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Structural, Spectroscopic and Computational Characterization of the Concomitant Polymorphs of the Natural Semiconductor Indigo Tommaso Salzillo, Simone D'Agostino, Arianna Rivalta, Andrea Giunchi, Aldo Brillante, Raffaele Guido Della Valle, Natalia Bedoya Martínez, Egbert Zojer, Fabrizia Grepioni, and Elisabetta Venuti J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b03635 • Publication Date (Web): 11 Jul 2018 Downloaded from http://pubs.acs.org on July 24, 2018

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The Journal of Physical Chemistry

Structural, Spectroscopic and Computational Characterization of the Concomitant Polymorphs of the Natural Semiconductor Indigo T. Salzillo*a†, S. d’Agostino*b, A. Rivaltaa, A. Giunchia, A. Brillantea, R.G. Della Vallea, N. BedoyaMartinezc, E. Zojer c, F. Grepionib, E. Venuti*a. a

Dipartimento di Chimica Industriale “Toso Montanari” and INSTM−UdR Bologna, University of Bologna, Viale del Risorgimento 4 – 40136 Bologna, Italy. b c

Dipartimento di Chimica ‘‘G. Ciamician’’, University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy.

Institute of Solid State Physics, NAWI Graz, Graz University of Technology, Petersgasse 16, 8010 Graz, Austria.

Abstract Indigo (2,2'-Bis(2,3-dihydro-3-oxoindolyliden)), a commonly used natural dye, has been shown to exhibit highly promising semiconducting behaviour, allowing for the realization of ambipolar devices. Nevertheless, up to date, it is still unclear which crystal structure is present in the thin films, a piece of information relevant for device applications. In this work we address this issue by an in-depth characterization of the polymorphs of Indigo in the bulk and in drop cast films. To do this, X-ray diffraction and micro-Raman spectroscopy have been employed jointly, with the support of state of the art Density Functional Theory calculations in the solid state. Structural and spectroscopic characterizations have established that the two known A and B polymorphs grow as concomitant in the bulk under most of the experimental conditions adopted in this work. In the drop cast films, X-ray diffraction cannot unambiguously identify the structure, but Raman spectroscopy is effective in establishing that only the B form is present. The calculations augment the experiments, providing valuable insight into the relative thermodynamic stability of the two forms as a function of temperature. They also allow for a more comprehensive characterization of the Raman modes.

†Present address: Institut de Ciéncia de Materials de Barcelona (CSIC), Campus de la UAB, 08193 Bellaterra (Spain) *Corresponding authors

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E-mail address: [email protected] E-mail address: [email protected] E-mail address: [email protected]

Introduction The high potential of organic systems in electronic applications has been widely demonstrated in recent years through mature OLED technology as well as by highly promising applications in Organic PhotoVoltaics (OPV)1–3 and Organic Field Effect Transistors (OFETs).4,5 Since the lifetime of a certain number of products based on organic semiconductors is expected to be short and some are designed for disposable applications, their increasing employment would reflect negatively on the waste load. Thus, the search for non-toxic, biodegradable, and biocompatible compounds is a hot topic in the field of Organic Electronics.6,7 Bio-inspired Organic Semiconductors (OSCs), which hold the promise of being environmentally friendly and of special relevance for bio-applications, have already been tested in organic thin film transistors (OTFTs),6,8– 10

featuring excellent performances.

Among systems of natural origin, Indigo [2,2'-Bis(2,3-dihydro-3-oxoindolyliden), Figure 1] has been shown to be a most promising biocompatible semiconductor material, exhibiting balanced ambipolar transport in OTFTs.10–14 Its properties in thin films were found to be strongly dependent on the surface on which the film is grown,15,16 with hydrocarbon-based materials such as polyethylene and tetratetracontane outperforming other dielectrics. Recently, this has been attributed to a polymorphic modification, induced by the dielectric acting as a template.16 This is particularly relevant, as polymorphs differ in the relative molecular arrangement resulting in different electronic couplings between neighboring molecules and, hence, in different charge transport properties. Consequently, polymorphism can be considered as an additional, highly promising degree of freedom for the design of organic semiconducting materials. Thus,17,18 a key 2 ACS Paragon Plus Environment

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issue in the growth of the active material is to exert control on the compound polymorphism, possibly also relying on the formation of surface induced phases (SIP),19 which may impact on electrical performances of the material. One point of interest in SIPs is the understanding of their structures also in relation to bulk crystals, as the molecular packing stabilized by the presence of the substrate may exist only as a metastable form in the bulk.20 Therefore, it is crucial to understand which polymorphs grow under specific conditions21 and under what circumstances the coexistence of several polymorphic structures has to be expected.

Figure 1 Molecular structure of Indigo (2,2'-Bis(2,3-dihydro-3-oxoindolyliden)).

The present work is concerned with the structural and Raman properties of crystalline Indigo, which is known in two polymorphic forms, named A and B, displaying similar structures.22–26 Both are monoclinic P21/n with Z=2 molecules per unit cell and similar unit cell parameters. We assess the relative stability of the A and B polymorphs employing Density Functional Theory in combination with a posteriori van der Waals corrections (DFT-vdW). A combination of single crystal and powder X-ray diffraction (XRD) techniques has been used to characterize bulk and films obtained by drop casting. The X-ray experiments provide a clear "picture" of the polymorphic composition in the bulk samples, showing that A and B modifications often coexist and that, at variance with some previous reports,24 phase B seems to be the predominant one. In the samples obtained by drop casting, the XRD cannot identify unambiguously which of the two polymorph is present, a complication that has already been 3 ACS Paragon Plus Environment


reported and discussed in detail in the literature for the thin films.15 Raman investigations performed on the bulk samples are used here to identify the vibrational fingerprint of each polymorph. Such a knowledge is thus successfully applied to characterize the drop cast samples and to reveal that polymorph coexistence is present at the micron scale in crystallites. The spectral investigation focuses both on the low energy region (10-150 cm-1), where the lattice phonons are recorded, and on selected intra-molecular modes (in the ranges 100-200 cm-1 and 1550-1600 cm1

), which have been found to be very sensitive to the H-bonds. These two energy regimes provide

excellent markers for Indigo polymorph discrimination. The knowledge of the phonon spectrum provided by the Raman measurements and DFT calculations27 also provides information that will be needed in future studies for understanding the role of vibrations for charge transport processes in these systems. 28

Experimental and Theoretical Methods Crystal Growth and drop cast Film Preparation Indigo (TCI Chemicals) was purified by double sublimation at 200 °C at low pressure of nitrogen to avoid thermal oxidation, obtaining microcrystals of irregular shape. Elongated single crystals about 200 μm long were grown by Physical Vapor Transport (PVT).29 For PVT growth the material was placed at one end of an evacuated glass ampule, which was sealed after three cycles of evacuation and nitrogen purging. The end of the ampule containing the material was then placed horizontally in a furnace kept at 250 °C. At equilibrium a temperature gradient of approx. 13 °C/cm was measured. Despite the low solubility of Indigo in most organic solvents, crystals were also obtained by dissolving the compound in boiling Dimethyl sulfoxide and leaving the resulting filtered solution to slowly evaporate. Crystalline films were obtained by drop casting filtered (0.2 μm filter) saturated solutions in 1,2-dichlorobenzene and acetonitrile onto a Si/SiOx wafer 4 ACS Paragon Plus Environment

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previously cleaned by an ultrasonic bath in acetone, isopropyl alcohol, and deionized water, and finally dried under nitrogen. After drop casting, the films were dried on a hot plate at 50 °C.

Raman Spectroscopy Raman spectra in the lattice phonon region (10-150 cm-1) were recorded with a Horiba Jobin Yvon T64000 spectrometer equipped with three monochromators in double subtractive configuration. The spectrometer was coupled to an Olympus BX40 confocal microscope equipped with 100x, 50x, 20x and 10x objectives, for a lateral resolution lower than 1 µm with the 100x objective. This allows gathering information on the polymorphic composition in crystal domains of micrometric dimensions. The excitation wavelength used was the 752.5 nm line from a tunable Kr+ gas laser, with a nominal power of 1 W. The power was reduced by neutral density filters to avoid sample damage. Raman spectra in the 100-2000 cm-1 wavenumber range were recorded on a single grating spectrometer Renishaw System 1000 equipped with a suitable notch filter and coupled to a Leica DMLM microscope, exciting the Raman scattering with the 785 nm wavelength of a diode laser with a nominal power of 500 mW.

X-ray Diffraction Single-crystal data for Indigo grown by physical vapour transport (PVT) were collected both at room and at low temperature (210 K) on an Oxford X’Calibur S CCD diffractometer equipped with a graphite monochromator (Mo-Kα radiation, λ = 0.71073 Å) and with an Oxford CryoStream800 cryostat. Data collection and refinement details are listed in Table S1. All non-hydrogen atoms were refined anisotropically. HCH atoms were added in calculated positions, HNH atoms were directly located on the N atoms and refined riding on their respective atoms. SHELX9730 was used 5 ACS Paragon Plus Environment


for structure solution and refinement on F2. The program Mercury31 was used to calculate intermolecular interactions and to simulate the Bravais–Friedel–Donnay–Harker (BHDF) crystal morphology, which was compared with the experimental one determined with the software

Oxford CrysAlisPro171.34.36.32 VESTA333 and Mercury31 were used for molecular graphics. Crystal data can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retrieving.htmL (or from the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB21EZ, UK; fax: (+44)1223336-033; or e-mail: [email protected]). CCDC numbers 1563460-1563461. For single crystal face indexing and for phase identification on polycrystalline samples and thin films (for the preparation see above), X-ray powder diffraction patterns (XRPD) were collected in the 2θ range between 5°–40°. This was done on a PANalytical X’Pert PRO automated diffractometer with Bragg-Brentano geometry equipped with an X'Celerator detector, in the 2θ range 5–40°, using Cu Kα radiation without a monochromator (step size, 0.02°; time/step, 20 s; 0.04 rad soller; 40 kV x 40 mA). The program Mercury31 was used for the simulation of X-ray powder patterns on the basis of single crystal data either retrieved from the Cambridge structural database (CSD) (polymorph B - with INDIGO04 as CSD refcode) or collected in this work (Indigo grown by PVT - identified as polymorph A). Chemical and structural identity between bulk materials and single crystal structures was always verified by comparing experimental and simulated powder diffraction patterns. For Rietveld refinement purposes, X-ray powder diffraction patterns (XRPD) in the 2θ range between 3–70° were collected on a PANalytical X’Pert PRO automated diffractometer equipped with Focusing Mirror and Pixcel detector in transmission geometry (step size 0.0260°, time/step 200 s, 0.02 rad soller; VxA 40 kV x 40 mA). Powder diffraction data were analyzed with the software TOPAS4.1.34 A shifted Chebyshev function with 7 parameters and a Pseudo–Voigt function (TCHZ type) were used to fit background and peak shapes, respectively. A spherical 6 ACS Paragon Plus Environment

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harmonics model was used to describe the preferred orientation. An overall thermal parameter for the C, N, O atoms was adopted. Refinements converged to Rwp = 7.2%, Rp = 5.3%; Rwp = 10.3%, Rp = 8.0% for sublimed and commercial powders, respectively. Figure S1 shows experimental, calculated, and difference curves for commercial powders and polycrystalline samples obtained after sublimation.

Computations To assess whether the crystal structures reported in the literature and in this work can all be safely assigned to either the A or B polymorph, the ”Crystal Inherent Structure” method was employed.35,36 Such an approach represents an efficient way of discerning/grouping experimental structures which, judging from the XRD data, appear to be very similar albeit not identical. The method relies on the calculation of the crystal structure of minimum energy, which in this work we have determined with an atom-atom potential model for the non-electrostatic interactions, combined with atomic point charges to treat the electrostatic contributions. Molecular geometries and atomic charges were obtained from an isolated molecule DFT calculation. The lattice energies were minimized starting from all available crystal structures,22–26 including the data from this work. Unit cell parameters, molecule orientations and distances within the cell were varied keeping the molecules rigid and interacting through the DREIDING37 atom-atom potential. The GAMESS38 program with the B3LYP/6-31G(d) functional and basis set combination was employed for equilibrium molecular geometries and ESP atomic charges. To assess the relative stability of the A and B polymorphs of Indigo, we used the density functional code VASP (Vienna Ab initio Simulation Package)39–42 with the PBE exchange correlation functional43 and projected-augmented wave (PAW) potentials (versions provide in the SI).44,45 The effects of the van der Waals (vdW) interactions have been included with either the pairwise 7 ACS Paragon Plus Environment


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method of Tkatchenko and Scheffler (TS)46 or the many-body dispersion (MBD) method of Tkatchenko et.al.. 47 Due to their structural similarity, energy convergence could be achieved with identical settings for the two polymorphs: a plane wave cutoff of 800 eV proved adequate in combination with

3 × 5 × 3 and 4 × 6 × 3 Monkhorst-Pack k-point grids for the TS and MBD calculations, respectively. Raising the cutoff energy from 800 to 1200 eV caused energy changes below 1 meV/atom, while increasing k-point sampling to 6 × 10 × 5 gave energy changes below 0.05 meV/atom. Lower k-point samplings actually are within the same accuracy. Cell parameters and atomic coordinates were fully relaxed, halting when residual forces fell below 1meV/Å. For both energy cutoff and k-point sampling, energy differences between polymorphs A and B converge faster than absolute energies to within 0.07 meV/atom (i.e. 0.05 kcal/mol of Indigo). The relative stability of the two phases as a function of temperature was analyzed by adding the

vibrational contribution,48 () = ∑ ℏ + ∑ ln 1 − exp "

ℏ#$

%& '

(), to the Helmholtz free

energy. Here, and are the Bolzmann constant and the absolute temperature. Fvib depends on the vibrational frequencies , and, therefore, on the details of the molecular packing. Phonon frequencies were computed with the PHONOPY software48 in combination with VASP, for an approximately cubic 2 × 3 × 2 supercell with sides of ~ 19 Å. Thanks to the larger computational cell and to the over converged k-point sampling of the primitive cell, the sizable computational cost could be reduced by limiting the k-point sampling to the Г point, which yielded convergence to 0.07 meV/atom. The sum over frequencies was replaced by the equivalent integral over the phonon density of states (DOS) -(), determined with 250 symmetry-inequivalent wave vectors over a 10 × 10 × 10 mesh in reciprocal space. Raman intensities were obtained by using the Python program VASP_RAMAN.py,49 which used the VASP code as backend.


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Results and Discussion The crystal structures of Indigo in the literature Five structures are contained in the CSD repository with refcode INDIGO, referring to a number of structural works on this compound.23–26,50 Refs. 23,25,50 all report the same monoclinic P21/c structure, denoted as polymorph A in the CSD files. In Ref. 22 the occurrence of a second structure (denoted as polymorph B) is mentioned for the first time: the reported cell parameters are such that, within the experimental error, only the cell length a and the monoclinic angle β differ from those of polymorph A. More information about form B can be found in Refs.

24,26

. In the former

work with crystallites grown by sublimation, polymorph B was always found to co-exist (10%) with polymorph A, while in the latter paper, single crystals of B were selectively grown at high temperature and ambient pressure near the decomposition limit of the compound. Structurally very similar to form A, form B is reported as monoclinic P21/c24 or P21/n.26 Its larger volume (about 3% at RT) suggests that B might be the structure stable at higher temperature, however no phase transition was detected by cooling down to 213 K.26 Polymorphs A and B contain two molecules per unit cell (Z=2) related by a 21 screw axis and possessing Ci molecular symmetry. Only very small deviations from the planar geometry and from C2h symmetry are found. The latter correspond to the minimum energy configuration determined by the DFT calculation for the isolated molecule. This shows that the influence of crystal packing on the molecular geometry is negligible. Both A and B polymorphs show the same interaction patterns: translationally equivalent molecules are arranged with parallel aromatic rings to form stacks with face-to-face π-π interactions, and a network of intra- and inter- hydrogen bonding interactions (see XRD characterization section). Even the packings are nearly identical and the main difference between the polymorphs is in a subtle reciprocal orientation of the molecules, which leads to slightly different stackings (see Figure 2). Although small, this difference could 9 ACS Paragon Plus Environment


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affect electrical properties of Indigo based thin film devices, hence the need to know exactly what polymorph we are dealing with.

Figure 2. (a) Overlay of the packing diagrams showing subtle differences in unit cell and reciprocal orientation of the molecules for Indigo form A (light blue) and B (pink), determined at 210 K (this work) and 213 K26), respectively. (b) Particular showing how these differences mirror in slightly different π-stacking interactions for form A (left) and B (right).

A summary of the published structures and of the data of this work, with cell parameters standardized to the P21/n space group, are reported in Table 1. This table also contains the values calculated by DFT discussed in more detail in the following section.

a

Table 1 Lattice parameters and sublimation energies ΔsubH (T) of crystalline Indigo. Experiments are compared to calculations, 46

47

either with the Tkatchenko-Scheffler (TS) or many-body dispersion (MBD) DFT method.

REFCODE/name

a

b

c

β

Volume

(Å)

(Å)

(Å)

(deg)

(Å3)


T

ΔsubH (T)

(K) (kcal/mol)

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9.2850(9)

5.7941(4)

11.5722(9)

108.710(10)

589.66(8)

295

9.1942(8)

5.7876(6)

11.4878(8)

108.268(9)

580.48(9)

210

INDIGO / A

9.24

5.77

11.50

108.73

580.65

RT

INDIGO0123 / A

9.23

5.74

11.59

108.95

580.82

RT

INDIGO03 / A

9.24

5.77

11.50

108.73

580.50

RT

INDIGO0224 / B

9.854

5.887

10.840

107.38

600.12

RT

INDIGO04 / B

9.7990

5.9064

10.7550

106.78

595.96

213

This work, calc (TS)/ A

9.107

5.741

11.489

108.53

569.60

45.5

This work, calc (MBD)/ A

9.148

5.779

11.465

108.81

573.71

37.4

This work, calc (TS)/ B

9.633

5.922

10.468

105.94

574.16

45.2

This work, calc (MBD)/ B

9.732

5.885

10.559

106.90

578.68

37.4

This work / A

50

25

26

3251

a) All the experimental structures have been standardized to P21/n space group.

Inherent structure analysis and polymorph relative stability. The inherent structure of a polymorph is the local minimum corresponding to the configuration of mechanical equilibrium35,36 reached by a steepest descent minimization, which starts from a given configuration of the system on the potential energy surface. In this context all structures of the same thermodynamic phase lie in the potential basin of the same local minimum and, thus, converge to the same inherent structure. In a case such as Indigo, where we are dealing with a collection of very similar structures measured over many years under various conditions and temperatures, the method enables us to identify which of the reported structures actually correspond to different polymorphs. The minimizations could be performed running DFT optimizations starting from all available experimental structures. When including high-level dispersion corrections, this would yield reliable lattice parameters and energies, but with the risk of wasting computer time by repeatedly reaching the same minimum, whenever supposedly 11 ACS Paragon Plus Environment


different experimentally determined structures actually correspond to a single polymorph. Luckily, in our experience it is not necessary to resort to expensive computational methodologies because, although the lattice parameters computed at the minimum obviously depend on the method adopted for the calculations, the identification of the various polymorphs is instead independent of the method itself (provided that it is realistic).52 For this reason, we have first determined all Indigo inherent structures using the potential model described in section “Experimental and Computational Methods”. The analysis does confirm that for all the experiments only two distinct minima can be identified, corresponding to form A (this work, and CSD refcodes INDIGO,50 INDIGO01,23 INDIGO325) and form B (INDIGO02,24 INDIGO0426). Notably, the adopted potential model reproduces satisfactorily the experimental sublimation enthalpy51 (ΔsubHexp(577 K) = 32 kcal/mol, ΔsubHcal = 34 kcal/mol). An useful way of comparing crystallographic structures is the distance comparison method,53,54 in which all the interatomic distances between a reference molecule and at least 14 neighboring molecules in a spherical coordination shell are listed, and pairs of structures are then compared by means of the root-mean-square-deviation (RMSD14) between their lists of distances. This analysis further supports the association of all measured structures with two polymorphs, yielding RMSD14 values clustered in two sets A and B. All A-A and B-B (same-set) RMSD14 distances are below 0.08 Å, whereas A-B (different-sets) RMSD14 distances exceed 0.40 Å. After this inexpensive screening, DFT calculations were run only for the two distinct polymorphs A and B, to obtain information about their relative stability. The lattice parameters computed at the minimum energy structure with TS46 and MBD47 DFT-vdW methods by relaxing both the atomic coordinates and the cell axes, are reported in Table 1. The agreement with the experimental parameters (Table 1) is excellent and can be regarded as a validation of the method, also considering that that calculations did not take thermal expansion into account, while experiments 12 ACS Paragon Plus Environment

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are done above 0 K. Furthermore, the RMSD14 distance analysis shows that the computed structures cluster together with the corresponding experimental ones. For the same sets (A-A or B-B), computed vs experimental RMSD14 distances are 0.10 and 0.16 Å for MBD and TS methods, respectively, whereas for different-sets (A-B or B-A) the RMSD14 distances exceed 0.45 Å. Following standard procedures,55,56 we have computed the sublimation enthalpy ΔsubHcal (T) by subtracting the energy of an isolated molecule from the calculated total energy per molecule in the solid, and by adding the 2RT Dulong-Petit term. The energy of the isolated molecule was estimated by embedding a single molecule in a cubic cell. The size of the cell was progressively increased from 20 to 35 Å until the energy converged, in order to avoid interaction between periodic images. The resulting ΔsubHcal (T), reported in Table 1, overestimates the experimental values by 13 and 5 kcal/mol for the TS and the MBD method, respectively. These differences are larger, but in the same direction as those found in recent benchmark calculations on a set of 23 molecular crystals,56 with the same PBE functional and van der Waals corrections but with an explicit treatment of the vibrational contributions instead of the Dulong-Petit term. In that study, on average, experimental ΔsubH were overestimated by 3 and 2 kcal/mol for the TS and MBD method, respectively. These differences are approaching the experimental uncertainties, estimated to be around 1 kcal/mol.57 Computed volumes for polymorph A are smaller than for polymorph B in agreement with the experiments. At 0 K, the A phase is predicted to be slightly more stable than the B phase, by 0.3 kcal/mol and 0.06 kcal/mol for the TS and MBD methods, respectively, in agreement with the rule of thumb that the higher density, the higher the stability. The energy difference especially in the MBD case is very small, as expected on the basis of the close structural similarities between the two forms, and indeed comparable to the computational accuracy for such differences of 0.05 kcal/mol (see Experimental and Computational Methods section). 13 ACS Paragon Plus Environment


When the temperature dependent vibrational contribution to the free energy () is included, the stability differences between the two phases decreases with increasing T. In fact, form B becomes more stable beyond 480 ±70 K or 110 ±70 K with either the TS or the MBD method, where the incertitude in the temperatures derives from the incertitude in the energy. These results support the experimental suggestion24,26 that form B is the stable one at high T.

X-ray diffraction characterization The samples grown by physical vapor transport, PVT, were analyzed with single crystal XRD both at room and low temperature (see details in Experimental and Computational Methods section) and unambiguously identified as A. The crystal structure was solved and refined in the monoclinic P21/n space group. At room temperature the crystal packing of Indigo form A is characterized by the presence of π-stacking and of a network of intra- and intermolecular hydrogen bonding interactions between N-H and C=O groups [with distances of 2.915(2) Å and 2.875(2) Å, respectively] leading to the assembly as shown in Figure S1. To confirm the absence of any phase transition upon cooling, additional data sets were acquired at 210 K and the unit cell was determined also at 150 K. In contrast, for commercial and sublimed Indigo no sufficiently large single crystals were accessible. Thus, we restricted the investigations on these samples to powder XRD. The corresponding diffractograms are reported in Figure S2. For the commercial product the peaks appear slightly broadened, but the pattern corresponds to that of polymorph B, with possible traces of A. After sublimation, a significant enrichment in polymorph A was detected, in agreement with what observed by Kettner et al..26 Notably, the amount of polymorph A increases with increasing the deposition temperature of the sublimation.

Rietveld refinement was used to evaluate the relative amounts of polymorphs before and after 14 ACS Paragon Plus Environment

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sublimation (see Figure S3. As anticipated, the commercial sample was found to consist mostly of polymorph B (ca. 93%) with a small amount of A (ca. 7%), while in the sublimed sample the polymorphic content in A was found to increase up to ≈ 30% and ≈50% with increasing the cold finger temperature from 30°C to 90°C, respectively. The thin films obtained by drop casting of solutions in 1,2-dichlorobenzene or acetonitrile were also subjected to powder XRD analysis (see Figure 3). They show very similar diffraction patterns with two peaks: the first at 10.7°, corresponding to a d-spacing value of 8.28 Å. Here, the degree of uncertainty is, however, too high to allow for a safe and unambiguous determination of the type of polymorph from these measurements. A similar problem has been previously encountered by Scherwitzl et al. 15 and by Anokhin et al. 16 in Indigo films grown from vapor on various substrates. Therefore, we resorted to Raman spectroscopy as an alternative tool for polymorph identification.20,58

Figure 3 XRD pattern of indigo deposited on Si/SiOx wafer by drop casting of 1,2-dichlorobenzene (green-line), and acetonitrile (blue-line).



Raman Characterization The first crucial step for using Raman spectroscopy to identify polymorphs is to measure and/or calculate the reference spectra for samples in which the actual structure has been identified (i.e., in our case for the bulk crystals)

Lattice phonon Raman spectra of the bulk crystals The lattice normal modes, i.e., translations and rotations of the molecule as a whole are found in the low wavenumber region of the vibrational spectrum. Their pattern is characteristic of the inter-molecular interactions. This makes Raman spectra in this range an optimal probe of structural properties, as here each polymorph displays its own, unique spectrum. To obtain the unique lattice phonon Raman pattern of polymorph A, Raman spectra were collected for the Indigo samples grown by PVT and identified by single crystal XRD. Moreover, some of the crystallites grown by sublimation were found to have dimensions and characteristics suitable for single crystal micro-Raman analysis. The lattice phonon Raman spectra of all these samples, together with that of the commercial powder, are shown in Figure 4. Random sampling of the specimens grown by sublimation confirmed that two different spectral patterns could be selectively detected on individual crystallites: the one corresponding to polymorph A, assigned on the basis of the analysis performed on the PVT crystals, and a second one, measured for the larger fraction of the crystallites. Based on the XRD investigations discussed above, this pattern was, thus, assigned to polymorph B and subsequently used to unambiguously identify the presence of this polymorph. As expected, the spectrum of the commercial product displays broader bands compared to the single crystals, but concerning spectral positions and shapes we can associate it with polymorph B, in agreement with the powder XRD results.


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Figure 4 Left: Lattice phonon Raman spectra of the various samples of crystalline Indigo, with the two unique patterns that can be identified from the analysis; Right: images of the samples.

The images of A and B crystals in Figure 4 show that morphology cannot be used to discriminate between the two polymorphs. It should be noticed that also the spectral patterns of the two crystal forms in the lattice phonon region are quite similar, reflecting the similarities of the lattices. To confirm the assignment, the experimental Raman spectra of the two polymorphs in the region of the lattice phonons are compared in Figure 5 to those calculated by DFT employing the MBD correction. The Γ-point vibrations are broadened by Lorenzian bands with a FWHM of 1.5 cm-1, chosen to match the experiments.



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Figure 5 Comparison of DFT-MBD and experimental Raman spectra for A and B indigo polymorphs in the lattice phonon region. -1

The experimental spectra have been deconvoluted as sums of Lorenzian bands. The 42 cm peak of the B polymorph can be resolved only in the Raman polarized spectra as shown in the SI.

Based on the P21/n crystal symmetry, which is the same for both polymorphs A and B of Indigo, six lattice modes of gerade symmetry 3Ag + 3Bg are predicted to be Raman active. The prediction is made on the assumption that Indigo can be treated as a rigid molecule, in which the lattice phonons lie at energies lower than those of molecular vibrations and can be considered separately. The six lattice modes correspond to either in-phase (Bg) or out-of-phase (Ag) rotations (librations) of the molecules in the unit cell around their axes of inertia and give rise to three doublets in the Raman spectrum. This preliminary analysis is the key to the interpretation of the spectral features, possibly with the aid of polarized Raman spectroscopy, as illustrated in the SI. 18 ACS Paragon Plus Environment

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Such an analysis is supported by the calculations. The eigenvectors of the six lowest gerade normal modes do correspond to pure librations, with no contribution of intramolecular vibrations. In the SI the visualization of these modes is available through animations. The agreement between simulated and experimental patterns is very good for polymorph A and less so for polymorph B, although close to the accuracy of the theoretical method in the calculation of the vibrational eigenvectors.27 By analyzing the displacements it is possible to pair corresponding modes in the two polymorphs. As can be seen in Figure 5, the experimental feature which most clearly distinguishes polymorph B from polymorph A, i.e. ,the presence of two almost degenerate lowest energy lattice phonons around 40 cm-1, is very well reproduced by the simulations. However, in the calculated spectra the differences between the higher energy phonons of the two polymorphs (70-110 cm-1) are larger than what appears from the experiments. Residual polarization effects due to sample orientation could explain changes in relative intensities, but further investigation might be needed. Nevertheless, the reproduction of the spectral features, especially for polymorph A, contributes to the validation of the assignment of Raman spectra to specific polymorph structures initially made with the aid of XRD measurements.

Raman analysis of the intra-molecular vibrations Intra-molecular vibrational spectra, either IR or Raman, often provide a valid diagnostic tool for the identification of conformational polymorphs. They are, however, usually ineffective for packing polymorphs, which share the same molecular geometry and, thus, the same spectral features for the intra-molecular modes. By contrast, Indigo A and B polymorphs can be discerned by some of the strongest bands of their intra-molecular Raman spectra. The central panel in Figure 6 shows these spectra for samples of the two polymorphs in the wavenumber region from 100 cm-



1

to 2000 cm-1, while at the sides two specific ranges have been zoomed in: i) 100-200 cm-1 and ii)

1450-1650 cm-1.

Figure 6 Raman spectra of Indigo polymorphs A (blue) and B (red) and of the commercial powder (black), which was found to be -1

composed mostly of B, in the wavenumber range 100-2000 cm . Centre: extended spectrum; left and right: zoom into the wavenumber intervals, in which polymorph discrimination can be made on the basis of intra-molecular vibrations.

As expected for packing polymorphs, most bands of forms A and B are overlapping. The lowwavenumber region shown in the right panel of Figure 6 highlights the bands corresponding to the intra-molecular mode of lowest energy. It is split into an Ag+ Bg doublet in the crystal with Z=2 molecules/cell, as a result of the Davydov coupling59 between vibrations involving pairs of molecules. In polymorph B, the two peaks lie at 132 and 139 cm-1, whereas in polymorph A at 136 and 142 cm-1. The Raman calculations on the crystals correctly reproduce the red shift of form B (yielding 135 and 144 cm-1) compared to A (140 and 151 cm-1). The eigenvectors describe this 20 ACS Paragon Plus Environment

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vibration as a large amplitude mode arising from internal rotations, which gives rise to ripples travelling the entire molecular scaffold (top images of Figure 7). The nature of this motion suggests it to be a sensitive probe of the strength of the intermolecular hydrogen bonds, as these could hinder internal rotations. Hence the frequency difference observed between the two forms is indeed determined by packing differences, making these bands excellent probes for polymorph identification. By comparison, frequency shifts are neither observed nor calculated for the weaker peaks of the following doublet, around 172 and 182 cm-1, also reported in Figure 6. The Raman spectra of the two polymorphs also differ in the doublet of the most intense and typical band of Indigo,60–62 shown in the right panel of Figure 6. In polymorph A, the doublet lies at 1578 and 1592 cm-1 (calculated 1568 and 1585 cm-1, respectively), in polymorph B at 1576 and 1587 cm-1 (calculated 1566 and 1580 cm-1, respectively). As can be seen in the eigenvector visualization of Figure 7 (bottom images), the corresponding mode is a combination of the central C=C and C=O stretchings, but actually comprises the motion of the entire functional system formed by the two C=O acceptor and the two N-H donor groups, called cross-conjugation chromophore.61,62 The mode is computed around 1596 cm-1 for the isolated molecule60,62 with a large red shift observed60–62 and calculated in the solid state. Such a variation has been interpreted on the basis of calculations on a dimer60 as a consequence of the strong intermolecular hydrogenbonds, which affect the vibrational dynamics of the functional groups involved in the interaction. The animation provided in the SI is useful for the description of the mode.



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-1

Figure 7 Top: visualization of the Ag intramolecular mode of lowest energy (calculated at 140.1 cm for the A polymorph); bottom: visualization of the Ag intramolecular mode corresponding to the most intense and typical band of Indigo (calculated at -1

1568.0 cm for the A polymorph). Arrows indicate the direction of the displacements, while blue and red geometries depict the 63

moving of the system.

The different splittings observed in forms A and B, together with different red shifts compared to the isolated molecule, suggest differences in the details of the interactions between the pairs of non-translationally equivalent molecules, in a way similar to what we observed for the previously described large amplitude motion. The calculations correctly reproduce the larger Davydov’s splitting of A compared to B, as well as the larger red shift of the latter but somehow the agreement is not fully satisfactorily. Probably, minimal structural variations of this extensively


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hydrogen-bonded system reflect on the local interaction strength and then on the coupling and the dynamics of the nuclear motions. From a practical point of view, these findings show that polymorphs A and B can be efficiently identified by inspecting their Raman bands in energy ranges easily accessible. More interestingly, they provide the spectroscopic evidence of a specific difference between the two forms which originates from the different dynamics of the H-bond motifs. Once the reference spectra for both bulk modifications are precisely known, Raman analysis can be safely used to identify polymorphs also for cases in which the co-existence of polymorphs occurs on the micrometric scale,64 affecting domain structures, morphology and grain boundaries of crystallites. An example for the co-existence of both indigo polymorphic arrangements in the same specimen identified by Raman spectroscopy is reported in the SI (section 7).

Raman analysis of the drop cast samples As mentioned above, the X-ray investigation of Indigo films may fail to recognize which crystal modifications are present. The high sensitivity displayed by Raman microscopy for Indigo suggested its application to the screening of the films.



Figure 8 Raman spectra of films of Indigo drop cast from solutions in chlorobenzene and acetonitrile. The wavenumber ranges suitable for polymorph identification are shown. For each spectrum the number indicates the image area of the sample where the Raman scattering has been collected.

Figure 8 shows the Raman spectra recorded on films obtained by drop-casting from 1,2dichlorobenzene and acetonitrile solutions on Si/SiO2. Choosing as polymorph markers the intramolecular modes illustrated in the previous section, we investigated phase identity and purity by performing extensive random sampling on the film surfaces. All measurements indicate that B is the only polymorph present. Notably, the films prepared for these measurements are thicker than those reported in previous works. Besides, solution techniques like that here adopted do not yield for Indigo films of the quality required to test charge transport. However, the technique clearly is very sensitive, as can be judged by the high signal/noise ratio of the spectra presented, and this makes it a good candidate for reliable polymorph identification also in very thin films 24 ACS Paragon Plus Environment

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Conclusions The characteristics of the concomitant Indigo A and B polymorphs have been revisited by single crystal and powder X-ray diffraction and lattice phonon Raman microscopy. Solid state DFT-TSVdW and DFT-MBD-VdW calculations have been employed to estimate the relative stability of the two forms, whereas a quick energy minimization based on a model potential has assured us that all the literature structures belong to two and only two forms. Polymorphs A and B are very similar, with close lattice parameters, almost identical packings and closely corresponding interatomic distances. With a threshold of 1 Å, typical in crystal predictions to identify different structures by comparing their lists of interatomic distances, indeed the two forms would be considered identical. Nevertheless, we here show that they are different: experimentally because they exhibit clearly different XRD and Raman spectra; computationally because they converge to distinct minima. The DFT calculations are in agreement with the empirically proposed energy ranking for the two polymorphs, although they assign the polymorphs to be nearly isoenergetic. At 0 K the form A is predicted to be more stable than B, by 0.1 to 0.3 kcal/mol, depending on the method. Such values are very small, but differences around 0.5 kcal/mol are commonly found by comparable theoretical methods for most non-conformational polymorphs.65 Moreover, the MBD approach adopted here has been reported to yield an accuracy of ca. 0.2 kcal/mol in the relative energies of a wide range of molecular crystals polymorphs.66 Our finding that the temperature dependent vibrational contribution to the free energy () favors polymorph B suggests that this is phase stable at high T.



From an experimental point of view we must notice that in contrast to what has been described literature, the commercial powder available to us is almost entirely composed of the B form, which since its first identification has been assumed to be not trivial to isolate and possibly metastable. The same applies to the product of sublimation, where the B form dominates, but which can be enriched in A by changing the deposition conditions. With the situation of the Indigo polymorphs clarified by the experiments in the bulk phase, and the correlation between structural and dynamic properties made, the characterization of the films has become possible. We have shown that even in cases in which the close similarities of the two structures impairs their identification by XRD investigations, the micro Raman technique is sensitive enough for polymorph discrimination, identifying the B form as the only one present in films obtained by drop casting. Measurements of films obtained by ultrahigh vacuum (UHV) deposition are under way to investigate the existence of surface-induced phases on substrate of technological interest. Acknowledgements We thank CINECA Supercomputing Center for providing computer time through the ISCRA scheme (project C - HP10CA2TWT). A.G. acknowledges funding by the exchange program “Erasmus+ Mobilità per tirocinio 2017/2018” (Convenzione n. 2017-1-IT02-KA103-035637). This work has been financially supported by the Austrian Climate and Energy Fund (KLIEN) and the Austrian Research Promotion agency (FFG) through the project “ThermOLED” [FFG No. 848905].

Supporting Information Description Projected-augmented wave (PAW) pseudopotentials, Network of intra- and inter-molecular hydrogen bonds form A, Crystal data and details of measurements for indigo A, powder XRD 26 ACS Paragon Plus Environment

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pattern comparison, Morphology of Indigo form A, Symmetry analysis of the lattice phonon Raman spectra and Polarized Raman spectra, Phase coexistence probed by lattice phonon Raman spectra and animations of the vibrational modes.

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Marom, N.; Distasio, R. A.; Atalla, V.; Levchenko, S.; Reilly, A. M.; Chelikowsky, J. R.; Leiserowitz, L.; Tkatchenko, A. Many-Body Dispersion Interactions in Molecular Crystal Polymorphism. Angew. Chemie - Int. Ed. 2013, 52 (26), 6629–6632.




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Figure 1 Molecular structure of Indigo (2,2'-Bis(2,3-dihydro-3-oxoindolyliden). 41x21mm (600 x 600 DPI)

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Figure 2. (a) Overlay of the packing diagrams showing subtle differences in unit cell and reciprocal orientation of the molecules for Indigo form A (light blue) and B (pink), determined at 210 K (this work) and 213 K24), respectively. (b) Particular showing how these differences mirror in slightly different πstacking interactions for form A (left) and B (right). 330x279mm (144 x 144 DPI)


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Figure 3 XRD pattern of indigo thin films deposited on Si/SiOx wafer by drop casting of 1,2-dichlorobenzene (green-line), and acetonitrile (blue-line). 244x125mm (150 x 150 DPI)



Figure 4 Left: Lattice phonon Raman spectra of the various samples of crystalline Indigo, with the two unique patterns that can be identified from the analysis; Right: images of the samples. 125x105mm (300 x 300 DPI)


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Figure 5 Comparison of DFT-MBD and experimental Raman spectra for A and B indigo polymorphs in the lattice phonon region. The experimental spectra have been deconvoluted as sums of Lorenzian bands. The 42 cm-1 peak of the B polymorph can be resolved only in the Raman polarized spectra as shown in the SI. 226x180mm (300 x 300 DPI)



Figure 6 Raman spectra of Indigo polymorphs A (blue) and B (red) and of the commercial powder (black), which was found to be composed mostly of B, in the wavenumber range 100-2000 cm-1. Centre: extended spectrum; left and right: zoom into the wavenumber intervals, in which polymorph discrimination can be made on the basis of intra-molecular vibrations. 289x173mm (300 x 300 DPI)


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Figure 7 Top: visualization of the Ag intramolecular mode of lowest energy (calculated at 140.1 cm-1 for the A polymorph); bottom: visualization of the Ag intramolecular mode corresponding to the most intense and typical band of Indigo (calculated at 1568.0 cm-1 for the A polymorph). Arrows indicate the direction of the displacements, while blue and red geometries depict the moving of the system.61 71x66mm (300 x 300 DPI)



Figure 8 Raman spectra of films of Indigo drop cast from solutions in chlorobenzene and acetonitrile. The wavenumber ranges suitable for polymorph identification are shown. For each spectrum the number indicates the image area of the sample where the Raman scattering has been collected. 70x54mm (300 x 300 DPI)


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