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Electronic Supplementary Information (ESI)
Amine-carboxylate Supramolecular Synthon in
Pharmaceutical Cocrystals
Duanxiu Li,ab Minmin Kong,ab Jiong Li,b Zongwu Deng,ab and Hailu Zhangab*
a Laboratory of Magnetic Resonance Spectroscopy and Imaging, Suzhou Institute of Nano-
Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China. Tel:
+86-512-62872713; Fax: +86-512-62603079; E-mail: [email protected].
b CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-
Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China.
Electronic Supplementary Material (ESI) for CrystEngComm.This journal is © The Royal Society of Chemistry 2018
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Contents
S1. Virtual cocrystal screening.................................................................................................S3
Table S1 Chemical structures and abbreviation of APIs.........................................................S4
Table S2 Calculated change in interaction site pairing energies (−ΔE in kJ mol-1) for the
reported pharmaceutical cocrystals of L-pro and their CSD refcodes......................................S6
Table S3 Results of virtual cocrystals screening.....................................................................S7
S2. Cocrystal preparation..........................................................................................................S8
Table S4 Crystallographic data for new obtained cocrystals of L-pro..................................S10
Table S5 Hydrogen bonds for new obtained cocrystals of L-pro..........................................S11
Fig. S1 The PXRD patterns of CNX-L-pro and starting materials........................................S12
Fig. S2 The PXRD patterns of FC-L-pro and starting materials............................................S13
Fig. S3 The PXRD patterns of CLX-L-pro and starting materials.........................................S13
Fig. S4 The PXRD patterns of SMZ-L-pro and starting materials.........................................S14
Table S6 CSD refcodes of cocrystals with N—H···–OOC synthon......................................S14
Fig. S5 Electrostatic potential surfaces (in kJ mol−1) of CNX molecules using different
starting conformations (extracted from structures of Form I-IV, respectively).....................S15
Table S7 The MEPmax values (in kJ mol−1) of COOH, Ph-OH, and NH, NH2 functional groups
in cocrystals of L-pro..............................................................................................................S16
References .............................................................................................................................S17
S3
S1. Virtual cocrystal screening
Gaussian 09 program[1] was used to optimize the geometry and calculate the MEPS using
DFT and a B3LYP/6-31G* basis set. Multiwfn_3.4.1 program[2] was used to extract local
maxima and minima from the MEP mapped onto the 0.002 Bohr Å−3 electron density
isosurface. The MEPS were then converted into αi and βj H-bond parameters using eqn (3)
and (4) and calculation of the energies of the pure and cocrystal solids, E, were performed
using Excel spreadsheets. Such mapped electrostatic potential surface has been plotted using
the GaussView 5.0 software. The stability of cocrystals compared to pure components was
estimated for all combinations based on the difference in the interaction site pairing energies,
ΔE, calculated using eqn (1) and (2).
E=−Σαiβj (1)
Comparison of the total SSIP of two pure components with cocrystals of various
stoichiometries gives an energy difference, i.e.
ΔE=Ecc−nE1−mE2 (2)
where E1 is the interaction site pairing energy of the pure form of component 1, E2 is the
interaction site pairing energy of the pure form of component 2, Ecc is the interaction site
pairing energy of the cocrystal of stoichiometry 1n2m, which is a measure of the probability of
forming a cocrystal.
α = 0.0000162MEPmax2 + 0.00962MEPmax (3)
β = 0.000146MEPmin2 − 0.00930MEPmin (4)
where MEPmin and MEPmax are local minima and maxima on the MEPS in kJ mol−1.
S4
Table S1 Chemical structures and abbreviation of APIs.
API Name Chemical structure Abbreviation Reference
L-proline NH2
COO L-pro
IpragliflozinO
HOS
FHO
OH
HO
Ipr [3]
C-aryl Glucoside Derivatives
OHO
HOOH
OH
R3R2
R1
R4 R5R6OA - [4]
NaproxenO
COOH Nap [5]
AprepitantF3C
CF3
ON
O
NH
NHN
F
O
Apr [6]
Ezetimibe F N
OH
O
F
OH
Eze [7]
(1S)-1-[4-chloro-3-(4-ethoxybenzyl)phenyl]-1,6-
dideoxy-D-glucose
O
HOOH
OH
Cl OEt
Ptt [8]
HelicidO O
HOOH
OHO
HO
Hel [9]
(1S)-1, 5-dehydrogenation-1-C-[3-[[5-(4-fluorophenyl)-2-
thienyl]methyl]-4-methylphenyl]-D-glucitol
O
HOS
HO
HO
F
Ptc [10]
BaicaleinOHO
OH OHO
Bai [11]
ChrysinOHO
OH O
Chr [11]
GenisteinOHO
OH OOH
Gen [11]
kaempferol OHO
OHOH
OH
O
Kae [11]
Luteolin OHO
OH
OH
OH
O
Lut [11]
Quercetin OHO
OHOH
OH
OH
O
Que [11]
Myricetin OHO
OHOH
OHOH
OH
O
Myr [12]
Nitrofurantoin OO2N N
N
NHO
O
Nft [13]
S5
ResveratrolOH
HO
OH
Rsv [14]
FlurbiprofenF
COOH Flu [15]
Reluzole S
NH2N
OCF3 Rlz [16]
Diclofenac acidHN
Cl
Cl
COOH
Dfa [17]
ClonixinHN
N
ClCH3 COOH
CNX √
Nitazoxanide O
O
NH
O S
N NO2
NTZ
SulfamerazineH2N
SHN
O O N
NSMR
SulfadiazineH2N
SHN
O O N
N SDZ
Celecoxib N N
S
H3C
CF3
H2N O
O
CLX √
Acyclovir NHN
N
N
OHO
O
NH2
ACV
Sulfathiazole NH
S NS
O
O
NH2
STZ
Sulfamethizole NNH
SN
SO O
NH2
SMZ √
5-Fluorouracil HN
HNO
FO
FU
Flucytosine N
HNO
FNH2
FC √
S6
Table S2 Calculated change in interaction site pairing energies (ΔE in kJ mol−1) for the
reported pharmaceutical cocrystals of L-proline and their CSD refcodes.
API Stoichiometry −ΔE Reference
Nap 1:1 4.5 FEVZUD [5]
Apr 1:1:1(MeOH) 3.9 [6]
Chr 1:1 5.6 EJEQAN [11]
Gen 1:2 9.2 EJEQER [11]
Kae 1:2 17.5 EJEPOA [11]
Lut 1:1 11.6 EJEPUG [11]
Que 1:2 19.1 EJERAO [11]
1:1 21.2 PEBZOO [14]Rsv
1:2 32.5 PEBZUU [14]
2:1 7.6 VEVKOZ [15]
1:1 6.0
VEVKEP, VEVKEP01,
VEVMUH, VEVMUH01,
VEVLEQ, VEVLEQ01,
VEVLOA [15]
1:2 6.3 VEVLAM [15]
Flu
1:3 6.4 VEVKUF [15]
Rlz 1:1 10.9 YEPJEL [16]
Dfa 1:1 8.1 RETNEM [17]
S7
Table S3 Results of virtual cocrystal screening. Experimentally observed cocrystals are denoted by ‘‘√’’.
API Stoichiometry −ΔE (kJ mol−1) Experimental results
NTZ 2:1, 1:1, 1:2 1.3, 1.3, 2.3
SMR 2:1, 1:1, 1:2 1.9, 1.5, 2.3
SDZ 2:1, 1:1, 1:2 3.1, 2.3, 3.1
CLX 2:1, 1:1, 1:2 2.4, 2.3, 4.1 √(1:2)
ACV 2:1, 1:1, 1:2 3.9, 3.3, 3.3
STZ 2:1, 1:1, 1:2 4.5, 4.0, 5.1
SMZ 2:1, 1:1, 1:2 5.7, 4.9, 5.2 √(1:1)
FU 2:1, 1:1, 1:2 6.1, 5.8, 6.5
FC 2:1, 1:1, 1:2 14.6, 11.7, 17.8 √(1:1)
CNX-I 2:1, 1:1, 1:2 5.2, 4.6, 4.8
CNX-II 2:1, 1:1, 1:2 0.5, 0.3, 0.4
CNX-III 2:1, 1:1, 1:2 18.4, 13.3, 13.8
CNX-IV 2:1, 1:1, 1:2 18.4, 13.3, 13.8
√(1:1)
S8
S2. Experimental Screening of cocrystals
Materials
L-proline (>98%) was purchased from Aladdin. Clonixin (CNX, form I, >98%) and
Sulfamethizole (SMZ, >98.5%) were purchased from TCI. Celecoxib (CLX, ≥99%) was
purchased from Dalian Meilun Biotech Co., Ltd. Flucytosine (FC, ≥97%) and solvents of
analytical grade were purchased from Sinopharm Chemical Reagent Co., Ltd. All chemicals
were used without further purification.
Preparation of CNX-L-pro cocrystal (1:1)
CNX (66 mg, 0.25 mmol) and L-pro (57 mg, 0.5 mmol) were mixed and dissolved in
anhydrous CH3OH (5 mL) and filtered through a 0.22 μm PTFE syringe filter. The resulting
solution was left to slowly evaporate at room temperature. Colorless crystals of CNX-L-pro
were harvested after 2-3 days. Large-scale crystallization of CNX-L-pro can be realized
through CH3OH-assisted grinding of a mixture of a 1:1 molar ratio of CNX and L-pro.
Preparation of FC-L-pro cocrystal (1:1)
FC (65 mg, 0.25 mmol) and L-pro (115 mg, 1.0 mmol) were mixed and dissolved in
anhydrous CH3OH (5 mL) and filtered through a 0.22 μm PTFE syringe filter. The resulting
solution was left to slowly evaporate at room temperature. Colorless crystals of FC-L-pro
were harvested after 2-3 days. Large-scale crystallization of FC-L-pro can be realized through
CH3OH-assisted grinding of a mixture of a 1:1 molar ratio of FC and L-pro.
Preparation of CLX-L-pro cocrystal (1:2)
CLX (95 mg, 0.25 mmol) and L-pro (57 mg, 0.5 mmol) were mixed and dissolved in
anhydrous CH3OH (5 mL) and then filtered through a 0.22 mm PTFE syringe filter. The
resulting solution was left to slowly evaporate at room temperature. Colorless crystals CLX-
L-pro can be harvested after 2-3 days. Large-scale crystallization of CLX-L-pro can be
realized through CH3OH-assisted grinding of a mixture of a 1:2 molar ratio of CLX and L-pro.
Preparation of SMZ-L-pro cocrystal (1:1)
Eqivmolar mounts of SMZ (54 mg, 0.2 mmol) and L-pro (23 mg, 0.2 mmol) were mixed and
dissolved in anhydrous CH3OH (5 mL). The resulting solution was filtered through a 0.22 μm
PTFE syringe filter and left to slowly evaporate at room temperature. Colorless crystals of
SMZ-L-pro were harvested after 2-3 days. Large-scale crystallization of SMZ-L-pro can be
realized through CH3OH-assisted grinding of a mixture of a 1:1 molar ratio of SMZ and L-pro.
S9
X-ray crystallographic analysis
Single crystal X-ray diffraction data of CNX-L-pro was collected on a Bruker Apex-II CCD
diffractometer using a graphite monochrome Mo-Kα (λ = 0.71073 Å) at 120 K. The collected
data was subjected to absorption corrections using the multi-scan method. The diffraction data
reduction was performed using the Bruker SAINT software. Single crystal X-ray diffraction
data of CLX-L-pro and SMZ-L-pro were collected on an Agilent Xcalibur diffractometer
CCD using a graphite monochrome Mo-Kα (λ = 0.71073 Å) at 293 K for CLX-L-pro and
193K for SMZ-L-pro. FC-L-pro was measured on an Agilent Xcalibur diffractometer CCD
using a graphite monochrome Cu-Kα (λ = 1.54184 Å) at 293 K. The collected data was
subjected to absorption corrections using the multi-scan method. The diffraction data
reduction was performed using the CrysAlisPro software (CrysAlis171. NET, Version
1.71.36.32).
The structures of the four cocrystals were solved by direct methods and refined on F2 by
full-matrix least squares using SHELXTL-2014.[18] All non-hydrogen atoms were refined with
anisotropic thermal parameters. The positions of hydrogen atoms associated with carbon
atoms were placed geometrically. The active hydrogen atoms on the O/N−H groups of all
structures were located from the difference Fourier maps with the O/N−H distance restrained
to 0.82/0.86 Å and thermal parameters constrained to Uiso(H) = 1.2Ueq(O/N). For form
CLX-L-pro, the CF3 functional group displayed the positional disorder with the relative ratio
of 0.65/0.35, two proline rings displayed positional disorder with the relative ratio of
0.80/0.20 and 0.63/0.37 refined for the two disordered components. Crystallographic data and
structural refinements for CNX-L-pro, FC-L-pro, CLX-L-pro, and SMZ-L-pro are
summarized in Table S4. Hydrogen bonding distances and angles for CNX-L-pro, FC-L-pro,
CLX-L-pro, and SMZ-L-pro are summarized in Table S5.
Powder X-ray diffraction (powder XRD)
Powder XRD of all the samples were recorded on a Bruker D8 Advance X-ray powder
diffractometer (Bruker AXS, Karlsruhe, Germany) equipped with a LynxEye detector (Cu Kα
radiation). The tube current and voltage of the generator were set to 40 mA and 40 kV,
respectively. The data were recorded over the 2θ range from 3° to 40° scanning with a step
size of 0.0194° at ambient temperature. For CNX-L-pro, CLX-L-pro, SMZ-L-pro and FC-L-
pro, comparisons of the experimental and simulated PXRD patterns are given in the Fig.
S1−S4.
S10
Table S4. Crystallographic data for new obtained cocrystals of L-pro.
Crystal data CNX-L-pro (1:1) FC-L-pro (1:1) CLX-L-pro (1:2) SMZ-L-pro (1:1)
Formula C18H20ClN3O4 C9H13FN4O3 C27H32F3N5O6S C14H19N5O4S2
Formula weight 377.82 244.23 611.63 385.46
Temperature/K 120(2) 293(2) 293(2) 193(2)
Crystal system Orthorhombic Triclinic Orthorhombic Monoclinic
Space group P212121 P1 P212121 P21
a/Å 5.7789(3) 5.5932(3) 9.5641(7) 11.1850(9)
b/Å 12.3293(7) 6.0945(4) 20.0364(10) 8.9191(9)
c/Å 24.9401(14) 16.8563(8) 30.4887(17) 17.2838(15)
α/° 90 97.308(4) 90 90
β/° 90 94.713(4) 90 96.393(9)
γ/° 90 107.291(5) 90 90
V/Å3 1776.98(17) 539.79(5) 5842.6(6) 1713.5(3)
Z 4 2 8 4
ρcalc/(g·cm−3) 1.412 1.503 1.391 1.494
μ (Mo−Kα)/mm−1 0.245 1.082 0.179 0.342
F (000) 792 256 2560 808
total reflections 42221 5933 28262 8982
unique reflections 4100(Rint = 0.0712)
3167(Rint = 0.0215)
10336(Rint = 0.0734)
5096(Rint = 0.0524)
no. observations 3404 3080 6707 3522
no. parameters 236 339 796 456
R1[I > 2σ(I)]/R1a 0.0361/0.1040 0.0417/0.0426 0.0657/0.1115 0.0405/0.0541
wR2[I > 2σ(I)]/wR2b 0.0559/0.1268 0.1117/0.1136 0.1271/0.1437 0.1099/0.1206
cGOF 0.933 1.047 1.009 1.025
Δρmax/Δρmin (e Å−3) 0.180/-0.271 0.356/-0.302 0.412/-0.317 0.416/-0.371
Flack parameter −0.01(3) 0.02(11) −0.07(13) −0.05(17)
CCDC 1850498 1850499 1850500 1850501aR1 =Σ||Fo| − |Fc||/Σ|Fo|. bwR2= [Σw(Fo
2−Fc2)2/ ΣwFo
2]1/2. cGOF = [Σw((Fo2 − Fc
2)2)/(n − p)]1/2, where n = number of reflections and p = total number of parameters refined.
S11
Table S5 Hydrogen bonds for new obtained cocrystals of L-pro.
D—H···A D—H/Å H···A/Å D···A/Å D—H···A/º Symmetry code
CNX-L-pro O1—H1···O3 0.84 1.74 2.568(3) 170.4
N2—H2A···O2 0.88 1.94 2.676(3) 140.4
N3—H3···O4 0.91 2.00 2.800(3) 145.4 x−1/2, −y+1/2, −z
N3—H3A···O3 0.91 1.82 2.719(3) 167.8 x−1, y, z
FC-L-pro N3—H3B···F1 0.77(5) 2.46(4) 2.762(3) 105(4)
N6—H6B···F2 0.94(5) 2.45(4) 2.767(4) 100(3)
N7—H7A···O4 0.91(4) 2.21(4) 2.650(3) 109(3)
N8—H8B···O6 0.82(5) 2.20(4) 2.657(4) 115(4)
N1—H1A···N5 0.88 1.89 2.762(3) 172.5 x, y+1, z
N3—H3A···O2 0.93(4) 2.05(4) 2.978(3) 173(3) x+1, y, z
N3—H3B···O3 0.77(5) 2.18(5) 2.936(4) 171(4) x, y, z−1
N4—H4A···N2 0.79 1.98 2.759(3) 164.8 x−1, y, z
N6—H6A···O1 0.86(4) 2.10(5) 2.962(4) 176(4) x, y−1, z
N6—H6B···O5 0.94(5) 2.23(5) 3.070(4) 149(4) x+1, y, z
N7—H7A···O6 0.91(4) 2.02(4) 2.862(4) 154(3)
N7—H7B···O3 0.88(5) 1.91(4) 2.753(3) 160(4) x−1, y, z
N7—H7B···O4 0.88(4) 2.45(4) 3.173(4) 139(3) x−1, y, z
N8—H8A···O5 0.78(6) 1.99(6) 2.749(3) 164(5) x+1, y, z
N8—H8B···O4 0.82(5) 2.06(4) 2.755(4) 142(4) x, y, z-1
CLX-L-pro N1—H1B···O12 0.86(5) 2.17(6) 3.024(8) 173(4)
N4—H4A···O1 0.86 2.34 2.841(7) 117.4
N4—H4B···O8 0.86 2.02 2.838(7) 158.4
N7—H7B···O5 0.84 2.07 2.664(6) 128.1
N7—H7C···O7 0.86 1.91 2.746(6) 163.1
N8—H8B···O7 0.86 2.28 2.725(6) 112.1
N9—H9B··· O8 0.83 2.17 2.859(6) 140.6
N9—H9B···O10 0.83 2.13 2.644(6) 119.8
N10—H10B···O9 0.92 2.39 3.005(7) 124.6
N10—H10B···O10 0.92 1.9 2.811(6) 174.1
N10—H10C···O12 0.93 2.25 2.716(6) 110.4
N1—H1A···O4 1.01(7) 1.94(7) 2.937(8) 168(5) x−1, y, z
N7—H7B···O6 0.84 2.28 2.868(6) 127.1 x−1/2, −y+1/2, −z+1
N9—H9C···O6 0.93 1.75 2.683(6) 173.7 x−1/2, −y+1/2, −z+1
N8—H8B···O9 0.86 2.02 2.702(7) 135 x+1, y, z
N8—H8C···O11 0.85 1.89 2.727(6) 171.6 x+1/2, −y+3/2, −z+1
S12
N10—H10C···O11 0.93 2.08 2.833(6) 137.3 x−1/2, −y+3/2, −z+1
SMZ-L-pro N1—H1A···O5 0.84 2.01 2.847(10) 171.5
N1—H1B···O2 0.96 2.04 2.987(9) 166.1 −x+1, y+1/2, −z+2
N3—H3A···O8 0.88(3) 1.88(3) 2.749(9) 166(8)
N5—H5A···O7 0.81 2.14 2.938(9) 169.3
N5—H5B···O4 0.81 2.23 2.996(9) 156.8 −x+2, y−1/2, −z+1
N7—H7A···O6 0.76 2.02 2.729(9) 156.7
N9—H9D···O6 0.91 2.06 2.893(10) 152.2 −x+2, y−1/2, −z+2
N9—H9E···O3 0.91 2.17 2.987(8) 148.9 −x+2, y−1/2, −z+2
N9—H9E···N6 0.91 2.41 3.058(9) 128.5 −x+2, y−1/2, −z+2
N10—H10A···O8 0.91 1.86 2.767(9) 179.5 −x+1, y+1/2, −z+1
N10—H10B···O1 0.91 2.43 3.161(8) 137.2 −x+1, y+1/2, −z+1
N10—H10B···N2 0.91 2.56 3.055(9) 115.2 −x+1, y+1/2, −z+1
5 10 15 20 25 30 35 402 (degree)
CNX-L-pro simulated CNX-L-pro L-pro CNX form I
Fig. S1 The PXRD patterns of CNX-L-pro and starting materials.
S13
5 10 15 20 25 30 35 40
FC-L-pro simulated FC-L-pro L-pro FC
2 (degree)
Fig. S2 The PXRD patterns of FC-L-pro and starting materials.
5 10 15 20 25 30 35 40
2 (degree)
CLX-L-pro simulated CLX-L-pro L-Pro CLX
Fig. S3 The PXRD patterns of CLX-L-pro and starting materials.
S14
5 10 15 20 25 30 35 40
2 (degree)
SMZ-L-pro simulated SMZ-L-pro L-pro SMZ
Fig. S4 The PXRD patterns of SMZ-L-pro and starting materials.
Table S6 CSD-refcodes of cocrystals with N—H···–OOC synthon.a
Search motif Refcodes of hits
NH2···–OOC(n=19)
BEJNAI, CIDBOH, PAVXIV, COKTEC,b WECXAF, WECXEJ, UFOQEN, DADMIH, WETHOV,
YEPJEL, VETVUM, PIRXOF,cNAQPON, DAYREA03/DAYREA06, DUMJEA10,c
HUZVUT, REGKUK, PAQMECacyclic-NH···–OOC
(n=7)WUSTAH, DUCMAQ, HACKII, HACKOO,
HACKUU, DUKJUP, CUKPUUc
cyclic-NH···–OOC (n=8)
ALIWEZ, UPIGOR, NOBYAE, WETJEN, WUYROX, CUKPUU,c DUMJEA10,c PIRXOFc
a. Interaction between two electroneutral molecules and NH group is not charged.b. This structure was not used in Fig. 6 for the hydrogen bond angle < 120º.c. Structures holding two kinds of NH···–OOC interactions.
S15
Fig. S5 Electrostatic potential surfaces (in kJ mol-1) of CNX molecules using different
starting conformations (extracted from structures of Form I-IV, respectively).
S16
Table S7 The MEPmax values (in kJ mol-1) of COOH, Ph-OH, and NH, NH2 functional groups
in cocrystals of L-pro.
API H-bond donor MEPmax (kJ mol-1)
Chr 2 Ph-OH 290.8, 63.3
Gen 3 Ph-OH 300.8, 280.3, 71.2
Kae 4 Ph-OH 304.4, 295.7, 172.8, 91.0
Lut 4 Ph-OH 304.6, 299.4, 299.3, 57.2
Que 5 Ph-OH 319.8, 303.2, 221.8, 168.1, 90.2
Rsv 3 Ph-OH 275.7, 275.5, 275.1
Nap COOH 250.9
Flu COOH 261.6
Dfa COOH; NH 273.6; 68.5
CNX COOH; NH 286.2; 54.0
Apr NH 211.7
Rlz NH2 251.4, 225.4
CLX NH2 242.6, 240.5
SMZ NH2; NH 220.3, 219.5; 246.6
FC NH2; NH 238.9, 216.7; 235.1
The values in bold font indicate the corresponding H-bond donor in supramolecular synthon O—H···–OOC or N—H···–OOC of cocrystals.
S17
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