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★声明:本文仅代表个人观点,笔者学识有限,资料整理过程中可能存在疏漏错误,请不吝指正。 晶体结构不是预期结构案例29 案例88: 本来是按照如图88所示(由ChemBioDraw[1]绘制),在催化剂的作用下使化合物A和化合物B反应生成化合物C,然而实验后处理完,培养晶体进行单晶X射线衍射(SC-XRD,single-crystal X-ray diffraction)实验得到晶体数据,经结构解析发现该晶体结构为单质硫/硫单质 [2](S8, Octathiocane, CAS: 10544-50-0.CCDC [3]: 1161500[2a], 1161501 [2b],267383 [2c], 757275 [2d],1161502-1161505 [2d], 757277 [2e], 856708 [2f],862658 [2g], 1555239 [2h], 1555240[2i], 1934705 [2j],1947735 [2k], 1992592 [2l], 2015061 [2m],1992592 [2n], 2097464 [2o], 2241156 [2p],2267093 [2q], 2150895 [2r], 2082127 [2s],2339024 [2t], 2415401 [2u], 930773 [2v],2474521 [2w], 2588694 [2x],2589570 [2y]),可能是反应中的副产物。
▲图88 案例88反应示意图 相关视频: 单晶结构解析练习791(非预期结构):https://www.bilibili.com/video/BV1ybeB6iE1t 案例89: 本来是按照如图89所示,利用四水合硝酸镉(Cd(NO3)2·4H2O, Cadmium nitrate tetrahydrate, CAS: 10022-68-1)和配体反应以N,N-二甲基甲酰胺 [4](DMF, N,N-dimethylformamide,CAS: 68-12-2, CCDC: 102756 [4a], 1869635–1869638[4b], 1869744–1869752 [4b])和水[5](H2O, water, CAS: 7732-18-5, CCDC: 2080050–2080051)作为溶剂在一定条件下反应,以期得到含该配体的镉配合物,然而所得红棕色晶体经SC-XRD实验得到晶体数据,经结构解析发现该晶体结构为碳酸镉 [6](CdCO3, Cadmium carbonate, CAS: 513-78-0, CCDC:156740 [6a], 156755[6a], 20181 [6b], 33662 [6c], 2589924[6d]),其中碳酸根可能来自DMF分解产生(参阅推文“DMF和DEF会为晶体结构带来什么”),也可能是空气中二氧化碳(CO2, Carbon dioxide, CAS: 124-38-9)进入体系中生成。
▲图89 案例89反应示意图 相关视频: 单晶结构解析练习795(CAP数据还原-非预期结构-非正定):https://www.bilibili.com/video/BV1RhaP6JEi2 案例90: 本来是按照如图90所示,利用氯(二甲基硫化)金(I)/氯化(二甲硫醚)金(I) [7](Me2SAuCl, Chloro(dimethyl sulfide)gold(I), CAS: 29892-37-3,CCDC: 1169763 [7a], 2116322–2116324 [7b], 2426918 [7c])和双(对甲氧基苯基)氧化膦(Bis(4-methoxyphenyl)phosphineoxide, CAS: 15754-51-5)以及其他成分以甲苯 [8](Tol,toluene, CAS: 108-88-3, CCDC: 1273751 [8a], 1273752 [8b], 1273753 [8c], 725245 [8d], 1430464–1430470 [8e], 2377542 [8f])和正己烷[9](C6H14, n-hexane,CAS: 110-54-3, CCDC: 103189)作为溶剂在一定条件下反应,以期得到多核金簇合物,然而所得晶体经SC-XRD实验得到晶体数据,经结构解析发现该晶体结构为双核金化合物。
▲图90 案例90反应示意图 相关视频: 单晶结构解析练习797(非预期结构-SHELXT无法直接给出结构模型):https://www.bilibili.com/video/BV142H76nEyW 参考文献 [1] (a)Klein, F. M. CS ChemDraw Pro,1 Version 3.1 for Windows. J. Chem. Inf. Comput. Sci. 1995, 35, 166–167. DOI: 10.1021/ci00023a026. (b)Cousins, K. R. ChemDraw 6.0 Ultra CambridgeSoft Corporation, 100 Cambridge ParkDrive, Cambridge, MA 02140. http://www.camsoft.com. Commercial Price: $1395.Academic Price: $699. J. Am. Chem. Soc. 2000, 122, 10257–10258. DOI: 10.1021/ja0047572.(c) Buntrock, R. E. ChemOffice Ultra 7.0. J. Chem. Inf. Comput. Sci. 2002, 42, 1505–1506. DOI: 10.1021/ci025575p. (d) Li, Z.; Wan, H.; Shi, Y.;Ouyang, P. Personal Experience with Four Kinds of Chemical Structure DrawingSoftware: Review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch. J. Chem. Inf. Comput. Sci. 2004, 44, 1886–1890. DOI: 10.1021/ci049794h.(e) Mendelsohn, L. D. ChemDraw8 Ultra, Windows and Macintosh Versions. J. Chem. Inf. Comput. Sci. 2004, 44, 2225–2226. DOI: 10.1021/ci040123t. (f) Cousins, K. R. ChemDrawUltra 9.0. CambridgeSoft, 100 CambridgePark Drive, Cambridge, MA 02140. www.cambridgesoft.com. See Web site for pricing options. J. Am. Chem. Soc. 2005, 127, 4115–4116. DOI:10.1021/ja0410237. (g) Zielesny, A. Chemistry Software PackageChemOffice Ultra 2005. J. Chem. Inf.Model. 2005, 45, 1474–1477. DOI:10.1021/ci050273j. (h) Mills, N. ChemDraw Ultra 10.0 CambridgeSoft, 100CambridgePark Drive, Cambridge, MA 02140. www.cambridgesoft.com. CommercialPrice: $1910 for download, $2150 for CD-ROM; Academic Price: $710 fordownload, $800 for CD-ROM. J. Am. Chem. Soc. 2006, 128, 13649–13650. DOI: 10.1021/ja0697875. (i) Kerwin, S. M.ChemBioOffice Ultra 2010 Suite. J. Am. Chem. Soc. 2010, 132, 2466–2467. DOI: 10.1021/ja1005306. (j) Milne, G. W. A. SoftwareReview of ChemBioDraw 12.0. J. Chem. Inf.Model. 2010, 50, 2053. DOI:10.1021/ci100385n. (k) Narayanaswamy, V. K.; Rissdörfer, M.; Odhav, B.Review on CambridgeSoft ChemBioDraw Ultra 13.0v. Int. J. Theor. Appl. Sci. 2013, 5, 43–49. [2] (a) Rettig, S. J.; Trotter, J. Refinement of the Structureof Orthorhombic Sulfur, α-S8. Acta Cryst. 1987, C43, 2260-2262. DOI:10.1107/S0108270187088152. (b) Gallacher, A. C.; Pinkerton, A. A. ARedetermination of Monclinic γ-Sulfur. Acta Cryst. 1993, C49, 125–126. DOI:10.1107/S0108270192009661. (c) Bolte, M. CCDC 267383: ExperimentalCrystal Structure Determination. CSD Commun. 2005, DOI: 10.5517/cc8z78q.(d) Goldsmith, L. M.; Strouse, C. E. Molecular Dynamics in the Solid State. TheOrder-Disorder Transition of Monoclinic Sulfur. J. Am. Chem. Soc. 1977, 99, 7580–7589. DOI:10.1021/ja00465a029. (e) David, W. I. F.; Ibberson, R. M.; Cox, S. F.J.; Wood, P. T. Order–Disorder Transition in Monoclinic Sulfur: A PreciseStructural Study by High-Resolution Neutron Powder Diffraction. Acta Cryst.2006. B62, 953–959. DOI:10.1107/S0108768106039309. (f) Fronczek, F. R. CCDC 856708: ExperimentalCrystal Structure Determination. CSD Commun. 2012, DOI: 10.5517/ccxrgrv.(g) Clegg, J. K.; Meng, W.; Nitschke, J. R. CCDC 862658: Experimental CrystalStructure Determination. CSD Commun. 2012, DOI: 10.5517/ccxynp5. (h)Batsanov, A. S. CCDC 1555239: ExperimentalCrystal Structure Determination. CSD Commun. 2017, DOI:10.5517/ccdc.csd.cc1p6c08. (i) Batsanov, A. CCDC 1555240: ExperimentalCrystal Structure Determination. CSD Commun. 2017, DOI:10.5517/ccdc.csd.cc1p6c19. (j) Bouteiller, H.; Pasturel, M.; Lemoine, P.CCDC 1934705: Experimental Crystal Structure Determination. CSD Commun. 2019, DOI: 10.5517/ccdc.csd.cc22y6v3. (k) Mikuriya,M.; Taniguchi, K.; Koyama, Y.; Watanabe, Y.; Yoshioka, D.; Mitsuhashi, R.;Asato, E. Crystal Structure of S8 Molecule from Thiourea. X-ray.Str. Anal. Online. 2020, 36, 1–2. DOI:10.2116/xraystruct.36.1. (l) Chen, W. CCDC 1992592: Experimental CrystalStructure Determination. CSD Commun. 2020, DOI:10.5517/ccdc.csd.cc24wg5p. (m) Zeukang, R. D.; Siwe-Noundou, X.;Fotsing, M. T.; Kuiate, T. T.; Mbafor, J. T.; Krause, R. W. M.; Choudhary, M.I.; de Théodore Atchadé, A. Cordidepsine is A Potential New Anti-HIV Depsidonefrom Cordia millenii, Baker. Molecules 2019, 24, 3202. DOI:10.3390/molecules24173202. (n) Chen, W.; Zhou, H.; Ren, B.-H.; Ren,W.-M.; Lu, X.-B. COS-Triggered Oxygen/Sulfur Exchange of Isatins:Chemoselective Synthesis of Functionalized Isoindigos and Spirothiopyrans viaSelf-Condensation and the Thio-Diels–Alder Reaction. Org. Biomol. Chem. 2022, 20, 678–685. DOI: 10.1039/d1ob02157e.(o) Wang, R.; Xie, K.-J.; Fu, Q.; Wu, M.; Pan, G.-F.; Lou, D.-W.; Liang, F.-S. Transformationof Thioacids into Carboxylic Acids via a Visible-Light-Promoted AtomicSubstitution Process. Org. Lett. 2022, 24, 2020–2024. DOI:10.1021/acs.orglett.2c00481. (p) Yu, Y. CCDC 2241156: ExperimentalCrystal Structure Determination. CSD Commun. 2023, DOI:10.5517/ccdc.csd.cc2f73c5. (q) Marupalli, S. S.; Arockiaraj, M.; Singh,G.; Rajeshkumar, V. Iodine-Catalyzed Synthesis of Benzo-β-carbolinesthrough Desulfurative Cyclization of 2‑(1H‑Indol-3-ylsulfanyl)-phenylamineswith Aryl Methyl Ketones. J. Org. Chem. 2023, 88, 12783–12791. DOI:10.1021/acs.joc.3c00657. (r) Rushworth, J. L.; Thawani, A. R.;Fajardo-Ruiz, E.; Meiring, J. C. M.; Heise, C.; White, A. J. P.; Akhmanova, A.;Brandt, J. R.; Thorn-Seshold, O.; Fuchter, M. J. [5]-Helistatins:Tubulin-Binding Helicenes with Antimitotic Activity. JACS Au 2022, 2, 2561–2570. DOI:10.1021/jacsau.2c00435. (s) Zeng, J.-S.; Liu, Y.-H.; Yang, S.-N.; Chien,S.-Y.; Wen, Z.-H.; Liu, H.-T.; Tsai, Y.-C.; Sung, P.-J. Isolation andIdentification of Cyclooctasulfur from the Octocoral Sinularia Humilis (vanOfwegen, 2008). Nat. Prod. Commun. 2021, 16, 1. DOI:10.1177/1934578X211040605. (t) Hong, D. CCDC 2339024: ExperimentalCrystal Structure Determination. CSD Commun. 2024, DOI:10.5517/ccdc.csd.cc2jhydd. (u) Rahimisheikh, S.; Hajizadeh, A.;Quintelier, M.; Stulens, S.; Hardy, A.; Hadermann, J. Crystal Structure ofSubmicron-Sized Sulfur Particles Using 3D ED Obtained in Atmospheric Conditions.Acta Cryst. 2025, C81, 56–63. DOI:10.1107/S2053229625000130. (v) Das, P.; Mondal, S.; Goswami, S.; Mondal,A.; Das, P.; Ray, S. A Completely Metal-Free Protocol for OxidativeDesulfitative C−N Coupling Reaction in Non-Basic Condition. Chem. Asian J.2025, 20, e202401575. DOI:10.1002/asia.202401575. (w) Johnson, N. T.; Waddell, P. G. CCDC 2474521:Experimental Crystal Structure Determination. CSD Commun. 2025, DOI: 10.5517/ccdc.csd.cc2p1y8z. (x) Hong,D. CCDC 2588694: Experimental Crystal Structure Determination. CSD Commun.2026, DOI: 10.5517/ccdc.csd.cc2swr8q.(y)Hong, D. CCDC 2589570: ExperimentalCrystal Structure Determination. CSD Commun. 2026, DOI: 10.5517/ccdc.csd.cc2sxnjx. [3] (a) Allen, F. H. The CambridgeStructural Database: A Quarter of a Million Crystal Structures and Rising. Acta Cryst. 2002, B58, 380–388. DOI: 10.1107/S0108768102003890. (b) Groom, C. R.;Bruno, I. J.; Lightfoot, M. P.; Ward, S. C. The Cambridge Structural Database. Acta Cryst. 2016, B72, 171–179. DOI: 10.1107/S2052520616003954. (c) Mitchell, J.;Robertson, J. H.; Raithby, P. R. Cambridge Crystallographic Data Centre (CCDC).Comprehensive Coordination Chemistry III2021, 413–437. DOI: 10.1016/B978-0-12-409547-2.14829-2. [4] (a)Borrmann, H.; Persson, I.; Sandström, M.; Stålhandske, C. M. V. The Crystal andLiquid Structures of N,N-Dimethylthioformamide and N,N-DimethylformamideShowing a Stronger Hydrogen Bonding Effect for C–H⋯S than of C–H⋯O. J.Chem. Soc. Perkin Trans. 2 2000, 393–402. DOI:10.1039/a904531g. (b) Ratajczyk,P.; Sobczak, S.; Katrusiak, A. High-Pressure Structure and Properties of N,N-Dimethylformamide(DMF). Cryst. Growth Des. 2019, 19, 896–901. DOI: 10.1021/acs.cgd.8b01452. [5] Salzmann, C. G., Loveday, J. S., Rosu-Finsen, A.;Bull, C. L. Structure and nature of ice XIX. Nat. Commun. 2021, 12, 3162. DOI: 10.1038/s41467-021-23399-z. [6] (a) Am.Mineral. 2007, 92, 829–836. DOI: 10.2138/am.2007.2315. (b) Doklady Akademii Nauk SSSR 1979, 245, 1099. (c) Skrifter utgitt av det NorskeVidenskaps-Akademi i Oslo 1: Matematisk-Naturvidenskapelig Klasse 1928, 1928, 1. (d) Hong, D. CCDC 2589924: Experimental CrystalStructure Determination. CSD Commun. 2026, DOI:10.5517/ccdc.csd.cc2sy0yq. [7] (a) Jones, P. G.; Lautner, J. Chloro(dimethylsulfide)gold(I). Acta Cryst. 1988, C44, 2089–2091. DOI:10.1107/S0108270188009151. (b) Pawlȩdzio, S.; Malinska, M.; Kleemiss,F.; Grabowsky, S.; Woźniak, K. Aurophilic Interactions Studied by QuantumCrystallography. Inorg. Chem. 2022, 61, 4235–4239. DOI:10.1021/acs.inorgchem.1c03333. (c) Al-Buthabhak, H.; Sobolev, A. N.; Baker, M. V. CCDC2426918: Experimental Crystal Structure Determination. CSD Commun. 2025, DOI: 10.5517/ccdc.csd.cc2mgdp6. [8] (a)Anderson, M.; Bosio, L.; Bruneaux-Poulle, J.; Fourme, R. Toluène: Structure Cristalline et Moléculairede la Variété Stable α et état Amorphe J. Chim. Phys. 1977, 74,68–73. DOI: 10.1051/jcp/1977740068. (b) Bosto, L.; Bruneaux-Poulle, J.; Defrain, A.;Dupont, M. C. R. Acad. Sci. Ser. C (Chim) 1973, 276, 1667.(c)Ibberson, R. M.; David, W. I. F.; Prager, M. Accurate Determination of HydrogenAtom Positions In Α-Toluene by Neutron Powder Diffraction. J. Chem. Soc.Chem. Commun. 1992, 1438–1439. DOI: 10.1039/c39920001438.(d) Nayak,S. K.; Sathishumar, R.; Row, T. N. G. Directing Role of Functional Groups inSelective Generation Of C–H⋯πInteractions: In Situ Cryo-Crystallographic Studies on BenzylDerivatives. CrystEngComm 2010, 12, 3112–3118. DOI: 10.1039/c001190h. (e) Marciniak, J.; Bąkowicz, J.; Dobrowolski, M.A.; Dziubek, K. F.; Kaźmierczak, M.; Paliwoda, D.; Rajewski, K. W.; Sobczak,S.; Stachowicz, M.; Katrusiak, A. Most Frequent Organic Interactions Compressedin Toluene. Cryst. Growth Des. 2016, 16, 1435–1441. DOI: 10.1021/acs.cgd.5b01538. (f) Andre, D.; Fourme, R.; Bruneaus-Poulle, J.;Bosio, L. Crystal Structure of the Metastable β-Phase of Toluene. J. Mol.Struct. 1982, 81, 253–259. DOI: 10.1016/0022-2860(82)85338-6. [9] Boese, R.; Weiss, H.-C.; Bläser, D. TheMelting Point Alternation in the Short-Chain n-Alkanes: Single-CrystalX-Ray Analyses of Propane at 30 K and of n-Butane to n-Nonane at90 K. Angew. Chem. Int. Ed. 1999, 38, 988–992. DOI: 10.1002/(SICI)1521-3773(19990401)38:7<988::AID-ANIE988>3.0.CO;2-0.
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