Aaa qualitative and dft analysis of endiynes for isha slideshare

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Aaa qualitative and dft analysis of endiynes for isha slideshare

  1. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 33. References
  34. 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. 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. 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. 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. 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. 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. 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. 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

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