,17)
125.62 (19)
125.7
125.7
127.1
127.0
126.6
126.5

    A (13,15,17)
110.82 (18)
111.3
111.4
109.9
110.1
110.4
110.6

    A (10,16,21)
110.36 (14)
112.7
112.7
112.2
112.0
112.2
112.1

    A (10,16,22)
108.77 (16)
109.5
109.6
109.2
109.1
109.4
109.3

    A (10,16,24)
113.45 (17)
113.0
112.9
112.4
112.4
112.7
112.8

    A (21,16,22)
101.95 (16)
101.7
101.7
102.0
101.8
101.8
101.6

    A (21,16,24)
102.96 (17)
102.2
102.2
102.7
102.7
102.5
102.5

    A (22,16,24)
118.4 (2)
117.0
117.0
117.8
118.1
117.4
117.8

    A (15,17,23)
120.50 (18)
122.7
122.7
120.2
120.1
120.8
120.7

    A (13,18,21)
103.57 (16)
102.8
102.8
103.3
103.5
103.2
103.3

    A (12,19,24)
102.19 (18)
101.7
101.7
101.9
101.8
101.9
101.9

    A (12,19,25)
101.94 (19)
101.9
101.9
102.1
102.1
102.0
102.1

    A (24,19,25)
107.8 (2)
107.2
107.2
107.6
107.4
107.3
107.2

    A (14,20,21)
114.0 (2)
113.1
113.1
113.7
113.6
113.5
113.5    

    A (21,20,25)
102.9 (2)
102.8
102.8
103.0
103.0
102.8
102.9

    A (12,21,16)
99.80 (15)
98.7
98.6
98.5
98.4
98.8
98.7

    A (12,21,18)
112.54 (17)
112.2
112.2
111.6
111.7
111.8
111.9

    A (12,21,20)
102.24 (16)
102.2
102.3
102.4
102.5
102.5
102.5

    A (16,21,18)
106.95 (16)
106.7
106.7
106.8
106.8
106.7
106.7

    A (16,21,20)
108.39 (16)
109.9
109.9
109.6
109.7
109.4
109.5

    A (18,21,20)
124.24 (19)
124.3
124.2
124.8
124.7
124.7
124.5

    A (13,22,16)
103.32 (17)
103.2
103.2
103.7
103.7
103.6
103.5

    A (17,23,26)
102.1 (2)
102.6
102.6
102.1
102.1
102.4
102.5

    A (17,23,30)
110.0 (2)
110.3
110.3
109.8
110.0
109.9
110.1

    A (17,23,34)
110.0 (2)
110.3
110.2
110.1
109.7
110.2
109.9

    A (26,23,30)
111.1 (3)
110.4
110.5
111.0
110.9
110.8
110.8

    A (26,23,34)
110.5 (3)
110.5
110.6
110.8
111.0
110.7
110.8

    A (30,23,34)
112.7 (3)
112.3
112.3
112.6
112.5
112.4
112.3

    A (16,24,19)
100.05 (3)
99.8
99.9
100.2
100.3
100.2
100.2

    A (19,25,20)
104.00 (19)
103.6
103.6
103.7
103.7
103.6
103.6

0.9929
0.9929
0.9961
0.9966
0.9964
0.9969

aThe  atom numbering scheme of the molecular structure is given in Figure 2(a).

br: correlation coefficient between optimized and experimental geometrical parameters.

cFrom [10].

(a)

(b)

Figure 2: The optimized molecular structure (Conformer 2) of the title compound (a), the single crystal structure of the title compound. Thermal ellipsoids are shown at the 50% probability level (b).

Based on this comparison, the bond lengths and angles calculated for the title compound show good agreement with experiment. However, according to our calculations, the optimized both bond lengths and bond angles obtained by DFT methods show the best agreement with the experimental values. The large difference between experimental and calculated DFT/B3LYP-6-31G(d,p) bond length and bond angle is 0.065 Å and 1.65 °, respectively.

2.3. Vibrational Assignments

Table 3 lists the wavenumbers of the bands observed in the FT-IR spectra of the tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate. The theoretical frequencies and infrared intensities calculated by HF, BLYP, and B3LYP methods of the title compound are gathered in Table 3. The last column of Table 3 shows the detailed vibrational assignment obtained from the calculated potential energy distribution (PED).

Table 3: Vibrational wavenumbers obtained for the title compounda.

HF
BLYP
B3LYP

Number
Exp.
6-31G(d)
6-31G(d,p)
6-31G(d)
6-31G(d,p)
6-31G(d)
6-31G(d,p)
IR intensity
Assignments, PED (%)b

Unscal
Sca.
Sca.
Unscal
Sca.
Sca.
Unscal
Sca.
Sca.
Unscal
Sca.
Sca.
Unscal
Sca.
Sca.
Unscal
Sca.
Sca.
Abs.
Rel.

1
3082
3418
3067
3060
3397
3065
3055
3134
3100
3117
3131
3102
3154
3226
3093
3101
3218
3093
3094
3
0
ν CH, C20, 96

2
3067
3386
3038
3031
3363
3035
3024
3100
3066
3083
3095
3066
3117
3194
3062
3071
3184
3060
3061
14
2
ν CH, C25, 95

3
3067
3342
2999
2992
3323
2999
2988
3090
3056
3073
3094
3065
3116
3174
3043
3051
3173
3050
3051
7
1
ν CH3, asym, C30, C34, 88

4
3067
3337
2995
2988
3320
2996
2985
3086
3052
3069
3089
3060
3111
3170
3039
3048
3168
3045
3046
3
0
ν CH3, asym, C30, C34, 90

5
3010
3336
2994
2987
3316
2992
2982
3073
3039
3056
3081
3052
3103
3158
3027
3036
3159
3036
3037
3
0
ν CH2, a sym, C22, 94

6
3010
3334
2992
2985
3311
2988
2977
3068
3034
3051
3066
3037
3088
3155
3025
3033
3149
3027
3027
26
4
ν CH, C19, 92

7
3010
3310
2970
2963
3294
2972
2962
3057
3024
3040
3060
3031
3082
3143
3013
3022
3142
3020
3021
6
1
ν CH2, asym, C24, 91

8
3003
3309
2969
2963
3290
2969
2958
3052
3019
3035
3054
3025
3076
3136
3006
3015
3134
3012
3013
50
7
ν CH3, asym, C26, 92

9
3003
3288
2951
2944
3272
2953
2942
3051
3018
3034
3052
3023
3074
3133
3003
3012
3131
3009
3010
30
4
ν CH3, asym, C26, 95

10
3003
3286
2949
2942
3271
2952
2941
3036
3003
3019
3041
3012
3063
3120
2991
3000
3120
2999
3000
18
3
ν CH3, asym, C26, C30, C34, 92

11
3003
3271
2935
2929
3256
2938
2928
3034
3001
3017
3039
3010
3061
3118
2989
2998
3118
2997
2998
7
1
ν CH3, asym, C30, C34, 97

12
3003
3269
2933
2927
3254
2936
2926
3025
2992
3008
3023
2995
3045
3116
2987
2996
3110
2989
2990
7
1
ν CH2, asym, C18, 96

13
2972
3261
2926
2920
3243
2926
2916
3011
2978
2994
3011
2983
3033
3094
2966
2975
3089
2969
2970
15
2
ν CH2, sym, C24, 97

14
2964
3256
2922
2915
3235
2919
2909
2985
2952
2969
2987
2959
3009
3072
2945
2953
3069
2950
2951
15
2
ν CH2, sym, C18, 95

15
2928
3241
2908
2902
3220
2906
2895
2984
2951
2968
2985
2957
3006
3064
2937
2946
3060
2941
2942
23
3
ν CH3, sym, C26, C30, C34, 91

16
2928
3223
2892
2886
3203
2890
2880
2978
2945
2962
2978
2950
2999
3057
2931
2939
3052
2933
2934
23
3
ν CH3, sym, C30, C34, 90

17
2928
3213
2883
2877
3193
2881
2871
2976
2943
2960
2976
2948
2997
3056
2930
2938
3051
2933
2933
10
1
ν CH3, sym, C26, C30, C34, 89

18
2928
3212
2882
2876
3192
2880
2870
2952
2920
2936
2955
2927
2976
3045
2919
2927
3042
2924
2925
30
4
ν CH2, sym, C22, 95

19
1686
1941
1742
1738
1939
1750
1744
1704
1685
1695
1700
1684
1712
1784
1710
1715
1781
1712
1712
384
57
ν C=O, C15-O11, 82

20
1474
1672
1500
1497
1657
1495
1490
1519
1502
1511
1507
1493
1518
1557
1493
1497
1543
1483
1483
17
2
δ CH3, deform., C26, C30, C34, 64

21
1460
1669
1498
1494
1653
1492
1486
1497
1481
1489
1483
1469
1494
1538
1474
1479
1519
1460
1460
1
0
δ CH2, sciss., C18, C22, 51

22
1460
1659
1489
1485
1643
1483
1477
1496
1480
1488
1477
1463
1488
1534
1471
1475
1519
1460
1460
4
1
δ CH2, sciss., C18, C22, 66

23
1451
1652
1482
1479
1636
1476
1471
1487
1471
1479
1471
1457
1482
1527
1464
1468
1511
1452
1453
3
0
δ CH2, sciss., C18, C22, 56

24
1451
1645
1476
1473
1629
1470
1465
1485
1469
1477
1471
1457
1482
1524
1461
1465
1508
1449
1450
16
2
δ CH3, deform., C30, C34, 58

25
1451
1643
1474
1471
1626
1467
1462
1484
1468
1476
1469
1455
1480
1521
1458
1462
1507
1448
1449
3
0
δ CH3, deform., C26, C30, 68

26
1431
1637
1469
1466
1620
1462
1457
1482
1466
1474
1467
1453
1478
1519
1456
1460
1501
1443
1443
0
0
δ CH3, deform., C26, C34, 70

27
1431
1636
1468
1465
1619
1461
1456
1475
1459
1467
1459
1445
1470
1515
1452
1457
1499
1441
1441
8
1
δ CH2, sciss., C24, 76

28
1427
1619
1453
1449
1601
1445
1440
1462
1446
1454
1447
1433
1457
1499
1437
1441
1483
1425
1426
1
0
δ CH3, deform., C26, C30, C34, 81

29
1409
1597
1433
1430
1594
1438
1433
1416
1401
1408
1398
1385
1408
1455
1395
1399
1445
1389
1389
674
100
ν NC, N13-C15, 53

30
1392
1585
1422
1419
1583
1428
1423
1387
1372
1379
1374
1361
1384
1443
1383
1387
1438
1382
1382
14
2
δ CH3, umbrella, C26, C30, C34, 51

31
1360
1584
1421
1418
1569
1416
1411
1380
1365
1372
1366
1353
1376
1435
1376
1380
1431
1375
1376
21
3

32
1360
1560
1400
1397
1545
1394
1389
1366
1351
1358
1364
1351
1374
1427
1368
1372
1412
1357
1357
14
2

33
1350
1559
1399
1396
1544
1393
1388
1362
1347
1355
1361
1348
1371
1422
1363
1367
1408
1353
1354
18
3

34
1350
1546
1387
1384
1538
1388
1383
1350
1335
1343
1339
1326
1349
1403
1345
1349
1394
1340
1340
23
3

35
1327
1521
1365
1362
1513
1365
1360
1335
1320
1328
1328
1316
1338
1383
1326
1330
1376
1323
1323
10
1

36
1305
1483
1331
1328
1477
1333
1328
1292
1278
1285
1290
1278
1299
1340
1285
1288
1337
1285
1285
2
0

37
1282
1472
1321
1318
1464
1321
1316
1280
1266
1273
1277
1265
1286
1332
1277
1281
1328
1276
1277
6
1

38
1259
1454
1305
1302
1449
1308
1303
1268
1254
1261
1262
1250
1271
1321
1266
1270
1315
1264
1264
5
1

39
1247
1420
1274
1271
1414
1276
1271
1246
1232
1239
1243
1231
1252
1293
1240
1243
1288
1238
1238
26
4

40
1228
1408
1263
1261
1401
1264
1260
1236
1222
1229
1230
1218
1239
1283
1230
1233
1278
1228
1229
15
2

41
1222
1395
1252
1249
1387
1252
1247
1233
1220
1226
1229
1217
1238
1282
1229
1233
1275
1225
1226
15
2

42
1211
1391
1248
1245
1387
1252
1247
1211
1198
1204
1209
1198
1218
1264
1212
1215
1262
1213
1213
9
1

43
1211
1374
1233
1230
1367
1234
1229
1210
1197
1203
1205
1194
1214
1256
1204
1208
1250
1201
1202
22
3

44
1180
1366
1226
1223
1362
1229
1225
1198
1185
1191
1191
1180
1200
1246
1194
1198
1242
1194
1194
27
4

45
1180
1364
1224
1221
1358
1225
1221
1193
1180
1186
1189
1178
1198
1241
1190
1193
1234
1186
1186
4
1

46
1180
1354
1215
1212
1349
1217
1213
1178
1165
1172
1170
1159
1178
1229
1178
1182
1224
1176
1177
9
1

47
1163
1336
1199
1196
1329
1199
1195
1171
1158
1165
1167
1156
1175
1218
1168
1171
1213
1166
1166
34
5

48
1163
1330
1193
1191
1324
1195
1191
1161
1148
1155
1154
1143
1162
1210
1160
1163
1204
1157
1158
372
55

49
1128
1289
1157
1154
1287
1161
1157
1100
1088
1094
1093
1083
1101
1152
1104
1108
1150
1105
1106
112
17

50
1109
1269
1139
1136
1266
1142
1138
1089
1077
1083
1087
1077
1095
1144
1097
1100
1138
1094
1094
4
1

51
1089
1247
1119
1116
1243
1122
1118
1075
1063
1069
1068
1058
1076
1140
1093
1096
1132
1088
1088
34
5

52
1061
1219
1094
1091
1216
1097
1093
1050
1039
1044
1044
1034
1052
1096
1051
1054
1092
1050
1050
16
2

53
1045
1212
1088
1085
1210
1092
1088
1040
1029
1034
1034
1024
1041
1080
1035
1038
1080
1038
1038
22
3

54
1033
1177
1056
1054
1174
1059
1056
1030
1019
1024
1026
1016
1033
1069
1025
1028
1063
1022
1022
1
0

55
1005
1174
1054
1051
1171
1057
1053
1024
1013
1018
1024
1014
1031
1062
1018
1021
1057
1016
1016
0
0

56
1005
1160
1041
1039
1153
1040
1037
1016
1005
1010
1007
998
1014
1061
1017
1020
1054
1013
1013
18
3

57
993
1157
1038
1036
1150
1038
1034
986
975
981
984
975
991
1038
995
998
1038
998
998
34
5

58
960
1128
1012
1010
1126
1016
1012
964
953
959
961
952
968
1014
972
975
1012
973
973
7
1

59
947
1109
995
993
1105
997
994
953
943
948
947
938
954
995
954
957
990
952
952
42
6

60
928
1067
957
955
1065
961
958
941
931
936
935
926
942
979
939
941
972
934
934
0
0

61
928
1062
953
951
1054
951
948
910
900
905
907
898
914
961
921
924
958
921
921
11
2

62
920
1026
921
919
1023
923
920
904
894
899
901
893
907
945
906
909
942
905
906
14
2

63
910
1014
910
908
1010
911
908
902
892
897
899
891
905
936
897
900
932
896
896
2
0

64
910
1012
908
906
1007
909
905
901
891
896
896
888
902
934
895
898
929
893
893
0
0

65
883
1009
905
903
1006
908
905
870
860
865
863
855
869
910
872
875
907
872
872
16
2

66
873
997
895
893
993
896
893
857
848
852
855
847
861
907
870
872
902
867
867
7
1

67
862
984
883
881
981
885
882
841
832
836
839
831
845
892
855
858
891
856
857
42
6

68
852
977
877
875
974
879
876
828
819
823
830
822
836
877
841
843
878
844
844
27
4

69
835
956
858
856
955
862
859
817
808
813
816
808
822
868
832
834
867
833
834
11
2

70
825
942
845
843
940
848
845
810
801
806
808
800
814
854
819
821
852
819
819
3
0

71
808
920
826
824
918
828
825
792
783
788
791
784
797
835
800
803
833
801
801
9
1

72
764
899
807
805
898
810
807
779
770
775
777
770
783
817
783
785
815
783
784
21
3

73
750
875
785
783
875
790
787
743
735
739
743
736
748
778
746
748
777
747
747
3
0

74
729
847
760
758
846
763
761
726
718
722
725
718
730
760
729
731
757
728
728
5
1

75
729
818
734
732
817
737
735
712
704
708
707
700
712
757
726
728
755
726
726
21
3

76
685
812
729
727
811
732
729
696
688
692
692
686
697
736
706
708
732
704
704
28
4

77
633
737
661
660
737
665
663
653
646
649
654
648
659
681
653
655
681
655
655
10
1

78
582
675
606
604
674
608
606
589
583
586
589
583
593
617
591
593
617
593
593
10
2

79
546
641
575
574
640
578
575
563
557
560
560
555
564
588
564
565
586
563
563
13
2

80
524
562
504
503
562
507
505
499
494
496
501
496
505
520
499
500
520
500
500
5
1

81
0
537
482
481
537
485
483
469
464
466
469
465
472
490
470
471
490
471
471
4
1

82
0
527
473
472
527
476
474
459
454
456
461
457
464
482
462
463
482
463
463
3
0

83
0
495
444
443
495
447
445
445
440
443
441
437
444
461
442
443
459
441
441
3
0

84
0
477
428
427
477
430
429
421
416
419
425
421
428
437
419
420
440
423
423
4
1

85
0
443
398
397
442
399
397
385
381
383
389
385
392
403
386
387
404
388
388
4
1

86
0
429
385
384
429
387
386
381
377
379
382
378
385
398
382
383
400
384
385
1
0

87
0
388
348
347
388
350
349
339
335
337
340
337
342
352
337
338
353
339
339
2
0

88
0
376
337
337
377
340
339
337
333
335
335
332
337
350
336
336
349
335
336
1
0

89
0
358
321
321
358
323
322
320
316
318
324
321
326
332
318
319
334
321
321
16
2

90
0
341
306
305
341
308
307
305
302
303
305
302
307
316
303
304
315
303
303
1
0

91
0
336
302
301
336
303
302
299
296
297
299
296
301
311
298
299
311
299
299
2
0

92
0
311
279
278
311
281
280
272
269
271
272
269
274
283
271
272
283
272
272
4
1

93
0
305
274
273
303
273
272
268
265
267
270
267
272
277
266
266
268
258
258
0
0

94
0
275
247
246
274
247
246
259
256
258
250
248
252
263
252
253
246
236
237
0
0

95
0
239
214
214
239
216
215
213
211
212
216
214
218
222
213
213
224
215
215
4
1

96
0
233
209
209
230
208
207
204
202
203
210
208
212
212
203
204
215
207
207
2
0

97
0
227
204
203
228
206
205
201
199
200
197
195
198
208
199
200
200
192
192
0
0

98
0
197
177
176
197
178
177
162
160
161
169
167
170
171
164
164
177
170
170
1
0

99
0
186
167
167
186
168
167
157
155
156
161
159
162
170
163
163
169
162
162
0
0

100
0
148
133
133
148
134
133
136
135
135
136
135
137
141
135
136
139
134
134
1
0

101
0
123
110
110
123
111
111
108
107
107
110
109
111
113
108
109
113
109
109
2
0

102
0
86
77
77
86
78
77
79
78
79
80
79
81
81
78
78
82
79
79
0
0

103
0
74
66
66
74
67
67
65
64
65
65
64
65
67
64
64
65
62
62
2
0

104
0
44
39
39
44
40
40
43
43
43
46
46
46
43
41
41
46
44
44
0
0

105
0
22
20
20
21
19
19
19
19
19
14
14
14
18
17
17
11
11
11
0
0

r

0.9997
0.9997
0.9997
0.9997
0.9997
0.9997
0.9998
0.9998
0.9998
0.9998
0.9998
0.9998
0.9999
0.9999
0.9999
0.9999
0.9999
0.9999

Mean deviation

190.49
14.55
11.01
181.49
15.05
9.60
12.73
−4.08
4.27
8.49
−5.89
19.52
66.71
0.96
5.32
61.31
−0.24
0.13

Mean absolute deviation

190.49
34.33
34.02
181.49
34.93
34.37
21.23
15.75
17.1
20.24
16.22
26.00
66.81
10.99
11.56
61.41
9.69
9.67

Average absolute error

13.61
2.69
2.57
13.08
2.77
2.59
1.48
1.39
1.36
1.41
1.42
1.61
4.47
0.96
0.99
4.07
0.86
0.86

RMSmol

201.95
37.40
37.61
191.47
37.94
38.43
26.65
18.49
20.81
25.40
19.37
34.91
76.04
13.40
14.29
71.20
12.34
12.34

RMSover

176.28
32.65
32.83
167.13
33.11
33.54
23.26
16.14
18.16
22.17
16.91
30.48
66.37
11.7
12.47
62.15
10.77
10.77

Scaling factor

1.000
0.8974
0.8953
1.000
0.9024
0.8992
1.000
0.9891
0.9945
1.000
0.9906
1.0072
1.000
0.9587
0.9614
1.000
0.9612
0.9614

aHarmonic frequencies (in cm⁻¹) and IR intensities (km/mol).

bν: stretching; : in-plane bending; : out-of-plane bending; : torsion; sym: symmetric; asym: asymmetric; R1: C19-O12-C21-C20-C25; R2: C19-O12-C21-C16-C24; R3: C16-C21-C18-N13-C22. PED less than 10% are not shown.

Comparison of the frequencies calculated at HF, BLYP, and B3LYP with experimental values reveals the overestimation of the calculated vibrational modes due to neglect of anharmonicity in real system. Inclusion of electron correlation in density functional theory to a certain extent makes the frequency values lower in comparison with the Hartree-Fock frequency data [17–20]. Reductions in the computed harmonic vibrations, though basis set sensitives are only marginal as observed in the DFT values using 6-31G(d) and 6-31G(d,p). Any way notwithstanding the level of calculations, it is customary to scale down the calculated harmonic frequencies in order to improve the agreement with the experiment [17–20]. Therefore, the scaling factor values of 0.8953/0.8992, 0.9614/0.9614, and 0.9945/1.0072 for HF, B3LYP, and BLYP (6-31G (d)/6-31G(d,p)), respectively, are used in our study [17, 21–25]. Experimental fundamentals are in better agreement with the scaled fundamentals which are found to have a good correlation for DFT/B3LYP/6-31G(d,p) () than HF method. The calculated frequencies (scaled) do not differ so much from the experimental ones that the maximum difference between two spectra is not more than 27 cm⁻¹ for DFT/B3LYP/6-31G(d,p) method. Also, the average absolute error of the calculated frequencies was found less than 0.86% for DFT/B3LYP/6-31G(d,p) method.

A general better performance of B3LYP and BLYP versus HF can be quantitatively characterized by using the mean deviation, mean absolute deviation, average absolute error, root mean square values, and coefficients of correlation () between the calculated and observed vibration frequencies and given in Table 3. All these values were calculated in this study by the PAVF 1.0 program [26] according to Scott and Radom [21]. The root mean square (RMS) values were obtained in this study using the following expression [21]:

The values for both DFT methods were greater than 0.9998, whereas for HF it was 0.9997. These values are very close to those reported in the literature [27–33]. These results indicate that the B3LYP calculations approximate the observed fundamental frequencies much be better than the HF results. The small difference between experimental and calculated vibrational modes is observed. It must be due to the fact that hydrogen bond vibrations present in crystal lead to strong perturbation of the infrared frequencies (and intensities) of many other modes. Also, we state that the experimental results belong to solid phase and theoretical calculations belong to gaseous phase [17, 19, 20, 23–25, 30–34].

Finally, we calculated the optimal scaling factors, which are crucial for IR spectral predictions, using the PAVF 1.0 program [26]. Without accounting for different vibrations, only single-uniform scaling factors were calculated. The values obtained are 0.8974/0.9024, 0.9587/0.9612, and 0.9891/0.9906 for the HF, B3LYP, and BLYP (6-31G(d)/6-31G(d,p)) methods, respectively. They are very close to those recommended by Scott and Radom [21] for the same levels of theory and increase in the same order of the HF, B3LYP and BLYP methods. Thus, for future IR spectral predictions for unknown derivatives of the title compound, one can recommend scaling factors of 0.897/0.902, 0.959/0.961, and 0.989/0.991 for the HF, B3LYP, and BLYP (6-31G(d)/6-31G(d,p)) methods, respectively.

The IR bands at 3082, 3067, and 3010 cm⁻¹ in FT-IR spectrum of the title compound have been designated to νCH stretching fundamentals of C20, C25, and C19 atoms, respectively [23, 35, 36]. The wavenumbers corresponding to the aliphatic νCH stretching are listed in Table 3. All the calculated values in each method are overestimated, as well known in theoretical quantum mechanic assignment concerning hydrocarbons. After we applied the scale factor both calculated in this research and given by Scott and Radom [21] for all the methods, we observed a good concordance between the experimental and the calculated values. The vibrational spectra show six bands in the aliphatic νCH stretching region and evident overlap between the different C–H stretching modes. The asymmetric and the symmetric νC–H stretching bands for –CH₂– group are listed in Table 3. These assignments were also supported by the literature [20, 23, 35, 37]. The in-plane and out-of-plane bending vibrations of C–H group have also been identified for the title compound and they are presented in Table 3.

The carbonyl stretching vibrations are found in the region 1780–1700 cm⁻¹ [38, 39]. The sharp intense band in IR spectrum at 1686 cm⁻¹ can be assigned to the carbonyl group νC=O stretching vibration.

The vibrational modes concerning the bond angle bending (–CH₂–), scissoring, wagging, twisting, and rocking are well defined in all the calculations. As seen from Table 3, the bands observed at 1460, 1451, and 1431 cm⁻¹ in FT-IR spectrum correspond to scissoring deformation of –C(18)H₂–, –C(22)H₂– and –C(24)H₂– group in the title compound, respectively [37, 40]. The theoretically computed values of scissoring deformation vibration modes show a good agreement with the experimental values. The wagging, twisting, and rocking vibrational modes are distributed in a wide range [36, 37, 40, 41]. Twisting and wagging vibrational modes of the –CH₂– groups were assigned in the range of 1350–1163 cm⁻¹. The above result is in close agreement with the literature values [36, 37, 40–42]. These vibrational modes are described in the tables by mean of the general symbol δCH₂. The rocking –CH₂– is assigned in the wavenumber range of 1109–852 cm⁻¹, and the wavenumber shift of these bands is due to the atom nature in which the –CH₂– group is bonded. The –CH₂– rocking vibrational modes are generally intensive bands which can be appreciating the vibrational coupling with other vibrational modes [36, 37]. These bands are assigned using calculated potential energy distribution.

For the assignments of CH₃ group frequencies, 15 fundamental vibrations can be associated to CH₃ groups. Nine stretching, three umbrella, and three rocking vibration modes are designated the motion of the methyl group. The CH₃ asymmetric and symmetric stretching frequencies are established at 3067, 3010, 3003, and 2923 cm⁻¹ in infrared spectrum. The three methyl hydrogen deformation modes are also well established in the spectrum. We have observed the methyl deformation mode at 1474, 1451, 1431, and 1409 cm⁻¹ in the infrared spectrum.

The C–C stretching vibrations in cyclic alkanes appeared as weak bands, so these vibrations are of little importance for structural study [43]. The IR bands appearing at 1360, 1247, 1222, 1211, 1180, 1163, 1128, 1109 1089, 1045, 993, 947, and 928 cm⁻¹ were assigned to νCC vibrations coupled with the δCCH for the title compound. So, in our study, the C–C stretching vibrations are observed as medium-intensity bands. These results were confirmed by Gunasekaran et al. [44].

The identification of CN vibrations is a difficult task, since the mixing of vibrations is possible in CN stretching vibration frequencies region. However, with the help of both the animation option of Gaussian programs and theoretical calculations (VEDA 4), the CN vibrations are identified and assigned in this study. The IR bands appearing at 1409, 1282 and 1211 cm⁻¹ are assigned to νCN vibrations. These results agree with Sundaraganesan et al. [45].

Epoxide group could be identified via its characteristic C–O stretching bands which gives two different absorption bands in the fingerprint region around ~800–950 and ~1250 cm⁻¹, respectively [46, 47]. There is also a third band in the range 750–850 cm⁻¹. The IR bands appearing at 1180, 993, and 883 cm⁻¹ are assigned to C–O stretching vibrations. These results agree with Evtushenko et al. [47]. The difference between observed and literature values is coming from the effects of the aromatic rings.

The νC–Cl stretching vibrations give generally strong bands in the region of 710–505 cm⁻¹. The band observed at 685 cm⁻¹ in FT-IR spectrum has been assigned to νC–Cl stretching vibration in the present investigation [37].

2.4. Other Molecular Properties

Several calculated thermodynamic parameters are presented in Table 4. The total energies and the changes in the total entropy of the title compound at room temperature at different methods also presented.

Table 4: Theoretically computed energies, zero-point vibrational energies, entropies and dipole moment for the title compound.

Thermodynamic parameter
HF
BLYP
B3LYP

6-31G(d)
6-31G(d,p)
6-31G(d)
6-31G(d,p)
6-31G(d)
6-31G(d,p)

Total energy (a.u.)
−1316.1201
−1316.1634
−1321.6722
−1321.6975
−1322.0277
−1322.0532

Zero-point vibrational energy (kcal/mol)
206.307
205.270
184.792
184.321
191.332
190.656

Entropy (cal/mol K)

    Total
130.140
130.324
138.036
130.906
135.418
128.758

    Translational
42.862
42.862
42.862
42.862
42.862
42.862

    Rotational
33.707
33.705
33.821
33.775
33.757
33.725

    Vibrational
53.571
53.758
61.353
54.269
58.799
52.170

Dipole moment (D)
4.4
4.4
3.8
3.7
4.0
3.9

3. Experimental

Dichloromethane (DCM) was distilled from calcium hydride. Reactions were monitored by thin layer chromatography (TLC) using precoated silica plates (Macherey Nagel sil G UV254). Compounds were visualized using ultraviolet fluorescence, alkaline potassium permanganate solution, or acidic cerium (IV) sulphate solution. Column chromatography was carried out using Macharey Nagel Kieselgel 60 (230–240 mesh).

3.1. Instrumentation

Melting points were determined using an Electrothermal-9300 Digital Melting Points Apparatus (Electrothermal Inc., Essex, UK). The ¹H and ¹³C NMR spectra were recorded on a BrukerAvance DPX-400 spectrometer at the TÜBİTAK Analytical Laboratory (Ankara, Turkey). The chemical shifts are quoted in ppm, as δ values downfield of tetramethylsilane (TMS) or relative to the residual solvent resonance. Electron ionisation mass spectra (EI, 70 eV) were obtained on a Perkin Elmer Clarus 500 mass spectrometer. Elemental analysis was carried on LECO CHNS 932, TÜBİTAK Analytical Laboratory (Ankara, Turkey). The room-temperature-attenuated total reflection Fourier transform infrared (FT-IR ATR) spectrum of the tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate was recorded using Varian FTS1000 FT-IR spectrometer with Diamond/ZnSe prism (4000–525 cm⁻¹; number of scans: 250; resolution: 1 cm⁻¹) in the solid (Figure 3).

Figure 3: FT-IR spectrum of tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate.

3.2. Synthesis of tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate

To a solution of meta-chloroperbenzoic acid (m-CPBA) (120 mg, 0.66 mmol), which had previously been purified and re-crystallized from dry diethyl ether, in dichloromethane (10 mL), cooled to 0 °C, was added dropwise a solution of tert-butyl 7a-chloro-1,6,7,7a-tetrahydro-3a,6-epoxyisoindole-2-carboxylate (0.66 mmol) in dichloromethane (10 mL) over a period of 3 min (Scheme 1). The reaction mixture was stirred at room temperature for 4 h and then diluted with cold 4% sodium bicarbonate solution (4 mL). The organic layer was separated, washed with water ( mL), and concentrated in vacuum. The residue was subjected to flash column chromatography. As white crystal (110 mg, 56%). M.p.: 137–139 °C, TLC, (hexane: ethyl acetate (7 : 3)): Rf: 0.26. ¹H NMR (400 MHz CDCl₃) δ: 4.63 (d, 1H, H4, ), 4.01–3.73 (m, 4H, H7, H8), 3.75 (d, 1H, H3, , AB ), 3.52 (d, 1H, H2, , AB ), 2.52 (dd, 1H, H5, , , AB), 1.90 (d, 1H, H5, , AB), 1.45 (s, 9H, H11, H12, H13). ¹³C NMR (75 MHz CDCl₃) δ: 154.0 (C9, q), 91.1 (C1, q), 80.2 (C10, q), 77.2 (C4), 75.3 (C6, q), 60.5 (C2), 49.1 (C7), 48.3 (C8), 45.3 (C5), 42.1 (C3), 28.4 (C11, C12, C13). GC-MS (m/z): 288 [M⁺, %100], 252 [M⁺–(Cl), %55], 213 [M⁺–(OtBu), % 45] 167 [M⁺–(C8H9N), %85]. Elemental analysis (%) for C₁₃H₁₈ClNO₄: theoretical (experimental) C, 54.26 (54.03); H, 6.31 (6.15); N, 4.87 (4.71).

3.3. Calculations Details

The conformation analysis study was performed by Spartan 06 program package [15, 16]. All the other calculations were performed with the Gaussian 03W program package on a double xeon/3.2 GHz processor with 8 GB Ram [48]. The molecular structure of the title compound, in the ground state, is optimized by using HF, BLYP and B3LYP methods with the standard 6-31G(d) and 6-31G(d,p) basis sets. The vibrational frequencies were also calculated with these methods. The frequency values computed at these levels contain known systematic errors [27–29, 49–53]. Therefore, we have used the scaling factor for HF, B3LYP, and BLYP methods [17, 21–25]. We have also calculated optimal scaling factors for all investigated methods. We have also calculated optimal scaling factors for all investigated methods. The assignment of the calculated wavenumbers is aided by the animation option of GaussView 3.0 graphical interface for gaussian programs, which gives a visual presentation of the shape of the vibrational modes [52]. Furthermore, theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using VEDA 4 program [54].

4. Conclusions

The frequency assignment for the tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate has been done for the first time from the FT-IR spectrum recorded. The conformation stability, equilibrium geometries, and harmonic frequencies of the title compound were determined and analyzed both at HF and DFT level of theories utilizing 6-31G(d) and 6-31G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Any discrepancy noted between the observed and the calculated frequencies may be due to the fact that the calculations have been actually done on a single molecule in the gaseous state contrary to the experimental values recorded in the presence of intermolecular interactions. The IR spectrum of the title compound was interpreted in terms of the potential energy distribution (PED) analysis. Optimal uniform scaling factors were calculated for the title compound. Taking into account small variations of the scaling factors for the derivatives of the title compound, for future IR spectral predictions for unknown compounds of this class, one can recommend scaling factors of 0.897/0.902, 0.959/0.961, and 0.989/0.991 for HF, B3LYP, and BLYP (6-31G(d)/6-31G(d,p)), respectively.

Acknowledgments

The authors are grateful to TÜBİTAK, The Scientific and Research Council of Turkey (Project no. 107T831), and Mersin University Research Fund (Project no. BAP.ECZ.F.TB.(HA).2006-1) for financial support of this work.

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