Substituent Control of s-interference Effects in the Transmission of Saturated Molecules
The single-molecule conductance of saturated molecules can potentially be fully suppressed by destructive quantum interference in their s-system. However, only few molecules with s-interference have been identified and the structure-property relationship remains to be elucidated. Here, we explore the role of substituents in modulating the electronic transmission of saturated molecules. In functionalized bicyclo[2.2.2]octanes, the transmission is suppressed by sinterference when fluorine substituents are applied. For bicyclo[2.2.2]octasilane andoctagermanes the transmission is suppressed when carbon-based substituents are used, and such molecules are likely to be highly insulating. For the carbon-based substituents we find a strong correlation between the appropriate Hammett constants and the transmission. The substituent effect enables systematic optimization of the insulating properties of saturated molecular cores.
MANUSCRIPT
<p>Saturated organic molecules are considered to be good molecular insulators and find widespread use in studies of electronic and magnetic communication between functional molecular units. [1][2] Destructive quantum interference in the s-system can further enable the design of saturated molecules where the electronic transmission is almost completely suppressed. [3][4][5] Destructive sinterference may appear in saturated molecules when all through-bond paths in the molecular backbone have at least one gauche defect, i.e., a dihedral angle approaching 0°. [3][4][5][6][7][8] However, full suppression of the single-molecule conductance is not often achieved and it is not always clear if the partial suppression is due to an interference effect. 5 For example, the gauche conformations of simple linear alkanes have lower conductance than the trans conformations; however, clear signatures of destructive quantum interference are missing, such as sharp antiresonance dips in the electronic transmission. [8][9][10][11][12][13][14][15][16] When s-interference effects manifest, the conductance is highly sensitive to details in the molecular geometry. Based on the extensive topological understanding of interference effects in p-systems, we expect a similar intuition should be found for s-systems. [17][18][19][20][21] However, it is an ongoing challenge to understand the structure-property relationships for the single-molecule conductance of saturated group 14 systems. 9,[22][23][24][25][26][27] We reported a surprising chemical sensitivity of the s-interference effect. 5 Despite the benign nature of the substituents, the electronic transmission of functionalized cyclohexane, cyclohexasilane, bicyclo[2.2.2]octane, and bicyclo[2.2.2]octasilane is systematically lower when the molecules are permethylated. This is exemplified in Figure 1  Substituent effects are well-established for destructive quantum interference effects in conjugated molecules. [28][29][30][31] The destructive p-interference effect can be systematically manipulated depending on the electron donating or withdrawing character of the substituent. [32][33][34][35][36][37][38][39][40] Here, we examine the substituent effect on the electronic transmission of methylthiomethyl-functionalized bicyclo[2.2.2]octane (C222), bicyclo[2.2.2]octasilane, and bicyclo[2.2.2]octagermane (Ge222).</p><p>Fully X-substituted C222-X, Si222-X, and Ge222-X structures are sampled using RDKit as described in Supporting Information part A. 41 Common to all the methylthiomethyl-functionalized bicyclo[2.2.2]-systems, the molecular core is chiral but has no conformational freedom. Therefore, the orientations of the two linkers relative to each other provide three conformations. These are shown in Figure 2 as a Newman projection along the bridgehead axis of the molecule, and as the optimized conformations of Si222-H. It is the Si-Si-CH 2 -S dihedral angles of the linkers that must be rotated to sample the three conformations. In accordance with previous work, we refer them as the anti, ortho, and cis conformers. We sample these three in all studied molecules. For a control system, we examine the equivalent linear molecule in its all-trans conformation as shown in bottom panel of Figure 2. All structures are optimized using density functional theory as implemented in Gaussian09 using the PBE exchange-correlation (XC) functional with 6-311G(d,p) basis set. [42][43] Single-molecule junctions were made by placing the optimized molecules between two four-atom Au pyramids on 5x5 Au fcc(111) surfaces. The initial junction structure is built using Au-S bond length of 2.5 Å and Au-S-C bond angle of 110°. The terminal methyl groups are rotated to a dihedral angle of ±90° in order to make space for the Au atoms in the transoid position (±170°). 44 Junctions are relaxed to a force threshold of 0.06 eV/Å using DFT with the PBE XC functional and double-z plus polarization basis set as implemented in ASE and GPAW. 43,[45][46][47] Finally, the Landauer transmission is calculated using the NEGF approach as implemented in ASE. 45 We devise an extensive list of substituents based on the criterion of some extent of chemical realism, though in some cases also on chemical curiosity. The different substituents on C222-X, Si222-X, and Ge222-X are to some extent limited by the size of the molecular frame, and therefore not all substituents can be used. Scheme 1 provides an overview of all 34 molecules studied.</p><p>Optimizations of cyano-substituted Ge222-CN did not converge. It is a molecule we do not expect to be experimentally realistic, but it would have been of interest because CN is a very strong electron acceptor. Scheme 1: Overview of substituents in C222-X, Si222-X, and Ge222-X.</p><p>In the low-bias regime we study here, an insulating molecule must have strong suppression of the transmission near the Fermi energy in all its conformers. The constrained structure of the bicyclo[2.2.2]octane frame makes them shorter than the equivalent butane-motif molecules (methylthiomethyl-functionalized C4-X, Si4-X, and Ge4-X). Despite being shorter molecules (shorter tunneling barriers), previously studied the bicyclo[2.2.2]octane systems have similar or lower transmission than their linear counterparts as testament to their superior insulating properties. 3-5, 25, 48  The transmission is plotted against energy for select Si222, Ge222, and C222 molecules in  3b), however, there is some variation of the transmission depending on the conformation. The transmission of Ge222-Me is a bit higher than in the equivalent Si222-Me, and phenyl substituents may offer slightly lower conductance for germanium than methyl.</p><p>Similar suppression and variation are seen in the ethyl, vinyl, and ethynyl substituted cases of Si222 and Ge222 (Figure S3 and S4). Carbon-based substituents thus seem particularly promising for fine-tuning the insulating properties of Si222 and Ge222 systems. Although alkyl and phenyl substituents are quite benign from a chemical point of view, they are particularly promising because they are realistic synthetical targets for silicon and germanium based molecular cores. [49][50][51][52][53][54][55][56][57] We hope these results will motivate studies of the properties of substituted cyclic and bicyclic silanes and germanes. The transmission suppression is less clear in the C222 systems than for the silanes and germanes. Shown in Figure 3c, the transmission of C222-Me and C222-F does have antiresonances for some conformers. However, looking broadly at the C222 systems in Figure S2, it appears there are few cases with s-interference. We note the transmission of linear alkanes is much lower than that of linear silanes and germanes in general, 58 and the suppression effect is thus quite small in C222. For example, the suppression of the transmission in C222-H is below an order of magnitude compared to C4-H, in good agreement with experimental results. 5,48 Peralkylated bicyclo[2.2.2]octanes are not the most realistic synthetic targets, while fluorinated alkanes make for more realistic targets for single-molecule junction studies. [59][60][61] The transmissions of all C222-F conformers are suppressed over a broad energy-range compared with C4-F. Of the substituents studied for C222, fluorinated bicyclo[2.2.2]octanes are thus an interesting prospect for organic interference-based singlemolecule insulators. Generally, however, they are still not as promising as the Si and Ge based systems as only the anti-conformer has a deep antiresonance near the Fermi energy.</p><p>Certain substituents seem to promote the insulating properties of the three molecular cores. We further assess substituents based on their electron withdrawing and donating properties. Such effects have been classified in the extensive physical organic chemistry literature. 62 In Figure 4a, the transmission at the Fermi energy is plotted for all substituted molecules sorted by their oftused Hammett constants s p , which are based on the substituent effect in para-substituted benzenes. 62 Except for F and Cl, the substituent effect is fairly similar across the C222, Si222, and Ge222 series. However, there is no clear correlation across the full transmission data set when plotted against s p . Motivated by the strong transmission suppression seen for many of the carbon-based substituents, we separate the data set into two types of substituents: those based on carbon (blue in Figure 4a) and the remaining that are not carbon based (red in Figure 4a). We search further for quantitative correlations in substituent parameters that are determined in systems with suppressed or separated p-conjugation. 62 In addition to s p , we plot the transmission values against the Hammett constant, s m , which are determined on meta-substituted benzenes and the inductive parameter F.</p><p>While all these parameters are determined empirically, F may provide a better measure of the substituent effect on the s-system as it uses a bicyclo[2.2.2]octane compound for reference. 62 Shown in Figure 4b, the transmission of the three cores with carbon-based substituents is plotted against the three different Hammett constants. While there is a weak correlation for C222, both Si222 and Ge222 transmission show strong correlation with all three empirical parameters. These correlations are consistently weaker for the non-carbon substituents as plotted in Figure 4c. There is some correlation for these substituents in the Ge222 with s m and F, but in the remaining systems there is no correlation between the transmission and the Hammett constants.</p><p>The carbon-based substituents (listed in blue in Figure 4a) stand out from their non-carbon counterparts. They enable the lowest transmission for the Si222 and Ge222 systems, and their transmission correlates with the electron withdrawing properties of the substituents as given by the empirical Hammett constants. These correlations are quite strong compared to the correlations reported in other single-molecule conductance studies. [63][64][65] Carbon-based substituents thus provide an opportunity for fine-tuning s-interference effects in silicon and germaniumbased compounds.</p><p>The carbon-based substituents we find here appear to be special for the silicon-and germaniumbased cores, but do not systematically promote interference effects in the carbon-based core. As previous studies have suggested, the s-interference effect is highly sensitive to several structural and electronic parameters. [3][4][5][6][7]24 We have tested for correlations with structural parameters in our dataset but have not found any clear correlation, see Supporting Information part B for details. This indicates the effect of substituents is electronic (donor/acceptor effect) rather than from the distortion of the structure in molecular core. While these two effects (electronic and structural) are not independent of each other, the clear correlation we see for the carbon-based substituents with the Hammett constants suggests the effect is primarily electronic. Most likely, carbon-based substituents are special because they tune the electronic structure within an ideal range where there is s-interference in the transmission. This balance of parameters that enables interference effects in saturated molecules is still not well-described, but clearly the s-interference effect is very sensitive to both chemical and structural changes.</p><p>To summarize, a wide range of substituents can result in significant destructive interference effects in the transmission of Si and Ge cores. These are substituents based on carbon, such as alkyl and phenyl substituents, and we show that this substituent effect is systematic by correlating the transmission with different Hammett constants. However, we find that fluorination appears to be the only substituent that is likely to result in significant conductance-suppression in the carbonbased bicyclo[2.2.2]octane we have studied here. s-interference thus appears to be much more sensitive to chemical changes than the more well-established p-interference effect. Until recently, we may have thought that saturated molecules are some of the simplest and best understood systems in molecular electronics. Recent results by us and other groups suggest there is much more potential, 5, 66 which may be applied for novel chemical designs. This letter is a step in this direction, and future work must continue to build on the electron transport structure-property relationship of saturated carbon molecules and their heavier group 14 analogues.</p>