Visualizing Noncovalent Interactions and Property Prediction of Submicron-Sized Charge-Transfer Crystals from ab-initio Determined Structures

The charge-transfer (CT) interactions between organic compounds are reﬂected in the (opto)electronic properties. Determining and visualizing crystal structures of CT complexes are essential for the design of functional materials with desirable properties. Complexes of pyranine (PYR), methyl viologen (MV), and their derivatives are the most studied water-based CT complexes. Nevertheless, very few crystal structures of CT complexes have been reported so far. In this study, the structures of two PYRs-MVs CT crystals and a map of the noncovalent interactions using 3D electron diﬀraction (3DED) are reported. Physical properties, e.g., band structure, conductivity, and electronic spectra of the CT complexes and their crystals are investigated and compared with a range of methods, including solid and liquid state spectroscopies and highly accurate quantum chemical calculations based on density functional theory (DFT). The combination of 3DED, spectroscopy, and DFT calculation can provide important insight into the structure-property relationship of crystalline CT materials, especially for submicrometer-sized crystals.


Introduction
In the past few decades, interactions between the electron-rich (donors, D) and electron-deficient (acceptors, A) molecules have Scheme 1.A schematic illustration of the CTCs and major methodologies in the study.a) Chemical structures of the PYRs (D) and MVs (A) derivatives, as well as the inert ANT.Different methods such as UV-vis, PL, and NMR are used for characterizing the CT interactions.b) Schematic illustration of the three-layer diffusion method for the growth of PYR-MV microcrystals (left), and one of the selected area electron diffraction (SAED) patterns for crystal structural resolving (right).c) Resolved crystal structure of PYR a -MV a complex (left) and calculated band structure, the conductivity of the CTC solid, and electronic excitation in the aqueous phase compared with the experimental UV-vis spectrum (right).
submicron crystals which are too small for X-ray crystallography. [17]Consequently, there are very few reported water-soluble CTC crystal structures, [18,19] and their structureproperty relationship is not well investigated.
Due to the stronger scattering ability of electrons than Xray photons, 3D electron diffraction (3DED) can determine structures from submicron or nano-sized crystals, such as zeolites, [20,21] metal-organic frameworks (MOFs), [22,23] small organic molecules, [24] and proteins. [25]The high-resolution 3DED datasets can provide essential information on structural details, such as hydrogen atoms positions, [26] charge, [27] and molecular chirality. [28]n this study, we use 3DED to obtain the high-accuracy structures of two submicron-sized CTCs crystals of pyranine (PYRs) and methyl viologen (MVs) derivatives (Scheme 1a,b).To the best of our knowledge, this is the first time that the crystal structures of aqueous CTCs were determined by 3DED.With the high-precision structures, we employed computational methods, e.g., density functional theory (DFT) and time-dependent DFT (TD-DFT), [29][30][31][32] to predict a range of physical properties such as electronic band structures, conductivities, CT mechanism, and optical excitations (Scheme 1c).In addition, we visualized different types of noncovalent interactions, including hy-drogen bonding, electrostatic interaction, … interactions, van der Waals (VDW) interactions, and CT interactions.The CT interactions and the packing geometries of the CTCs were also investigated using Ultraviolet-visible (UV-vis) spectroscopy, photoluminescence (PL) spectroscopy, and nuclear magnetic resonance (NMR).Additionally, we studied the interaction between the PYRs/MVs with another widely used CT molecule as a control (2-anthryltrimethylammonium, ANT). [33]With our combined experimental and theoretical investigation workflow, we have successfully visualized and comprehensively analyzed the CTCs of PYRs and MVs in both crystalline and aqueous phases.

Crystal Structures of PYR-MV Complexes
In PYR a -MV a with a chemical formula of Na(C 15 N 2 H 16 )(C 19 O 10 S 3 H 9 ), two sulfonate anions of PYR a 3− link with two crystallographic independent Na + ions to yield a 1D chain through strong O─Na bonds along the crystallographic b-axis, which was further connected into a 2D network via bc plane (Figure 1a; Table S1, Supporting Information). [34]We have calculated the distances and/or angles of … interactions and hydrogen bonds through Platon (Tables S2 and S3, Supporting Information). [35]The MV a 2+ ions are intercalated into PYR a 3− stacks and form a 1:1 mixed D-A-D-A 1D CT chain (… contacts, 3.61 and 3.86 Å).The adjacent 2D networks stack along a-axis, forming a 3D framework through nonclassical hydrogen bonds (H…O, 2.46 Å) (Figure 1b). Figure 1c shows the structure of one individual D-A pair, in which the … stacking deviates from the geometry center caused by the steric alkynyl group at the end of MV a molecule.All of the hydrogen atoms were found during structural refinement.As shown in Figure 1d, the Hirshfeld surface (HS) was plotted for both donor and acceptor molecules over normalized contact distance, d norm . [36,37]he darker red regions indicate the presence of the C─H…O hydrogen bonds and lighter ones are weaker short contacts.
The … interaction between the donor and acceptor can be visualized by the triangular-shaped regions (highlighted by white dash circles) on the HS plotted over the shape index (Figure S1, Supporting Information).The … interaction areas deviated from the center of both donor and acceptor molecules, which is consistent with the off-center stacking geometry of D-A pair in Figure 1c.In the electrostatic potential map (Figure 1e), the electrostatic potential enveloped both the disordered Na + ions and all hydrogen atoms, which further proved the high accuracy of the refined structure.Different from PYR a -MV a , the unit cell of PYR b -MV b with a chemical formula of (C 12 N 2 H 14 ) 1.5 (C 16 O 10 S 3 H 7 ) contains one and a half MV b 2+ and one PYR b 3− , and no host network is formed due to the lack of bridging Na + ions. [34]In Figure 2a for charge balancing lies between the 1D chains without participating in the CT interaction.A similar structure was reported in the perylene-TCNQ crystals. [38]A 3D network is further formed via hydrogen bonds between sulfonate anion and hydroxy group (H…O, 2.11 Å) and nonclassical hydrogen bonds (H…O, 2.36 and 2.38 Å) between MV b 2+ and sulfonate anion (Figure 2b).From Figure 2c, we found the D-A pair in PYR b -MV b is more symmetrical and well aligned via the molecular center, compared to PYR a -MV a .In Figure 2d, both C─H…O and O─H…O hydrogen bonds are presented as red areas in the HS plot.The shape index plot shows … interaction areas in PYR b -MV b are located more loosely (Figure S2, Supporting Information), compared with that in PYR a -MV a (Figure S1, Supporting Information).The interaction areas are also closer to the molecule centers, due to the higher symmetry.As shown in Figure 2e, H atoms are enveloped by the electrostatic potential, confirming the existence of H atoms from experimental data.

Electronic Structures of PYR-MV Complexes
From the crystal structure, we calculated the electronic structures of the two CTCs (Figure 3a,b).The two materials have similar electronic structures as indicated by the atom-projected density of states (PDOS).The states form a continuous band below −1 eV and have a series of intense peaks between −0.1 and 4 eV.The states from C atoms are mixed throughout the energy range.The intense peak just below the Fermi level has contributions from O states and the sharp, unoccupied ones between 2.5 and 4 eV have contributions from H and N states.Thus, the charge is expected to transfer from the PYR electron donor to the MV electron acceptor.This is also illustrated by the charge density of the topmost occupied and bottom unoccupied bands in PYR a -MV a (Figure 3c,d The conductivity difference in the two complexes indicates the structure of the crystal and the donor can largely tune the conductivity of CTCs. [39,40]We then compare the experimental conductivity with the calculated isotropic conductivity (Figure 3e,f), which is the mean conductivity in different directions.Assuming both CTCs are p-type doping as typical in organic crystals, [41] we speculate the band transport is the major transport mechanism and the conduction is occurring at E − E F < −0.6 eV, where the calculated conductivities of PYR a -MV a is higher than that of PYR b -MV b , consistent with the measured values.Both crystals are indirect gap materials as seen in the electronic band structure (Figure S7, Supporting Information).The band dispersion near the Fermi level is weak and likely limits the electrical conductivity via band transport.However, there are direct transitions at slightly higher energy.The lowest energy transition is 2.59 eV from Γ to D in PYR a -MV a and 2.58 eV from Y to U in PYR b -MV b .The direct bandgap is at the Γ-point and is 2.62 eV and 2.73 eV for PYR a -MV a and PYR b -MV b , respectively.

UV-Vis and PL Study of PYR-MV Complexes
Spectroscopy characterizations, i.e., UV-vis and PL are employed to further investigate the CT interactions in both solid-state and aqueous phases.We have acquired the solid-state UV-vis and PL spectra from thin film samples drop-cast from the solutions of PYRs, MVs, or their 1:1 mixture.From UV-vis spectra (Figure 4a    A more efficient quenching was found in PYR b -MV b than in PYR a -MV a , evidenced by the incomplete quenched peak at ca. 700 nm in the 1:1 mixture of PYR a 3− and MV a 2+ (Figure S8, Supporting Information).This is also caused by the closer packing and stronger CT interaction of PYR b 3− and MV b 2+ in the crystal structure.
The CT interaction between PYRs and MVs in the aqueous phase is crucial for their functional and structural diversity, [17,42] thus important to investigate.Besides, the samples are dispersed homogenously in the liquid state, providing more reliable data for quantitative analysis.[31][32] The calculations show that the band on the low-energy shoulder is a CT excitation.The PYR a -MV a complex had electronic transition energies of 447 and 361 nm from the ground state to the S 1 and S 2 excited states, respectively.The electron density difference of the S 0 →S 1 excitation reveals that electronic charge is shifted from the PYR electron donor to the MV electron acceptor (Figure S10, Supporting Information).The oscillator strength of the CT excitation was weaker than the intramolecular S 0 →S 2 electronic excitation (vertical dash lines in Figure 5a).) where c PYR 3-/c complex = 1-F 0 /F. [44]Then we can get the concentration of unassociated MVs (c' MV 2+ ) as c' MV 2+ = c MV 2+ -c complex , where c MV 2+ is the initial MVs concentration.The ratio of F 0 to F as a function of the concentration of unassociated MVs (c' MVa 2+ or c' MVb 2+ ) was plotted in Figure 5e,f.By fitting the data with a parabola function: where K s and K d are the static and dynamic quenching constant respectively. [42]In the case of PYR a 3− -MV a 2+ , we observe a linear relationship between F 0 /F and c' MVa 2+ where the slope K s is 2.48 × 10 4 m −1 and K d is 0 m −1 , indicating an absence of the dynamic quenching process. [44]In the case of PYR b 3− -MV b 2+ , we got a K s of 2.10 × 10 4 m −1 and a K d of 7.7 × 10 3 m −1 , consistent with previous findings. [42]We speculate that the extra half acceptor in the crystal structure of PYR b -MV b contributes to this dynamic quenching process.The maximum emission also blue-shifted dramatically from 430 nm in PYR a 3− to 510 nm PYR b 3− which consists of the previously reported amphiphilic pyranines. [45]

NMR Study of PYR-MV Complexes
For further studying the structures of CTCs in the aqueous phase, we performed the 1 H NMR for PYRs, MVs, and their 1:1 mixture in D 2 O and analyzed the chemical shifts (Figure 6).In Figure 6a,b, we have observed an obvious upfield chemical shifting of 1 H on pyrene of PYRs and pyridine of MVs, meaning the shielding effect is mainly from the … stacking of the donor complex is more aligned to the molecule center due to its higher symmetry.This observation consists very well with their crystal structures (Figures 1c and 2c).On the other hand, all the chemical shift values in PYR b -MV b complex (hollow circles) are larger than in PYR a -MV a complex (hollow squares), indicating a stronger inter-action, which is consistent with the results from UV-vis, PL measurements, and DFT calculation.In Figure S11 (Supporting Information), we also studied the chemical shift of PYR a -MV b and PYR b -MV a complexes.The same trend was observed where the center H atoms have a higher chemical shift.
The derivatives of anthracene are common electron donors in CT pairs.However, in the UV-vis and 1 H NMR of the mixture of ANT + and MVs (Figure S12, Supporting Information), no CT band or 1 H chemical shift was observed, meaning ANT + (Scheme 1a) lost the electron donor property when introducing a quaternary amino group on the  position.We have also studied the interaction between PYR b 3− and ANT + as shown in the UV-vis and 1 H NMR data in Figure 7.In the UV-vis spectra (Figure 7a), there was no obvious CT band in the 1:1 mixture of PYR b 3− and ANT + indicating the absence of CT interaction.Although without any color change, we have observed a notable 1 H chemical shift when mixing PYR b 3− and ANT + (Figure 7b), caused by the shielding effect from the electrostatic attraction of the oppositely charged molecules.By studying the chemical shift pattern (Figure 7c), we found regions close to H d1 and H d3 in PYR b 3− and H n4 in ANT + encountered the largest shielding effect as the green shaded area marked in Figure 7d.These areas are likely to overlap due to electrostatic attraction.Our attempt to crystalize PYR b 3− and ANT + has failed.These results implied that the opposite charge or the existence of electron donor/acceptor moiety does not necessarily lead to CT interaction between two conjugated systems, implying rational molecular design is important for water-based CTCs.

Conclusion
We have determined the crystal structures and obtained the entire range of noncovalent interactions of two submicron-sized crystals (PYR a -MV a and PYR b -MV b ) using 3DED.Our efforts of combining experiments and DFT calculation also enable us to quantitatively analyze the physical properties in both solid state and aqueous phase.Owing to the various molecular designs, distinct structural topologies and/or symmetries were found in their crystal structures and complexes in the aqueous phase.The different CT intensities in the two complexes lead to various physical properties, e.g., conductivities, CT absorption intensity, PL quenching, etc., which were confirmed experimentally and theoretically in both phases.To be more specific, we have listed the detailed characteristics of the two CT complexes in Table 1.Besides, the spectroscopy study of PYR b 3− and ANT + also suggests that electrostatic interaction between conjugated molecules does not adequately allow intermolecular CT.
In summary, we have demonstrated how the structure and properties of crystalline CT materials, especially for small crystals that cannot be investigated by X-ray diffraction, can be investigated by a combination of 3DED, spectroscopy, and DFT calculation.The novel insights into the structure and properties of crystalline CT materials could advance the use of crystal engineering for various applications, i.e., organic electronics.

Figure 1 .
Figure 1.Crystal structure of PYR a -MV a complex.a) The coordination environments of Na1 and Na2, and the 2D network of NaPYR a 2− filled with MV a 2+ guest ions.b) The 3D framework of PYR a -MV a is stacked by the 2D networks via nonclassical hydrogen bonds.c) A projection of the 1:1 D-A pair from b-axis.The hydrogen atoms are omitted for clarity.d) Hirshfeld surface for the donor (left, −0.85 < d norm <1.53) and acceptor (right, −0.45 < d norm <1.69).Red, white, or blue surface color represents shorter, equal, or longer contact distance compared to the sum of the VDW radii, respectively.e) The electrostatic potential map from experimental data (isosurface value: 0.2 V).
, a similar 1:1 D-A-D-A 1D CT chain was formed between the neighboring PYR b 3− and MV b 2+ (… contacts, 3.50 and 3.76 Å).The closer … packing in PYR b -MV b implies a stronger CT interaction than in PYR a -MV a .We speculate that the closer packing in PYR b -MV b is the major reason for their structural difference, where there is not enough space to form a 1D sulfonate sodium chain.Instead of Na + , an extra half MV b 2+

Figure 2 .
Figure 2. Crystal structure of PYR b -MV b complex.a) The 2D network is formed by 1D D-A-D-A 1D CT chains via classical and nonclassical hydrogen bonds.b) The 3D framework of PYR b -MV b is stacked by the 2D networks via nonclassical hydrogen bonds.c) A projection of the 1:1 D-A pair from a-axis.The hydrogen atoms are omitted for clarity.d) Hirshfeld surface for the donor molecule (left, −1.21 < d norm <1.61) and acceptor (right, −0.806 < d norm <1.932).Red, white, or blue surface color represents shorter, equal, or longer contact distance compared to the sum of the VDW radii, respectively.e) The electrostatic potential map from experimental data (isosurface value: 0.2 V).
).As expected, the charge density is located on the electron donor molecule in the topmost band and on the electron acceptor molecule in the bottom band.We also confirm that the extra half b 2+ in PYR b -MV b does not contribute to the CT interaction (Figure S3, Supporting Information).The crystal conductivities along a, b, and c axes are obtained from the band structures (Figure S4, Supporting Information).Particularly, both crystals are more conductive along the D-A … stacking direction, i.e., b-axis for PYR a -MV a and a-axis for PYR b -MV b .The experimental conductivities () of the two CTCs are measured from drop-casting thin films on a four-probe setup.The drop-cast thin films of the two complexes have the same structures as their crystals, which is confirmed by comparing the thin film X-ray diffraction patterns with the simulated XRD pattern from the crystallography structure (Figure S5, Supporting Information).The average isotropic conductivity of PYR a -MV a is 3.5 ± 1.7 × 10 −4 S m −1 from six individual samples with a thickness of 300-500 nm (Figure S6, Supporting Information).The conductivity of PYR b -MV b is much lower ( < 4 × 10 −7 S m −1 ).
,b), we can clearly observe a CT band at ca. 460−480 nm in both PYR a -MV a and PYR b -MV b .The CT peak is more intensive in PYR b -MV b than in PYR a -MV a , in consistency with the stronger CT interaction between PYR b 3− and MV b 2+ from structural analysis.The quenching effect of PYR by MV was observed in the solid-state PL of both PYR a -MV a and PYR b -MV b , indicating the CT interaction between PYRs and MVs (Figure 4c,d).

Figure 3 .
Figure 3.The calculated atom projected density of states (PDOS) of crystals a) PYR a -MV a and b) PYR b -MV b .The band-projected charge density of the c) topmost occupied band and d) bottom unoccupied band of PYR a -MV a .The isovalue is 1 × 10 −3 e a 0 −3 .e) Calculated isotropic electric conductivity of PYR a -MV a and PYR b -MV b .f) The zoom in conductivity between −0.7 and −0.4 eV.

Figure 4 .
Figure 4. Solid-state UV-vis spectra of a) Na 3 PYR a , MV a Cl 2 , and their 1:1 mixture.b) Na 3 PYR b , MV b Cl 2 , and their 1:1 mixture.Photoluminescence spectra of c) Na 3 PYR a and its 1:1 mixture with MV a Cl 2 .d) Na 3 PYR b and its 1:1 mixture with MV b Cl 2 .The samples are prepared by casting 50 μL of 0.01 m solution on a 1.5 cm × 1.5 cm cover glass pretreated with O 2 plasma.

Figure 5 .
Figure 5. UV-vis spectra of a) PYR a 3− -MV a 2+ , and b) PYR b 3− -MV b 2+ in water.The concentrations were 2 × 10 −5 M (main) and 1.67 × 10 −3 m (inset).The TD-DFT calculated electronic excitations were plotted as vertical dash lines with the same PL spectra of c) PYR a 3− -MV a 2+ , and d) PYR b 3− -MV b 2+ with different concentration ratios in water.The initial concentration for PYRs (c 0 ) is 4 × 10 −6 m.The emission spectra (solid curve) were excited by 395 nm light, and the excitation spectra used a maximum emission of 430 nm for PYR a 3− -MV a 2+ and 510 nm for PYR b 3− -MV b 2+ .e,f) are the plots and fitting curves of the ratio of initial PL intensity (F 0 ) to quenched PL intensity (F) as a function of the concentration of unassociated MVs (c' MVa 2+ or c' MVb 2+ , plotted in logarithmic scale).

b 3 −
itself has a weak intermolecular CT indicated by the weak CT bands at 460 nm as the blue curve shown in the insets of Figure 5b.However, this CT band was inhibited in PYR a 3− due to the existence of the propargyl group.The CT bands in PYR b -MV a /MV b complexes are stronger than those in PYR a -MV a /MV b complexes (Figure 5; Figure S9, Supporting Information), also indicating a decreased donor ability of PYR a 3− due to the steric effect of the propargyl group.The UV-vis spectra of PYR a 3− and PYR b 3− are very similar, implying a similar molecular orbital structure.

Figure 6 .
Figure 6.NMR and photos of a) PYR a 3− -MV a 2+ , and b) PYR b 3− -MV b 2+ donor-acceptor pairs in D 2 O, with all concentrations of 0.01 m (solvent peak of H 2 O, 4.8 ppm).The 1 H atoms were numbered and marked as H an or H dn in the chemical structures in (d).The red and blue dash lines indicate chemical shifts of 1 H atoms to the upfield and downfield, respectively.c) Chemical shift value of 1 H atoms in PYR a -MV a (hollow squares) and PYR b -MV b (hollow circles) complexes.The error bars represent the standard deviations of multiple 1 H atoms. d) Schematic illustration of a PYR a 3− (dark blue and blue)/PYR b 3− (dark blue) and MV a 2+ (dark red and red)/MV b 2+ (red) complex.
Similar results were obtained for the PYR b -MV b complex.The lowest-energy electronic excitations occur at 467 and 361 nm and CT occurs in the S 0 →S 1 excitation.The binding energies of the complexes show that their formation is energetically favorable (−59 and −67 kJ mol −1 for the PYR a -MV a and PYR b -MV b complexes, respectively).A stronger bonding energy in PYR b -MV b is consistent with its stronger CT band compared to PYR a -MV a .Figure 5c,d show the PL spectra of PYRs with different amounts of added MVs, as the ratio of initial PL intensity (F 0 ) to quenched PL intensity (F) of PYRs can indicate the ratio of PYR-MV complexes concentration (c complex ) to the initial PYRs concentration (c PYR

Figure 7 .
Figure 7. a) UV-vis spectra of PYR b 3− and ANT + in water.The concentrations were 2 × 10 −5 m (main) and 1.67 × 10 −3 m (inset).b) NMR and photos of PYR b 3− and ANT + in D 2 O, with all concentrations of 0.01 m (solvent peak of H 2 O, 4.8 ppm).The 1 H atoms on the PYR or ANT molecules were numbered and marked as H an or H in respectively, in the chemical structures in (d).The red dash lines indicate chemical shifts of 1 H atoms to the upfield.c) Chemical shift value of 1 H atoms in PYR b 3− and ANT + .The error bars represent the standard deviations of multiple 1 H atoms. d) Schematic illustration of a PYR b 3− (dark blue) and ANT + (grey).

Table 1 .
A comparison of major characteristics of PYR a -MV a and PYR b -MV b complexes.Chemical formula Na(C 15 N 2 H 16 )(C 19 O 10 S 3 H 9 ) ( C 12 N 2 H 14 ) 1.5 (C 16 O 10 S 3 H 7 )