共晶化合物/鹽類其晶體固態氫鍵鍵結與其在水中溶解度之關係

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研究生：	林子淳 Zih-Chun Lin
論文名稱：	共晶化合物/鹽類其晶體固態氫鍵鍵結與其在水中溶解度之關係 Relating the Solubility in Water of Co-crystals/Salts with Their Solid-State Hydrogen Bonding Network
指導教授：	李度 Tu Lee
口試委員:
學位類別：	碩士 Master
系所名稱：	工學院 - 化學工程與材料工程學系 Department of Chemical & Materials Engineering
畢業學年度：	99
語文別：	英文
論文頁數：	141
中文關鍵詞：	共晶化合物、氫鍵、鹽類
外文關鍵詞：	hydrogen bonding, salt, co-crystal
相關次數：	點閱：14 下載：0
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結晶材料的物理性質主要是受到固體狀態下的分子排列所影響，更細一步說是受到分子擺放位置和彼此間的作用力所影響。而共晶和鹽類更是近年來的熱門研究議題，當中最值得深入探討的作用力即為氫鍵。
在篩選共晶/鹽類的結晶工程中，我們著重探討於產物的物理性質譬如熔化熱，溶解於水中的焓，溶解於水中的熵，和在水中的溶解度是否受到固態狀態下形成之氫鍵影響。所以說除了再重覆前人發展出一套鑒定的共晶鹽類篩選跟檢測流程，實驗室常見的分析工具，如PXRD，DSC，TGA，IR，OM，和SXD被用來了解超分子結構，並確認共晶化合物/鹽類的生成。結果共產生2:1 cytosine－fumaric acid、2:1 cytosine－acetylenedicarboxylic dihydrate的共晶化合物，和2:1cytosine－tartaric acid的鹽類化合物。在本研究中的最大特色就是提出氫鍵數的探討。
在這個實驗過程中，不同以往的是我們使用固態氫鍵數企圖解釋共晶化合物在水中的溶解度而非使用溶度積。

It is well-known that crystalline materials obtain their fundamental physical properties from the molecular arrangement within the solid, and altering the placement and/or interactions between these molecules. Most studies were interested in the formation and structure of co-crystal/salt compound, the hydrogen bonding played an important role to affect physical properties.
In crystal engineering for screening co-crystals/salts, this thesis focused on relating the physical properties such as the heat of fusion, the enthalpy of dissolution, the entropy of dissolution, and the solubility in water. Common laboratory analytical tools such as PXRD, DSC, TGA, FT-IR, OM, and SXD were used to understand the supramolecular architectures and to ensure the quality of co-crystals. 2:1 co-crystal of cytosine-fumaric acid, 2:1 co-crystal of cytosine-acetylenedicarboxylic acid, and 2:1 salt of cytosine-tartaric acid were manufactured. The significance of our research is to offer concept to study the solid state hydrogen bonding.
In the experimental process, we used hydrogen bonding number in the solid-state to attempt to explain the co-crystal solubility in the liquid state, rather than using the solubility product in the liquid state to explain the co-crystal solubility in the liquid state.

Table of Contents
摘要	i
Abstract	ii
Acknowledgement	iii
Table of Contents	iv
Chapter 1	Executive Summery	1
1.1 Introduction	1
1.2 Brief Introduction of Cytosine	5
1.3 Conceptual Framework	6
1.4 Reference	8
Chapter 2	Analytical Instruments	11
2.1 Introduction	11
2.2 Crystallography	14
2.2.1 Powder X–ray Diffraction (PXRD)	14
2.2.2 Single-Crystal X-ray Diffraction (SXD)	18
2.3 Spectroscopic Instrument	20
2.3.1 Fourier Transform Infrared (FT-IR) Spectroscopy	20
2.3.2 Photoluminescence Spectroscopy (PL)	23
2.4 Thermal Analysis	25
2.4.1 Differential Scanning Calorimetry (DSC)	25
2.5 Microscopic Methods	31
2.6 Conclusions	33
2.8 References	34
Chapter 3	Solubility, Crystallinity, Crystal Habits of Cytosine by Initial Screening Procedures	37
3.1 Introduction	37
3.1.1 Solubility	39
3.1.2 Crystal Habits	40
3.1.3 Polymorphism	41
3.1.4 Crystallinity	44
3.2 Materials	44
3.2.1 Cytosine	44
3.2.2 Solvents	49
3.3.1 Initial Solvent Screening	53
3.3.1.1 Temperature Cooling Method	54
3.3.2 Instrumental Analysis	55
3.3.2.1 Powder X-ray Diffractometry (PXRD)	55
3.3.2.2 Differential Scanning Calorimetry (DSC)	55
3.3.2.3 Thermogravimetric Analysis (TGA)	56
3.3.2.4 Fourier Transform Infrared Spectroscopy (FT-IR)	56
3.3.2.5 Optical Microscopy (OM)	57
3.4 Results and Discussion	58
3.4.1 Solubility	58
3.4.2 Crystal Habits	63
3.4.3 Polymorphism	64
3.4.4 Crystallinity	67
3.6 References	69
Chapter 4	Relating the Solubility in Water of Co-crystals/Salts with Their Solid-State Hydrogen Bonding Network	73
4.1 Introduction	73
4.1.1 The Introduction of Hydrogen Bonding	75
4.1.2 The aim of co-crystal/salt comparison	78
4.1.3 Review of co-crystal/salt screening/manufacturing	79
4.2 Materials	82
4.3 Experimental Section	84
4.3.1 Screening of Cocrystal/Salt Formation	84
4.3.1.1 Co-crystal Screening by Solvent Drop Grinding	84
4.3.1.2 Co-crystal Screening by Differential Scanning Calorimetry (DSC)	84
4.3.2 Manufacturing of Co-crystal /Salt	85
4.3.3 Analytical Instruments	86
4.3.3.1 Optical Microscopy (OM)	86
4.3.3.2 Powder X-ray Diffractometry (PXRD)	86
4.3.3.3 Fourier Transform Infrared (FT-IR) Spectroscopy	87
4.3.3.4 Differential Scanning Calorimetry (DSC)	88
4.3.3.5 Thermal Gravimetric Analysis (TGA)	89
4.3.3.6 Single-Crystal- X-Ray Diffraction (SXD) (Hydrogen Bonding Network)	89
4.3.4 The Solubility test for Co-crystal/Salt	90
4.4 Results and Discussions	91
4.4.1 Screening Results	91
4.4.2 Characterization	95
4.4.2.1 Optical Microscopy (OM)	96
4.4.2.2 Powder X-Ray Diffraction (PXRD)	97
4.4.2.3 Differential Scanning Calorimetry (DSC) and Thermal Gravimetric Analysis (TGA)	97
4.4.2.5 Single Crystal X-ray Diffraction (SXD)	107
4.4.3 Solubility Study	125
4.4.3.1 Solubility Determination	125
4.4.3.2 Phase Solubility Diagram (PSD)	129
4.5 Conclusions	134
4.6 Reference	135
Chapter 5	Conclusions and Future Works	141
List of Tables
Table 2.1 Summary on the characterization capacities of the analytical apparatuses	13
Table 3.1 23 kinds of solvents in our experiments.	50
Table 3.2 Form space of cytosine, the solvents were arranged by Hildebrand values.	59
Table 3.3 Molar enthalpy and entropy of dissolution of cytosine in different solvents.	63
Table 3.4 The enthalpy of melting and crystallinity of cytosine crystals by temperature cooling in 2 kinds of good solvents.	67
Table 4.1 The information of the chemicals.	83
Table 4.2 IR assignments of cytosine, dicarboxylic acids, and co-crystals of cytosine with dicarboxylic acids.	107
Table 4.3 Crystallographic data of co-crystals/salts	113
List of Figures
Figure 1.1 Schematic map of the common solid forms and their respected compounds.	3
Figure 1.2 The molecular structure of anhydrous cytosine.	6
Figure 2.1 Diffraction of Bragg’s Law.	15
Figure 2.2 A Bruker Axs D8 Advance PXRD.	17
Figure 2.3 Schematic representation of a four-circle diffractometer.	19
Figure 2.4 A Siemens SMART CCD-based X-ray diffractometer equipped with Oxford Cryosystems low temperature device.	20
Figure 2.5 A Perkin Elmer Spectrum One FT-IR spectrometer (Perkin Elmer, New York, USA).	22
Figure 2.6 A Perkin Elmer Spectrum One FT-IR spectrometer (Perkin Elmer, New York, USA).	22
Figure 2.7 Schematic illustration of luminescence processes.	24
Figure 2.8 Perkin Elmer LS-55 Fluorescence spectrometer.	25
Figure 2.9 Schematic diagram of a DSC. The triangles are amplifiers that determine the difference in the two input signals.  The sample heater power is adjusted to keep the sample and the reference at the same temperature during the DSC scan.	27
Figure 2.10 (a) Heat flux DSC, (b) power-compensated DSC (S = Sample pan; R = Reference pan).	28
Figure 2.11 A Perkin Elmer DSC 7 differential scanning calorimeter.	28
Figure 2.12 A Perkin Elmer TGA 7 thermogravimetric analyzer.	30
Figure 2.13 Light paths of the optical microscopy 	32
Figure 2.14 Olympus SZII (Tokyo, Japan) optical microscopy.	32
Figure 3.1 Typical solubility curve and a cooling crystallization path from A to D.	40
Figure 3.2 Solubility diagram for enantiotropic polymorphism.  Form I was the stable form below the transition temperature, while Form II was the metastable one.  Above the transition point (Ttr), Form I became metastable, while Form II became stable.	42
Figure 3.3 Solubility diagram for monotropic polymorphism.  Form I was considered the thermodynamically stable polymorph, while Form II was the kinetically stable (metastable) polymorph.	43
Figure 3.4 The molecular structure of anhydrous cytosine.	45
Figure 3.5 The structure (a) cytidine is the nucleoside of cytosine in RNA and (b) deoxycytidylate is the nucleotide of cytosine in DNA.	46
Figure 3.6 (a) The Watson-Crick base pair, cytosine forms three hydrogen bonds with guanine and (b) the Hoogsteen base pair, thymine forms two hydrogen bonds with adenine.	46
Figure 3.7 Cytosine has two tautomeric forms, the amino form and imino form.	47
Figure 3.8 (a) TGA data and (b) DSC thermogram at a heating rate of 10oC/min of the purchased cytosine for use test.	48
Figure 3.9 The recrystallization of cytosine by temperature cooling.	54
Figure 3.10 Solubility curve of cytosine in the good solvents (a) water, and (b) DMSO	60
Figure 3.11 The Van’t Hoff plots of the solubility values of cytosine in 2 different kinds of good solvents (a) DMSO, and (b) water.	63
Figure 3.12 OM images of cytosine monohydrate solids grown from water.	64
Figure 3.13 (a) TGA data and (b) DSC thermogram of cytosine monohydrate re-crystallized from water by cooling.	65
Figure 3.14 The PXRD patterns of (a) cytosine monohydrate, and (b) the purchased cytosine.	66
Figure 3.15 The FT-IR spectra of (a) the cytosine monohydrate and (b) the purchased cytosine .	66
Figure 4.1 Different types of hydrogen bridges. (a) Normal hydrogen bond with one acceptor, (b) Bifurcated hydrogen bond, and (c) Trifurcated hydrogen bond. d is the distance of H atom to A atom.	77
Figure 4.2 Molecular Structures of (a) cytosine, (b) fumaric acid, (c) succinic acid, (d) l-tartaric acid, (e) d-tartaric acid	83
Figure 4.3 PXRD patterns of (a) cytosine, (b) fumaric acid, (c) water-drop ground mixture of cytosine and fumaric acid where indicates the new appearing diffraction peak, and (d) solution crystallized co-crystal of CymFuAn.  (* represented the new peak relative to the starting materials.)	93
Figure 4.4 PXRD patterns of (a) cytosine, (b) succinic acid, (c) water-drop ground mixture of cytosine and succinic acid where indicates the new appearing diffraction peak, and (d) solution crystallized co-crystal of CymSuAn.  (* represented the new peak relative to the starting materials.)	93
Figure 4.5 PXRD patterns of (a) cytosine, (b) acetylenedicarboxylic acid, (c) water-drop ground mixture of cytosine and acetylenedicarboxylic acid where indicates the new appearing diffraction peak, and (d) solution crystallized co-crystal of CymAcAn (* represented the new peak relative to the starting materials.)	94
Figure 4.6 PXRD patterns of (a) cytosine, (b) l-tartaric acid, (c) solution crystallized co-crystal of CymLTAn (* represented the new peak relative to the starting materials.)	94
Figure 4.7 PXRD patterns of (a) cytosine, (b) d-tartaric acid, (d) solution crystallized co-crystal of CymDTAn (* represented the new peak relative to the starting materials.)	95
Figure 4.8 The optical micrographs of the co-crystal/salt of (a) CymFuAn, (b) CmSuAn, (c) CmAcAn, (d) CymLTAn, (e) CymDTAn, and (f) cytosine monohydrate.	97
Figure 4.9 (a) TGA and (b) DSC scans of solution crystallized co-crystal of CymFuAn	99
Figure 4.10 (a) TGA and (b) DSC scans of solution crystallized co-crystal of CymSuAn	99
Figure 4.11 (a) TGA and (b) DSC scans of solution crystallized salt of Cy2AcA1•2H2O	100
Figure 4.12 (a) TGA and (b) DSC scans of solution crystallized salt of Cy2LTA1•H2O	100
Figure 4.13 (a) TGA and (b) DSC scans of solution crystallized salt of Cy2DTA1•H2O	101
Figure 4.14 Effect of X1-N-H … O-X2 hydrogen bonding on X~O bond lengths.  The quantity Δd/d0 is the difference between the donor X1-N and and the acceptor O-X2 bond length (d0 ＝ value for fragments free of hydrogen bonding; ￭: the co-crystal of Cy2FuA1; •: the co-crystal of Cy2SuA1; ▲: the co-crystal of Cy2AcA1.2H2O; ▼: the salt of Cy2LTA1.H2O; ◄: the salt of Cy2DTA1.H2O	103
Figure 4.15 Effect of X1-C-H … O-X2 hydrogen bonding on X~O bond lengths.  The quantity Δd/d0 is the difference between the donor X1-C and the acceptor O-X2 bond length (d0 ＝ value for fragments free of hydrogen bonding; ￭: the co-crystal of Cy2FuA1; •: the co-crystal of Cy2SuA1; ▲: the co-crystal of Cy2AcA1.2H2O; ▼: the salt of Cy2LTA1.H2O; ◄: the salt of Cy2DTA1.H2O	104
Figure 4.16 FTIR spectra of (a) cytosine, (b) cytosine monohydrate, (c) fumaric acid, and (d) the co-crystal of Cy2FuA1.	104
Figure 4.17 FTIR spectra of (a) cytosine, (b) succinic acid, and (c) the co-crystal of Cy2SuA1.	105
Figure 4.18 FTIR spectra of (a) cytosine, (b) cytosine monohydrate, (c) acetylenedicarboxylic acid, and (d) the co-crystal of Cy2AcA1•2H2O.	105
Figure 4.19 FTIR spectra of (a) cytosine, (b) cytosine monohydrate, (c) l-tartaric  acid, and (d) the salt of Cy2LTA1•H2O.	106
Figure 4.20 FTIR spectra of (a) cytosine, (b) cytosine monohydrate, (c) d-tartaric  acid, and (d) the salt of Cy2DTA1•H2O.	106
Figure 4.21 (a) PXRD pattern from solution crystallization by cooling, and (b) theoretical PXRD pattern from SXD of 2:1 co-crystal of Cy2FuA1.	110
Figure 4.22 (a) PXRD pattern from solution crystallization by cooling, and (b) theoretical PXRD pattern from SXD of 2:1 salt of Cy2SuA1.	111
Figure 4.23 (a) PXRD pattern from solution crystallization by cooling, and (b) theoretical PXRD pattern from SXD of 2:1:1 co-crystal of Cy2AcA1. 2H2O	111
Figure 4.24 (a) PXRD pattern from solution crystallization by cooling, and (b) theoretical PXRD pattern from SXD of 2:1 co-crystal of Cy2LTA1•H2O.	112
Figure 4.25 (a) PXRD pattern from solution crystallization by cooling, and (b) theoretical PXRD pattern from SXD of 2:1 co-crystal of Cy2DTA1•H2O.	112
Figure 4.26 Visualization of the (a) ORTEP plot of the molecular entities in the asymmetric unit of the co-crystal Cy2FuA1, (b) supramolecular arrangements of cytosine and fumaric acid in the co-crystal Cy2FuA1 translating along a axis, and (c) the packing moiety of the hydrogen bonding network with fumaric acid molecule as the center surrounded by other components in the co-crystal Cy2FuA1 as depicted by a computer software (Diamond 3.1, Crystal Impact Gbr, Brandenberg, Germany).	116
Figure 4.27 Visualization of the (a) ORTEP plot of the molecular entities in the asymmetric unit of the cocrystal Cy2SuA1, (b) supramolecular arrangements of  cytosine and succinic acid in the cocrystal Cy2SuA1, and (c) the packing moiety the hydrogen bonding network with succinic acid molecule as the center surrounded by other components in the co-crystal Cy2SuA1 as depicted by a computer software (Diamond 3.1, Crystal Impact Gbr, Brandenberg, Germany).	118
Figure 4.28 Visualization of the (a) ORTEP plot of the molecular entities in the asymmetric unit of the cocrystal Cy2AcA1.2H2O, (b) supramolecular arrangements of  cytosine and acetylenedicarboxylic acid in the co-crystal Cy2AcA1.2H2O, and (c) the packing moiety of the hydrogen bonding network with acetylenedicarboxylic acid molecule as the center surrounded by other components in the co-crystal Cy2AcA1.2H2O as depicted by a computer software (Diamond 3.1, Crystal Impact Gbr, Brandenberg, Germany).	120
Figure 4.29 Visualization of the (a) ORTEP plot of the molecular entities in the asymmetric unit of the salt Cy2LTA1•H2O, (b) hydrogen bonded formed by cytosine and water molecules in the salt Cy2LTA1•H2O, and (c) the packing moiety of the hydrogen bonding network with l-tartaric acid molecule as the center surrounded by other components in the salt Cy2LTA1.H2O as depicted by a computer software (Diamond 3.1, Crystal Impact Gbr, Brandenberg, Germany). (d) L/D-tartaric acid crystal structure is plotted compared to Cy2LTA1•H2O and Cy2LTA1•H2O, distinguishing the chiral/racemic crystal structure.	122
Figure 4.30 Visualization of the (a) ORTEP plot of the molecular entities in the asymmetric unit of the salt Cy2DTA1•H2O, (b) hydrogen bonded formed by cytosine and water molecules in the salt Cy2DTA1•H2O, and (c) the packing moiety of the hydrogen bonding network with d-tartaric acid molecule as the center surrounded by other components in the salt Cy2DTA1.H2O as depicted by a computer software (Diamond 3.1, Crystal Impact Gbr, Brandenberg, Germany).	124
Figure 4.31 The solubility curve of (a) cytosine, (b) the salt of Cy2LTA1•H2O, (c) the salt of Cy2DTA1•H2O, (d) cytosine monohydrate, (e) the co-crystal of Cy2SuA1, (f) the co-crystal of Cy2AcA1.H2O, and (g) the co-crystal of Cy2FuA1.	126
Figure 4.32 The solubility values in water at 25℃ of (a) Cy2FuA1, (b) Cy2AcA1.2H2O, (c) Cy2SuA1, compared with hydrogen bonding number.	127
Figure 4.33 The solubility values in water at 25℃ of (a) Cy2FuA1, (b) Cy1AcA1.2H2O, (c) Cy2SuA,  compared with the solubility values in water at 25℃ of (a) fumaric acid, (b) acetylenedicarboxylic acid, (c) succinic acid.	128
Figure 4.34 The mole fraction in water at 25℃ of (a) Cy2FuA1, (b) Cy1AcA1.2H2O, (c) Cy2SuA, compared with hydrogen bonding number.	128
Figure 4.35 Effect of cytosine concentration and fumaric acid concentration the solubility of 2:1 cocrystal of Cy2FuA1 at 37℃ showing reactant total solution concentrations ([cyt]T and [FuA]T) at equilibrium with 2:1 cocrystal of Cy2FuA1. Measured solubility of cytosine and 2:1 cocrystal of Cy2FuA1 in water were indicated by green ▼ and red ▲, respectively. Predicted solubility dependence on 2:1 cocrystal of Cy2FuA1 is represented by the solid line [cyt]T = (Ksp/[FuA]T)0.5 with Ksp = 9.95 × 10-6 m3. The dashed line represented reactant stoichiometry in solution corresponding to that of cocrystals.	131
Figure 4.36 Effect of cytosine concentration and succinic acid concentration the solubility of 2:1 cocrystal of Cy2SuA1 at 37℃ showing reactant total solution concentrations ([cyt]T and [SuA]T) at equilibrium with 2:1 cocrystal of Cy2SuA1. Measured solubility of cytosine and 2:1 cocrystal of Cy2SuA1 in water were indicated by green ▼ and red ▲ , respectively. Predicted solubility dependence on 2:1 cocrystal of Cy2SuA1 is represented by the solid line [cyt]T = (Ksp/[SuA]T)0.5 with Ksp = 4.35 × 10-5 m3. The dashed line represented reactant stoichiometry in solution corresponding to that of co-crystals.	132
Figure 4.37 Effect of cytosine concentration and acetylenedicarboxylic acid concentration on the solubility of 2:1 cocrystal of Cy2AcA1. 2H2O at 37℃ showing reactant total solution concentrations ([cyt]T and [AcA]T) at equilibrium with 2:1 co-crystal of CyAcA. 2H2O. Measured solubility of cytosine and 2:1 co-crystal of Cy2AcA1. 2H2O in water were indicated by green ▼ and red ▲ , respectively. Predicted solubility dependence on 2:1 salt of CyLTA. H2O is represented by the solid line [cyt]T = (Ksp/[AcA]T)0.5 with Ksp = 1.21 × 10-4 m3. The dashed line represented reactant stoichiometry in solution corresponding to that of co-crystals.	133

                                

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