education

1. Using Maestro and Gaussian 09 in the Qualitative analysis of
Endiynes (enyne-allenes)
Abstract
By Dr. Robert D. Craig,Ph.D.
-8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec 2- yne,4-ene,6-yne
Students in my group have carried out DFT and various Analytical techniques to study an
enyne-allene OR Enediyne- C11H5O4. Mapping the synthesize of C11H5O4 was done with alpha-
butanone. The FT-NMR (1
H and 13
C) and FT-Raman were obtained . The spectra was adequate to
analyze and were compared to literature values. . The FT-NMR (1H and 13C) and FT-Raman was
calculaed The Mulliken, Lowdin, and NBO analysis were also carried out on the enediynes. Students
became familiar with DFT analysis , and using the molecule, completed with respect each instrument
(UV-VIS, FT-NMR, and FT-IR) using the B-3-YLP/6-311++(2p,3d), MP2, and RHF-STO-3G-basis sets. The
calculated HOMO and LUMO values were compared with spectra taken on the Cary Fluorescence
spectrophotometer.
Introduction
Ref 1
Enediynes undergo a Bergman cyclization reaction to form the labile 1,4-didehy-
drobenzene (p-benzyne) biradical. (1-3) The energetics of this reaction and the related
Schreiner–Pascal reaction as well as that of the Myers–Saito and Schmittel reactions of enyne-
allenes are discussed on the basis of a variety of quantum chemical and available experimental
results. (4-6) a family all nine national products is having a common remember system
bicyclo[7.3.0] dodecadiynene. Of the nine natural products are: necarzinostatin, kedarcidin, c-
1027 fifth with, an maduropeptin and N that1199A2. Although all the known nine membered
enediynes that contain a common bicyclo[7.3.0] dodecadiynene chromphore, only five have
complete structures The computational investigation of enediynes has been beneficial for both
experimentalists and theoreticians because it has led to new synthetic challenges and new
computational methodologies. The computer-assisted drug design of new antitumor antibiotics
based on the biological activity of natural enediynes in now very popular for the understanding
of catalyzed enediyne reactions

2. Figure one shows 8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec 2- yne,4-ene,6-yne
Or molecule 72- C11H5O4 and Molecule 73- C17H11O4
Figure xx: molecule 72 or 8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec
2- yne,4-ene,6-yne

3. Figure xx: molecule 73 or 8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec
2- yne,4-ene,6-yne
Figure xx: molecule 72 or 8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec
2- yne,4-ene,6-yne
Table xx: data for 8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec 2-
yne,4-ene,6-yne

4. Zero-point vibrational energy
385897.3 (Joules/Mol)
Molecular mass: 202.02661 amu.
This molecule is an asymmetric top: C1
Rotational symmetry number 1.
energy value Units units
E (Thermal) 100.229 KCal/Mol (Joules/Mol)
CV 48.707 Cal/Mol-Kelvin (Joules/Mol-Kelvin
S 112.669 Cal/Mol-Kelvin (Joules/Mol-Kelvin
Ref 2
8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec 2- yne,4-ene,6-yne =drawn with Maestro
2. computational Methods
This protocol is intended to provide chemists who discover or make new organic compounds
with a valuable tool for validating the structural assignments of those new chemical entities.
Experimental 1
H and/or 13
C NMR spectral data and its proper interpretation for the compound of
interest is required as a starting point. The approach involves the following steps: (i) using

5. molecular mechanics calculations (with, e.g., Maestro) to generate a suitable structure; (ii) using
density functional theory (DFT) calculations (with, e.g., Gaussian 09) to determine optimal
geometry, infrared absorptions and chemical shifts (iii) comparing the computed chemical shifts
for two or more candidate structures with experimental data to determine the best fit.
Below in Table xx, is a brief summary of the steps
Table XX: obtaining computational data for your molecule of interest
1. Draw your biologically significant molecule using Maestro by Schrodinger (i3 processor is fine)
2. produce an "SDF" file
3. open the SDF file in Avogadro-run the Geometry optimization
4. send the Geometry optimized z-matrix to Gaussian 09 (HPCC "Bob")
5 run the FT-IR, Raman, conformation analysis, and FT NMR using the B-3-YLP/6-311++(2p,3d), MP2,
and RHF-STO-3G-basis sets
6. You can run PC Gamess/Firefly and "MASK" to get adequate HOMO and LUMO and VPE on an "i3" Core
3. Results and discussion
3.1 geometry
Inport second
The optimized geometry parameters, i.e., bond lengths and bond angles, computed at the
B3LYP/6-311G* level were compared with those found by single crystal X-ray diffraction (
Table xxx. According to the X-ray single crystal data, the molecule 72 might be linked by
intermolecular hydrogen bonds between the hydroxyl group and O atoms of the C-0-C bridge.
Our calcultations give C1(non-planar) geometry for molecule 72 with an intramolcular H-bbond
neighboring OH and C-O-C ethoyond neighboring OH and C-O-C ethoxide
Also O26-H27…O27. The calculated h-bond distance between O26…O27 is 2.54 angstrom. In
the x-ray structure the same distance is 2.54 angstrom. Bearing in mind that in the crystal both
O-atoms participate additionally in two intermolecular H-bonds, we consider that the
computational method gives good results

6. BOND DISTANCE ANGLE DIHEDRAL
O 1 1.39557
C 2 1.39313 C-0 1 109.26779 C-0
C 3 1.45267 C-O-C 2 114.36653 C1-O-C3-C4 1 130.43435
C 4 1.42546 C4-C3-C2 3 118.35424 C4-C3-C2-C5 2 321.82219
C 5 1.20105 C5-C4-C3 4 158.03028 C5-C4-C3-C1 3 351.94693
C 1 1.42807 C1-C5-C4 2 112.68811 C1-C5-C4-C7 3 242.50450
C 7 1.20447 C7-C1-C5 1 156.10698 C7-C1-C5-C8 2 26.23735
C 8 1.42627 C8-C7-C1 7 155.44570 C8-C7-C1-H9
1
1.28760
H 9 1.08095 H9-C8-C7 8 123.22098 H9-C8-C7-C9
7
3.48912
C 9 1.30232 C9-C8-C7 8 110.39850 C9-C8-C7-C1
7
3.48912
C 1 1.50966 C1-C9-C8 2 107.78562 C1-C9-C8-H12 3 25.22114
H 12 1.09623
H12-C1-
C9 1 107.24384 H12-C1-C9-012 2 87.56819
O 12 1.42033
O12-C1-
C9 1 115.54686 O12-C1-C9-H14 2 206.52303
H 14 0.97118
H14-O12-
C1 12 108.47071 H14-O12-C1-C3 1 21.64786
C 3 1.51168
C3-H14-
012 2 110.17080 C3-H14-012 1 347.59809
H 16 1.09524
C3-H16-
016 3 111.38565 2 236.79634
O 16 1.42728
C2-H18-
016 3 111.19669 2 115.60460
H 18 0.97445 C2-H18 16 105.91438
O 4 1.37381 O4-H20 3 116.09753
H 20 0.97412 04-H20 4 110.77349
3.2 the vibrational frequencies
From the Heart!!!!

7. Chiavassa et al. for similar compounds. The assignment of the normal modes in the
C-H stretching regions (3200-2700 cm-) is not obvious because there are fewer bands in the
experimental spectrum than predicted by calculations. The highest frequency experimental bands
observed in the IR spectrum (3079-3000 cm-) are assigned to the C-H stretches, There are only two C-H
bonds
The bands at 4046.68 cm- and 3996.325 cm- have intensities of 123.72 kJ/mol and 119.8242 kJ/mol and
are the asymmetric stretches of the C-H bonds. There is another at 3953.4 cm- with a intensity of
117.1cm- and another at 3351.3 cm- with low intensity (8.2315 kJ/mol) and another which is somewhat
higher at 3271.63 cm- and a reading of 55.4 kJ/mol
experimental and theorectical spectra., the theory predicts two modes associated with C-O-H
vibrations.
The 1779.804 cm- with intensity 14.2064 km.mol- is assigned to symmetric C-0-H mode, while the
band at 1727.664 cm- with intensity 13.4021 km.mol- corresponds to the asymmetric mode. So, the
former band was NOT weaker than the latter and could not be seen in the theorectical spectra within
the scale used
There are 4 C-C type “in plane” bands in the 1600 to 1500 cm- region, with only one being relatively
intense. They are due to C=C double bond and C=C triple bond vibrations.
They are 1592.574 , 1575.74 with intensities of16.0328 km.mol- and 15.1968 km.mol- respectively. The
strongest band is 1539.011 cm- at 80.0522 km.mol-. The last C-H in plane mode is 1511.852 cm-
There are 3 C-C stretching peaks , two of which have intense vibrations. They are 1169.967 cm- at,
106.6948 km.mol , 1146.463 cm- at 125.6572 km.mol-. and , 1105.053 cm- which is apparent but weak
The energy of 1060.969 cm- is C-H out-of-plane bending
Out of plane bending modes appear at 939.3541 and 917.6558 for the C-H groups
Although the main subject of this study was to measure and interpret the experimental
vibrational spectra of molecule 72. We believe that it is useful to show the spectra obtained both
in the solid state and in different solvents. The theorectical and Raman and FT-IR spectrum of
molecule 72 are shown in figure 2.
figure 2: The theorectical and Raman
Raman scattering force constants

8. (mDyne/A
activities (A**4/AMU),
114.0259 10.2999
45.3208 10.0378
32.8367 9.8082
188.6873 STRONG 7.1901
236.5857 STRONG 6.8506
45.864 6.7721
7.0758
4.5977
10.8595
2.3589
5.3518
6.4395
17.6114
7.8888
18.163

9. 0.8424 0.2615
1.0281 0.9465
0.7698 0.7436
2.1891 0.6212
0.7769 0.3537
1.9845 0.5357
4.2925
1.282
2.8739
2.8166
2.337
4.6515
0.9753
3.4525
3.596
figure 2: The theorectical FT-IR

10. Harmonic frequencies IR intensities (KM/Mole
(cm**-
1),
4046.668 asym C-H stretching regions 123.7181
3996.325 sym C-H stretching regions 119.8242
3953.383
plus
ring C-H stretching regions 117.0801
3351.26
plus
ring C-H stretching regions 8.2315 NO DIPOL
CHANGE WITH
VIB
3271.628 asym
C-H stretching
regions
C-H + C-
H 55.353 NO DIPOL
3253.31 sym
C-H stretching
regions
C-H + C-
H 6.4605
1779.804 C-O-H vibration 13.4021
1727.664 C-O-H vibration 14.2064
1592.574 C=C double bond 16.0328
C=C double bond
1575.74 C=C double bond 15.1968
1539.011 C=C double bond 80.0522 STRONG
1511.852 C=C double bond 0.792
1489.661 C-H in-plane 12.3021
1484.942 C-H in-plane 16.4951
1436.836 C-H in-plane 5.2138
1430.197 C-H in-plane 16.5024
1422.439 C-H in-plane 76.1422 STRONG
1368.217 C-H in-plane 137.5125 STRONG
1330.388 C-H in-plane 11.8842
1304.207 C-H in-plane 5.1197
1281.358 C-H in-plane 163.0389 STRONG
1235.983 C-H in-plane 122.8856 STRONG
1169.967 C-H in-plane 106.6948 STRONG
1146.463 C-H in-plane 125.6572 STRONG
1105.053 six C-H in-plane 45.9391
1060.969 C-C stretching peaks 39.886
939.3541 C-C stretching peaks 29.2604
917.6558 C-C stretching peaks 16.088
849.807 C-C ring brething 13.7702
806.3163 out-of-plane bending 22.1696

11. 795.5685 out-of-plane bending 19.8076
765.1576 out-of-plane bending 19.6704
695.1723 C-C-C IN PLANE BENDING 30.6751
680.9222 C-C-C IN PLANE BENDING 21.9926
633.2742 C-C-C IN PLANE BENDING 7.9044
595.0455 C-C-C IN PLANE BENDING 32.1228
506.6196 C-C-C “OUT OF” PLANE BENDING 189.1074 STRONG
492.176 C-C-C “OUT OF” PLANE BENDING 100.3815 STRONG
471.4012 C-C-C “OUT OF” PLANE BENDING 4.8989
456.3225 C-C-C “OUT OF” PLANE BENDING 7.0674
418.0662 2.5737
392.476 12.3402
376.9907 4.1473
352.3439 13.7006
336.987 11.0296
278.6581 123.3328 STRONG
266.8744 67.7691
218.8519 1.4898
202.9863 3.3298
178.4513 10.7903
155.9329 2.1698
103.9909 2.1074
90.2773 1.2068
46.443 1.0666
3.2 the vibrational frequencies-focus here –no nmr-write without it
Although the main subject of this study was to measure and interpret the experimental
vibrational spectra of molecule 72. We believe that it is useful to show the spectra obtained
both in the solid state and in different solvents. So these calculations were attempted
The theorectical and experimental Raman spectrum of molecule 72 are shown in figure
l and experimental IR spectra, measured in KBr pellet and
different solvents in the middle region are compared in figure 3. Examination of Figures 2
and 3 reveals that the experimental spectra of the studied compound are, in general, similar
to that based on quantum chemical calculations for the isolated molecule. However one
cannot expect complete coincidence between experimental vibrational data and theorectical
data for the isolated molecule. The explanation for this difference is the effect of the
hydrogen bonding interaction in the solid state

12. Skip to next page
From the Heart!!!!
and Chiavassa et al. for similar compounds. The assignment of the normal modes in the
C-H stretching regions (3200-2700 cm-) is not obvious because there are fewer bands in the
experimental spectrum than predicted by calculations. The highest frequency experimental
bands observed in the IR spectrum (3079-3000 cm-) are assigned to the C-H stretches,
There are only two C-H bonds
The bands at 4046.68 cm- and 3996.325 cm- have intensities of 123.72 kJ/mol and 119.8242
kJ/mol and are the asymmetric stretches of the C-H bonds. There is another at 3953.4 cm-
with a intensity of 117.1cm- and another at 3351.3 cm- with low intensity (8.2315 kJ/mol)
and another which is somewhat higher at 3271.63 cm- and a reading of 55.4 kJ/mol
The bands at 4046.68 cm- and 3996.325 cm- have intensities of 123.72 kJ/mol and 119.8242
kJ/mol and are the asymmetric stretches of the C-H bonds. There is another at 3953.4 cm- with
a intensity of 117.1 kJ/mol and another at 3351.3 cm- with low intensity (8.2315 kJ/mol) and
another which is somewhat higher at 3271.63 cm- and a reading of 55.4 kJ/mol
DESCRIBE NOW
predicts two modes associated with C-O-H vibrations. The 1779.804 cm- band with intensity
14.2064 km.mol- is assigned to symmetric C-0-H mode, while the band at 1727.664
cm- with intensity 13.4021 km.mol- corresponds to the asymmetric mode. So, the
former band was NOT weaker than the latter and could not be seen in the theorectical spectra
within the scale used.

13. FROM THE HEART
1592.574
1575.74
1539.011
1511.852
There are 4 C-C type “in plane” bands in the 1600 to 1500 cm- region, with only one being
relatively intense. They are due to C=C double bond and C=C triple bond vibrations.
They are 1592.574 , 1575.74 with intensities of16.0328 km.mol- and 15.1968 km.mol-
respectively. The strongest band is 1539.011 at 80.0522 km.mol-. The last C-H in plane mode is
1511.852 cm-
These are C-C stretch
1169.967 106.6948 STRONG
1146.463 125.6572 STRONG
1105.053
out-of-plane bending
1060.969 six C-H out-of-plane bending
out-of-plane bending
939.3541 C-H out-of-plane bending i
917.6558 C-H out-of-plane
C-C ring brething
849.807 C-C ring brething
out-of-plane bending
806.3163 C-H out-of-plane
795.5685 C-H out-of-plane bending vibration

14. 765.1576 C-H out-of-plane bending vibration
700-550 C-C-C IN PLANE BENDING
695.1723 C-C-C IN PLANE BENDING
680.9222 C-C-C IN PLANE BENDING
633.2742 C-C-C IN PLANE BENDING
595.0455 C-C-C IN PLANE BENDING
550 -434 C-C-C “OUT OF” PLANE BENDING
506.6196
492.176
471.4012
456.3225
3.2.1 C-H
8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec 2- yne,4-ene,6-yne
The C-H stretch vibrations of an aliphatic ring (26) are expected in the region of 3000- 3120 cm-.
the calculated values of the target molecule have been found to be
Frequencies -- 3253.3104 3271.6279 3351.2596, 3953.3827 3996.3253
4046.6678
at the using the B-3-YLP/6-311++(2p,3d) level of calculation.
The theorectical computed C-H vibrations by the B-3-YLP/6-311++(2p,3d), are reported here, as
this molecule has no been synthesized

15. The C-H in-plane and out-of-plane bending vibrations generally lie in the range of 1000-1300 cm- and
800-950 cm- (27-29), respectively.
Frequencies -- 1146.4633 1169.9673 1235.9834
Frequencies -- 1281.3576 1304.2065 1330.3879
Frequencies -- 1368.2170
has aromatic ring structures that can easily be determined due to relation of the C-H and C=C-C
ring vibrations. For simplicity, the modes of the vibrations of aromatic compounds are
considered as separate C-H and C-C vibrations. The C-H stretching occurs above 3000 cm-and is
typically exhibited as a multiplicity of weak to moderate bands, compared with that of aliphatic
C-H stretching (25). The C-H stretch vibrations of an aliphatic ring (26) are expected in the
region of 3000- 3120 cm-. the calculated values of the target molecule have been found to be
3223.5, 3223.0, 3207.7, 3207.6, 3159.6 and 3187.7 cm- at the using the B-3-YLP/6-311++(2p,3d)
level of calculation.
The theorectical computed C-H vibrations by the B-3-YLP/6-311++(2p,3d), are reported here, as this
molecule has no been synthesized
The C-H in-plane and out-of-plane bending vibrations generally lie in the range of 1000-1300 cm- and
800-950 cm- (27-29), respectively. In the present case, twelve C-H in-plane bending vibrations of the
present compound are identified at the range of 1055.8 -1503.3 cm-.
1060.9691 1105.0525 1146.4633 1169.9673 1235.9834 1281.3576 1304.2065 1330.3879
1368.2170 1422.4390 1430.1970 1436.8364 1484.9419 1489.6613
Frequencies -- 1511.8523 1539.0105 1575.7404 Frequencies -- 1592.5735

16. The six C-H out of plane bending vibrations are observed at the range of 750.2-1011.3 cm- and
678.1 cm-. However, as in many complex molecules there are overtones and interactions of these
vibrations to weak to be displayed in the spectrum
1060.969 six C-H in-plane
939.3541 six C-H in-plane
917.6558 six C-H out-of-plane
849.807 six C-H out-of-plane
806.3163 six C-H out-of-plane
795.5685 C-H out-of-plane bending vibration
765.1576 C-H out-of-plane bending vibration
Inport third
The C-H stretching occurs above 3000 cm- and is typically exhibited as aliphatic C-H stretch
(25). In 1994, Roeges (26) showed that, the C-H stretching vibrations of the phenyl (MY CASE
IS THE FIVE MEMEBERED RING) are expected in the region 3000-3120 cm. The calculated
values of these modes for the target molecule have been found to be 3220.5, 3223.0, 3207.7,
3207.6, 3159.6 and 3183.7 cm- at B3LYP/6-31+G(d,p) level of calculation.
Harmonic frequencies
IR intensities
(KM/Mole
(cm**-
1),
1 4046.668 asym C-H + C-H 123.7181
2 3996.325 sym C-H + C-H 119.8242
3 3953.383 plus ring C-H + C-H 117.0801
4 3351.26 plus ring C-H + C-H 8.2315
5 3271.628 asym plus ring C-H + C-H 55.353

17. 6 3253.31 sym plus ring C-H + C-H 6.4605
1060.969 six C-H in-plane
939.3541 six C-H in-plane
917.6558 six C-H out-of-plane
849.807 six C-H out-of-plane
806.3163 six C-H out-of-plane
795.5685 C-H out-of-plane bending vibration
765.1576 C-H out-of-plane bending vibration
695.1723 C-H out-of-plane bending vibration
680.9222 C-H out-of-plane bending vibration 21.9926
633.2742 C-H out-of-plane bending vibration 7.9044
595.0455 C-H out-of-plane bending vibration 32.1228
506.6196 189.1074
492.176 100.3815
471.4012 4.8989
456.3225 7.0674
418.0662 2.5737
392.476 12.3402
376.9907 4.1473
352.3439 13.7006
336.987 11.0296
278.6581 123.3328
266.8744 67.7691
218.8519 1.4898
202.9863 3.3298
178.4513 10.7903
155.9329 2.1698
103.9909 2.1074
90.2773 1.2068
46.443 1.0666
3.2.2 C-C

18. Asymmetric, symmetric, bending, C-C modes
3.2.3 C-0-C
Asymmetric, symmetric, bending, wagging C-0-C modes 1200 cm- to 950 cm-
They are the Frequencies , 939.3541 cm- , 1060.9691 cm- , 1105.0525 cm- , 1146.4633 cm-
1169.9673 cm- , 1235.9834 cm-
3.2.4 C=C-DOUBLE
Asymmetric, symmetric occur in 1575 cm- to 1675cm-
Frequencies -- 1511.8523 1539.0105 1575.7404, 1592.5735
1727.6637 1779.8043
NMR of yne-allene-C11H5O4
The 1
H FT-NMR and 13
C FT-NMR were recorded of the two synthesized molecules. Table XXX and Table
XXX show the spectra and DFT analysis , as well as prior results (ref xx). Students in my group were able
• To relate spectra to data found in the NIST data base. We also carried out FT-NMR and FT-IR
calculations for B-3-YLP/6-311++(2p,3d), MP2, and RHF-STO-3G-basis sets via the HPCC
supercomputer which hosts G09. Gaussview 5 was used to adjust the appropriate z-matrices,

19. and Maestro (Schrodinger Inc.) was available on a “i3” core Pentium to produce accurate
depictions of the molecule.-Rebecca!! The three OH groups resemble aliphatic signals and
reside at 0.5-2.0 ppm (depend on Concentration). Intramolecular hydrogen bonding deshield
OH and render it less sensitive to concentration. Usually there is an OH exchange rapidly (no
coupling with neighbors). In DMSO or Acetone, the exchange rate is slower, there is coupling
with neighbors. There are peaks to signify Intramolecular bond  12-10 ppm, As in the case
of Carboxylic Acids that Exist as Dimers  13.2-10 ppm

20. Figure xxx: The 1H FT-NMR and 13 FT-NMR of molecule 72 and Molecule 73 taken on
The 1H FT-NMR and 13 FT-NMR of yne-allene-C11H5O4 molecule 72 and Molecule 73 taken on
Example 1H NMR spectrum (1-dimensional) of a mixture of menthol enantiomers plotted as
signal intensity (vertical axis) vs. chemical shift (in ppm on the horizontal axis). Signals from
spectrum have been assigned hydrogen atom groups (a through j) from the structure shown at
upper left
The 1
H FT-NMR and 13
C FT-NMR of yne-allene-C11H5O4 molecule 72 and Molecule 73 taken on

21. Table 3: proton FT-NMR of yne-allene-
C11H5O4 molecule 72
Exp J(Hz) MP2 RHF
H15 H1 OH-5.35 ppm
H19 H2 OH-5.35 ppm
H3 H-C 6.1 ppm
Hc-2
peaks
H3
H4
H-C 7.1 ppm
Hc-2
peaks
Hb
4 peaks 2.2 ppm-
lone OH

22. Table 4: carbon 13
C FT-NMR of yne-allene-
C11H5O4 molecule 72
Exp B3LYP MP2 RHF
C1
c-0-c 82
to 73
O2
C3
c-0-c 82
to 73
C4-----65.6
ppm
C5—128
ppm
C6-128
ppm
C7-128
C8-128
C9-128
ppm
C10
C12 --65.6
carbon
c-oh 65.6 G98
73.1 G98
c-0-c 82 to 73
c=c 128-130 G98
UV-Vis of yne-allene-C11H5O4 Molecule 72

23. Below are the pictures of the Homo and lumo of Molecule 72 (figure xx).
In table xx, we give the data for the energies of the homo and lumo for yne-allene-C11H5O4
Molecule 72 and molecule 73. The Homo and lumo of biologically interesting molecules are the frontier
orbitals. They are the states in which the molecules resides, and thus the states needed to examined
the most
Figure xxx: Homo- of yne-allene-C11H5O4 Molecule 72
Figure xxx: Lumo of yne-allene-C11H5O4 Molecule 73
Table xx: energies of the homo and lumo for yne-allene-C11H5O4 Molecule 72

24. Some of the calculated energy values of yne-allene-C11H5O4 molecule 72 in its ground state
with triplet
Symmetry at the RHF-STO-3G
methods
RHF-STO-3G
Lowest MO Eigen
value (a.u.) -20.3173
Highest MO Eigen
value (a.u.) 1.4306
HOMO (a.u.) -0.0173
LUMO (a.u.) 0.1506
HOMO-LUMO gap, delta E
(a.u.) 0.1679
The Highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital are very
important parameters for quantum chemistry. We can determine the way the molecule interacts with
other species ; hence they are called frontier orbitals. HOMO, which can be thought the outermost
orbital containing electrons, tend to give these electrons such as an electron donor. On the otherhand,
LUMO can be thought the innermost orbital containing free places to accept electrons. (35) . Owing to
the interaction between HOMo and LUMO orbital of a structure transition state transition state pi-pi*
type observed with regard to molecular orbital theory (36) . Therefore,while the energy of the HOMO is
directly related to the ionization potential, LUMO energy is directly related to the electron affinity.
Energy difference between HOMO and LUMO orbital is called as energy gap that is an important stability
for structures (37) . A large HOMO –LUMO gap implies high kinetic stability and low chemical
reactivity, because it is energetically unfavorable to add electrons to a high-lying LUMO, and to extract
electrons from low-lying HOMO (38) . The magnititude of the HOMO-LUMO energy separation could
indicate the reactivity pattern for the molecule(39) . In addition, 3D plots of the highest occupied
molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are shown in figure XXX and
figure XXX
molecular geometry

25. CALCULATED BOND DISTANCES AND
EXPERIEMENTAL X-RAY DATA
the endiyne allene –could possibly be linked with intramolecular hydrogen bonding . The table xxx
shows the theroectical (B3YLP/6-311G*) bond lengths (degrees) and bond angles (degrees) compared
with x-ray data. Bonding for certain carbons with a bond angle of 158.0563 is obviously under strain
CALCULATED BOND DISTANCES AND EXPERIEMENTAL X-RAY DATA
Table xxx: theroectical (B3YLP/6-311G*) bond lengths (degrees) and bond angles (degrees) compared with x-ray data
(B3YLP/6-311G*) EXP
bonds *need this
C1-O2 1 1.39593
02-C2 2 1.39219
C2-C3 3 1.45256
C4-C5 4 1.42562
C5-C6 5 1.20113
angles 1 109.2654
C1-O2-C2 2 114.4001
02-C2-C3 3 118.3062
C4-C5-C6 4 158.0563
ATOM1 LENGTH ATOM2 ANGLE ATOM 3 DIHEDRAL
1 1.39593
2 1.39219 1 109.2654
3 1.45256 2 114.4001 1 130.4463
4 1.42562 3 118.3062 2 -38.1813
5 1.20113 4 158.0563 3 -8.1545

26. NBO ANALSIS OF yne-allene-C11H5O4 MOLECULE 72
This analysis is carried out by examining all possible interactions between "filled" (donor)
Lewis-type NBOs and "empty" (acceptor) non-Lewis NBOs, and estimating their energetic
importance by 2nd-order perturbation theory. Since these interactions lead to donation of
occupancy from the localized NBOs of the idealized Lewis structure into the empty non-Lewis
orbitals (and thus, to departures from the idealized Lewis structure description), they are referred
to as "delocalization" corrections to the zeroth-order natural Lewis structure. For each donor
NBO (i) and acceptor NBO (j), the stabilization energy E(2) associated with delocalization ("2e-
stabilization") i j is estimated as
where qi is the donor orbital occupancy, i, j are diagonal elements (orbital energies)
and F(i,j) is the off-diagonal NBO Fock matrix element
Mulliken atomic charges:
#UHF/6-311G** Units=AU Field=F(2)10 Scf=Tight
1 Atom Mulliken Lowdin
1 C 0.106580 1 C 0.13 0.09
2 O -0.464684 2 O -0.23 -0.14
3 C 0.237856 3 C 0.1 0.05
4 C 0.929137 4 C 0.11 0.08
5 C -0.946121 5 C -0.04 -0.04
6 C -0.119745 6 C -0.04 -0.04
7 C 0.517174 7 C -0.09 -0.1
8 C 0.091799 8 C -0.02 -0.02
9 C -1.048213 9 C -0.09 -0.06
10 H -0.304253 10 H 0.1 0.06
11 C 0.528524 11 C 0.07 0.08
12 C 1.454406 12 C 0.06 0.07
13 H -0.511770 13 H 0.08 0.04
14 O -0.314870 14 O -0.29 -0.21
15 H -0.215294 15 H 0.2 0.14

27. 16 C 1.937672 16 C 0.06 0.07
17 H -0.717993 17 H 0.07 0.03
18 O -0.366829 18 O -0.29 -0.21
19 H -0.408051 19 H 0.2 0.14
20 O -0.209599 20 O -0.29 -0.19
21 H -0.175723 21 H 0.22 0.16
Mulliken atomic charges:
#UHF/6-311G** Units=AU Field=F(2)10 Scf=Tight
1
1 C 0.106580
2 O -0.464684
3 C 0.237856
4 C 0.929137
5 C -0.946121
6 C -0.119745
7 C 0.517174
8 C 0.091799
9 C -1.048213
10 H -0.304253
11 C 0.528524
12 C 1.454406

28. 13 H -0.511770
14 O -0.314870
15 H -0.215294
16 C 1.937672
17 H -0.717993
18 O -0.366829
19 H -0.408051
20 O -0.209599
21 H -0.175723
-----------------ADDITIONAL INFORMATION-----------------
---Calculated Charges---
Atom Mulliken Lowdin
1 C +0.13 +0.09
2 O -0.23 -0.14
3 C +0.10 +0.05
4 C +0.11 +0.08
5 C -0.04 -0.04
6 C -0.04 -0.04
7 C -0.09 -0.10
8 C -0.02 -0.02
9 C -0.09 -0.06
10 H +0.10 +0.06
11 C +0.07 +0.08
12 C +0.06 +0.07

29. 13 H +0.08 +0.04
14 O -0.29 -0.21
15 H +0.20 +0.14
16 C +0.06 +0.07
17 H +0.07 +0.03
18 O -0.29 -0.21
19 H +0.20 +0.14
20 O -0.29 -0.19
21 H +0.22 +0.16
CALCULATED BOND DISTANCES AND EXPERIEMENTAL X-RAY DATA
UV -VIS
Next is the spectrum taken by our group of 8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec 2-
yne,4-ene,6-yne
Bicyclo(7:2:2) 2,4,6-yne-allene-4,12,16 triol on the Cary Flourescence spectrophometer. Figure xxx is
shown first. It shows pi to pi* transitions of the 1,9 diene,3 –yne-doca-aryne ring
Figure xxx: Flourescence of molecule Bicyclo(7:2:2) 2,4,6-yne-allene-9,10,13 triol
taken on the Cary Flourescence spectrophometer

30. FT-IR of Molecule 72
FT-IR spectroscopy of 8,10,11 trihydroxy- 9- oxoBicyclo(7:2:2)undec 2- yne,4-ene,6-yne
Bicyclo(7:2:2) 2,4,6-yne-allene-9,10,13 triol
molecule 72 was performed on fourier-tranformed infrared spectrophotometer (Bruker VECTOR 22)
equipped with a detector (DTGS) which has a resolution of 4 cm-1 . The pellets of the samples (10 mg)
an potassium bromide (200 mg) were prepared by compressing the powders at 5 bars for 5 minutes on
KBr press and the spectra were scanned on the wave number range of 4000-850 cm-1 .
The vibrational frequencies of molecule 72 and molecule 73 were calculated on “Bob” of the HPCC at
the College of Staten island. To assign the frequencies, the gaussview program was used.
Before a Z-matrix is generated to obtain any of the vibrational frequencies, electronic transitions or
nuclear magnetic resonances of molecule 72 and molecule 73, we sent the “pds” file to AVOGADRO.
This piece of software automatically does a geometry opimitization of the ground state of the
molecules.
The molecular structure and vibrations frequecies in figure xxx, are optimized by HF, beck 3-Lee-Yang-
Parr (B3LYP) and Moller-Plesset pertubation theory (MP2) functions using 6-31+G(d,p) basis set.
6-31+G(d,p)
basis
Frequencies
Approximate Selected Freq.
(cm-1) type of mode Value Rating
46.443
90.2773
103.9909
155.9329
178.4513
202.9863
336.987
352.3439
376.9907
392.476
418.0662 Ring deform 410 C
456.3225
471.4012
492.176
506.6196
595.0455 Ring deform 606 C

31. 633.2742
680.9222 CH bend 673 B
695.1723 Ring deform 703 E
765.1576
795.5685
806.3163
849.807
917.6558
939.3541 Ring str 992 C
1060.9691 Ring str Ring deform 1010 C
1105.0525 Ring deform 1010 C
1146.4633 CH bend 1150 C
1169.9673 CH bend 1150 C
1235.9834 CH out-of-plane
1281.3576 CH out-of-plane
1304.2065 Ring str 1310 C
1330.3879 CH bend 1326 E
1368.217
1422.439
1430.197
1436.8364 Ring str + deform 1486 B
1489.6613
1511.8523
1539.0105
1575.7404
1592.5735
1727.6637
1779.8043
3253.3104
3271.6279
3351.2596
3953.3827
3996.3253
4046.6678

32. Figure xxx: FT-IR spectra of molecule 72 taken on the (Bruker VECTOR 22) spectrophotometer
Sym. No Approximate Selected Freq. Infrared
Exp B3LYP
Species type of mode Value Rating Value Phase
a1g 1 CH str 3062 C ia
a1g 2 Ring str 992 C ia
a2g 3 CH bend 1326 E ia
a2u 4 CH bend 673 B 673 S gas
b1u 5 CH str 3068 C
3067.57
VW
sln.
b1u 6 Ring deform 1010 C 1010 W sln.
b2g 7 CH bend 995 E ia
b2g 8 Ring deform 703 E ia
b2u 9 Ring str 1310 C 1310 W liq.
b2u 10 CH bend 1150 C 1150 W liq.
e1g 11 CH bend 849 C ia
e1u 12 CH str 3063 E 3080 S liq.
e1u 12 CH str 3063 E 3030 S liq.
e1u 13
Ring str +
deform
1486 B 1486 S gas
e1u 14 CH bend 1038 B 1038 S gas
e2g 15 CH str 3047 C ia
e2g 16 Ring str 1596 E ia
e2g 16 Ring str 1596 E ia
e2g 17 CH bend 1178 C ia
e2g 18 Ring deform 606 C ia
e2u 19 CH bend 975 C 975 W liq.
e2u 20 Ring deform 410 C 417.7 S sln.
e2u 20 Ring deform 410 C 403.0 S sln.

33. References

34. 1. Editorial [ Enediynes and Related Structures in Medicinal and
Biorganic Chemistry Guest Editor: Ajoy Basak ] Ajoy Basak, Scientist,
Ottawa Health Research Institute University of Ottawa Canada..
Current Topics in Medicinal Chemistry (Impact Factor: 3.7). 03/2008;
8(6):435-435
2. DNA damage by C1027 involves hydrogen atom abstraction and
addition to nucleobases, Joanna Maria N. San Pedroa, Terry A.
Beermanb, Marc M. Greenberga, DOI: 10.1016/j.bmc.2012.06.004
Ref 1
Elfi Kraka, Dieter Cremer, ”Enediynes, enyne‐allenes, their reactions, and beyond”, Corros. Sci. 50 (2013)
1174
Published Online: Oct 08 2013
DOI: 10.1002/wcms.1174
 How to cite this article
Ref 1
Masahiro Hirama, Kimio Akiyama, Parthasarathi Das, Takashi Mita, Martin J Lear, Kyo-Ichiro Iida, Itaru Sato,
Fumihiko Yoshimura, Toyonobu Usuki, Shozo Tero-Kubota
DIRECT OBSERVATION OF ESR SPECTRA OF BICYCLIC NINE-MEMBERED ENEDIYNES AT
AMBIENT TEMPERATURE
Thioxanane paper
(35) G.Gece, Corros. Sci. 50 (2008) 2981.
(36) K. Fukui, Theory of Orientation and Stereoselection, Springer-Verlag, Berlin
1975, see also: K.Fukui, Science 218 (1987) 747.
(37) D.F. V. Lewis, C. Loannides, D.V Parke, Xenobiotica 24 (1994) 401.

35. (38) B. Chattophadhyay, S. Basu, P. Chakraborty, S.K. Choudhury, A.K.
Mukherjee, M. Mukherjee, J.Mol. Structu 932 (2009) 90.
7. Willoughby, P. H., Jansma, M. J. & Hoye, T. R A guide to small-molecule structure
assignment through computation of (1
H and 13
C) NMR chemical shifts. Nature Protocols 9, 643–
660 (2014)
-----------------ADDITIONAL INFORMATION-----------------
hyperfine coupling constant ANALSIS OF MOLECULE 72 AND 73
The Fermi contact interaction is the magnetic
interaction between an electron and an atomic nucleus
when the electron is inside that nucleus.
The parameter is usually described with the symbol A
and the units are usually megahertz. The magnitude of A is given
by this relationship:
and
where A is the energy of the interaction, μn is the
nuclear magnetic moment, μe is the
electron magnetic dipole moment, and Ψ(0) is the
electron wavefunction at the nucleus.[1]
Isotropic Fermi Contact Couplings
Atom a.u. MegaHertz Gauss 10(-4) cm-1

36. 1 C(13) 0.00557 3.12884 1.11645 1.04367
2 O(17) -7.32027 2218.75973 791.70862 740.09858
3 C(13) 0.08773 49.31008 17.59506 16.44807
4 C(13) -0.00196 -1.10284 -0.39352 -0.36787
5 C(13) 0.16043 90.17561 32.17690 30.07935
6 C(13) -0.02609 -14.66527 -5.23293 -4.89181
7 C(13) -0.01794 -10.08221 -3.59758 -3.36306
8 C(13) 0.04146 23.30617 8.31622 7.77410
9 C(13) -0.04895 -27.51333 -9.81744 -9.17746
10 H(1) 0.11483 256.62910 91.57164 85.60225
11 C(13) -0.03890 -21.86817 -7.80310 -7.29443
12 C(13) 0.08430 47.38385 16.90774 15.80555
13 H(1) 0.00825 18.44452 6.58146 6.15243
14 O(17) 0.03129 -9.48379 -3.38405 -3.16345
15 H(1) 0.00103 2.31284 0.82528 0.77148
16 C(13) 0.09058 50.91252 18.16685 16.98259

37. Hyperfine coupling
The hyperfine coupling constant is not only responsible for splittings of resonance lines in EPR
and NMR, for radicals it is by far the most dominating contribution to the nuclear shielding
tensor. The hyperfine coupling tensors are normally written as two parts, an isotropic Fermi
contact (FC) part which describes the unpaired electron density at a given nucleus and a spin-
dipole (SD) part which corresponds to the classic magnetic-dipole interaction energies
---- Spin Dipole Couplings ----
3XX-RR 3YY-RR 3ZZ-RR
--------------------------------------------------------
1 Atom -0.164225 0.007692 0.156533
2 Atom -0.006756 -0.062927 0.069682
3 Atom 0.032228 -0.168110 0.135883
4 Atom 0.112677 -0.021661 -0.091016
5 Atom -0.143209 0.087145 0.056064
6 Atom 0.186629 -0.102087 -0.084542
7 Atom 0.156190 -0.102238 -0.053952
8 Atom 0.352607 -0.216188 -0.136419
9 Atom 0.041656 -0.022740 -0.018916
10 Atom 0.027530 -0.048113 0.020583
11 Atom 0.203798 -0.337718 0.133920
12 Atom 0.054929 -0.008471 -0.046458
13 Atom 0.021091 -0.004540 -0.016551
14 Atom -0.005654 0.014177 -0.008523
15 Atom -0.007976 0.008170 -0.000194
16 Atom 0.031856 -0.038100 0.006244
17 Atom 0.015051 -0.003889 -0.011162

38. 18 Atom 0.037047 -0.030982 -0.006065
19 Atom 0.006681 -0.007006 0.000324
20 Atom 0.028179 0.058941 -0.087120
21 Atom 0.015479 0.008048 -0.023527
Within an atom, only s-orbitals have non-zero electron density at the nucleus, so the contact
interaction only occurs for s-electrons. Its major manifestation is in electron paramagnetic
resonance and nuclear magnetic resonance spectroscopies, where it is responsible for the
appearance of isotropic hyperfine coupling. Roughly, the magnitude of A indicates the extent to
which the unpaired spin resides on the nucleus. Thus, knowledge of the A values allows one to
map the singly occupied molecular orbital.[3]
Magnetic dipole–dipole interaction, also called dipolar coupling, refers to the direct
interaction between two magnetic dipoles.
Dipolar coupling and NMR spectroscopy
The direct dipole-dipole coupling is very useful for molecular structural studies, since it depends
only on known physical constants and the inverse cube of internuclear distance. Estimation of
this coupling provides a direct spectroscopic route to the distance between nuclei and hence the
geometrical form of the molecule, or additionally also on intermolecular distances in the solid
state leading to NMR crystallography notably in amorphous materials
The potential energy of the interaction is as follows:
where ejk is a unit vector parallel to the line joining the centers of the two dipoles. rjk is the
distance between two dipoles, mk and mj.
For two interacting nuclear spins
where is the magnetic constant, , are gyromagnetic ratios of two spins, and rjk is the
distance between the two spins.

39. Force between two magnetic dipoles:
where is unit vector pointing from magnetic moment to , and is the distance between
those two magnetic dipole moments.

40. Figure xxx: Isotropic Fermi Contact Couplings of molecule 72 and Molecule 73 taken on
calculated on “Bob” of the HPCC at the College of Staten island
Isotropic Fermi Contact Couplings
Atom a.u. MegaHertz Gauss 10(-4) cm-1
1 C(13) 0.00557 3.12884 1.11645 1.04367
2 O(17) -7.32027 2218.75973 791.70862 740.09858
3 C(13) 0.08773 49.31008 17.59506 16.44807
4 C(13) -0.00196 -1.10284 -0.39352 -0.36787
5 C(13) 0.16043 90.17561 32.17690 30.07935
6 C(13) -0.02609 -14.66527 -5.23293 -4.89181
7 C(13) -0.01794 -10.08221 -3.59758 -3.36306
8 C(13) 0.04146 23.30617 8.31622 7.77410
9 C(13) -0.04895 -27.51333 -9.81744 -9.17746
10 H(1) 0.11483 256.62910 91.57164 85.60225
11 C(13) -0.03890 -21.86817 -7.80310 -7.29443
12 C(13) 0.08430 47.38385 16.90774 15.80555
13 H(1) 0.00825 18.44452 6.58146 6.15243
14 O(17) 0.03129 -9.48379 -3.38405 -3.16345
15 H(1) 0.00103 2.31284 0.82528 0.77148
16 C(13) 0.09058 50.91252 18.16685 16.98259

41. NBO ANALSIS OF MOLECULE 72 AND 73
Mulliken atomic charges:
1
1 C 0.106580
2 O -0.464684
3 C 0.237856
4 C 0.929137
5 C -0.946121
6 C -0.119745
7 C 0.517174
8 C 0.091799
9 C -1.048213
10 H -0.304253
11 C 0.528524
12 C 1.454406
13 H -0.511770
14 O -0.314870
15 H -0.215294
16 C 1.937672
17 H -0.717993
18 O -0.366829
19 H -0.408051
20 O -0.209599
21 H -0.175723