請用此 Handle URI 來引用此文件：
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/82378完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 趙聖德(Sheng-Der Chao) | |
| dc.contributor.author | Yu-Chi Cheng | en |
| dc.contributor.author | 鄭詠琦 | zh_TW |
| dc.date.accessioned | 2022-11-25T07:30:00Z | - |
| dc.date.available | 2025-01-01 | |
| dc.date.copyright | 2022-02-17 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2022-01-11 | |
| dc.identifier.citation | P. Politzer, J. S. Murray, and Z. Peralta-Inga, “Molecular surface electrostatic potentials in relation to noncovalent interactions in biological systems,” Int. J. Quantum Chem. 85, 676–684 (2001). L. R. Ferguson and W. A. Denny, “Genotoxicity of non-covalent interactions: DNA, intercalators,” Mutat. Res., Fundam. Mol. Mech. Mutagen. 623, 14–23 (2007). G. Natile and L. G. Marzilli, “Non-covalent interactions in adducts of platinum drugs with nucleobases innucleotides and DNA as revealed by using chiral substrates,” Coord. Chem. Rev. 250, 1315–1331 (2006). P. Jurečka, et al. 'Benchmark database of accurate (MP2 and CCSD (T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs.' Physical Chemistry Chemical Physics 8.17 (2006): 1985-1993. T. Takatani, et al. 'Basis set consistent revision of the S22 test set of noncovalent interaction energies.' The Journal of chemical physics 132.14 (2010): 144104. 張育銘, “利用量子化學方法建立分子二聚體分子間作用力數據庫與SAPT分析,” 碩士論文, 國立台灣大學, 2017. 黃星翔, “利用量子化學方法建立混和型二聚體分子間作用力數據庫與混合法的比較分析.” 碩士論文, 國立台灣大學, 2017. O. Tyagi, Harender S. Bisht, and K. Alok Chatterjee. 'Phase transition, conformational disorder, and chain packing in crystalline long-chain symmetrical alkyl ethers and symmetrical alkenes.' The Journal of Physical Chemistry B108.9 (2004): 3010-3016. P. Hobza, and Rudolf Zahradník. Intermolecular complexes: the role of van der Waals systems in physical chemistry and in the biodisciplines. Vol. 52. Elsevier Science Ltd, 1988. W. Saenger and G. A. Jeffrey. Hydrogen bonding in biological structures. Springer-Verlag, Berlin, 1991. A. J . Stone,. 'The Theory of Intermolecular Forces Oxford University Press.' New York (1996). M. J. Frisch.; G. W. Trucks,; H. B. Schlegel; G. E. Scuseria; M. A. Robb; J. R. Cheeseman; J. A. Montgomery, Jr.; T. Vreven; K. N.Kudin; J. C.Burant; J. M. Millam; S. S. Iyengar; J Tomasi.; V. Barone; B. Mennucci; M . Cossi; G. Scalmani; N. Rega; G.A. Petersson; H. Nakatsuji; M. Hada; M. Ehara; K. Toyota.; R. Fukuda; J. Hasegawa; M. Ishida; T. Nakajima; Y. Honda; O. Kitao; H. Nakai; M. Klene; Li, X.; J. E. Knox; H. P. Hratchian; J. B. Cross; V. Bakken; C. Adamo; J. Jaramillo; R. Gomperts; R. E. Stratmann; O.Yazyev; A. J. Austin;R. Cammi; C. Pomelli; J. W. Ochterski; P. Y. Ayala; K.Morokuma;G.A.Voth;P. Salvador; J. J. Dannenberg; V. G.Zakrzewski; S.Dapprich; A. D.Daniels; M. C. Strain; O. Farkas; D. K. Malick; A. D.Rabuck; K. Raghavachari; J. B.Foresman; J. V.Ortiz; Q.Cui; A. G.Baboul;S.Clifford; J .Cioslowski; B. B. Stefanov; G. Liu; A. Liashenko; P. Piskorz; I. Komaromi; R. L. Martin; D. J. Fox; T Keith.; M. A. Al-Laham; C. Y.Peng; A.Nanayakkara; M.Challacombe; P. M. W. Gill; B. Johnson;W. Chen; M. W. Wong; C. Gonzalez; and J. A. Pople. Gaussian 03, RevisionD. 01; Gaussian, Inc.: Wallingford, CT, 2004. Trent M .Parker, et al. 'Levels of symmetry adapted perturbation theory (SAPT). I. Efficiency and performance for interaction energies.' The Journal of chemical physics 140.9 (2014): 094106. H. Dunning, 'A road map for the calculation of molecular binding energies.' The Journal of Physical Chemistry A 104.40 (2000): 9062-9080. A. Stone. The theory of intermolecular forces. OUP Oxford, 2013. S. Grimme, et al. 'A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu.' The Journal of chemical physics 132.15 (2010): 154104. O. Marchetti, and Hans-Joachim Werner. 'Accurate calculations of intermolecular interaction energies using explicitly correlated coupled cluster wave functions and a dispersion-weighted MP2 method.' The Journal of Physical Chemistry A 113.43 (2009): 11580-11585. K. Raghavachari, et al. 'A fifth-order perturbation comparison of electron correlation theories.' Chemical Physics Letters 157.6 (1989): 479-483. S. F. Boys, , and Fiorenza de Bernardi. 'The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors.' Molecular Physics 19.4 (1970): 553-566. B. Jeziorski,M. Robert, and Krzysztof Szalewicz. 'Perturbation theory approach to intermolecular potential energy surfaces of van der Waals complexes.' Chemical Reviews 94.7 (1994): 1887-1930. J. Hoja,F. Alexander. Sax, and Krzysztof Szalewicz. 'Is Electrostatics Sufficient to Describe Hydrogen‐Bonding Interactions?.' Chemistry-A European Journal 20.8 (2014): 2292-2300. M. Marques AL, and Eberhard KU Gross. 'Time-dependent density functional theory.' Annu. Rev. Phys. Chem. 55 (2004): 427-455. O. Tyagi,O. Harender S. Bisht, and Alok K. Chatterjee. 'Phase transition, conformational disorder, and chain packing in crystalline long-chain symmetrical alkyl ethers and symmetrical alkenes.' The Journal of Physical Chemistry B108.9 (2004): 3010-3016. E.G. Hohenstein and C. David Sherrill. 'Wavefunction methods for noncovalent interactions.' Wiley Interdisciplinary Reviews: Computational Molecular Science 2.2 (2012): 304-326. P.R. Surján., István Mayer, and István Lukovits. 'Second-quantization-based perturbation theory for intermolecular interactions without basis set superposition error.' Chemical physics letters 119.6 (1985): 538-542. I. Mayer 'Improved chemical energy component analysis.' Physical Chemistry Chemical Physics 14.1 (2012): 337-344 J.M. Turney, et al. 'Psi4: an open‐source ab initio electronic structure program.' Wiley Interdisciplinary Reviews: Computational Molecular Science2.4 (2012): 556-565. Daniel Berthelot, Weekly reports of the sessions of the Academy of Sciences, 126 pp. 1703-1855 (1898) T. Helgaker, et al. 'Basis-set convergence of correlated calculations on water.' The Journal of chemical physics 106.23 (1997): 9639-9646. P. Jurečka, et al. 'Benchmark database of accurate (MP2 and CCSD (T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs.' Physical Chemistry Chemical Physics 8.17 (2006): 1985-1993. M.J. Frisch 'Guassian 09, Gaussian, Wallingford, CT.' There is no corresponding record for this reference (2009). J.M. Turney, et al. 'Psi4: an open‐source ab initio electronic structure program.' Wiley Interdisciplinary Reviews: Computational Molecular Science2.4 (2012): 556-565. S. Tsuzuki, et al. 'Estimated MP2 and CCSD (T) interaction energies of n-alkane dimers at the basis set limit: Comparison of the methods of Helgaker et al. and Feller.' The Journal of chemical physics 124.11 (2006): 114304. S. Tsuzuki, et al. 'Magnitude of interaction between n-alkane chains and its anisotropy: High-level ab initio calculations of n-butane, n-petane, and n-hexane dimers.' The Journal of Physical Chemistry A 108.46 (2004): 10311-10316. K.S. Kim, S. Karthikeyan, and N. Jiten Singh. 'How Different Are Aromatic π Interactions from Aliphatic π Interactions and Non-π Stacking Interactions?.' Journal of chemical theory and computation 7.11 (2011): 3471-3477. V. Dyczmons. 'Dimers of ethanol.' The Journal of Physical Chemistry A108.11 (2004): 2080-2086. J.M. Hermida-Ramón., and Miguel A. Rı́os. 'Ab initio molecular orbital analysis of acetaldehyde dimers.: Thermodynamic properties.' Chemical physics letters 290.4 (1998): 431-436. J.M. Hermida-Ramón, and Miguel A. Ríos. 'The energy of interaction between two acetone molecules: a potential function constructed from ab initio data.' The Journal of Physical Chemistry A 102.15 (1998): 2594-2602. Y. Matsuda, et al. 'Infrared spectroscopy for acetone and its dimer based on photoionization detection with tunable coherent vacuum-ultraviolet light.' Chemical Physics Letters 471.1 (2009): 50-53. J. Chocholoušová, Jaroslav Vacek, and Pavel Hobza. 'Acetic acid dimer in the gas phase, nonpolar solvent, microhydrated environment, and dilute and concentrated acetic acid: ab initio quantum chemical and molecular dynamics simulations.' The Journal of Physical Chemistry A 107.17 (2003): 3086-3092. R. Sedlak., T. Janowski.,M. Pitoňák.,J. Řezáč.,P. Pulay., P. Hobza. (2013). Accuracy of quantum chemical methods for large noncovalent complexes. Journal of chemical theory and computation, 9(8), 3364-3374. Z. L Glick, D. P. Metcalf, A. Koutsoukas, S. A. Spronk, D. L Cheney and C. D sherrill, '.AP-Net: An atomic-pairwise neural network for smooth and transferable interaction potentials. ' The Joural of Chemical Physics, 2020. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/82378 | - |
| dc.description.abstract | 先前透過量子化學計算方法，建立出常見官能基二聚體的數據庫，但隨著分子系統越大計算也會越複雜，且需要的計算資源也會越來越高，因此我們實驗室的數據庫停留在10-20個重原子之間，然而自然界中的分子系統通常都屬於大分子，並不是目前的CPU-based可以應付的，所以需要架構出一種模型去預測更大的大分子系統，便進一步去了解相互作用如何得來的。 我們對八種常見的官能基二聚體的鍵結模式和相互作用力進行量子化學的研究，包括烷類-烯-炔類(AAA group)、醇-醛-酮類(AAK group)、羧酸-酰胺(CAA group)。我們為了得到這些官能基相互作用新的物理見解，使用基於對稱適應微擾理論(SAPT)進行了一系列的分解計算，我們進一步提出了基於特定官能基中化學可辨識團基的團基相互作用模型，我們希望這些模型可用於預測較大的分子系統的相互作用能，並透過預測出來的結果去構建粗粒化的力場。 我們使用PSI4軟體裡的SAPT方法，將相互作用分解成四個不同物理意義的作用力，分別是靜電能、誘導能、交換能與色散能，透過這些能量去分析分子間作用力的吸引力和排斥力是如何對分子二聚體的穩定性造成影響。我們希望透過此模型比SAPT分析更仔細的去探討這四項能量分別是由哪些分子中的團基相互作用而來的，並探討Dimer與Bimer相互作用的不同。從上述八類官能基，由炭數小的分子出發，去找出構成相互作用的規則，並最終能應用於預測大分子系統的相互作用能。 | zh_TW |
| dc.description.provenance | Made available in DSpace on 2022-11-25T07:30:00Z (GMT). No. of bitstreams: 1 U0001-0601202217002100.pdf: 4827595 bytes, checksum: 090ad3030ceada785beaaa2e5e838e9b (MD5) Previous issue date: 2021 | en |
| dc.description.tableofcontents | 口試委員會審定書 # 致謝 I 摘要 II ABSTRACT III 目錄 V 圖目錄 XII 表目錄 XV 第1章 緒論 1 1.1 研究動機 1 1.2 分子間作用力介紹 2 1.3 計算分子間作用力方法介紹 3 第2章 基本理論介紹 6 2.1 量子力學理論 6 2.1.1 薛丁格方程式(Schrödinger equation) 6 2.1.2 波恩奧本海默近似(Born-Oppenheimer Approximation) 8 2.2 Ab initio 分子軌域理論 10 2.2.1 自洽理論 Hartee-Fock approximation(HF) 11 2.2.2 微擾理論Møller-Plesset perturbation theory 14 2.2.3 耦合簇理論 Coupled Cluster Method(CC) 17 2.2.4 對稱性匹配微擾理論Symmetry-Adapted Perturbation Theory (SAPT) 18 第3章 計算方法與模型建立 21 3.1 計算方法 21 3.2 模型建立 21 3.2.1 團基分類 22 3.2.2 靜電能模型 23 3.2.3 誘導能模型 24 3.2.4 交換能模型 24 3.2.5 色散能模型 25 第4章 計算、預測結果與討論 27 4.1 靜電能模型計算與預測 27 4.1.1 烷類靜電能團基相互作用計算與預測 27 4.1.2 烷類烯類相同型與混和型靜電能團基相互作用計算與預測 29 4.1.3 烷類炔類相同型與混和型靜電能團基相互作用計算與預測 32 4.1.4 醇類靜電能團基相互作用計算與預測 33 4.1.5 烷類醇類混和型二聚體靜電能團基相互作用計算與預測 35 4.1.6 烯類醇類混和型二聚體靜電能團基相互作用計算與預測 36 4.1.7 醛類靜電能團基相互作用計算與預測 38 4.1.8 烷類醛類混和型二聚體靜電能團基相互作用計算與預測 40 4.1.9 烯類醛類混和型二聚體靜電能團基相互作用計算與預測 41 4.1.10 羧酸類靜電能團基相互作用計算與預測 43 4.1.11 醯胺類靜電能團基相互作用計算與預測 45 4.1.12 烷類羧酸類混和型二聚體靜電能團基相互作用計算與預測 46 4.1.13 烯類羧酸類混和型二聚體靜電能團基相互作用計算與預測 47 4.1.14 醇類羧酸類混和型二聚體靜電能團基相互作用計算與預測 48 4.1.15 醛類羧酸類混和型二聚體靜電能團基相互作用計算與預測 50 4.1.16 烷類醯胺類混和型二聚體靜電能團基相互作用計算與預測 51 4.1.17 烯類醯胺類混和型二聚體靜電能團基相互作用計算與預測 53 4.1.18 醇類醯胺類混和型二聚體靜電能團基相互作用計算與預測 54 4.1.19 醛類醯胺類混和型二聚體靜電能團基相互作用計算與預測 55 4.1.20 醯胺類羧酸類混和型二聚體靜電能團基相互作用計算與預測 57 4.1.21 靜電能預測結果討論 58 4.2 誘導能模型計算與預測 60 4.2.1 烷類誘導能團基相互作用計算與預測 60 4.2.2 烯類烷類誘導能團基相互作用計算與預測 62 4.2.3 烷類炔類相同型與混和型誘導能團基相互作用計算與預測 64 4.2.4 醇類誘導能團基相互作用計算與預測 66 4.2.5 烷類醇類混和型二聚體誘導能團基相互作用計算與預測 68 4.2.6 烯類醇類混和型二聚體誘導能團基相互作用計算與預測 70 4.2.7 醛類誘導能團基相互作用計算與預測 71 4.2.8 烷類醛類混和型二聚體誘導能團基相互作用計算與預測 73 4.2.9 烯類醛類混和型二聚體誘導能團基相互作用計算與預測 74 4.2.10 羧酸類誘導能團基相互作用計算與預測 76 4.2.11 醯胺類誘導能團基相互作用計算與預測 77 4.2.12 烷類羧酸類混和型二聚體誘導能團基相互作用計算與預測 79 4.2.13 烯類羧酸類混和型二聚體誘導能團基相互作用計算與預測 80 4.2.14 醇類羧酸類混和型二聚體誘導能團基相互作用計算與預測 81 4.2.15 醛類羧酸類混和型二聚體誘導能團基相互作用計算與預測 83 4.2.16 烷類醯胺類混和型二聚體誘導能團基相互作用計算與預測 84 4.2.17 烯類醯胺類混和型二聚體誘導能團基相互作用計算與預測 85 4.2.18 醇類醯胺類混和型二聚體誘導能團基相互作用計算與預測 86 4.2.19 醛類醯胺類混和型二聚體誘導能團基相互作用計算與預測 88 4.2.20 醯胺類羧酸類混和型二聚體誘導能團基相互作用計算與預測 89 4.2.21 誘導能預測結果討論 90 4.3 交換能模型計算與預測 92 4.3.1 烷類交換能團基相互作用計算與預測 92 4.3.2 烯類烷類交換能團基相互作用計算與預測 94 4.3.3 烷類炔類相同型與混和型交換能團基相互作用計算與預測 97 4.3.4 醇類交換能團基相互作用計算與預測 99 4.3.5 烷類醇類混和型二聚體交換能團基相互作用計算與預測 101 4.3.6 烯類醇類混和型二聚體交換能團基相互作用計算與預測 103 4.3.7 醛類交換能團基相互作用計算與預測 104 4.3.8 烷類醛類混和型二聚體交換能團基相互作用計算與預測 105 4.3.9 烯類醛類混和型二聚體交換能團基相互作用計算與預測 107 4.3.10 羧酸類交換能團基相互作用計算與預測 109 4.3.11 醯胺類交換能團基相互作用計算與預測 111 4.3.12 烷類羧酸類混和型二聚體交換能團基相互作用計算與預測 112 4.3.13 烯類羧酸類混和型二聚體交換能團基相互作用計算與預測 114 4.3.14 醇類羧酸類混和型二聚體交換能團基相互作用計算與預測 115 4.3.15 醛類羧酸類混和型二聚體交換能團基相互作用計算與預測 116 4.3.16 烷類醯胺類混和型二聚體交換能團基相互作用計算與預測 118 4.3.17 烯類醯胺類混和型二聚體交換能團基相互作用計算與預測 119 4.3.18 醇類醯胺類混和型二聚體交換能團基相互作用計算與預測 120 4.3.19 醛類醯胺類混和型二聚體交換能團基相互作用計算與預測 122 4.3.20 醯胺類羧酸類混和型二聚體交換能團基相互作用計算與預測 123 4.3.21 交換能預測結果討論 125 4.4 色散能模型計算與預測 126 4.4.1 烷類色散能計算與預測 126 4.4.2 烯類色散能計算與預測 128 4.4.3 炔類色散能計算與預測 131 4.4.4 醇類色散能計算與預測 133 4.4.5 烷類醇類混和型二聚體色散能計算與預測 135 4.4.6 烯類醇類混和型二聚體色散能計算與預測 135 4.4.7 醛類色散能計算與預測 136 4.4.8 烷類醛類混和型二聚體色散能計算與預測 137 4.4.9 烯類醛類混和型二聚體色散能計算與預測 138 4.4.10 羧酸類色散能計算與預測 139 4.4.11 醯胺類色散能計算與預測 140 4.4.12 烷類羧酸類混和型二聚體色散能計算與預測 142 4.4.13 烯類羧酸類混和型二聚體色散能計算與預測 143 4.4.14 醇類羧酸類混和型二聚體色散能計算與預測 144 4.4.15 醛類羧酸類混和型二聚體色散能計算與預測 144 4.4.16 烷類醯胺類混和型二聚體色散能用計算與預測 145 4.4.17 烯類醯胺類混和型二聚體色散能用計算與預測 146 4.4.18 醇類醯胺類混和型二聚體色散能團基相互作用計算與預測 146 4.4.19 醛類醯胺類混和型二聚體色散能團基相互作用計算與預測 147 4.4.20 醯胺類羧酸類混和型二聚體色散能計算與預測 148 4.4.21 色散能預測結果 148 4.5 分子間作用力總能預測結果 150 4.6 與機器學習比較 156 第5章 結論及未來展望 157 5.1 結論 157 5.2 未來展望 157 REFERENCE 158 附錄 161 | |
| dc.language.iso | zh-TW | |
| dc.title | 利用SAPT方法建立團基粗粒化模型並分析與預測分子間作用力 | zh_TW |
| dc.title | Using SAPT method makes a segmental coarse-grained model analysis and intermolecular forces predictions | en |
| dc.date.schoolyear | 110-1 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 林立強(Hsin-Tsai Liu),李奕霈(Chih-Yang Tseng),周佳靚,蔡政達 | |
| dc.subject.keyword | 相互作用能數據庫,非共價相互作用力,分子間作用力,SAPT,團基相互作用, | zh_TW |
| dc.subject.keyword | Intermolecular interaction energy database,Noncovalent interaction,SAPT,functional groups interaction,segmental groups interaction, | en |
| dc.relation.page | 183 | |
| dc.identifier.doi | 10.6342/NTU202200021 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2022-01-12 | |
| dc.contributor.author-college | 工學院 | zh_TW |
| dc.contributor.author-dept | 應用力學研究所 | zh_TW |
| dc.date.embargo-lift | 2025-01-01 | - |
| 顯示於系所單位： | 應用力學研究所 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| U0001-0601202217002100.pdf | 4.71 MB | Adobe PDF | 檢視/開啟 |
系統中的文件，除了特別指名其著作權條款之外，均受到著作權保護，並且保留所有的權利。