Title

氮,氮-雙(4-吡啶甲基)草酰胺與反式-4,4'-偶氮-1,2,4-三唑分子之鍵結特性─實驗和理論的電荷密度研究

Translated Titles

Bond Characterization of N,N'-bis(4-pyridylmethyl)oxalamide and trans-4,4'-azo-1,2,4-triazole─A Combined Experimental and Theoretical Charge Density Study

DOI

10.6342/NTU.2012.00172

Authors

仲文君

Key Words

電荷密度 ； 鍵結特性 ； 電荷密度二次微分 ； X光繞射 ； pi–pi堆積作用力 ； 氫鍵作用力 ； charge density ； bond characterization ； Laplacian density ； X-ray diffraction ； pi–pi interaction ； hydrogen bond

PublicationName

臺灣大學化學研究所學位論文

Volume or Term/Year and Month of Publication

2012年

Academic Degree Category

碩士
Advisor

王瑜
Content Language

繁體中文
Chinese Abstract

本篇論文主要是藉由高解析度單晶X-ray繞射儀在低溫下(100 K)收得實驗數據與理論計算產生之電荷密度分佈來探討兩個有機分子N,N'-bis(4-pyridylmethyl)oxalamide (4py-ox, C14H14N4O2) 和trans- 4,4'-azo-1,2,4-triazole (atrz, C4H4N8)的分子內與分子間鍵結性質。這兩個化合物的分子結構在分子中心的位置皆具有反轉中心(inversion center)，前者是由草酰胺分子(oxalamide group)連結兩個吡啶甲基分子(pyridylmethyl fragments)所組成，相鄰分子間藉由兩組N–H...N和C–H...O分子間氫鍵作用力維繫整個三維之晶體結構；後者則由偶氮分子(azo group)連結兩個三唑五環分子(triazole five-member rings)形成一個平面分子，在此晶體結構中可觀察到兩組C–H...N弱氫鍵作用力和一組由三唑五環形成之強pi–pi堆積作用力，其環平面與環平面間垂直距離約為3.17 Å。電子密度的研究將藉由變形電子密度和電子密度二次微分的分佈來描述，從變形電子密度可發現所有共價鍵的部分在鍵中心處皆有變形電子密度的聚集，而電荷密度二次微分的分佈顯示了原子的混成方式與VSEPR的觀念相互吻合。我們利用拓樸性質分析探討分子內和分子間作用力的鍵結特性，從結果顯示，藉由鍵臨界點的電荷密度(rhoBCP)和總能量密度(HBCP)值說明C–N、C–C、C–O和N–N鍵具有共價鍵的特性，並且從C–O鍵之鍵臨界點的位置，說明了C–O鍵具有極化的特性。所有分子間作用力包括氫鍵作用力和pi–pi堆積作用力，皆可找到通過其鍵臨界點(BCP)及相關鍵結路徑(BPs)。
English Abstract

A combined study of experimental and theoretical charge density (CD) are performed on two organic molecules, N,N'-bis(4-pyridylmethyl) oxalamide (4py-ox, C14H14N4O2) and trans-4,4'-azo-1,2,4-triazole (atrz, C4H4N8). The experimental data is collected at 100 K using high resolution single-crystal X-ray diffraction. The molecular structures of these two compounds have inversion center locating at middle of molecules. The former, two pyridylmethyl fragments are connected by an oxalamide group. Adjacent molecules are then linked through intermolecular N–H...N and C–H...O hydrogen bonds. The later is a planar molecule which two triazole five-member rings are connected by an azo group. Two weak C–H...N hydrogen bonds and strong pi–pi interaction with the inter-planar distance of 3.17 Å are observed. Electron densities are depicted via deformation density and Laplacian distribution. The deformation density shows significant charge accumulation in all covalent bonding regions. The Laplacian distribution applies good agreement with VSEPR concept. The bond characterization of intra- and intermolecular interactions are discussed in terms of topological properties. According to the results, the covalent bond character of C–N, C–C, C–O, and N–N bonds are well described in terms of electron density (rhoBCP) and total energy density (HBCP) at the bond critical points. The BCP position of C–O bond clearly indicates polarization character. All the intermolecular interactions including the hydrogen bonding interactions as well as strong pi–pi interaction are allocated through the BCP and the associated bond paths (BPs).
Topic Category 基礎與應用科學 > 化學
理學院 > 化學研究所
Reference
  1. (2) Hansen, N. K.; Coppens, P. Acta Crystallogr A 1978, 34, 909.
    連結：
  2. (3) Tzeng, B. C.; Chen, B. S.; Lee, S. Y.; Liu, W. H.; Lee, G. H.; Peng, S. M. New J Chem 2005, 29, 1254.
    連結：
  3. (5) Tzeng, B. C.; Huang, Y. C.; Chen, B. S.; Wu, W. M.; Lee, S. Y.; Lee, G. H.; Peng, S. M. Inorg Chem 2007, 46, 186.
    連結：
  4. (6) Lee, G. H.; Wang, H. T. Acta Crystallogr C 2007, 63, M216.
    連結：
  5. (7) Lee, G. H. Acta Crystallogr C 2010, 66, O241.
    連結：
  6. (8) Pang, S. P.; Qi, C.; Li, S. H.; Li, Y. C.; Wang, Y. A.; Chen, X. K. J Mater Chem 2011, 21, 3221.
    連結：
  7. (12) Srinivasan, P.; Asthana, S. N.; Pawar, R. B.; Kumaradhas, P. Struct Chem 2011, 22, 1213.
    連結：
  8. (14) H. C. Chang, S. L. C., R. H. Chen, Eric J. Gabe, T. J. Lee, L. K. Liu, Peter Main, Norio Kato, S. M. Peng, Robert A. Sparks, Y. Wang, S. N. Yang Proceedings of the Crystallographic Computing Workshop, Taipei 1986.
    連結：
  9. (16) Crystal Structure analysis A primer, J. P. G., Kenneth, Oxford.
    連結：
  10. (18) Abramov, Y. A. Acta Crystallogr A 1997, 53, 264.
    連結：
  11. (19) Bader, R. F. W.; Gatti, C. Chem Phys Lett 1998, 287, 233.
    連結：
  12. (20) Gatti, C. Z Kristallogr 2005, 220, 399.
    連結：
  13. (21) Gatti, C.; Lasi, D. Faraday Discuss 2007, 135, 55.
    連結：
  14. (22) Gatti, C.; Cargnoni, F.; Bertini, L. J Comput Chem 2003, 24, 422.
    連結：
  15. (23) Hohenberg, P.; Kohn, W. Phys Rev B 1964, 136, B864.
    連結：
  16. (24) Kohn, W.; Sham, L. J. Phys Rev 1965, 140, 1133.
    連結：
  17. (26) Spackman, M. A.; McKinnon, J. J. Crystengcomm 2002, 378.
    連結：
  18. (27) Spackman, M. A.; Jayatilaka, D. Crystengcomm 2009, 11, 19.
    連結：
  19. (28) Mcweeny, R. Rev Mod Phys 1960, 32, 335.
    連結：
  20. (32) 劉啟村 Department of Chemistry, National Taiwan University, Master Thesis, 2005.
    連結：
  21. (35) Allen, F. H. Acta Crystallogr B 1986, 42, 515.
    連結：
  22. (42) Kluwer: Dordrecht International Tables for Crystallography, 1992.
    連結：
  23. (45) Lin, K. J.; Wang, C. C.; Wang, Y. J Chin Chem Soc-Taip 1991, 38, 505.
    連結：
  24. (46) Macchi, P.; Proserpio, D. M.; Sironi, A. J Am Chem Soc 1998, 120, 13429.
    連結：
  25. (48) Parthasarathi, R.; Subramanian, V.; Sathyamurthy, N. J Phys Chem A 2006, 110, 3349.
    連結：
  26. (49) Parthasarathi, R.; Subramanian, V. Struct Chem 2005, 16, 243.
    連結：
  27. (1) Bader, R. F. W. Atoms in molecules : a quantum theory; Clarendon Press: Oxford ; New York, 1990.
  28. (4) Tzeng, B. C.; Yeh, H. T.; Wu, Y. L.; Kuo, J. H.; Lee, G. H.; Peng, S. M. Inorg Chem 2006, 45, 591.
  29. (9) 劉敏憲; 陳成; 洪耀勳; 劉權文 CHEMISTRY（THE CHINESE CHEM. SOC., TAIPEI） 2004, 62, 315.
  30. (10) Chen, Y. S.; Stash, A. I.; Pinkerton, A. A. Acta Crystallogr B 2007, 63, 309.
  31. (11) Stephen, A. D.; Kumaradhas, P.; Pawar, R. B. Propell Explos Pyrot 2011, 36, 168.
  32. (13) Meents, A.; Dittrich, B.; Johnas, S. K. J.; Thome, V.; Weckert, E. F. Acta Crystallogr B 2008, 64, 519.
  33. (15) Laue, F. K. Sitz.ber. Bayer. Akademie d. Wiss. 1912.
  34. (17) X-ray Structure determination, G. H. S., Lyle H. Jensen, WILEY.
  35. (25) Boys, S. F.; Bernardi, F. Mol Phys 1970, 19, 553.
  36. (29) Silberberg., M. S. Chemstry: The Molecular Nature of Matter and Change, Fourth Edition 2006.
  37. (30) Nguyen, T. L.; Scott, A.; Dinkelmeyer, B.; Fowler, F. W.; Lauher, J. W. New J Chem 1998, 22, 129.
  38. (31) Pang, S. P.; Li, S. H.; Li, X. T.; Yu, Y. Z.; Zhao, X. Q. Chinese Chem Lett 2007, 18, 1176.
  39. (33) Sheldrick, G. M. SADABS. University of Gottingen, Germany 2000.
  40. (34) Sheldrick, G. M. SHELXL97 and SHELXS97. University of Gottingen, Germany. 1997.
  41. (36) Sheldrick, G. M.; Schneider, T. R. Macromolecular Crystallography, Pt B 1997, 277, 319.
  42. (37) T. Koritsanszky, S. H., T. Richter, Z. Su, P. R. Mallinson, N. K., ; Hansen, B. E. XD. Computer Program Package for Multipole Refinement and Analysis of Electron Density from X-Ray Diffraction Data. Free University of Berlin, Germany, 1996.
  43. (38) AEleen Frisch, M. J. F., Fernando R. Clemente, Gary W. Trucks Gaussian 09 User's Reference.
  44. (39) Bader, R. F. W. AIMPAC: a set of programs for the theory of atoms in molecules, McMaster University, Hamilton, Ontario (Canada L8S 4M1) 1994.
  45. (40) Jose Carlos Ortiz Alba, Carles Bo Jane, Xaim - X Atoms in Molecules Interface Version 1.0. Universitat Rovira i Virgili Tarragona Spain. 1998.
  46. (41) Volkov, A.; Koritsanszky, T.; Chodkiewicz, M.; King, H. F. J Comput Chem 2009, 30, 1379.
  47. (43) Hummel, W.; Raselli, A.; Burgi, H. B. Acta Crystallogr B 1990, 46, 683.
  48. (44) Burgi, H. B.; Raselli, A. Struct Chem 1993, 4, 23.
  49. (47) Konovalova, I. S.; Nelyubina, Y. V.; Lyssenko, K. A.; Paponov, B. V.; Shishkin, O. V. J Phys Chem A 2011, 115, 8550.
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