Hydrates of Cyclobutylamine: Modifications of Gas Clathrate Types sI

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Hydrates of cyclobutylamine – modifications of gas clathrate types sI and sH Lukasz Dobrzycki, Kamila Pruszkowska, Roland Boese, and Micha# K. Cyra#ski Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.5b01846 • Publication Date (Web): 23 Feb 2016 Downloaded from http://pubs.acs.org on March 14, 2016

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Crystal Growth & Design

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Hydrates of cyclobutylamine – modifications of gas clathrate types sI and sH

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Lukasz Dobrzycki*, Kamila Pruszkowska, Roland Boese, Michał K. Cyrański

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The Czochralski Laboratory of Advanced Crystal Engineering, Faculty of Chemistry, University of

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Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland

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Abstract

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Cyclobutylamine (cBA) and its four new hydrates were crystallized using in situ crystallization

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technique with a focused IR laser beam procedure on a single crystal diffractometer. Two groups of

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hydrates, separated by a gap, can be identified: the “lower hydrates” (the known hemi- and new

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monohydrate); plus the “higher hydrates”: (6 3/7, approx. 7 ½ and 9 1/2). The “lower hydrates” are

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fully-ordered structures with well-defined stoichiometries, in contrast the “higher hydrates” which are

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severely disordered with water molecules organized in 3-D networks, similar to clathrate hydrate type sI

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(hydrate 7 ½) and sH (hydrates 6 3/7 and 9 ½). The latter two structures can be considered as extensions

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of the hexagonal clathrate hydrate sH with addition of water segments in a manner which preserves the

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hexagonal/trigonal symmetry of the lattice, changing only the c edge of the unit cell. Such a variation is

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commonly used in engineering for modifying standard structures to ‘extended’ versions, like creating a

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limousine from an economy car.

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*Phone: +0048225526360, Fax: +0048228222892, E-mail: [email protected]

21 ACS Paragon Plus Environment


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Hydrates of cyclobutylamine – modifications of gas

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clathrate types sI and sH

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The Czochralski Laboratory of Advanced Crystal Engineering, Faculty of Chemistry, University of

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Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland

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*Phone: +0048225526360, Fax: +0048228222892, E-mail: [email protected]

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Abstract

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Cyclobutylamine (cBA) and its four new hydrates were crystallized using in situ crystallization

9

technique with a focused IR laser beam procedure on a single crystal diffractometer. Two groups of

10

hydrates, separated by a gap, can be identified: the “lower hydrates” (the known hemi- and new

11

monohydrate); plus the “higher hydrates”: (6 3/7, approx. 7 ½ and 9 1/2). The “lower hydrates” are

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fully-ordered structures with well-defined stoichiometries, in contrast the “higher hydrates” which are

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severely disordered with water molecules organized in 3-D networks, similar to clathrate hydrate type sI

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(hydrate 7 ½) and sH (hydrates 6 3/7 and 9 ½). The latter two structures can be considered as extensions

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of the hexagonal clathrate hydrate sH with addition of water segments in a manner which preserves the

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hexagonal/trigonal symmetry of the lattice, changing only the c axis of the unit cell. Such a variation is

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commonly used in engineering for modifying standard structures to ‘extended’ versions, like creating a

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limousine from an economy car.

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Introduction

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There exist a relatively small number of crystal structures containing cyclobutylamine (cBA) in either

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neutral or protonated form, as revealed by a search of the Cambridge Structural Database1 which results

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in just 12 records. The non-protonated cBA is used to obtain new coordination complexes with a Pt

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central ion2-5 as potential anti-tumor agents, similar to cisplatin6 or carboplatin.7 The cationic form of

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cBA is applied for preparation of inorganic-organic hybrid crystals8-11 or a salt with the terephthalate

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dianion.12 All of the above-mentioned crystals with amine coordinatively bonded to the metal or

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forming salts can exist at ambient conditions. This is not the case for the cBA hemihydrate13 which has

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a melting point around 210K. Due to the low melting point, the crystals were obtained using an IR laser

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assisted in situ technique14 directly on the goniometer of the single crystal diffractometer.

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There exist many examples of aliphatic amines forming a large number of hydrates15 with tert-

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butylamine holding the record of 7 hydrates.16-20 It seems that the frequent occurrence of hydrates is

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characteristic for aliphatic amines: the hydrophilic amino group, even in case of tertiary amines, is able

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to form hydrogen bonds (HBs) with water molecules. Simultaneously, the presence of the aliphatic

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residues in amines is able to develop weak hydrophobic homo-molecular interactions. With the increase

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of the number of water molecules per amine, the architecture of the HB network changes. Starting with

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a relatively small molar ratio of H2O:amine no water-water HBs are observed, as demonstrated by the

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structure of cBA hemihydrate.13 With higher ratios water molecules start to form linear arrangements, as

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found for the monohydrate of tert-butylamine16,17 or layers occur, as found for the hexahydrate of

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piperazine.21,22 A higher amount of water molecules results in the formation of three-dimensional

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arrangements of HB-interacting water frameworks with amine molecules incorporated. These kinds of

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hydrates can be described as semi-clathrates23,24 with pyrrolidine hexahydrate25 as one example. In the

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latter case, strong hydrogen bonds also exist between the amino group and water molecules, whereas the

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aliphatic ring of the amine resides in niches formed by water species. Finally, with enough water

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molecules available, water networks start to be similar to those of natural gas clathrate hydrates.16,17

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Amine molecules are now fully encapsulated in the cavities formed by water species.

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There are three main types of clathrate hydrates: sI, sII and sH.26 While the first two examples belong to

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the cubic system, the latter is hexagonal. Furthermore, there also exists a tetragonal clathrate structure

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III.27-29 In this type of compound, water molecules interacting via HBs form a three-dimensional host

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network with guest molecules (mostly severely disordered) located in cavities. In this case, there are no

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classical HBs30 present between host and guest molecules. Not only hydrocarbons form clathrate

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hydrates.31-33 The following compounds are known to co-crystallize with water giving the same

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structures: Cl2,34 Br2,27 CO2,35 THF (tetrahydrofuran)25,36 or other ethers,36-38 etc. As pointed out earlier,

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there are several examples of amines forming structures similar to clathrate hydrates. In fact, HBs in

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these structures are present between amines and H2O molecules. Frequently, the water framework

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exhibits positional disorder of O atoms. In spite of the structural similarity to clathrate hydrates, these

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entities cannot be treated as host-guest systems; they resemble an O-disordered variant.16,17 More

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examples of O-disordered clathrate hydrates are structures with ammonia/THF,39 Cl2/Br229 or complex

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systems containing tert-butylamine, Xe and H2S.40

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With respect to the above statements regarding the tendency of aliphatic amines to form multiple

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hydrates exemplified by tert-butylamine, we wondered whether the lack of further hydrates of cBA is

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due to lack of interest or any other reason, such as feasibility and/or crystal stability.

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Experimental Section

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Crystallization and single crystal X-ray diffraction. Samples suitable for single crystal X-ray

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experiments were grown in thin wall glass capillaries mounted on the goniometer of a Bruker D8

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Venture diffractometer equipped with LT device and using an IR laser-assisted in situ crystallization

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technique.14 All data were collected with a Mo sealed tube and TRIUMPH monochromator with a

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Photon1000 area detector and processed using the Bruker suite of programs.41 All measurements were

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performed using the φ scan method with the positioning of the LT device not allowing χ angles

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deviating much from 0° because otherwise the capillary is not completely flushed by the cold gas ACS Paragon Plus Environment

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stream. Therefore, in some cases the final completeness of the data set does not achieve the commonly

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recommended 98%. The structures were solved by direct methods and refined using the SHELXL

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program suite42 and in some cases using the WinGX package43 to convert the data (see Supporting

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Information). The atomic scattering factors were taken from the International Tables.44 Crystal data and

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refinement parameters are presented in Table 1. Thermal ellipsoid plots at the 50% probability level are

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shown in Figure S1, Figure S2 and Figure S3 in the Supporting Information. For the preparation of the

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figures, the Diamond 3.2 software45 was used. A detailed description on the refinement of the obtained

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crystal structures is given in the Supporting Information. The crystal structures were deposited in the

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Cambridge Crystallographic Data Centre with the following numbers: CCDC 1442577-1442592.

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X-ray powder diffraction. Crystalline samples were prepared by flash cooling of the liquid, sealed in

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thin wall glass capillaries containing the desired amount of water and the amine in the following molar

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ratios: 0:1, 0.5:1, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1 and 8:1. The data were collected at T = 170K on a

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Bruker D8 Discover diffractometer equipped with capillary stage, sealed tube with Cu anode, Goebel

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focusing mirror and LynxEye detector. The 2θ range for the data collection was 5°-60°. Further

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processing of the data was performed in the DIFFRAC EVA46 and Mathematica packages.47

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Results and Discussion

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Crystal structure of cyclobutylamine and its monohydrate. As pointed out in the Introduction, the

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crystal structure of cyclobutylamine and water was only known for the cBA hemihydrate.13 No

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structural information was available for the neat amine except for some spectroscopic data for the

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solidified compound.48,49

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Single crystals of cBA were obtained by the in situ crystallization process using the neat cBA (Sigma

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Aldrich, catalogue number: 225185, 98%) and for the monohydrate from the mixture of 1:1 molar

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fraction with water, respectively. X-ray data were collected at 100K and 170K for cBA as well as 100K, ACS Paragon Plus Environment


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202K for cBA monohydrate, respectively. No phase transitions were detected within the temperature

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ranges applied. For cBA, the hemi- and monohydrate (both hydrates referred to as ‘lower hydrates’) the

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unit cell contents are presented in Figure 1. The cBA crystal lattice contains two non-equivalent

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molecules. In the first molecule (A) only one hydrogen atom of the amino group is involved in HBs,

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whereas the second H atom is dangling free. The amino group in the second molecule (B) has both H

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atoms forming HBs. In contrast to the crystalline neat cBA, the crystal lattice of the hemihydrate13 has

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two symmetry-independent cBA molecules, each with one -NH2 hydrogen atom involved in HBs. The

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new structure of the cBA monohydrate contains four amine-H2O pairs in the asymmetric part of the unit

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cell. Here, all amine hydrogen atoms are involved in HBs.

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The HBs in the neat amine form 1-D networks based on ribbons consisting of four-membered, planar

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rings with N-H···N contacts. cBA hemihydrate maintains a 1-D HB topology with molecules forming

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centrosymmetric and heteromolecular four-membered rings linked by two amine molecules resulting in

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a columnar arrangement. Finally, the monohydrate structure adopts a 2-D topology of HBs. Here the 1-

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D zigzag chains of hydrogen bonded water molecules (along [100]) are linked via rows of separated

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amine molecules above and below [see Figure 1 c)]. Thus no N-H···N HBs occur.

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All the structures of the neat amine and “lower hydrates” mentioned here are ordered, even including

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the positions of all hydrogen atoms. An analysis of the HBs based on graph set notation50-52 allows

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discrimination of the R44(8) motif as the common feature of the structures discussed so far. All these

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rings have homodromic53,54 arrangements of the hydrogen atoms. This means that the directionality of

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the N-H bonds is preserved within each four-membered ring.

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In spite of the different environment of the amine molecules in the crystals of neat compound and the

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“lower hydrates”, the conformation of cBA is almost the same [see Figure S4 in the Supporting

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Information and Table 2 with values of H-N-C-H torsion angles presented]. The molecules which

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deviate most from the trans-gauche conformation (expected dihedral angle equal to 60°) are found for ACS Paragon Plus Environment

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the cBA monohydrate. In molecules (B) and (C) the H-N-C-H angle is even smaller than 40°. This is

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obviously a result of the packing of four symmetry-independent molecules with more conformational

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freedom.

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Table 2. H-N-C-H torsion angles in cyclobutylamine in the structures of the neat compound, hemi- and monohydrate. Compound

H-N-C-H torsion angle

Neat amine (molecule A) T=170K Neat amine (molecule B) T=170K Hemihydrate (molecule 1) T=205K Hemihydrate (molecule 2) T=205K Monohydrate (molecule A) T=202K Monohydrate (molecule B) T=202K Monohydrate (molecule C) T=202K Monohydrate (molecule D) T=202K

56.7° 55.0° 49.5° 45.1° 54.4° 38.6° 36.0° 57.4°

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Crystal structure of other hydrates of cBA

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Crystals containing more water molecules per cBA are now referred to as “higher hydrates”.

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Surprisingly, in situ crystallization of the amine:water mixture in the molar ratio 1:2 at T = 170K did not

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result in a dihydrate; instead, a crystal containing 6 3/7 H2O molecules per cBA was obtained, which we

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hereafter refer to as the 6 3/7 hydrate. After melting, the crystals in the sealed capillary and subsequent

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crystallization at T = 195K resulted in the formation of a different, non-stoichiometric phase with

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composition close to a 7 ½ hydrate, hereafter denoted as “7 ½”. Both networks are distinct. The first is

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trigonal (P-3m1) or alternatively hexagonal P6/mmm (see comments on the space group choice in the

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Supporting Information) while the second has cubic Pm-3n symmetry. Finally, the third “higher

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hydrate”, a 9 ½ hydrate, was crystallized from a 1:8 amine to water molar ratio. The space group choice

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can be either trigonal P-31m or hexagonal P6/mmm (see comments on the space group choice in the

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Supporting Information).

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In contrast to the “lower hydrates”, all “higher hydrate” structures are severely disordered, including

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both the amine and water molecules. Moreover, the “higher hydrates” of cBA consist of 3-D water

3

frameworks with the amine molecules located in the voids, similar to the clathrate hydrates. Yet, only

4

the “7 ½” hydrate can be considered as topologically equivalent to clathrate type sI – see Figure 2 a).

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However, due to a partial substitution of the water molecules by the amino groups in the crystal lattice,

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this hydrate contains slightly less H2O species than can be derived from a 100% occupancy model

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(7.543 instead of expected 7 ⅔). A detailed analysis of the “7 ½” hydrate structure shows that the water

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framework is disordered, including the positions of oxygen atoms. Some of H2O molecules are

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disordered over two or even five sites with the main components (occupancies in the range from 0.880

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to 0.955) mimicking the host network of the clathrate hydrate type sI [see Figure 2 b)]. The framework

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disorder is due to classical HB formation between the host and guest molecules, which should not be

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present according to the basic definition of clathrates. This structure is another case of O-disordered

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clathrate type sI, apart from the mixed Br2/Cl2 hydrate example.29 However, in the cBA “7 ½” hydrate

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only the bigger 51262 cages are occupied, while the smaller dodecahedron-like 512 cavities are left

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empty. This is due to the size of the 512 cages, which are too small for incorporating the amine. The “7

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½” hydrate of cBA has a bigger unit cell [a = 12.3320(5) Å at 195K] than the mixed Br2/Cl2 analogue

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form reference 29 [a = 11.9619(4) Å at 173K]. This results from the relatively big cBA molecule

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‘elbowing’ in the 51262 cages with ca. 6% of the amine molecule incorporated in the water framework,

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thus decreasing the amount of H2O species in the unit cell. The other cubic structures of aliphatic amine

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hydrates having comparable unit cell dimensions to cBA “7 ½” hydrate are ethylamine and

21

dimethylamine hydrates.15 The edge length of the unit cell is equal to 12.17(1) Å and 12.55(1) Å for

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ethylamine and dimethylamine hydrates respectively, established at 238K.

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Due to the lack of atomic coordinates (crystals measured using the Weissenberg method without

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establishing the structure) further analysis of crystal packing and comparison with cBA“7 ½” hydrate is

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not feasible. However, the edge length of the unit cell of dimethylamine hydrate is quite big for such a ACS Paragon Plus Environment

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small molecule, in comparison to cyclobutylamine “7 ½” hydrate. Moreover, dimethylamine hydrate

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contains probably 8 ⅔ water molecules per amine. This suggest the water framework of this hydrate is

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different to the cases of cBA “7 ½” and ethylamine 7 ⅔ hydrates. We are going to shed some more light

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on the mysterious case of dimethylamine 8 ⅔ hydrate in a following paper dedicated to amine hydrates.

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The other two structures – 6 3/7 and 9 ½ hydrates of cBA – have no obvious similarity to the clathrate

7

hydrates archetypes. However, they can be derived from clathrate hydrate type sH as displayed in

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Figure 3 a) to c). The 6 3/7 hydrate of cBA is similar to the octahydrate of iso-propylamine,55 the

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packing diagram for which is presented in Figure 3d). In both of the hydrates there are two types of

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voids present – closed cages and 2-D channels occupied by the amine molecules displayed in Figures 4

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a) and b). Regarding the relative orientations of 2-D channels, both hydrates can be considered as

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polytypic structures. However, the c unit cell parameter of the iso-propylamine hydrate is not twice that

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of the corresponding cyclobutylamine hydrate. The water framework in the cBA hydrates is different,

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containing empty 4662 and occupied 51262 and 51263 cages, whereas the iso-propylamine hydrate has no

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51262 cages. Instead, the framework has empty 512 cages incorporated. This is another reason why the

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stoichiometry of both structures is so different.

17 18

The water framework in the iso-propylamine octahydrate is also disordered with one of the water

19

molecules distributed over two sites [the alternative O atom is displayed in orange in the Figure 4 b)].

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The water framework in the cBA 6 3/7 hydrate is disordered as well. This is manifested by the

21

elongated thermal ellipsoids of the O atoms common for the two 51262 cages (cyan) occupied by the

22

amine. The disorder is associated with the interaction between cBA and the afore-mentioned oxygen

23

atoms of the water molecules. Moreover, this disordered O atom is partially substituted by the amino

24

group of the cBA occupying the 51262 cages. The summed occupancy of disordered O atoms is 5/6. The

25

distances between these disordered atoms are ca. 3.2 Å, so the common hexagonal face of two adjacent



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51262 cages is bigger than in typical clathrate hydrates. If the occupancies of all the O atoms were 100%,

2

the composition of the hydrate would result in one amine to 6 4/7 water molecules.

3 4

Finally, the 9½ hydrate of cBA can be considered as an extended variant of the clathrate hydrate type H

5

by placing an additional water layer intercepting the center of the unit cell. This results in a conversion

6

of the smaller 435663 cage to 51263. The bigger 51268 one is transformed to a dual cage consisting of two

7

distorted 51262 voids shearing one hexagon face. In this hexagon, the O···O distances are much longer

8

than expected in typical water frameworks – 3.16 Å (T = 100K) instead of 2.7-2.8Å. These O atoms –

9

similar to the case of 6 3/7 hydrate of cBA – are disordered, They have elongated thermal ellipsoids and

10

are split over two positions as a result of interaction of the amine with the water framework. In the 9 ½

11

hydrate, one of the oxygen atoms is also partially substituted by the amino group of cBA as observed in

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the 6 3/7 hydrate. In the 9 ½ hydrate, the summed occupancy of the O atoms forming the common

13

hexagon of two adjacent 51262 polyhedra is ⅔. If the occupancies of these atoms were 100%, the

14

formation of a decahydrate could be expected.

15 16

Due to the size of the amine for the 51262 cage, the number of water molecules has to be reduced by

17

partial substitution of waters with amino groups. Such a modification of the clathrate hydrate type H, as

18

described for the 9 ½ cBA hydrate, is also reported in the literature albeit with slightly different

19

stoichiometries – the decahydrate of n-propylamine15 and 10 ¼ hydrate of trimethylamine.56 In the latter

20

case, there are additional water molecules with partial occupancies, resulting in an excess of water

21

molecules compared to the expected 10 water molecules per one amine.

22 23

Powder diffraction

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During in situ crystallization on the single crystal diffractometer, in most cases, the composition of

25

obtained hydrate was not in agreement with the composition of the aqueous solution of the cBA. Indeed,

26

6 3/7 and “7 ½” hydrates were obtained from a 1:2 amine:water molar ratio. Thus, to check the phase ACS Paragon Plus Environment

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behavior of the cBA-H2O system we decided to analyze the results of flash cooling crystallization at

2

different dilution ratios using powder diffraction. The comparison of calculated powder patterns (top

3

diagrams) for the neat amine and all described hydrates with experimental powder patterns (bottom

4

diagrams) recorded for molar ratios amine:water from 1:0 up to 1:8 is presented in Figure 5. The powder

5

patterns are displayed as density plots, similar to a Guinier-Simon presentation;57 instead of temperature

6

the dilution of the cBA is listed.

7 8

Starting from the neat amine (bottom, 1:0), the pattern corresponds to its calculated diffractogram (top,

9

0), as indicated by the blue link on the left. Increasing the concentration to 1:0.5 results in formation of

10

the hemihydrate (cyan linking line) and monohydrate, as indicated by the green bracket. Moreover, the

11

monohydrate is achieved in the range up to 1:6 and coexists with 6 3/7 hydrate (molar ratios from 1:2 to

12

1:4, as indicated by the pink bracket) and 9 ½ hydrate (molar ratios from 1:4 to 1:6, as indicated by the

13

red bracket). For the 1:7 and 1:8 molar ratios, only the pure 9 ½ cBA hydrate crystallizes. Surprisingly,

14

the cubic “7 ½” hydrate of cBA cannot be located on the experimental powder patterns; yet, it was

15

obtained by in situ crystallization techniques on the single crystal diffractometer from the 1:2 mixture

16

(top pattern, as indicated by a black square in Figure 5).

17 18 19 20

Conclusions

21

In the dilution series of aliphatic amines with water using a LT in situ crystallization technique, four

22

new crystalline hydrates of cyclobutylamine (cBA) were obtained, in addition to the known

23

hemihydrate. The series consists of two groups – “lower hydrates” and “higher hydrates”. The hemi-

24

and monohydrates of cBA belonging to the first group are fully ordered structures with well-defined

25

stoichiometries and water molecules binding the amines via hydrogen bonds (HBs). The second group

26

includes crystals with molar cBA:H2O ratios of 6 3/7, approx. 7 ½ - denoted as “7 ½” and 9 ½, all of ACS Paragon Plus Environment


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them severely disordered. Unlike in “lower hydrates”, in the second group water molecules form 3-D

2

networks with HBs consisting of polyhedra with voids. Some of these are filled with amines, and the

3

smaller ones are empty.

4 5

The series has many similarities to the previously determined crystal structures of seven tert-butylamine

6

hydrates. It exhibits a gap in the stoichiometry between the mono- and 7 ¼ hydrate, which was

7

attributed to a fuzzy situation during the crystal nucleation processes. Likewise, tert-butylamine

8

hydrates of cBA are disordered as well with some of them being similar to clathrate hydrates. The “7 ½”

9

non-stoichiometric hydrate of cBA and 17 hydrate of tert-butylamine are O-disordered water framework

10

variants of clathrate types cI and cII, respectively.

11 12

Based on the unit cell parameters or packing, the “higher hydrate” crystal structures of cBA can be

13

compared to those of other amines.15,56 Indeed, ethylamine and dimethylamine have the same cubic

14

symmetry and similar unit cell volumes as the “7 ½” hydrate of cBA. In spite of the lack of atomic

15

coordinates, the former two structures are believed to be clathrate hydrates with composition 7 ⅔.

16

However the dimethylamine hydrate, which is believed to be 8 ⅔ hydrate, due to slightly bigger unit cell

17

[a = 12.55(1) Å at 238K, while a larger cyclobutylamine gives “7 ½” hydrate with a = 12.3320(5) at

18

195K] probably has a different water framework. Comparable unit cell parameters are also observed for

19

a 9 ½ hydrate of cBA and n-propylamine decahydrate or 10 ¼ hydrate of trimethylamine. Finally, some

20

similarities can be found between the 6 3/7 hydrate of cBA and iso-propylamine octahydrate. In the

21

latter case, the similarity is based on the three-dimensional water network.

22 23

It can be considered an unusual feature that such different molecules can form comparable hydrates.

24

This can be explained in Figure 6 which presents the considered amines with structural fragments

25

common to cBA highlighted. The formation of comparable crystal structures is not affected by the order

26

of the amine but it seems to be based, in the first instance, on the shape of these compounds. The ACS Paragon Plus Environment

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1

mentioned amines can adopt either an oblate spheroid or banana shape. As the biggest molecule among

2

presented in Figure 6, cyclobutylamine forms comparable hydrates but with smaller amounts of water in

3

each case, in comparison to other amines. This results from partial substitution of water molecules by

4

the amino group of cBA.

5 6

With the refinement of 6 3/7 and 9 ½ hydrates of cBA, we faced a situation with an ambiguous choice

7

of the crystal system – hexagonal or trigonal. From Figures 3 b) and c), the presence of a mirror plane

8

perpendicular to [001] is expected. In the case of 6 3/7 hydrate, modeling the disorder in trigonal space

9

group improved the discrepancy factor by more than 1% at both temperatures (100K and 210K); yet, for

10

the 9 ½ hydrate, the difference was not so pronounced. Moreover, while at 100K the refinement in the

11

trigonal system was better, at 270K the situation was reversed. This can be explained by an averaging of

12

the structure approaching the melting point and better modeling the disorder in a higher symmetry space

13

group. Both variants of the crystal structure refinements for 6 3/7 and 9 ½ hydrates are displayed in

14

Table 1. In the case of 6 3/7 hydrate, refinement in the trigonal system is preferred; no preference is

15

found for the 9 ½ hydrate. When comparing similar hydrates based on their symmetries, this point

16

should be considered. This is clearly a matter of crystal structure refinement based on single crystal data

17

and can hardly be evaluated by powder diffraction data, especially if there is no phase transition

18

detected, as in the present case. Moreover, the cubic “7 ½” hydrate of cBA was not detected using

19

powder diffraction after flash cooling of mixtures of the amine and water in ratios from 1:0.5 to 1:8 (see

20

Figure 5). This was only achieved by in situ crystallization with a CO2 IR laser on the single crystal

21

diffractometer.

22 23

Comparison of the 6 3/7 hydrate of cBA and octahydrate of iso-propylamine reveals some similarities

24

typical for polytypes, when relative positions of layers consisting of 2-D channels are shifted with

25

respect to each other. In this case, this modification simultaneously changes the composition of the

26

hydrates. The 6 3/7 hydrate of cBA can be considered as a last member of the family of the hydrates ACS Paragon Plus Environment


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Page 14 of 26

1

with extended water framework, starting from the clathrate hydrate type sH. Indeed, adding some water

2

molecules to this structure in the (002) plane results in formation of the water framework which can be

3

found in the 9 ½ hydrate of cBA [see Figure 3 b)]. The following modification of the 9 ½ hydrate, but in

4

this case based on the simultaneous cloning of the water layer (002) and extending it along [001], results

5

in a new structure realized in the 6 3/7 hydrate of cBA. Such cut-copy-paste modification is mimicked

6

by a Janus-headed stretch limousine built by cutting a standard car into two pieces and inserting an

7

extension, thus giving more space for passengers. Indeed the highest extended cBA hydrate (6 3/7) can

8

accommodate more “guest” molecules than a smaller version i.e. 9 ½. Put simply: a smaller amount of

9

construction material (water in hydrates, steel in the limousine) is necessary to host the guests (amine

10

molecules in hydrates, passengers in the limousine).

11 12

ASSOCIATED CONTENT

13

Supporting Information

14

The Supporting Information is available free of charge on the ACS Publications website at DOI:

15

XXXXXXXXXX.

16

Single crystal X-ray diffraction data and refinement information, thermal ellipsoid plots,

17

overlay of the amine molecules from the structures of the neat compound, hemihydrate and

18

monohydrate (PDF).

19 20

Acknowledgements

21

All experiments were performed in the Czochralski Laboratory of Advanced Crystal Engineering

22

(Faculty of Chemistry, University of Warsaw) established by generous support from the Polish Ministry

23

of Science and Higher Education (grant No. 614/FNiTP/115/2011). The research was supported by the

24

Foundation for Polish Science (Homing Plus/2011-4/5 grant based on the European Union Regional

25

Development Fund) and National Science Center (grant NCN 2011/03/B/ST4/02591). The proof-

26

reading assistance of Dr Siân Howard is gratefully acknowledged. ACS Paragon Plus Environment

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1 2 3

References

4

(1)

Allen, F. H., Acta Crystallogr. 2002, B58, 380. Version 1.17, 2014.

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(2)

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(3)

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(11) Billing, D. G.; Lemmerer, A., CrystEngComm 2009, 11, 1549.

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(12) Lemmerer, A., Crystal Growth & Design 2011, 11, 583.

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(13) Allan, D. R., Acta Crystallogr. E, 2006, 62, o751.

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(14) Boese, R., Z. Kristallogr. 2014, 229, 595.

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(15) McMullan, R. K.; Jordan, T. H.; Jeffrey, G. A., J. Chem. Phys. 1967, 47, 1218.

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(16) Dobrzycki, Ł; Taraszewska, P.; Boese, R.; Cyrański, M. K.; Cirkel, S. A., Angewandte Chemie

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International Edition 2015, 54, 10138-10144. (17) Dobrzycki, Ł; Taraszewska, P.; Boese, R.; Cyrański, M. K.; Cirkel, S. A., Angewandte Chemie 2015, 127, 10276–10282. ACS Paragon Plus Environment


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(19) G. A. Jeffrey, Acc. Chem. Res. 1969, 11, 344.

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(20) D. Staben, D. Mootz, J. Incl. Phen. Mol. Recogn. Chem.1995, 22, 145.

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(21) Schwarzenbach, D., J. Chem. Phys. 1968, 48, 4134.

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(22) Jeffrey, G. A.; Mastropaolo, D.; Shen, M. S., Acta Crystallogr., Sect. A: Cryst. Phys., Diffr.,

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Theor. Crystallogr. 1975, 31, S177.

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(23) Fowler, D. L.; Loebenstein, W. V.; Pall, D. B.; Kraus, C. A., J. Am. Chem. Soc., 1940, 62, 1140.

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(24) G. A. Jeffrey, R. K. McMullan, Progress in Inorganic Chemistry, Wiley, New York, 1967, vol. 8,

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p. 43. (25) Dobrzycki, L.; Taraszewska, P.; Boese, R.; Cyrański, M. K., Crystal Growth & Design, 2015, 15, 4804–4812. (26) Sloan, E. D.; Koh, C. A., “Clathrate Hydrates of Natural Gases”, 3rd Edition, Taylor & Francis/CRC Press, Boca Raton, FL, USA, 2008. (27) Jeffrey, G. A. In Comprehensive Supramolecular Chemistry; Atwood, J. L., Davies, J. E. D., MacNicol, D. D., Vögtle, F., Eds.; Pergamon: Oxford, U.K., 1996; Vol. 6, p 757. (28) Alavi, S.; Udachin, K. A.; Ratcliffe, C. I.; Ripmeester, J. A. Clathrate Hydrates. In Supramolecular Chemistry: From Molecules to Nanomaterials; John Wiley & Sons, Ltd.: Chichester, U.K., 2011.

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(29) Udachin, K. A.; Alavi, S.; Ripmeester, J. A., J. Phys. Chem. C 2013, 117, 14176−14182.

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(30) Desiraju, G. R.; Steiner, T., “The Weak Hydrogen Bond: In Structural Chemistry and Biology”,

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IUCr Monographs on Crystallography, Vol. 9, Oxford: Oxford University Press/International

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(32) Udachin, K. A.; Ratcliffe, C. I.; Ripmeester, J. A., J. Supramol. Chem., 2001, 2, 405

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(33) Kirchner, M. T.; Boese, R.; Billups, W. E.; Norman, L. R., J. Am. Chem. Soc. 2004, 126, 9407.

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(34) Davy, H. P., Trans. R. Soc. 1811, 101, 155. ACS Paragon Plus Environment

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(35) Wróblewski, S., Acad. Sci. Paris, Comptes rendus 1882, 94, 212-213.

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(36) Sargent, D. F.; Calvert, L. D., J. Phys. Chem., 1966, 70, 2689.

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(37) McMullan, R. K. ;Jeffrey, G. A., J. Chem. Phys., 1965, 42, 2725.

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(38) Udachin, K. A.; Ratcliffe, C. I.; Ripmeester, J. A., J. Phys. Chem.B, 2007, 111, 11366.

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(39) Shin, K.; Alavi, S.; Udachin, K. A.; Ripmeester, J. A., Proc. Natl. Acad. Sci. U.S.A. 2012, 109,

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14785.

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(40) Alavi, S.; Udachin, K.; Ripmeester, J. A., Chem.-Eur. J., 2010, 16, 1017.

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(41) SAINT,. Bruker AXS Inc., Madison, Wisconsin, USA, 2013; SADABS,. Bruker AXS Inc.,

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Madison, Wisconsin, USA, 2012; TWINABS,. Bruker AXS Inc., Madison, Wisconsin, USA,

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2012.

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(42) Sheldrick, G. M., Acta Crystallogr., 2008, A64, 112–122.

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(43) Farrugia, L. J., J. Appl. Cryst. 2012, 45, 849-854.

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(44) International Tables for Crystallography, Ed. Wilson A. J. C., Kluwer: Dordrecht, 1992, Vol. C.

14

(45) Diamond - Crystal and Molecular Structure Visualization, Crystal Impact - Dr. H. Putz & Dr. K.

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Brandenburg GbR, Kreuzherrenstr. 102, 53227 Bonn, Germany.

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(46) DIFFRAC EVA, Bruker AXS, Madison, Wisconsin, USA, 2012.

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(47) Wolfram Research, Inc., Mathematica, Version 7.0, Champaign, IL, 2008.

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(48) Kalasinsky, V. F.; Guirgis, G. A.; Durig, J. R., J. Mol. Struct., 1977, 39, 51–65.

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(49) Durig, J. R.; Ganguly, A.; El Defrawy, A. M.; Guirgis, G. A.; Gounev, T. K.; Herrebout, W. A.;

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van der Veken, B. J., J. Mol. Struct., 2009, 918, 64–76.

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(50) Etter, M. C.; MacDonald, J. C.; Bernstein J., Acta Crystallogr. B-struct. Sci., 1990, 46, 256-262

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(51) Bernstein, J; Davis, R. E.; Shimoni, L.; Chang, N.-L., Angew. Chem. Int. Ed. Engl., 1995, 34

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1555-1573.

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(52) Bernstein, J; Shimoni, L.; Davis, R. E.; Chang, N.-L., Angew. Chem., 1995, 15, 1689-1708.

25

(53) Saenger W., Inclusion Compounds, Vol. 2, edited by J. L. Atwood, J. E. D. Davies & D. D.

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MacNicol, ch. 8, p. 253. London: Academic Press. 1984. ACS Paragon Plus Environment


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(54) Merz, K.; Kupka, A., Cryst. Growth Des., 2015, 15, 1553–1558.

2

(55) McMullan, R. K.; Jeffrey, G. A.; Panke, D., J. Chem. Phys., 1970, 53, 3568-3577.

3

(56) Panke, D., J. Chem. Phys., 1968, 48, 2990.

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Page 19 of 26

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1 2 3 4


Fig. 1. Crystal packing of a) neat amine, b) hemihydrate [based on ref. 13], c) monohydrate of cyclobutylamine.



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1 2 3 4

Page 20 of 26

Fig. 2. Packing diagram of the “7 ½” hydrate of cBA a). Closest environment of the 512 and 51262 cages, yellow spheres indicates alternative position of the oxygen atoms of the disordered water framework b).

5 6


Page 21 of 26

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1 2 3 4 5


Fig. 3. Packing diagram of the model structure of clathrate hydrate type sH (from the ref. 33) - a) compared to the crystal packing of the cyclobutylamine 63/7 hydrate b). Comparison of cyclobutylamine 9 ½ hydrate c) and iso-propylamine octahydrate d).



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Page 22 of 26

1 2 3

Fig. 4. Interior of the 2-D channels in the cyclobutylamine 6 3/7 hydrate a) and iso-propylamine octahydrate b).

4 5 6 7 8

Fig. 5. Comparison of the calculated powder patterns based on single crystal structures of cBA and its hydrates with powder diffractograms obtained for flash-cooled liquids containing amine and water at different dilutions. The color scale used is the same as on typical hypsometric maps.


Page 23 of 26

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1

2 3 4 5

Fig. 6. Comparison of cBA to other amines revealing common fragments and topological similarities. Compounds heaving similar phases or structural motifs are grouped in rows.

6



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48

1

Table 1. Crystal data and structure refinement for described compounds. Composition

Amine 100K C4H9N

Amine 170K C4H9N

Monohydrate 100K C4H9N + H2O

Monohydrate 202K C4H9N + H2O

6 3/7 100K in P-3m1 C28H153N7O45

6 3/7 100K in P6/mmm C28H153N7O45

6 3/7 210K in P-3m1 C28H153N7O45

6 3/7 210K in P6/mmm C28H153N7O45

M

71.12

71.12

89.14

89.14

1308.56

1308.56

1308.56

1308.56

T/ K

100(2)

170(2)

100(2)

202(2)

100(2)

100(2)

210(2)

210(2)

λ/ Å

0.71073

0.71073

0.71073

0.71073

0.71073

0.71073

0.71073

0.71073

Size[mm]

0.3×0.3×0.6

0.3×0.3×0.6

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

Space group unit cell parameters/ Å, °

P-1 a=5.2838(2) Å b=9.4857(5) Å c=9.4903(5) Å α=97.0785(17)° β=96.0194(15)° γ=94.2314(15)° 467.62(4) 4, 1.010

P-1 a=9.1525(3) Å, b=10.4739(4) Å c=12.1391(5) Å α=86.0525(12)° β=79.1339(11)° γ=89.9472(10)° 1140.02(7) 8, 1.039

P-1 a=9.3650(4) Å b=10.5296(7) Å c=12.1428(7) Å α=86.453(2)° β=78.8420(10)° γ=89.8970(10)° 1172.45(11) 8, 1.010

P-3m1 a=12.2342(4)Å

P6/mmm P-3m1 a=12.2342(4)) Å a=12.3507(5) Å

P6/mmm a=12.3507(5) Å

c=14.7456(5) Å

c=14.7456(5) Å

c=14.8036(6) Å

c=14.8036(6) Å

V [Å3] Z, Dx/ g·cm-3

P-1 a=5.2389(2)Å b=9.4368(5)Å c=9.4507(5)Å α=97.7261(15)° β=96.3342(15)° γ=94.1419(13)° 458.36(4) 4, 1.031

1911.37(14) 1, 1.137

1911.37(14) 1, 1.137

1955.60(18) 1, 1.111

1955.60(18) 1, 1.111

µ [mm-1]

0.062

0.061

0.074

0.072

0.106

0.106

0.103

0.103

F(000)

160

160

400

400

730

730

730

730

θmin, θmax

3.31°, 25.03°

2.87°, 25.05°

2.97°, 25.05°

2.96°, 25.05°

3.33°, 25.10°

3.33°, 25.10°

3.30°, 25.10°

3.30°, 25.10°

8937*/1526 [Rint=0.0432 for 2θmax=50.74°]* (HKLF5 – one)* 92.0%** 0.960, 0.980

17949*/3818 [Rint=0.0633 for 2θmax=52.82°]* (HKLF5 – two)* 94.5%** 0.978, 0.964

11513/3827 [Rint=0.0498]

21194/1316 [Rint=0.0227]

21194/739 [Rint=0.0230]

22195/1336 [Rint=0.0158]

22198/750 [Rint=0.0160]

Completeness Tmax, Tmin

9557*/1495 [Rint=0.0443 for 2θmax=50.77°]* (HKLF5 –one)* 92.1%** 0.960, 0.980

92.0%** 0.979, 0.965

99.6% 0.970, 0.900

99.5% 0.970, 0.890

99.6% 0.970, 0.940

99.5% 0.970, 0.940

Reflections/ constrains/ parameters

1495 / 0 / 107

1526 / 0 / 107

3818 / 2 / 265

3827 / 3 / 281

1316 / 54 / 162

739 / 40 / 105

1336 / 54/ 162

750 / 40 / 105

1.039

1.092

1.145

1.055

1.187

1.189

1.142

1.107

R1=0.0429 wR2=0.1131 R1=0.0452 wR2=0.1150

R1=0.0447 wR2=0.1270 R1=0.0477 wR2=0.1300

R1=0.0624 wR2=0.1585 R1=0.0856 wR2=0.1779

R1=0.0614 wR2=0.1624 R1=0.0917 wR2=0.1901

R1=0.0557 wR2=0.1637 R1=0.0644 wR2=0.1783

R1=0.0680 wR2=0.1994 R1=0.0752 wR2=0.2145

R1=0.0599 wR2=0.1921 R1=0.0663 wR2=0.2031

R1=0.0730 wR2=0.2282 R1=0.0780 wR2=0.2393

0.217, -0.231

0.198, -0.172

0.323, -0.318

0.479, -0.205

0.330, -0.286

0.381, -0.267

0.298, -0.306

0.334, -0.271

Reflections collected/ independent

2

GooF on F

R [I>2σ(I)] R (all data) ρmax, ρmin/ e·Å-3

2 3 4 5 6 7

Page 24 of 26

* **

Crystal twinned by pseudomerohedry. Data reduction and scaling based on two twin components. Final refinement preformed on merged data using refined twin fractions (“HKLF5 – one” = reflections from the major twin component + composites; “HKLF5 – two” – reflections from two twin components + composites). Data is completeness lowered due to scanning along φ axis with κ = 0 of crystals grown in capillary in an oriented manner due to their morphology. The angular restrictions results from LT device nozzle positioning.


Page 25 of 26

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1


Table 1. Crystal data and structure refinement for described compounds (continuation) 9 ½ 100K in P/6mmm C4H28NO9.5

9 ½ 150K in P-31m C4H28NO9.5

9 ½ 15K in P/6mmm C4H28NO9.5

9 ½ 270K in P-31m C4H28NO9.5

9 ½ 270K in P/6mmm C4H28NO9.5

620.80

242.27

242.27

242.27

242.27

242.27

242.27

100(2)

195(2)

100(2)

100(2)

150(2)

150(2)

270(2)

270(2)

0.71073

0.71073

0.71073

0.71073

0.71073

0.71073

0.71073

0.71073

“7 ½“ 195K

Composition

C16H82N4O22.628

M

620.80

T/ K λ/ Å Size[mm]

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

0.3×0.3×0.5

Space group unit cell parameters/ Å, °

Pm-3n a=12.2629(5) Å

Pm-3n a=12.3320(5) Å

P-31m a=12.0105(5) Å

P6/mmm a=12.0105(5) Å

P-31m a=12.0384(5) Å

P6/mmm a=12.0384(5) Å

P-31m a=12.1608(17) Å

P6/mmm a=12.1608(17) Å

c=12.3732(6) Å

c=12.3732(6) Å

c=12.3998(6) Å

c=12.3998(6) Å

c=12.499(2) Å

c=12.499(2) Å

V [Å3] Z, Dx/ g·cm-3

1844.1(2) 2, 1.129

1875.4(2) 2, 1.110

1545.73(15) 4, 1.041

1545.73(15) 4, 1.041

1556.26(15) 4, 1.034

1556.26(15) 4, 1.034

1600.8(5) 4, 1.005

1600.8(5) 4, 1.005

µ [mm-1]

0.106

0.104

0.101

0.101

0.101

0.101

0.098

0.098

F(000)

692

692

540

540

540

540

540

540

θmin, θmax

5.26°, 25.08°

5.23°, 25.06°

3.77°, 25.07°

3.39°, 25.07°

3.76°, 25.08°

3.38°, 25.08°

3.73°, 25.07°

3.35°, 25.07°

27249***/599 [Rint=0.0325 for 2θmax=50.70°]*** (HKLF4)*** 98.8% 0.970, 0.950





Reflections collected/ independent

16681/315 [Rint=0.0218]

11104/318 [Rint=0.0167]

Completness Tmax, Tmin

97.2% 0.970, 0.950

97.2% 0.970, 0.950


Reflections/ constrains/ parameters

315 / 7 / 47

318 / 7 / 47

1004 / 8 / 92

599 / 4 / 67

1015 / 8 / 92

605 / 4 / 67

1035 / 10 / 92

618 / 6 / 66

1.214

1.202

1.133

1.131

1.143

1.113

1.232

1.258

R1=0.0536 wR2=0.1430 R1=0.0566 wR2=0.1474

R1=0.0511 wR2=0.1371 R1=0.0551 wR2=0.1450

R1=0.0391 wR2=0.1002 R1=0.0442 wR2=0.1036

R1=0.0400 wR2=0.1116 R1=0.0432 wR2=0.1149

R1=0.0415 wR2=0.1051 R1=0.0492 wR2=0.1101

R1=0.0416 wR2=0.1147 R1=0.0462 wR2=0.1192

R1=0.0641 wR2=0.1465 R1=0.0726 wR2=0.1521

R1=0.0630 wR2=0.1453 R1=0.0672 wR2=0.1480

0.349, -0.184

0.285, -0.163

0.228, -0.193

0.226, -0.218

0.194, -0.213

0.194, -0.227

0.179, -0.282

0.235, -0.257

2

GooF on F

R [I>2σ(I)] R (all data) ρmax, ρmin/ e·Å-3

2 3

C16H82N4O22.628

9 ½ 100K in P-31m C4H28NO9.5

“7 ½“100K

*** Sample including two differently oriented crystals – data scaling based on two components with the option HKLF4.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

For Table of Contents Use Only

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2 3

Page 26 of 26

Hydrates of cyclobutylamine – modifications of gas clathrate types sI and sH

4 5


6

7 8

Synopsis

9

Crystalline cyclobutylamine and its four new hydrates are presented. Two of the hydrates can be

10

considered as extensions of the hexagonal clathrate hydrate sH with some relation to modifying standard

11

structures into stretched versions, much like creating a limousine from an economy car.


Hydrates of Cyclobutylamine: Modifications of Gas Clathrate Types sI

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