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報告學生：彭家瑜 報告日期： 2012/03/12

Theoretical Study of Hydrogen Bonding in Homodimers and Heterodimers of Amide, Boronic Acid, and Carboxylic Acid, Free and in Encapsulation Complexes. 報告學生：彭家瑜 報告日期： 2012/03/12. 出處： J. Am. Chem. Soc. 2011 , 133 , 16977–16985 作者： Demeter Tzeli, Giannoula Theodorakopoulos

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報告學生：彭家瑜 報告日期： 2012/03/12

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  1. Theoretical Study of Hydrogen Bonding in Homodimers and Heterodimersof Amide, Boronic Acid, and Carboxylic Acid, Free and in EncapsulationComplexes 報告學生：彭家瑜 報告日期：2012/03/12

  2. 出處： J. Am. Chem. Soc. 2011, 133, 16977–16985 作者： Demeter Tzeli, Giannoula Theodorakopoulos and Ioannis D. Petsalakis* Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou, Athens 116 35, Greece Dariush Ajami and Julius Rebek The Skaggs Institute for Chemical Biology & Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States

  3. Abstract 氫鍵在化學以及生物化學中都扮演著非常重要的角色。本篇的作者曾在2011年，利用encapsulation 的實驗技術，將 carboxylic acids (C)，amides (A) 和 boronic acids (B) 所組成的 heterodimer 和 homodimer 包覆在 capsule 中，透過混合溶液中各 dimer 的比例來推論氫鍵強度。此實驗技術使 dimer 存在的時間延長，以利 NMR 的觀測。 本研究透過理論計算，驗證並解釋實驗所得到的結果。使用 M06-L、M06-2X、MP2 等理論搭配基底 6-31G(d,p) 和 6-311+G(d,p) 計算 dimer 的結構及能量，同時考慮在 DMF 和 CCl4中的溶劑效應。Capsule 和dimer 所形成的錯合物則使用 ONIOM [M06-2X/6-31G(d,p) ; PM6]，ONIOM [MP2/6-31G(d,p); PM6] 和 M06-2X/6-31G(d,p) 方法做計算。由計算結果得知氣態下各 dimer 的 dimerization energy 介於 0.74 到 0.35 eV 之間，作用力的強度順序為：CC > AC > AA > BC > AB > BB。而包覆在 capsule 中的 dimer 其 dimerization energy 的範圍和作用力的強度順序則相差不大，部分結果驗證了作者先前的實驗策略並不會對原本的 dimer 性質有太大的影響。

  4. Introduction The dimers in DNA： Adenine-Thymine and Cytosine-Guanine base pair

  5. 1982Raman spectra of HCOOH dimer J. Chem. Phys.1982, 76, 886–894. • 2005 Theoretical study of HCOOH, CH3COOH, HCONH2 and PCA dimers by MP2 thoery J. Phys. Chem. A 2005, 109, 6397–6405. • 2006 Theoretical study of HB(OH)2 dimers by MP2 and CCSD thoeryJ. Phys. Chem. A 2006, 110, 10633–10642 • 2009Rebek Hydrogen-Bonded Cylindrical Capsules J. Org. Chem. 2009, 74, 6584–6591. • 2011.06Rebek Boronic Acid Hydrogen Bonding in Encapsulation Complexes J. Am. Chem. Soc. 2011, 133, 9689–9691 • 2011.09Petsalakis Theoretical study of Dimers, Free and in Encapsulation Complexes J. Am. Chem. Soc. 2011, 133, 16977–16985

  6. J. Org. Chem.2009, 74, 6584–6591 Free Dimer nanosecond lifetimes Encapsulated Dimer millisecond ~ hours J. Am. Chem. Soc. 2011,133, 9689–9691.

  7. J. Am. Chem. Soc. 2011,133, 9689–9691.

  8. Computational Methods For geometry of dimers : M06-2X, M06-L functionals and MP2 theory with 6-31G(d,p) and 6-311+G(d,p) basis sets PCM (solvent=DMF, CCl4) For geometry of encapsulation complexes : ONIOM [M06-2X/6-31G(d,p) ; PM6] ONIOM [MP2/6-31G(d,p) ; PM6] M06-2X/6-31G(d,p) Program : Gaussian 09

  9. Results and Discussion • Methyl and p-Ethyl-Phenylene Substituents • Combinations of Different Funtional Groups In the conditions： • Gas-Phase and Solvent Effect (DMF, CCl4) • Free Dimers and Encapsulated Dimers methyl substituents (primed) p-ethyl-phenylene substituents (unprimed)

  10. Calculated Structures and Relative Energies (Te)of Monomers (H=white spheres, C=gray spheres, O=red spheres, and N=blue spheres) boronic acids (B and B’) Te calculated at : M06-2X/6-31G(d,p) M06-2X/6-311+G(d,p) M06-L/6-311+G(d,p) MP2/6-31G(d,p) MP2/6-311+G(d,p) levels amides (A and A’) carboxylic acids (C and C’)

  11. Calculated Dimers of Amides (A and A’), Boronic Acids (B and B’), and Carboxylic Acids (C and C’) (H = white spheres, C=gray spheres, O=red spheres, B=pink spheres, and N=blue spheres) methyl substituents (primed) p-ethyl-phenylene substituents (unprimed)

  12. Dimerization Energies in eV of the Dimers in the Gas Phase at Various Levels of Theory

  13. Dimerization Energies in eV of the Dimers in the Gas Phase, in DMF and CCl4Solvents at Various Levels of Theory

  14. Four Types of H-Bonds C=O … H-O C=O … H-N -O … H-N -O … H-O

  15. Hydrogen Bond Distances (Å) of the Dimers in the Gas Phase, in DMF and CCl4Solvents at Various Levels of Theory a J Phys. Org. Chem. 2008, 21, 472–482 b The Trans Dimers of the CC, AC, AA, BC, AB, and BB Species

  16. Calculated Structures of Two Capsules 1.24.1 (H=white spheres, C=gray spheres, O=red spheres, and N=blue spheres) Capsule a deduced from NMR for the first time in 2009 J. Org. Chem. 2009, 74, 6584–6591 4*4 (glycoluril-cavitand) +) 2*4 (glycoluril-glycoluril) 24 H-bonds ←More stable than capsule a by 0.09 eV 4*4 (glycoluril-cavitand) +) 2*4 (glycoluril-glycoluril) 24 H-bonds

  17. Dimerization Energies in eV of the Dimers in the Gas Phase and in Capsulesat Various Levels of Theory a Oniom-[high layer] b All low layers are the capsules calculated at PM6 level cAll convergence problems denoted by “ - ” d Trans/cis

  18. Hydrogen Bond Distances (Å) of the Dimers in the Gas Phase and in Capsulesat Various Levels of Theory R1 R1 R3 R2 R2 R4 R2 R2 R4 a Oniom-[high layer] b All low layers are the capsules calculated at PM6 level cAll convergence problems denoted by “ - ” d The trans dimers of the CC, AC, AA, BC, AB, and BB species

  19. Dimerization Energy ΔE (eV) of the Dimers in the Capsulea, Interaction Energy of the Capsule with the Dimers ΔE1(eV), and the Total Interaction Energy ΔE2(eV) of the Capsule with the Two Guest Molecules ΔE ΔE1 ΔE2 a at the M06-2X/6-31G(d,p) level

  20. Encapsulated Dimer % Distribution of the CC, AC, AA, BC, AB, and BB Species at Various Levels of Theory Ni = degeneracy (gi) * dimerization energy (∆E) gi = 1 (AA, CC), 2 (AC, AB, BC), 4 (BB) a J. Am. Chem. Soc. 2011, 133, 9689–9691.

  21. Encapsulated Dimer % Distribution of the CC, AC, AA, BC, AB, and BB Species at Various Levels of Theory Ni (in paper) = gi * dimerization energy (∆E) gi = 1 (AA, CC), 2 (AC, AB, BC), 4 (BB) Ni (Bolzmann distribution) = gi * a J. Am. Chem. Soc. 2011, 133, 9689–9691.

  22. Conclusions • In this research, all dimers calculated by M06-2X and M06-L functionals and MP2 theory with 6-31G(d,p) and 6-311+G(d,p) basis sets in the gas phase and in solvents (DMF and CCl4), and Oniom methods in the capsule. • Dimerization energy (ΔE) order is carboxylic homodimers > amide-carboxylic dimers > amide-homodimers > boronic-carboxylic dimers > amide-boronic dimers > boronic-homodimers, and it ranges from 0.74 to 0.43 eV at M06-2X/6-311+G(d,p) level in the gas phase. • In CCl4 solvent, the energy order is retained except that the amide homodimers and boronic-carboxylic have nearly the same interaction energy.

  23. In DMF solvent, the energy order is retained except that the amide homodimers have the smallest ΔE values. In the capsule, the energy order is the same as that in the gas phase except that amide-boronic dimer is slightly more stable than the boronic-carboxylic dimer. Finally, maybe the calculated % distributions of the encapsulated dimers in solution are in general agreement with the experimental distribution, because it performed by the wrong way of dealing with their dimerization energy.

  24. Thanks for your attention !

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