Electronic Enhancement Effect of Copper Modification of Base Pairs

ARTICLE pubs.acs.org/JPCC

Electronic Enhancement Effect of Copper Modification of Base Pairs on the Conductivity of DNA Haiying Liu,†,‡ Genqin Li,† Hongqi Ai,§ Jilai Li,|| and Yuxiang Bu*,† †

The Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China School of Physics, University of Jinan, Jinan 250022, P. R. China § School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, P. R. China

)

‡

ABSTRACT: The effect of the new designed multicopper modification of base pairs on the conductivity of DNA was investigated by the nonequilibrium Green’s function method combined with density functional theory. Electronic transport calculations revealed that the equi-number H-by-Cu replacement can significantly enhance the conductivity of DNA from two aspects: transverse base-to-base communication along the hydrogen-bond direction and longitudinal transport along the DNA duplex. Furthermore, the enhancement effect on the longitudinal direction is more notable than that on the transverse. A tunneling mechanism is suggested for the short DNA segments. The decay factor of conductance in CuDNA decreases by half compared with the native DNA, thus making it more promising for constructing nanowires. In addition, Cu-DNA may prefer electron migration to hole transport with the lengthening of DNA segments. This work will shed some light on the design of promising DNA-based molecular wires.

1. INTRODUCTION DNA is one of the most potential candidate materials for constructing nanoelectronic devices1,2 because of its unique effect of nanosize and superior properties of self-recognition and self-assembly. Therefore, DNA conductance has attracted significant attention in the past decades.314 However, it is wellknown that the intrinsic conductivity of DNA has not been well characterized. The obtained controversy results cover the entire range from insulating,3 semiconducting,4,5 and conducting6,7 to even induced superconductivity.8 Thus, the development of functionalized DNA with modified components shifts into the limelight due to the limitations of the conductive property of native DNA. Among various modification schemes, the metal modification of DNA (M-DNA)1519 is one of the most promising avenues toward the goal of constructing complex functional nanoarchitetures since transition metals are good carriers of many functions, such as electronic and magnetic properties. The ability to convert normal DNA into metalized DNA and the resultant drastic change of DNA conductivity open up a whole new range of opportunities for molecular electronic engineering and provide us a new degree of freedom in molecular electronics and sensor designs. In 2001, Rakitin et al.15 used a metal ion Zn2+ to replace the imino proton of every base pair and observed a drastic change in the conductivity of DNA. In 2003, Shionoya's group16 systematically incorporated one to five Cu2+-mediated base pairs of hydroxypyridone nucleobases into the middle of a DNA duplex, resulting in DNA-bound metal arrays of various lengths in solution. Subsequently, they modified DNA so that it serves as a scaffold for one-dimensional arrays of metal ions. Each array is a r 2011 American Chemical Society

combination of Cu2+ and Hg2+ ions, arranged in an order defined by the DNA sequence.20 So far, many metal ions, such as Hg2+, Cu2+, Zn2+, Ag2+, Ni2+, Co2+, Mn3+, and Fe3+, have been used for the modified DNA.19 The major common property of metal base pairing is an enhancement of the thermal duplex stability.19 This feature might make metalbase pairing valuable for the construction of stable nanoarchitectures based on DNA. In spite of the large progress of M-DNA, the exact structures and electronic properties of the formed metal-DNA complexes are, however, less clear.19 Many issues about modulation of metal modification of DNA should be elucidated. Recently, our group also designed a class of multicoppermediated DNA.21 A three-copper-mediated guanine-cytosine base pair (G3CuC) and a two-copper-mediated adenine-thymine base pair (A2CuT) were obtained by substituting all the Watson Crick H-bond protons with Cu(I) (see Figure 1). The geometrical and electronic analyses indicated that the equi-number H-by-Cu replacement can not only enhance transverse electronic communication but also have a positive effect on the conductivity of DNA. However, the study was only limited to theoretical prediction from aspects of structural and electronic properties. Therefore, a question arises: whether it might be possible to use measurable parameters to more directly reflect and to further quantify the enhancing effects of the Cu modification on DNA conductivity? Received: July 22, 2011 Revised: October 4, 2011 Published: October 10, 2011 22547

dx.doi.org/10.1021/jp2070198 | J. Phys. Chem. C 2011, 115, 22547–22556

The Journal of Physical Chemistry C

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Figure 1. Geometries of copper-modified base pairs (G3CuC and A2CuT) and natural pairs (GC, AT).

Herein, a detailed investigation on electronic transport of the above multicopper-mediated DNA is presented by the nonequilibrium Green’s function method combined with density functional theory with some measurable parameters, such as current and conductance. It is verified that the Cu modification indeed enhances the conductivity of DNA from two aspects: transverse base-to-base communication along the hydrogen-bond direction and longitudinal transport along the DNA duplex. Longitudinal transport calculation indicates that an electron transfer mechanism is a superexchange for the short DNA segments with repeating stacked GC or G3CuC. Moreover, as a most essential aspect, the decrease of decay factor implies charge could migrate farther in the designed Cu-DNA than in native DNA. This variation is definitely in favor of constructing molecular wires. In addition, the analysis of transmission spectra implied that Cu-DNA may prefer electron migration to hole transport with the lengthening of DNA segments. This work will be helpful in the design of promising DNA-based molecular wires.

2. COMPUTATIONAL DETAILS 2.1. Geometry Optimizations. The relevant isolated base pairs (including natural GC, AT, the modified G3CuC and A2CuT, and =SH linked extended molecules) were optimized and then were anchored on two gold (111) surfaces through strong AuS covalent interaction. All optimizations were carried out with the Gaussian 03 software package,22 at the spin-restricted hybrid DFT/B3LYP23,24 level of theory with the 6-311++G(p,d)2528 base set for H, C, N, and O atoms and the LANDL2DZ29 for the Cu atom. In addition, examination at the spin-unrestricted level indicates that all results in geometries, energies, and electronic properties obtained at both levels are almost the same, and thus the spin effect is negligible in these calculations. 2.2. Electronic Transport Calculations. Quantum transport properties of base pairs were calculated with the ATK software package,3033 which is based on the combination of DFT with nonequilibrium Green’s function technique. This method has been successfully applied to study some systems with weak interactions, such as the hydrogen bond3436 and the π-stack effect.37,38 The

Figure 2. Schematic illustration of the transverse electronic transport model. The G3CuC base pair is sandwiched between two Au(111) surfaces, and two S anchoring atoms are located at the hollow sites. The scattering region used contains the optimized molecule together with 48 gold atoms and two 4 3 layers of Au surfaces for the left and right.

method’s premise is to divide the system into three regions: (i) the left electrode, (ii) the right electrode, and (iii) the scattering region between them. In transverse conduction calculations, the direction of charge transport is along the hydrogen bonds between pairing bases. The scattering region used contains the optimized molecule together with the surface gold atoms: there are two 4 3 layers of Au surfaces for the left and right. The electrode calculations were performed under periodic boundary conditions, with the unit cell being three layers along the transport direction, and the Brillouin zone was sampled with 3 3 500 points within the MonkhorstPack k-point sampling scheme in the case of our three-dimensional two-probe systems. To determine the conduction currents, the optimized SH-substituted base pairs (i.e., the hydrogens of the C8 site of G, A and of the C6 site of C, T were substituted by the SH fragments and then were optimized) were translated into the gold junction on the (111) surface. Dithiol was assumed to lose both hydrogen atoms upon interaction with the two gold electrodes (Figure 2). The distance between the sulfur atom and the gold surface was set to 1.90 Å, which is in a reasonable range of 1.902.40 Å that was used in most previous work.3942 Since the core part related to Cu modification is far from the moleculeelectrode contact region, 22548

dx.doi.org/10.1021/jp2070198 |J. Phys. Chem. C 2011, 115, 22547–22556


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Figure 3. Schematic illustration of the longitudinal electronic transport model. The planes of the G3CuC base pairs are parallel to the gold surface. The scattering region used contains four-layer-stacked base pairs together with 144 gold atoms and two 6 6 layers of Au surfaces for the left and right.

large changes in geometry after attachment to the gold surface were not expected.34 The effect of charge transfer between the molecule and electrodes on the transport properties was also checked, and the results indicate that it is very small and does not change the enhancement trend of copper modification of the base pairs. Considering the efficiency and the calculation time, the influence of the gold electrode surfaces was not considered in the optimizations. For the longitudinal electronic calculation, the 5 4 and 6 6 cell electrodes were applied, and the MonkhorstPack k-point sampling was set as 3 3 100. First, the multilayer stacks of GC, AT and G3CuC and A2CuT were constructed using the same structural parameters as those in B-DNA but without any further optimizations, i.e., the interplane distance being 3.4 Å and the helical angle being 36°. For simplicity, the sugarphosphate skeleton was removed, and the NEGF-DFT calculations were performed on ππ stacked base pairs. The simplification of the model is justified from the study of Tada et al.,12 which has shown that the conductance is achieved through ππ stacked bases, while the sugarphosphate skeleton has insulating properties. This simple model was also applied by other theoretical studies.13,43 Second, multilayer-stacked base pairs were inserted into the gold electrodes to compose two-probe systems with the planes of base pairs parallel to electrode surfaces, as shown in Figure 3. The distance between the base pair plane and the electrode surface was set as 3.5 Å, which is the absorption distance of a base or a base pair on the gold (111) surface.44,45 This distance was also used in another similar study.13 The LDA.PZ exchange/correlation function46 with a DZP basis set on the center molecules and with a SZP basis set47 on the Au clusters was used for the electric current calculations. Selfconsistent calculations were performed with a mixing rate set to 0.01. The tight convergence criterion was 105 eV. The electrostatic potentials were determined on a real-space grid with a mesh cutoff energy of 150 Ry to achieve a balance between the calculation efficiency and the accuracy.

3. RESULTS AND DISCUSSION 3.1. Transverse Electronic Transport. Our previous electronic properties calculation21 has pointed out that the copper modification would enhance the transverse base-to-base electronic communication. To further quantify the enhancement, transverse electronic transport calculations were performed. The calculated currents as a function of the applied bias for GC and G3CuC were shown as IV

Figure 4. Transverse IV curves of one-layer GC, G3CuC, and G3HC junctions. Here G3HC represents that the copper atoms are replaced by H atoms with the same geometry of G3CuC. The inset is the comparison of the IV curve between GC and G3HC junctions.

curves in Figure 4. Within the applied bias range from 0.5 to 0.5 voltages, the current increases almost linearly with the rising of the biases, showing an Ohmic signature. The order of magnitude of the calculated transverse currents of the base pairs is at nA level, consistent with the generally measured values.48 This further proves the feasibility of the applied methods. The transverse currents of the G3CuC junction are notably enhanced compared with those of the GC junction. In the bias range from 0.5 to 0.5 V, the concrete increase ratio is from 12.90 to 20.99. The variation of the transverse currents along hydrogen bonds directly indicates that the inserted copper atoms really enhance the transverse electronic communication of pairing G and C bases. In addition, the optimized results21 have indicated that G3CuC and A2CuT have great geometrical resemblances to the natural GC and AT with a size expansion of about 1.0 Å due to the larger radii of Cu(I). Moreover, it can be seen from Figure 1 that the inserted copper atoms are almost at the middle of the pairing bases. Obviously, these configuration changes will also affect the electronic transport properties of the systems. To elucidate this effect, the copper atoms were replaced with hydrogen atoms with fixing the geometry of G3CuC (labeled by G3HC). Then G3HC was translated into the two electrodes following the above-mentioned method, and its current was calculated (see the inset in Figure 4). Clearly, the currents of the G3HC junction decrease about 6 times compared with that of the native GC in the applied biases range. Therefore, it can be deduced that the increase of the transverse currents of G3CuC is not caused by the geometrical variations derived from the Cu modification. The important change of geometry is the expanded size of G3CuC by about 1 Å. So this change results in the elongation of the distance of electrodes by the same length. The increase of the electrodes should lead to the reduction of the current, while herein the transverse currents increase largely instead. Thus, the enhancement of the transverse currents should be purely a result of the change of electronic properties caused by the introduction of copper atoms. This is exactly the target we should elucidate. In addition, the 1 Å elongation of the distance of electrodes actually decreases the currents by almost 1 order of magnitude. This indicates that the mechanism of transverse electronic transport in the related systems is tunneling, for which the main character is the strong distance dependence of conductivity.49 22549



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Figure 5. Transverse IV curves of single-layer AT and A2CuT junctions.

The influence of the copper modification on transverse electronic transport of AT was also explored. The calculated IV curves are depicted in Figure 5. Within the applied bias range from 0.5 to 0.5 voltages, the current also increases almost linearly with the rising of the biases. The transverse currents of the A2CuT junction are largely enhanced, and the increase in ratio is about 17 related to those of AT. Comparing the currents in Figure 4 and Figure 5, it can be found that the currents of the GC junction are clearly larger than those of the AT junction, in agreement with the reported rule.50 It demonstrates that the electronic communication between G and C is stronger than that between A and T. In addition, the increased ratios of the transverse current of AT (from 11.78 to 23.81) are slightly larger than those of GC (from 12.90 to 20.99) due to the introduction of copper atoms. Clearly, for A2CuT, the inserted two Cu atoms produce an enhancement effect on transverse current similar to that of the three Cu atoms in G3CuC, which indicates that the transverse electronic communication of AT may be more sensitive to the copper modification than that of GC. In general, the current I can be explained as a function of the applied bias V by the LandauerB€uttiker formula30 IðV Þ ¼ G0

Z ∞ ∞

nðEÞTðE, V ÞdE

ð1Þ

where G0 = 2e2/h (quantum conductance); n(E) is the distribution function; and T(E,V) is the transmission coefficient for electrons with energy E for bias V. n(E) can be expressed as nðEÞ ¼ f ðE μL Þ f ðE μR Þ

ð2Þ

where f is the Fermi function, and μL and μR are the electrochemical potentials of each electrode. From the expression of n(E), it can be expected that only electrons with energies within a range around the Fermi level (Ef) contribute to the total current. A general approximation for this threshold is a range of [V/2, V/2], which is considered as the bias window.30 Since the current is the integral of the transmission coefficient in the bias window, analysis of the transmission spectra may give a clear understanding of the electronic transport behavior in DNA. Figure 6 shows the transmission spectra T(E,V) of the four related species at zero bias. The averaged Fermi level (Ef) is set as zero,30 which corresponds to the averaged value of the chemical

potentials of the left and the right electrodes. There is a large band gap of approximately 3 eV separating the occupied peaks (assigned to the occupied MOs) from the unoccupied peaks (assigned to the unoccupied MOs). Thus, the transverse currents of the four species are very weak compared with those of the common conjugated polymers,5153 which are always higher than the μA threshold and even some up to mA, while the calculated currents here are only at a nA level. Although the whole conductivity is low, the differences between the coppermediated products and their corresponding natural base pairs are distinct. First, the number of transmission peaks of G3CuC and A2CuT obviously increases compared to those of the natural GC and AT, respectively. This means that there are more new transport channels in the copper-modified base pairs than in the native. Second, more broad and strong peaks for G3CuC and A2CuT are observed, while the spectrum peaks for the natural GC and AT are rather narrow and low, thus leading to smaller currents. Third, also more importantly, the transmission peaks of G3CuC and A2CuT are closer to the Fermi level (Ef) from both right and left sides. For example, for the transmission spectrum of GC, its unoccupied peak, which is closest to Ef, is at 1.41 eV with the transmission coefficient reaching 0.83, while for G3CuC, the highest peak is at 0.76 eV with the coefficient up to 0.89. Therefore, the conductive gaps for G3CuC and A2CuT are narrower than those of GC and AT. It is should especially be noted that there is one small peak very close to the Fermi level for both G3CuC and A2CuT, respectively. Although the two peaks are very small, with a peak value of only about 0.03, due to their special locations, their contribution to the conductivity of systems can not be ignored. The above variations are the main reasons that the transverse currents of G3CuC and A2CuT are obviously higher than those of GC and AT. To understand the origin of the transmission peaks, the eigenvalues of the molecular projected self-consistent Hamiltonian (MPSH) were also calculated and plotted on the tops of panels in Figure 6. MPSH represents the MOs of the bridge molecules, which are modified by the electrodes.30 The energy positions of the MPSH states generally match with the transmission peaks. This means that these MPSH orbitals just are charge transport channels. One important character that should be pointed out is that the higher occupied peaks are nearer to Ef than the relatively smaller unoccupied peaks, and thus the former are expected to dominate transport. Table 1 lists the energy levels of the MPSH HOMO and LUMO and their corresponding transmission coefficients for GC, G3CuC, AT, and A2CuT. For G3CuC, its HOMO is at 0.30 eV, while its LUMO is at 1.78 eV, far from Ef. More importantly, the coefficient of the former reaches to 0.05, while that of the latter is only 0.02, decreased by one time. The above analyses confirm that the occupied orbitals, especially HOMO, dominant the charge transport, and thus the transverse charge transport should also be hole transfer.54 In addition, the HOMO energies of the four junctions including the influence of the electrodes for GC, G3CuC, AT, and A2CuT are 0.46, 0.30, 0.68, and 0.31 eV, respectively. Despite the difference of the absolute values, the relative energy order of the natural GC and AT is consistent with the previous study.55 This further illustrates the credibility of the results. The energy level of the HOMO is an indicator of hole-injection barrier from the electrode to the base pairs and ionization potential.55 Related to the GC junction, the lift of the HOMO level of G3CuC makes the hole transport barrier decrease 0.70 eV. This finding indicates that it is easier to inject a hole from the 22550



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Figure 6. Transmission spectra of GC, G3CuC, AT, and A2CuT junctions at zero bias for the transverse electronic transport model. The red dots on the top of each picture represent the molecular projected self-consistent Hamiltonian (MPSH) eigenvalue positions. The solid dots represent the occupied molecular orbital energies, and the hollow dots correspond to the unoccupied molecular orbital energies. The averaged Fermi level is set as zero.

Table 1. Frontier molecular orbital energy levels (in eV), HOMO-LUMO gap (in eV) and the corresponding transmission coefficients (in parentheses) of GC, G3CuC, AT and A2CuT junctions GC

G3CuC

AT

A2CuT

HOMO

0.46 (0.0029)

0.30 (0.0494)

0.68 (0.0089)

0.31 (0.0080)

LUMO

2.48 (0.0024)

1.78 (0.0220)

2.78 (0.0064)

2.33 (0.0615)

gaps

2.94

2.08

3.46

2.64

electrode to a G3CuC base pair than to a GC pair. For the A2CuT junction, the charge-migration barrier decreases 0.45 eV compared with that of the AT junction. Therefore, the lift of the HOMO level also is one of the main reasons that the conductivity of copper-mediated DNA is enhanced. Table 1 also lists the HOMOLUMO gaps of the junctions composed of the base pairs and the electrodes. The gaps are 2.94, 2.08, 3.46, and 2.64 eV for GC, G3CuC, AT, and A2CuT junctions, respectively. For the G3CuC junction, the introduction of copper atoms reduces the gap 0.86 eV and by 29.2% compared with that of the GC junction. Related to the A2CuT junction, the modification of copper decreases the gap 0.82 eV and by 23.7%. The shrink of the HOMOLUMO gap also contributes to the enhancement of the base-to-base transverse electronic communication. 3.2. Longitudinal Electronic Transport. To investigate the effect of the Cu modification on charge migration along the DNA

duplex, longitudinal electronic transport calculations of the multilayer-stacked GC and G3CuC base pairs were carried out. The stacking base pairs were inserted into the gold electrodes to compose two-probe systems with the planes of the base pairs parallel to the electrode surfaces, as shown in Figure 3. Longitudinal Electronic Transport of Two-Layer-Stacked Base Pairs. The IV curves of two-layer-stacked base pairs were depicted in Figure 7. The contact distance between the nearest base pair plane and the electrode surface was set as 2.8 Å.55 The 5 4 cell electrodes were applied. The currents in the bias range from 0.5 to 0.5 V are generally at the μA level. The currents of the two-layer-stacked G3CuC junction are higher than those of the corresponding GC junction with an average increasing ratio of about 9 times. This well illustrated that the multicopper modification can enhance not only transverse electronic communication but also charge migration along the DNA duplex. 22551



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Figure 7. Longitudinal IV curves of two-layer GC, G3CuC, and G3HC (replace Cu with H using the geometry of G3CuC) junctions. The contact distance is 2.8 Å, and the electrode cell is 5 4.

Figure 9. Longitudinal IV curves of three-layer repeating stacked GC (3-GC), G3CuC (3-G3CuC) junctions. The contact distance is 3.5 Å, and the electrode cell is 6 6.

Figure 8. Longitudinal IV curves of two-layer GC (GC:GC), G3CuC (G3CuC:G3CuC) junctions. The contact distance is 3.5 Å, and the electrode cell is 6 6.

between the copper atoms themselves and between the copper atoms and other atoms in the DNA fragments. The impact of the skeleton change due to the copper modification on longitudinal transport accounts for a small proportion, only about one-third. To reveal effects of the contact distance and the size of the electrode surface on the conductivity of systems, the IV curves (as shown in Figure 8) were further investigated with the contact distance as 3.5 Å and the electrode as a 6 6 cell. Taking into account the symmetry of the systems, the currents only in the range from 0 to 0.5 V were calculated. The results in Figure 8 show that the copper modification largely enhances longitudinal conduction along the DNA duplex with an average increase ratio being about 26. The ratio is higher by approximately 3 times than that of the currents change shown in Figure 7. This finding indicates that following the elongation of contact distance the enhancement of the copper modification becomes more prominent, while the effect of electrodes size on the DNA conductivity becomes smaller. The currents of two-layer-stacked GC:GC were calculated with contact distance as 2.8 Å and electrodes as a 6 6 cell. The results with a 6 6 electrode cell are slightly larger than those values with a 5 4 cell. This demonstrates that the effect of the electrode size on the charge migration in DNA is small. The currents of GC:GC were compared with the same 6 6 cell electrode but different contact distances. The corresponding currents decrease by about 20 times when the contact distance changes from 2.8 to 3.5 Å. Obviously, the conductivity of the systems is very sensitive to contact distance between the nearest base pair plane and the electrode surface. This indicates that the mechanism of longitudinal electronic transport in the related systems is tunneling, for which the main character is the strong distance dependence of conductivity.49 A tunneling barrier is introduced when the contact distance is increased. Therefore, the effect of the copper mediation on the conductivity of systems becomes more notable though the conductivity itself sharply decreases. Longitudinal Electronic Transport of Three-Layer-Stacked Base Pairs. To investigate the effect of copper modification on the conduction of DNA in more depth, the three-layer-stacked GC and G3CuC (short as 3-GC and 3-G3CuC) were further

Similar to the transverse electronic transport analyses, the effect of the geometrical variations introduced by the copper modification on longitudinal transport was also studied. The two-probe system of two-layer-stacked G3HC:G3HC is constructed by replacing Cu with H atoms and fixing the framework of G3CuC:G3CuC. For the sake of comparison, the calculated currents are also depicted in Figure 7. Obviously, the currents of G3HC:G3HC are between those of G3CuC:G3CuC and GC:GC. They increase about 3 times compared with those of the natural GC:GC. The variation can be understood from two aspects. First, it is confirmed that the geometrical changes triggered by the introduction of copper atoms improve the ππ stacking between base pairs in the DNA duplex, thus increasing the longitudinal currents. Second, the above improving of currents is still weaker than that brought by copper modification. Clearly, the increase of the longitudinal currents mainly comes from the inserted copper atoms, namely, from the interactions both

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The Journal of Physical Chemistry C studied. Figure 9 shows the IV curves of 3-GC and 3-G3CuC under the bias range from 0 to 0.5 V. The conductivity of 3-G3CuC is significantly enhanced by about 3 orders of magnitude compared with that of 3-GC. Moreover, the increasing ratio is higher than that of the two-layer-stacked base pairs. This finding can be understood from the following aspect. The distance between two electrodes increases about 3.4 Å with the inserted DNA fragments changing from two to three layers. Since tunneling current is very sensitive to the change of electrode distance, the currents of 3-GC decrease by 2 orders of magnitude compared with the corresponding values of GC:GC. On the contrary, the currents of 3-G3CuC are only slightly smaller than those of 3-GC. This indicates that with the lengthening of poly(G3CuC) the modulating effect of the copper atoms on DNA conduction may become more significant. Figure 10 shows the MPSH30 energy levels of 3-GC and 3-G3CuC junctions in the energy range from 4.0 to 4.0 eV. It is

Figure 10. Energy levels of three-layer repeating stacked GC (3-GC), G3CuC (3-G3CuC) junctions for the longitudinal transport model in the energy region from 4.0 to 4.0 eV. The average Fermi level is set as zero.

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clear that there are more and denser energy levels in the 3-G3CuC than in the 3-GC junction. Figure 10 also shows the change trend of HOMOLUMO gaps of the two junctions. Relative to the 3-GC junction, the HOMO of the 3-G3CuC junction rises by 0.44 eV, and its LUMO lowers by 0.45 eV, inducing a very smaller HOMO LUMO gap of only 0.81 eV, which reduced by 52.3%. Such a drastic change of energy levels and the shrinking of HOMOLUMO gaps will undoubtedly enhance longitudinal charge transport of DNA. To gain insight into the mediation effect of the inserted copper atoms, the transmission spectra and MPSH energy levels of 3-GC and 3-G3CuC junctions in the energy range from 4.0 to 4.0 eV were explored, as shown in Figure 11. For the natural DNA fragment of 3-GC, the occupied peaks are very dense and high, especially in the range from 4.0 to 2.0 eV, while the unoccupied peaks are relatively sparse. Therefore, the occupied orbitals corresponding to the above peaks become the main transport channels. Since the transmission peaks mainly locate in the range from 4.0 to 2.0 eV, it can be inferred that the currents of the 3-GC junction should notably increase when the applied bias exceeds 4 V. This finding is in agreement with the previous experimental4 and theoretical13 results. The differences between the transmission spectrum of the 3-GC junction and that of 3-G3CuC are demonstrated in Figure 11. First, more broad and strong peaks are observed in the transmission spectrum of the 3-G3CuC junction, while for the 3-GC junction the transmission peaks are rather narrow and low, thus resulting in smaller currents. For example, in the transmission spectrum of the 3-GC junction, there is an about 1.70 eV wide nonconduction platform. However, this gap almost disappears in the transmission spectrum of the 3-G3CuC junction with some new peaks of middle strength emerging. Because the distances between these peaks and the Fermi energy are very near, they have large contributions to the conductivity though their peak values are not very high. Second, the copper modification leads to MPSH energies close to the Fermi energy from both sides. Accordingly, the corresponding transmission peaks also have this trend. From formula 1, it can be inferred that the nearer the distance of the transmission peak from the Fermi energy, the

Figure 11. Transmission spectra of three-layer repeating stacked base pair 3-GC, 3-G3CuC junctions at zero bias for the longitudinal electronic transport model. The red dots on the top of each picture represent the molecular projected self-consistent Hamiltonian (MPSH) eigenvalue positions. The solid dots represent the occupied molecular orbital energies, and the hollow dots correspond to the unoccupied molecular orbital energies. The averaged Fermi level is set as zero. 22553


The Journal of Physical Chemistry C larger the contribution of the peak to the conductivity. Therefore, the above-mentioned trend of transmission peaks is also one of the most important reasons that the conductivity of the 3-G3CuC junction is higher than that of 3-GC.

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Mechanism of Charge Transport. The length dependence of conductance of the DNA fragments at zero bias was explored to probe the physical mechanism of charge migration. It is wellknown that if the mechanism of charge transport is tunneling the related conductance should exponentially depend on the length of the central molecule in a two-probe system,5557 namely, the conductance of the systems should vary with the length, L, of the DNA fragment as G ≈ expð βLÞ

Figure 12. Linear fits for the natural logarithmic conductance (G) on stacking base pairs for GC and G3CuC. The conductance is calculated at zero bias.

ð3Þ

where β is the characteristic falloff parameter (decay factor). Figure 12 shows the linear fits for the natural logarithmic conductances on the lengths of multilayer-stacked base pairs. The calculated conductances of the systems well correlate with the fitting lines. This indicates that the mechanism of charge transport for the short repeating sequence DNA fragments is superexchange (tunneling). The obtained decay factor is 0.61 Å1 for the stacking G3CuC base pairs, while that for the repeating GC stacking is 1.22 Å1. The decay rate of charge transport in Cu-DNA decreases by half compared with that of native DNA, thus preventing the excessive decay of tunneling currents. Therefore, the multicopper-mediated DNA is more suitable for constructing DNA-based nanowires since the charge can transport farther along the Cu-DNA duplex. The reported

Figure 13. Transmission spectra of the multilayer repeating stacked base pair junctions at zero bias for the longitudinal electronic transport model. 3-GC indicates three-layer-stacked GC base pairs, and other labels have similar means. The red dots on the top of each picture represent the molecular projected self-consistent Hamiltonian (MPSH) eigenvalue positions. The solid dots represent the occupied molecular orbital energies, and the hollow dots correspond to the unoccupied molecular orbital energies. The averaged Fermi level is set as zero. 22554


The Journal of Physical Chemistry C decay factor for natural DNA is in a large range from 0.1 to 1.5 Å1,56,58 even small to 0.05 Å1 measured by the Barton group.59 However, more experimental decay factors for DNA are about 1.0 Å1.60 So the calculated decay factors are rational and reliable. More importantly, the focus should be on the contrast of decay factors between the copper-mediated DNA and the natural DNA. This variation precisely demonstrates the modulation effect of the introduction of copper atoms on the DNA conductivity. Therefore, it can be safely concluded from Figure 12 that the copper modification can enhance the longitudinal conductivity of DNA along the duplex. Transformation of Transport Carrier. Figure 13 draws the transmission spectra of the multilayer (1 to 3 layers) repeating stacked base pairs for Cu-DNA and natural DNA at zero bias. With the increase of the stacking layers of base pairs, the transmission spectra, for both GC and G3CuC, all manifest the clearly decaying trends, mainly indicated by the overall decrease of the transmission peak values. For example, for the single-layer GC (1-GC), the transmission coefficient of the highest peak is about 2.3, while that of 3-GC is only 0.8. As for Cu-DNA, the coefficient of the highest transmission peak changes from 3.0 to 1.4 with the stacked layers varied from one to three. In addition, the number of transmission peaks notably reduces, resulting in the spectra of multilayer base pairs not as strong as those of the single layer. Therefore, the conductances of the systems exponentially drop with the length of the DNA fragments. It should be specially pointed out that the transmission spectra of the stacking GC and G3CuC base pairs show an important change trend. For the multilayer stacking GC fragments, the contribution of the occupied orbitals to charge transport is higher than that of the unoccupied orbitals. It can be found from both the peak strengths and their distances to the Fermi energy. This confirms that the occupied orbitals of poly(GC) construct the main transport channels. This is in good agreement with the previous reports that the charge transport in DNA pertains to hole migration through π stacks.9,10,61 However, the carrier of charge transport is supposed to shift to electron in the multicopper-mediated DNA. From the transmission spectra of the single-layer G3CuC, it can be seen that the hole still mainly participates in charge transfer. However, with the lengthening of the Cu-DNA fragment, the distance of the unoccupied orbitals to the Fermi energy is longer than that of the occupied orbitals though they all approach the Fermi energy from both sides. For 3-G3CuC, its LUMO is at 0.32 eV, while the HOMO is at 0.49 eV. Clearly, the LUMO is closer to the Fermi energy by 0.17 eV than that of the HOMO. Moreover, the transmission coefficient corresponding to the LUMO of 3-G3CuC is 0.46, much higher than that of the HOMO, which is only 0.02. The above analyses implicate that the transport carrier in Cu-DNA would transform from initial hole to free electron as the stacking layers of base pairs increase. The transformation of carrier may root in metallicity of the inserted copper atoms. For the natural DNA, the NH bonds in the hydrogen-bond region are covalent and strongly polarized. When the hydrogen atoms are replaced by coppers, NCu bonds have ionic bond character to some extent though they are still covalent bonds. The number of the inserted copper atoms increases with the lengthening of poly(G3CuC), and thus metallicity of the formed Cu-DNA fragments becomes more obvious. Therefore, it is supposed that the multicopper-mediated DNA may prefer electron transfer rather than hole migration.

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4. CONCLUSIONS In summary, a detailed theoretical investigation was presented to clarify the regulation effects of the multicopper modification of base pairs on electronic transport properties of DNA. First, an increase of the transverse currents in G3CuC and A2CuT fully confirms that Cu modification can significantly enhance transverse base-to-base electronic communication of pairing bases, compared with the canonical base pairs. Second, the analyses of longitudinal electronic transport along natural DNA and the CuDNA helix indicate that the enhancement effect of Cu modification is more notable than on the transverse. Furthermore, it is found that the electronic transfer mechanism is tunneling for the short repeating stacked base pairs. The decrease of decay factor implies that the charge could transfer farther in Cu-DNA than in native DNA. Clearly, this is more promising for constructing a molecular wire. Moreover, Cu-mediated DNA may prefer electron migration to hole transport. The obtained interesting results could possibly provide some good ideas for the design of a biomolecular device, like a molecular wire. It should also be noted that the proposed DNA-based molecular junctions are only ideal models and probably can not be directly applied in a realistic experimental situation because some other factors need considering in realization of a promising molecular device. Therefore, the obtained currents must be used more as a guide to rationally predict change trends in the conductivities of the designed systems rather than to quantify their absolute values. In addition, since Cu is a good carrier of various properties, such as magnetic and optical properties, more research about the CuDNA is in progress. Other metal-mediated pairs are also under investigation to pursue appropriate building blocks of electronic devices with various properties. ’ AUTHOR INFORMATION Corresponding Author

*E-mail: [email protected].

’ ACKNOWLEDGMENT This work was supported by NSFC (20633060, 20973101, 20973084), NCET, the Independent Innovation Foundation (2009JC020) of Shandong University, and the Foundation of State Key Laboratory of Theoretical and Computational Chemistry, Jilin University. A part of the calculations was carried out at High-Performance Supercomputer Center at SDU, HighPerformance Computational Platform at SDU Chem School, and Computational Platform at UJN. ’ REFERENCES (1) Okamoto, A.; Tanaka, K.; Saito, I. J. Am. Chem. Soc. 2004, 126, 9458–9463. (2) Lisdat, F.; Ge, B.; Scheller, F. W. Electrochem. Commun. 1999, 1, 65–68. (3) de Pablo, P. J.; Moreno-Herrero, F.; Colchero, J.; G omezHerrero, J.; Herrero, P.; Baro, A. M.; Ordejon, P.; Soler, J. M.; Artacho, E. Phys. Rev. Lett. 2000, 85, 4992–4995. (4) Porath, D.; Bezryadin, A.; de Vries, S.; Dekker, C. Nature 2000, 403, 635–638. (5) Yoo, K. H.; Ha, D. H.; Lee, J. O.; Park, J. W.; Kim, J.; Kim, J. J.; Lee, H. Y.; Kawai, T.; Choi, H. Y. Phys. Rev. Lett. 2001, 87, 198102. (6) Okahata, Y.; Kobayashi, T.; Tanaka, K.; Shimomura, M. J. Am. Chem. Soc. 1998, 120, 6165–6166. 22555


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Electronic Enhancement Effect of Copper Modification of Base Pairs

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