Electronic structures of π-conjugated DNA topoisomerase inhibitors

For initial screening of promising organic semiconductors, we selected DNA topoisomerase inhibitors that exhibit π-conjugation, high co-planarity, and are rich in hydrogen bond donors and/or acceptors such as amine, amide, carbonyl, ester, ether, hydroxyl groups (Fig. 1). We calculated their electronic structure theoretically at the DFT(B3LYP)/6–311 + G(d,p) level. Corresponding highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO) and bandgap (E g ) are shown in Fig. 1. The theoretical calculations indicate that all six DNA topoisomerase inhibitors are wide-bandgap semiconductors, with E g close to or exceeding 3 eV (for single molecules in vacuum). The experimentally measured optical bandgap in solution and in thin films ranged from 2.5 to 3.1 eV, which is substantially larger than typical organic semiconductors (Supplementary Fig. 1 and Supplementary Table 1). We note that organic semiconductors with wide bandgaps and uncompromised electronic performance have been pursued owing to their improved air stability, reduced photooxidation and light sensitivity, and high transparency to visible light28,29. Ellipticine, which is a plant alkaloid with anticancer properties, exhibits a calculated HOMO level in proximity to those of typical p-type organic semiconductors, making it most practical for charge injection from common metal electrodes among the six compounds evaluated. Therefore, we select ellipticine for further structure and charge transport property analysis.

Fig. 1 Molecular and electronic structures of DNA topoisomerase inhibitors tested. The top row shows the molecular structures of selected compounds possessing planar conjugated segments and hydrogen-bonding moieties (amine, amide, carbonyl, ester, ether, hydroxyl etc.) The bottom row shows corresponding optimized frontier orbitals and schematic energy level diagram of anticancer drugs as calculated using the B3LYP functional and 6–311 + G(d,p) basis set Full size image

Crystal structure and calculated charge transport properties of ellipticine

In this section, we discuss the role of π–π stacking and H-bonding in guiding the assembly of ellipticine and the emergent charge transport properties predicted from quantum-chemical simulations on the basis of experimental crystal structures (see Methods). Using various single-crystal growth and solution printing techniques30, we obtained two different crystal polymorphs of ellipticine. Their single-crystal structures are shown in Fig. 2a, b, Supplementary Table 2 and Supplementary Fig. 2. The two polymorphs exhibit similar packing motifs, featuring co-facial π stacks and H-bonding linkages between adjacent π stacks. Guided by these H-bond linkages, the columns of π stacks are arranged in a zig-zag fashion for both polymorphs, but at distinct dihedral angles of 87.9° for polymorph I vs. 35.7° for polymorph II (Fig. 2a, b and Supplementary Fig. 3). We note that such packing motif does not fall under the categories commonly observed in organic semiconductor systems, such as 1D slip-stack, 2D brick-wall, or 2D herringbone packing motifs31,32. We attribute the distinction to the presence of H-bonding in the ellipticine system. Specifically, polymorph I exhibits π−π stacking along the a axis at a distance of 3.45 Å; the corresponding hole transfer integral J π–π is calculated as 36.9 meV (Fig. 2a). In comparison, polymorph II’s π−π stacking occurs along the b axis at a comparable distance of 3.44 Å, with a much higher J π–π value of 83.0 meV associated with improved wavefunction overlap relative to polymorph I (Supplementary Fig. 2). Such a high hole transfer integral is on par with or even exceeds those of high-performance organic semiconductors such as C12-BTBT isomers33 and TIPS-pentacene34. Orthogonal to the π−π stacking direction is the H-bonding direction, which is along the c- and a axis for polymorph I and II, respectively. Again, the H-bond lengths are closely matched (1.95 Å and 2.02 Å for I and II, respectively) but the hole transfer integral is substantially higher for polymorph II, with J H bond of 16.9 meV vs. 7.1 meV for polymorph I. This difference is attributed to a lower dihedral angle between the molecular planes of the H-bonding pair for polymorph II (35.7° vs. 87.9° for polymorph I). The hole transfer integrals for other molecular pairs are summarized in Supplementary Fig. 4, which are relatively low given large intermolecular distances and/or small overlap. Altogether, we expect higher hole mobility for ellipticine polymorph II, with non-negligible contribution from the H-bond direction.

Fig. 2 Crystal structures and calculated hole mobilities for ellipticine. a, b Crystal structures of a polymorph I and b polymorph II viewed from the π−π stacking and the H-bonding directions. The corresponding calculated charge transfer integrals and the measured stacking distances were labeled. The blue dash lines denote H-bonds (NH to N). The yellow dash lines enclose one unit cell of the crystal lattice. c, d Calculated hole mobilities (in cm2 V−1 s −1) of ellipticine c polymorph I and d polymorph II. In both cases, 0° corresponds the H-bonding direction, and 90° the π−π stacking direction Full size image

Besides charge transfer integrals, we further calculated reorganization energies and predicted the hole mobilities in the hopping limit (Fig. 2c, d and Supplementary Fig. 5). The electron transfer integrals and electron mobility distributions are also computed (Supplementary Fig. 4 and 6), however not discussed owing to the practical challenge of electron injection for charge transport property measurements of ellipticine. With a calculated hole reorganization energy of 128 meV, we obtained higher hole mobilities for polymorph II owing to its higher charge transfer integrals. Both polymorphs exhibit anisotropic hole mobility distributions, with the highest mobilities appearing along the π−π stacking direction, and lower but considerable hole mobilities along the H-bonding direction. Notably, the calculated hole mobilities for polymorph II are as high as 1.0 cm2 V−1 s−1 and 3.7 cm2 V−1 s−1 along the H-bonding and the π−π stacking directions, reaching the range of high-performance organic semiconductors despite limited π conjugation of ellipticine. The predicted high mobility along the H-bonding direction suggests the important role of H-bonds in contributing to charge transport, which is rarely considered for the molecular design of organic semiconductors.

An intriguing question is how H-bond contributes to the calculated charge transfer integral and charge carrier mobilities along the H-bonding direction. Do H-bonds directly participate in or indirectly facilitate electronic wavefunction overlap? The answer is both as we detail in the analyses below. We first investigated how the H-bonding strength and the bond length impact the hole transfer integral, and compared with the case without the H-bond by replacing N with CH for both polymorphs (Fig. 3 and Supplementary Fig. 7). We found that varying the H-bonding strength while keeping the bond length does not significantly impact the charge transfer integral along both the H-bonding and π-stacking directions (Supplementary Fig. 7 and 8). On the other hand, increasing the bond length of NH…N causes rapid drop in charge transfer integral for both polymorphs (Fig. 3a, c). This seems to suggest that the role of the H-bond is to bring closer the molecular pairs engaged in the H-bond, as to indirectly facilitate overlap of the electronic wavefunction of the conjugated molecular backbone. To validate this hypothesis, we removed the H-bond by replacing N with CH on one molecule of a dimer pair (Fig. 3b, d). For polymorph II, this change mandates an increase of the intermolecular distance from the original 2.92 Å (N–N) to 4.30 Å (N–C) and thus reduces the charge transfer integral from 16.9 to 4.2 meV; restoring the H-bond at this large distance of 4.30 Å did not improve the charge transfer integral. Same conclusion is obtained for polymorph I. This result suggests that H-bond indirectly contribute to electronic coupling by reducing the intermolecular distance. However, a more-direct evidence for H bond-mediated charge transport is afforded by a closer examination at the HOMO versus LUMO transfer integrals in terms of the respective shape of these orbitals. From Fig. 3e, a major difference between the bonding–antibonding pattern of the frontier molecular orbitals is that, while there is a large contribution to the wavefunction originating from NH in the HOMO, this contribution vanishes for the LUMO. In polymorph II, the absence/presence of a node on the NH unit correlates with J HOMO being ~4 times larger than J LUMO for the H-bonding pair (16.9 vs. 4.4 meV; Supplementary Fig. 4). This clearly points to the positive effect on the transfer integral of spreading the electronic density on the hydrogen bonding NH unit. We further note that for polymorph I, where the close-to-90° dihedral angle electronically decouples the H-bonding pair, smaller and comparable transfer integrals are predicted for the HOMO and LUMO orbitals (7.1 vs. 9.8 meV; Supplementary Fig. 4). These analyses lead us to the conclusion that a low dihedral angle and a close distance of the H-bonding pair together with wavefunction delocalization over the H-bonding moieties act in concert to raise the electronic coupling between molecules along the H-bond direction.

Fig. 3 Theoretical calculations on the role of H-bond on electronic coupling. a, c Calculated hole transfer integral along the H-bonding direction as a function of NH…N distance for ellipticine with polymorph I and II. See Methods section for details. b, d Comparison of hole transfer integrals with and without H-bond for two polymorphs. The molecular pair without H-bond was created by replacing N with CH. Removal of H-bond requires adjustment of intermolecular distance from the original ~ 2.9 Å (N to N) to 4.3 Å (N to C) so that the two hydrogen atoms are separated by the sum of their van der Waals radii. We note that an intermolecular distance of 2.87 Å and 2.92 Å (N to N) corresponds to a H-bond length of 1.95 Å and 2.02 Å (N to H) in a for polymorph I and II, respectively. e Frontier molecular orbital topologies of ellipticine comparing the contribution of NH to HOMO vs. LUMO. The nitrogen atoms in the NH bonds are labeled in the HOMO and LUMO to facilitate direct comparison. Please note that this is a single molecule calculation result Full size image

Fabrication and structure characterizations of highly aligned ellipticine films

To validate theoretical predictions, it is necessary to fabricate highly crystalline, highly aligned ellipticine thin films with controlled polymorphism for measuring intrinsic and extrinsic charge transport properties in field-effect-transistor devices. High degree of alignment and crystallinity will allow us to compare charge carrier mobilities along the π−π vs. the H-bonding directions. The ability to control polymorphs offers the opportunity to determine how varying π−π and H-bonding interactions influence intrinsic charge transport properties. Towards this end, we developed solution-processing methods to controllably access polymorph I and II of ellipticine and prepared highly crystalline samples with high degree of alignment for polymorph II.

We applied the meniscus-guided solution coating method to entrap the neat phase of polymorph II (metastable at room temperature as determined from solvent vapor annealing) by varying coating speeds when deposited from tetrahydrofuran (THF) solution on plasma-treated Si wafer (Supplementary Fig. 9). Using this method, the kinetic stability of metastable forms can be substantially enhanced by the combined mechanism of nanoconfinement and kinetic trapping as demonstrated in our previous works30,34,35,36,37. The alignment, crystallinity, and polymorph identity of the solution coated ellipticine thin films were characterized using a combination of cross-polarized optical microscopy (CPOM), atomic force microscopy (AFM) and grazing incidence X-ray diffraction (GIXD) (Fig. 4, Supplementary Figs 10–12). Using CPOM, we observed millimeter to centimeter sized crystalline domains that extinguished cross-polarized light at the same time, indicative of high degree of alignment (Fig. 3a). AFM revealed well-defined crystalline ribbons and a terraced topology, which are characteristics of high crystallinity (Fig. 4b and Supplementary Fig. 12b). A single terrace height is 1.1–1.2 nm, comparable to the thickness of one molecular layer (1.04 nm) along the c axis of polymorph II. This indicates that the c axis is oriented normal to the substrate plane, confirmed by GIXD. We observed sharp, well-defined diffraction peaks from GIXD patterns. GIXD peak indexing against the single-crystal structures led to assignment of polymorph II to the solution coated ellipticine thin films (Supplementary Fig. 11). By comparing the diffraction patterns probed parallel (par) and perpendicular (perp) to the coating direction, the orientation of the crystalline domains was further analyzed as the following (Fig. 4c, d). First, for both sample orientations (par and perp), the GIXD patterns showed out-of-plane diffraction peaks at q z = 0.61 Å−1, corresponding to the (002) plane spacing of polymorph II. This indicates that the c axis is normal to the substrate plane, consistent with the AFM inference. With regard to in-plane diffraction features, (10 L), (20 L), and (30 L) Bragg rods appeared only in the perpendicular scan; at the same time, (01 L), (02 L), (03 L), and (04 L) Bragg rods were observed only in the parallel scan. This phenomenon points to the high degree of in-plane alignment in crystalline thin films prepared via meniscus-guided coating, consistent with the CPOM observation. It can be further deduced that the b axis (π−π stacking) is oriented parallel to the coating direction and the a axis (H bonding) perpendicular to coating (Fig. 4c, d). In addition to coating from THF solutions, aligned crystalline thin films of polymorph II were also obtained when coating from dimethyl sulfoxide (DMSO) solutions (Supplementary Figs 10b and 12).

Fig. 4 Structural characterizations of ellipticine thin films. The films were prepared via meniscus-guided coating from its 3 mg ml−1 THF solution at 0.05 mm s−1. a Cross-polarized optical microscopy (CPOM) images of ellipticine thin films as deposited (see Methods). b AFM height image and the cross-sectional height profile of the printed thin film along the white dotted line. The step heights are ~ 1.1–1.2 nm, comparable to the thickness of a single molecular layer of ellipticine (1.04 nm). The white arrows in panel a and b denote the coating direction. c, d Schematic of GIXD experiments and the GIXD patterns. The incident X-ray beam was set c parallel and d perpendicular to the coating direction. The (hkl) miller indices were labeled for corresponding diffraction peaks or Bragg rods. The inset schematic illustrates the inferred orientation of crystalline domains respective to the incident X-ray beam and the coating direction Full size image

Neat crystals of polymorph I were also fabricated, but using slow evaporation from bulk DMSO solution instead (see Methods). Owing to its slow nucleation and growth kinetics, neat polymorph I was not accessible using meniscus-guided coating; instead, mixed phases of I and II were obtained even at low coating speeds. Aligned crystalline films of polymorph I was prepared by laminating needle-shaped single crystals of polymorph I onto dielectric substrates for charge transport property characterizations (Supplementary Fig. 13a). Single-crystal diffraction confirmed that the long axis of the crystal is parallel to the a-axis which is along the π−π stacking direction (Supplementary Fig. 13b).

Measuring intrinsic charge carrier mobility

Aligned ellipticine samples were used for measuring intrinsic charge carrier mobility using two noncontact microwave-based techniques: flash-photolysis and field-induced time-resolved microwave conductivity, abbreviated as flash-photolysis time-resolved microwave conductivity (FP-TRMC) and field-induced time-resolved microwave conductivity (FI-TRMC), respectively. TRMC measures short-range, nano-scale mobility of charge carriers resonant with an oscillating microwave electric field; the measured mobility is free from grain boundary and contact effects38,39. In the FP-TRMC technique (Fig. 5a), charge carriers are generated by a photoinduced charge separation process, and resonate as they absorb the incident microwaves, resulting in a change in the power of the reflected microwaves ΔP r whose kinetic traces are monitored. Owing to photoexcitation induced ionization, both holes and electrons are generated together. Complementing to FP-TRMC, FI-TRMC can evaluate hole and electron mobilities separately at the semiconductor/dielectric interface using the metal insulator-semiconductor (MIS) structure (Fig. 5a). In this technique, the electrons or holes are induced by applying a positive or negative gate bias (hence, the name field-induced) rather than through photolysis.

Fig. 5 Intrinsic carrier transport properties via microwave conductivity. a Schematic of flash-photolysis and field-induced time-resolved microwave conductivity (FP- and FI-TRMC) techniques. b FP-TRMC response of ellipticine samples of polymorph I and II. ϕ∑μ denotes the product of charge separation quantum yield (ϕ) and the sum of photo-generated hole and electron mobilities (∑μ); ϕ∑μ is proportional to photoinduced conductivity change. c Gate bias effect on FI-TRMC signals for hole transport along the π−π stacking and the H-bonding directions. ΔP r denotes the change in the power of reflected microwave during gate bias pulsing; ΔP r is proportional to field-induced conductivity change. d Correlation between holes number ΔN and pseudo electrical conductivity ΔNμ along the π−π stacking and H-bonding directions Full size image

Using the FP-TRMC technique, we compared charge carrier mobilities of the two polymorphs, as the technique is applicable to both single-crystal and thin film samples. Monitoring the kinetic traces of ΔP r informs the transient photoconductivity of the generated charge carriers Δσ, which is proportional to ΔP r /P r . Owing to the electric field polarization of the microwaves40, the in-plane anisotropy of the photoconductivity in aligned samples can be measured. For data analysis, Δσ is evaluated as ϕΣμ where ϕ is the quantum yield of charge carrier generation per absorbed photon and Σμ is the sum of hole and electron mobilities41. Shown in Fig. 5b, the (ϕΣμ) max value of polymorph II is ~ 7 times that of polymorph I along the π−π stacking direction, and ~4 times that of polymorph I along the H-bonding direction. In comparison, the calculated II/I mobility ratios are ~2.5 and 3 along the π−π stacking and the H-bonding direction, respectively. For polymorph II, the total charge carrier mobility measured through the H-bond is significant considering the absence of π orbital overlap, albeit lower than through the π−stack given the same ϕ. For comparison, we applied the same technique to thermally evaporated pentacene thin film – a benchmark organic semiconductor, and obtained similar (ϕΣμ) max values as the polymorph I case (Supplementary Fig. 14). We note that owing to the low density of photoinduced charge carriers in these materials, precise evaluation of charge carrier mobility using FP-TRMC is challenging42,43.

We next evaluated intrinsic hole mobilities using FI-TRMC. For sample fabrication in the MIS geometry, polymorph II thin films were solution coated on poly(methyl methacrylate) (PMMA) dielectric substrates, which showed exceptionally high degree of alignment (Supplementary Fig. 15). Limited by the MIS geometry, we were not able to use polymorph I single-crystal needles in this technique. Figure 5c presents the gate bias-dependent ΔP r kinetic traces along the π−π stacking direction vs. the H-bonding direction. ΔP r is proportional to the change in the pseudo electrical conductivity ΔNμ, wherein ΔN is the change in charge carrier number43. In the MIS geometry, ΔN of injected carriers is calculated from the applied voltage ΔV using ΔN = C ox ΔV/e, where C ox is the capacitance of the insulator. Hence, the charge carrier mobility μ can be extracted from the ΔN–ΔNμ plot shown in Fig. 5d. We measured intrinsic hole mobilities as high as 6.5 cm2 V−1 s−1 and 4.2 cm2 V−1 s−1 along the π−π stacking and the H-bonding directions, respectively, which is in reasonable agreement with the theoretical predications (Fig. 2d). Using the same technique, comparable hole mobilities were obtained for pentacene (6.3 cm2 V−1 s−1)43 and BBTBDT (4.5 cm2 V−1 s−1)44, attesting to the potential of ellipticine serving as a high-performance organic semiconductor and the viability of utilizing H bond pathway for efficient carrier transport. We further deduced interfacial trap density from the x axis intercept of the linear region45 in Fig. 5d, and obtained 4.2 × 1012 cm−2 and 2.7 × 1012 cm−2 measured along the π−π stacking and the H-bonding directions, respectively. These values are on the same order of magnitude but slightly higher than literature reports (~1 × 1012 cm−2 45,46,).

Application of ellipticine in field-effect transistors and chemical sensors

To evaluate long-range charge transport over device-relevant length scales and to demonstrate potential for practical applications, we fabricated OFETs with the conductive channel along the π−π stacking and the H-bonding directions of ellipticine polymorph II (Fig. 6). The ellipticine layer was deposited via meniscus-guided solution coating on SiO 2 substrates pre-patterned with Au source-drain electrodes of 5–10 μm channel lengths. The as-deposited crystalline films exhibited domain sizes spanning hundreds of microns to millimeters in width, sufficiently large to cover an entire OFET device (Supplementary Fig. 16). The high degree of alignment was evident from the observation that the part of the film covering the device channel region extinguished cross-polarized light at once, consistent with the GIXD results (Fig. 3c, d, and Supplementary Fig. 12c). AFM further revealed a single-crystalline domain bridging the source-drain electrode (Fig. 6b). These morphology characteristics allow us to compare device performance along the π−π and H-bond directions directly (Fig. 6c).

Fig. 6 OFET device performance of solution coated ellipticine polymorph II thin films. a Schematic of device fabrication via the meniscus-guided solution-coating process. b Atomic Force Microscopy (AFM) tapping mode height images of the device channel region with the channel parallel (π−π) and perpendicular (H-bond) to the coating direction. Scale bars are 2 μm. The white arrows denote the coating direction. c Schematic of Organic Field-Effect Transistor (OFET) device configuration and molecular orientation in the conductive channels when measured in the parallel or perpendicular direction. The OFET device shown was used in the top-gate bottom-contact (TGBC) geometry with CYTOP as the dielectric layer or in the bottom-gate bottom-contact (BGBC) geometry with SiO 2 as the dielectric layer. d, e Transfer and output curves of ellipticine-based TGBC OFET. Performance of BGBC devices are shown in Supplementary Fig. 17 Full size image

The OFET device performance in various device configurations was summarized in Fig. 6, Supplementary Table 3, 4 and Supplementary Fig. 17. Fig. 6d, e show the representative transfer and output curves of top-gate bottom-contact devices fabricated via solution process, which yielded apparent hole mobilities of up to 1.3 ×10–3 cm2 V−1 s−1 and 0.4 × 10–3 cm2 V−1 s−1 along the π−π stacking and H-bonding directions, respectively. Here, we emphasize that the OFET device performance is strongly affected by the enormous charge injection barrier at the semiconductor/electrode interface owing to the deep HOMO level of ellipticine; the resulting large contact resistance is manifested in the S-shaped output curves at low V DS . On top of that, there exists a high interfacial trap state density exceeding 1.5 × 1013 eV−1 cm−2 for top-gate devices estimated from the subthreshold swing region of the transfer curve (see Methods), which is substantially higher than the values reported in high-performance small molecule organic semiconductor OFET devices (~ 1012 eV−1 cm−2)47,48. Such high-trap density may be induced by trace amount of water or residual polar solvents49,50. Both factors combined, the apparent mobility is three orders of magnitude lower than the intrinsic mobility measured by TRMC techniques. Exhaustive optimization of FET device performance is not the focus of this work and is therefore beyond the scope. Nonetheless, the measured charge transport anisotropy along the π−π stacking vs. the H-bonding directions is consistent with the theoretical prediction and TRMC results. This is one of the few reports on measurable hole transport along the H-bonding direction over microns length scale in dry solid-state electronic devices. We note that proton transport through H-bond networks have been demonstrated in field-effect transistors51, however, we ruled out the mechanism of proton transport in our case (Supplementary Fig. 18).