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year-2011

Publications during 2011

Article Reference A computational study of ultrafast acid dissociation and acid-base neutralization reactions. II. The relationship between the coordination state of solvent molecules and concerted versus sequential acid dissociation
We investigate the role played by the coordination state of pre-existing water wires during the dissociation of moderately strong acids by means of first-principles molecular dynamics calculations. By preparing 2,4,6-tricyanophenol (calc. pKa similar to 0.5) in two different initial states, we are able to observe sequential as well as concerted trajectories of dissociation: On one hand, equilibrium dissociation takes place on a similar to 50 ps timescale; proton conduction occurs through three-coordinated water wires in this case, by means of sequential Grotthus hopping. On the other hand, by preparing 2,4,6-tricyanophenol in a hydration state inherited from that of equilibrated phenol (calc. pKa = 7.6), the moderately strong acid finds itself in a presolvated state from which dissociation can take place on a similar to 1 ps timescale. In this case, concerted dissociation trajectories are observed, which consist of proton translocation through two intervening, four-coordinated, water molecules in 0.1 -1.0 ps. The present results suggest that, in general, the mechanism of proton translocation depends on how the excess proton is injected into a hydrogen bond network. In particular, if the initial conditions favour proton release to a fourfold H-bonded water molecule, proton translocation by as much as 6-8 angstrom can take place on a sub-picosecond timescale. (c) 2011 American Institute of Physics. [doi:10.1063/1.3554654]
Article Reference A Revisited Picture of the Mechanism of Glycerol Dehydration
The dehydration mechanism of neutral glycerol in the gas phase was investigated by means of metadynamics simulations. Structures, vibrational frequencies, Gibbs free energy barriers, and rate constants at 800 K. were computed for the different steps involved in the pyrolytic process. In this article, we provide a novel mechanism for the dehydration of neutral glycerol, proceeding via formation of glycidol with a barrier of 66.8 kcal/mol. The formation of glycidol is the rate limiting step of the,overall decomposition process. Once formed, glycidol converts into 3-hydroxypropanal With a barrier of 49.5 kcal/mol. 3-Hydroxypropanal can decompose further into acrolein or into formaldehyde and vinyl-alcohol with barriers of 53.9 and 35.3 kcal/mol, respectively. These findings offer, new insights to available experimental data based on glycerol pyrolysis studies performed with isotopic labeling and on the interpretation of the chemistry of glycerol and sugars in pyrolytic conditions.
Article Reference A theoretical study of the XP and NEXAFS spectra of alanine: gas phase molecule, crystal, and adsorbate at the ZnO(10(1)over-bar0) surface
The adsorption of alanine on the mixed-terminated ZnO(10 (1) over bar0) surface is studied by means of quantum-chemical ab initio calculations. Using a finite cluster model and the adsorption geometry as obtained both by periodic CPMD and embedded cluster calculations, the C1s, N1s and O1s X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra are calculated for single alanine molecules on ZnO(10 (1) over bar0). These spectra are compared with the spectra calculated for alanine in the gas phase and in its crystalline form and with experimental XPS and NEXAFS data for the isolated alanine molecule and for alanine adsorbed on ZnO(10 (1) over bar0) at multilayer and monolayer coverage. The excellent agreement between the experimental and calculated XP and NEXAFS spectra confirms the calculated adsorption geometry: A single alanine molecule is bound to ZnO(10 (1) over bar0) in a dissociated bidentate form with the two O atoms of the acid group bound to two Zn atoms of the surface and the proton transferred to one O atom of the surface. Other possible structures, such as adsorption of alanine in one of its neutral or zwitterionic forms in which the proton of the -COOH group remains at this group or is transferred to the amino group, can be excluded since they would give rise to quite different XP spectra. In the multilayer coverage regime, on the other hand, alanine is in its crystalline form as is also shown by the analysis of the XP spectra.
Article Reference Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl
The potential of mean force for the dissociation of a Ca-Cl ion pair in water is calculated from ab initio molecular dynamics simulations. The constraint-force method is employed to enhance sampling over the entire range of the reaction coordinate (Ca-Cl distance) from 2.2 to 6.5 angstrom. Particular attention is paid to equilibration of the system as it is found that the potential of mean force is highly sensitive to the hydration number of the Ca(2+) ion. The structure and polarization of hydration waters are examined in detail at three ion-ion separations of interest: the contact-ion position, the solvent-separated-ion position, and the transition state between them. The ab initio results are compared to the classical ones obtained using the CHARMM force field and the parameters of Dang and Smith. There are substantial differences between the polarization of hydration waters of Ca(2+) and Cl(-) ions at all distances, which indicates that an accurate description of Ca-Cl dissociation with nonpolarizable force fields may not be feasible. The ab initio results presented here for the Ca-Cl ion pair complements our earlier results for Na-Cl, and together they provide useful benchmarks for polarizable force fields under construction. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3595261]
Article Reference Ab initio modeling of fused silica, crystal quartz, and water Raman spectra
Fused silica light-scattering properties are important for many industrial and laboratory applications. In this work, ab initio molecular dynamics employing periodic boundary conditions are used to simulate its structure and Raman scattering. Fused silica geometry is modeled as a frozen liquid, and the spectra are compared to those of crystal quartz. The method is tested also on Raman spectra of liquid water. Structural similarities between water and fused silica are discussed. The modeling agrees with experiment and suggests that most fused silica spectral features can be explained within the harmonic approximation. The combination of Raman spectroscopy with theoretical computations thus appears useful for structural studies of amorphous materials. (C) 2011 Elsevier B. V. All rights reserved.
Article Reference Anthramycin−DNA Binding Explored by Molecular Simulations
The anticancer drug anthramycin inhibits replication and transcription processes by covalently binding to DNA. Here, we use molecular simulations to investigate the interaction between this ligand and the dodecanucleotide d[GCCAACGTTGGC]2. We start from the X-ray structure of the adduct anthramycin-d[CCAACGTTG*G]2, in which the drug binds covalently to guanine.1 We focus on the noncovalent complexes between the oligonucleotide and the anhydro and hydroxy forms of the drug. Molecular dynamics (MD) simulations show that only the hydroxy form lies in front of the reactive center for the whole simulation (?20 ns), while the anhydro form moves inside the minor groove to the nearest base pair after ?10 ns. This sliding process is associated to both energetic and structural relaxations of the complex. The accuracy of our computational setup is established by performing MD simulations of the covalent adduct and of a 14-mer complexed with anhydro-anthramycin. The MD simulations are complemented by hybrid Car?Parrinello quantum mechanics/molecular mechanics (QM/MM) simulations. These show that in the noncovalent complexes the electric field due to DNA polarizes the hydroxy and, even more, the anhydro form of the drug as to favor a nucleophilic attack by the alkylating guanine. This suggests that the binding process may be characterized by a multistep pathway, catalyzed by the electric field of DNA. The anticancer drug anthramycin inhibits replication and transcription processes by covalently binding to DNA. Here, we use molecular simulations to investigate the interaction between this ligand and the dodecanucleotide d[GCCAACGTTGGC]2. We start from the X-ray structure of the adduct anthramycin-d[CCAACGTTG*G]2, in which the drug binds covalently to guanine.1 We focus on the noncovalent complexes between the oligonucleotide and the anhydro and hydroxy forms of the drug. Molecular dynamics (MD) simulations show that only the hydroxy form lies in front of the reactive center for the whole simulation (?20 ns), while the anhydro form moves inside the minor groove to the nearest base pair after ?10 ns. This sliding process is associated to both energetic and structural relaxations of the complex. The accuracy of our computational setup is established by performing MD simulations of the covalent adduct and of a 14-mer complexed with anhydro-anthramycin. The MD simulations are complemented by hybrid Car?Parrinello quantum mechanics/molecular mechanics (QM/MM) simulations. These show that in the noncovalent complexes the electric field due to DNA polarizes the hydroxy and, even more, the anhydro form of the drug as to favor a nucleophilic attack by the alkylating guanine. This suggests that the binding process may be characterized by a multistep pathway, catalyzed by the electric field of DNA.
Article Reference Anthrax Lethal Factor Investigated by Molecular Simulations
The anthrax disease is caused by the lethal toxin secreted by the bacterium Bacillus anthracis. The toxin is a protein aggregate which contains a Zn-based hydrolase called anthrax Lethal Factor (LF). In this work, we investigate the structure of its Michaelis complex with an optimized MAPKK-like substrate using several computational methods including density functional theory, molecular dynamics, and coarse grained techniques. Our calculations suggest that (i) the presence of second-shell ligands is crucial for tuning the structure, energetics, and protonation state of the metal binding site, as found in other Zn-based enzymes; (ii) the nucleophilic agent is a Zn-bound water molecule; (iii) substrate binding to the active site groove is mainly stabilized by van der Waals interactions; (iv) the bonds most likely involved in the substrate hydrolysis are only mildly polarized by the protein scaffold; and (v) part of helix α19, which is present in one solid state structure of LF (PDB: 1JKY), assumes a coiled conformation. The anthrax disease is caused by the lethal toxin secreted by the bacterium Bacillus anthracis. The toxin is a protein aggregate which contains a Zn-based hydrolase called anthrax Lethal Factor (LF). In this work, we investigate the structure of its Michaelis complex with an optimized MAPKK-like substrate using several computational methods including density functional theory, molecular dynamics, and coarse grained techniques. Our calculations suggest that (i) the presence of second-shell ligands is crucial for tuning the structure, energetics, and protonation state of the metal binding site, as found in other Zn-based enzymes; (ii) the nucleophilic agent is a Zn-bound water molecule; (iii) substrate binding to the active site groove is mainly stabilized by van der Waals interactions; (iv) the bonds most likely involved in the substrate hydrolysis are only mildly polarized by the protein scaffold; and (v) part of helix α19, which is present in one solid state structure of LF (PDB: 1JKY), assumes a coiled conformation.
Article Reference Car-Parrinello molecular dynamics simulations of infrared spectra of crystalline imidazole
Car-Parrinello molecular dynamics was used to calculate geometry, power and infrared spectra of crystalline imidazole. The results were compared with the results of ab initio MP2/6-311++G** static calculations previously performed for the imidazole dimer. The reconstruction of the nu(N-H) bandshape obtained by CPMD method was compared with the results of quantum mechanical model of vibrational couplings in hydrogen-bonded dimer and with the experimental data. (C) 2010 Elsevier B.V. All rights reserved.
Article Reference Car–Parrinello Molecular Dynamics Simulations of Tensile Tests on Si⟨001⟩ Nanowires
Theoretical simulations of tensile tests on Si⟨001⟩ nanowires have been carried out using Car–Parrinello molecular dynamics. H-passivation was used to model experimentally occurring passivation in Si nanowires. First-principle molecular dynamics simulations at ambient temperature reveal the governing role of size, overall shape, and composition of the surface layer for the mechanical properties. Our results indicate that SiH2 groups in the outer layer and the octahedral shape of the wire soften Young’s modulus and allow wire to handle larger transverse strains than SiH groups in wires with the tetrahedral shape. The importance of the overall shape of the wire has been discussed by comparing the behavior of surface layers of 100 and 110 facets. The presence of the 100 facets helps to relax the transverse strain during tension. On the basis of changes in structural parameters, we have presented the schematic motion of Si atoms in core and surface layers before the fracture appeared.
Article Reference Changes of structure and dipole moment of water with temperature and pressure: A first principles study
The changes of structure and distribution of dipole moment of water with temperatures up to 2800 K and densities up to 2.2 g/cm(3) are investigated using ab initio molecular dynamics. Along the isochore of 1.0 g/cm(3), the structure of liquid water above 800 K is dramatically different from that at ambient conditions, where the hydrogen-bonds network collapses. Along the isotherm of 1800 K, the transition from the liquid state to an amorphous superionic phase occurs at 2.0 g/cm(3) (32.9 GPa), which is not observed along the isotherm of 2800 K. With increasing temperature, the average dipole moment of water molecules is decreased arising from the weakened polarization by the collapse of the hydrogen-bonds network, while it is contrarily increased with compression due to the strengthening effect upon the polarization of water molecules. Both higher temperature and pressure broaden the distribution of dipole moment of water molecules due to the enhanced intramolecular charge fluctuations. (C) 2011 American Institute of Physics. [doi:10.1063/1.3608412]
Article Reference Chemical response of aldehydes to compression between (0001) surfaces of alpha-alumina
First-principles molecular dynamics simulations are used to investigate the chemical response of acetaldehyde molecules (MeCHO) to compression and decompression between (0001) surfaces of a-alumina (Al(2)O(3)), with pressures reaching approximately 40 GPa. The results demonstrate that the MeCHO molecules are transformed into other chemical species through a range of chemical processes involving the formation of C-O and C-C bonds between MeCHO monomers as well as proton transfer. The mechanistic details of a representative set of the observed reactions are elucidated through analysis of maximally localized Wannier functions. Analysis of the changes in structure demonstrates that the main role of compression is to reduce the distances between MeCHO molecules to facilitate the formation of C-O bonds. Additional examination of the electronic structure demonstrates that the surface plays a role in facilitating proton transfer by both rendering hydrogen atoms in adsorbed MeCHO molecules more acidic and by acting as a proton acceptor. In addition, adsorption of the MeCHO molecules on the surface renders the sp(2) carbon atoms in these molecules more electrophilic, which promotes the formation of C-C and C-O bonds. It is suggested that the reaction products may be beneficial in the context of wear inhibition. Comparison of the surface structure before compression and after decompression demonstrates that the aldehydes and reaction products are capable of inhibiting irreversible changes in the structure as long as there is at least a monolayer coverage of these species. As a whole, the study sheds light on the chemical behavior of the aldehydes in response to uniaxial compression in nanoscopic contacts that likely applies to other molecules containing carbonyl groups and other metal oxide surfaces. (C) 2011 American Institute of Physics. [doi:10.1063/1.3528980]
Article Reference CIF2Cell: Generating geometries for electronic structure programs
The CIF2Cell program generates the geometrical setup for a number of electronic structure programs based on the crystallographic information in a Crystallographic Information Framework (CIF) file. The program will retrieve the space group number, Wyckoff positions and crystallographic parameters, make a sensible choice for Bravais lattice vectors (primitive or principal cell) and generate all atomic positions. Supercells can be generated and alloys are handled gracefully. The code currently has output interfaces to the electronic structure programs ABINIT, CASTEP, CPMD, Crystal, Elk, Exciting, EMTO, Fleur, RSPt, Siesta and VASP.
Article Reference Combined Theoretical and Mass Spectrometry Study of the Formation-Fragmentation of Small Polyoxomolybdates
We investigate the assembly of small polyoxomolybdates using Car-Parrinello molecular dynamics simulations which show that there is an expansion of the coordination sphere of the Mo center from four to six in molybdate anions when the acidity of the solution is increased. With the help of complementary static density functional theory (DFT) calculations and electrospray ionization mass spectrometry experiments, we are able to postulate tentative mechanisms, with energy-cascade profiles, for the formation of the Lindqvist [Mo(6)O(19)](2)(-) anion. Similar to the family of isopolytungstates, it can be proposed that the [Mo(6)O(19)](2)(-) is formed by the aggregation of one molybdenum unit at a time; however, significant differences with respect to isopolytungstates are also found. The different behavior of chromates with respect to molybdates and tungstates is also considered.
Article Reference Constructing simple yet accurate potentials for describing the solvation of HCl/water clusters in bulk helium and nanodroplets
The infrared spectroscopy of molecules, complexes, and molecular aggregates dissolved in superfluid helium clusters, commonly called HElium NanoDroplet Isolation (HENDI) spectroscopy, is an established, powerful experimental technique for extracting high resolution ro-vibrational spectra at ultra-low temperatures. Realistic quantum simulations of such systems, in particular in cases where the solute is undergoing a chemical reaction, require accurate solute-helium potentials which are also simple enough to be efficiently evaluated over the vast number of steps required in typical Monte Carlo or molecular dynamics sampling. This precludes using global potential energy surfaces as often parameterized for small complexes in the realm of high-resolution spectroscopic investigations that, in view of the computational effort imposed, are focused on the intermolecular interaction of rigid molecules with helium. Simple Lennard-Jones-like pair potentials, on the other hand, fall short in providing the required flexibility and accuracy in order to account for chemical reactions of the solute molecule. Here, a general scheme of constructing sufficiently accurate site-site potentials for use in typical quantum simulations is presented. This scheme employs atom-based grids, accounts for local and global minima, and is applied to the special case of a HCl(H(2)O)(4) cluster solvated by helium. As a first step, accurate interaction energies of a helium atom with a set of representative configurations sampled from a trajectory following the dissociation of the HCl(H(2)O)(4) cluster were computed using an efficient combination of density functional theory and symmetry-adapted perturbation theory, i.e. the DFT-SAPT approach. For each of the sampled cluster configurations, a helium atom was placed at several hundred positions distributed in space, leading to an overall number of about 400 000 such quantum chemical calculations. The resulting total interaction energies, decomposed into several energetic contributions, served to fit a site-site potential, where the sites are located at the atomic positions and, additionally, pseudo-sites are distributed along the lines joining pairs of atom sites within the molecular cluster. This approach ensures that this solute-helium potential is able to describe both undissociated molecular and dissociated (zwitter-) ionic configurations, as well as the interconnecting reaction pathway without re-adjusting partial charges or other parameters depending on the particular configuration. Test calculations of the larger HCl(H(2)O)(5) cluster interacting with helium demonstrate the transferability of the derived site-site potential. This specific potential can be readily used in quantum simulations of such HCl/water clusters in bulk helium or helium nanodroplets, whereas the underlying construction procedure can be generalized to other molecular solutes in other atomic solvents such as those encountered in rare gas matrix isolation spectroscopy.
Article Reference Density Functional Theory Combined with Molecular Mechanics: The Infrared Spectra of Flavin in Solution
The photophysics and photochemistry of flavin dyes determine the functional dynamics of a series of blue light photoreceptors that include the so-called BLUF (blue light sensors using flavin) domains. To enable molecular dynamics (MD) simulation studies of such signaling processes, we derived molecular mechanics (MM) models of flavin chromophores from density functional theory (DFT). Two 300 K ensembles of lumiflavin (LF) in aqueous solution were generated by extended MM-MD simulations using different MM potentials for the water. In a DFT/MM hybrid setting, in which LF was treated by DFT and the polarizing environment at atomistic resolution by MM, we applied instantaneous normal mode analyses (INMA) to these ensembles. From these data we determined the inhomogeneously broadened solution spectra as mixtures of Gaussian bands using a novel automated procedure for mode classification. Comparisons with vibrational spectra available in the literature on native and isotopically labeled flavins in aqueous solution serve us to determine suitable frequency scaling factors and to analyze the accuracy of our scaled DFT/MM-INMA approach. We show that our approach not only agrees with established computational descriptions but also extends such methods substantially by giving access to inhomogeneous line widths and band shapes.
Article Reference Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases-A comparative molecular dynamics study
We have studied substituent effects on the properties of the intramolecular hydrogen bond of some ortho-hydroxy Schiff bases using density functional theory (DFT) based first-principle molecular dynamics (FPMD) and path integral molecular dynamics. The studied compounds possess a strong intramolecular hydrogen bond (r((O ... N)) <= 2.6 angstrom), which can be tuned by substitution to either (i) enhance the basicity of the acceptor moiety by induction effects or (ii) decrease the hydrogen bond length through steric repulsion. DFT calculations and FPMD were employed to investigate structural and dynamical properties of the selected molecules, while quantum effects on the structural properties were assessed using path integral FPMD. The simulations were performed in vacuo and in the solid state to study the influence of the environment on the hydrogen bond and spectroscopic properties. We give computational support to the suggestion that induction effects are less effective to tune the intramolecular hydrogen bond properties of the discussed ortho-hydroxy Schiff bases than the steric or the environmental effects. (C) 2011 American Institute of Physics. [doi:10.1063/1.3528721]
Article Reference Duocarmycins Binding to DNA Investigated by Molecular Simulation
Duocarmycins are a potent class of antitumor agents, whose activity arises through their covalent binding to adenine nucleobases of DNA.1-3 Here, we perform molecular dynamics (MD) and hybrid Car?Parinello QM/MM simulations to investigate aspects of duocarmycin binding to the d(pGpApCpTpApApTpTpGpApC) oligonucleotide. We focus on the derivatives (+)-duocarmycin SA (DSA) and (+)-duocarmycin SI (DSI), for which structural information of the covalent complex with the oligonucleotide is available, as well as on the related, but less reactive, NBOC?duocarmycin SA (NBOC?DSA), interacting with the same oligonucleotide. Comparison is made with adenine alkylation reaction in water performed by the smallest of these compounds (NBOC?DSA). The MD calculations suggest that, in noncovalent complexes, (i) drug binding causes a partial dehydration of the minor groove, without inducing a significant conformational changes, and (ii) DSA and DSI occupy a more favorable position for nucleophilic attack than NBOC?DSA, consistently with the lower reactivity of the latter. The QM/MM calculations, which are used to investigate the first step of the alkylation reaction, turn out to provide strongly underestimated free energy barriers. Within these approximations, our calculations suggest that an important ingredient for the experimentally observed DNA catalytic power is the polarization of the drug by the biomolecular scaffold. Duocarmycins are a potent class of antitumor agents, whose activity arises through their covalent binding to adenine nucleobases of DNA.1-3 Here, we perform molecular dynamics (MD) and hybrid Car?Parinello QM/MM simulations to investigate aspects of duocarmycin binding to the d(pGpApCpTpApApTpTpGpApC) oligonucleotide. We focus on the derivatives (+)-duocarmycin SA (DSA) and (+)-duocarmycin SI (DSI), for which structural information of the covalent complex with the oligonucleotide is available, as well as on the related, but less reactive, NBOC?duocarmycin SA (NBOC?DSA), interacting with the same oligonucleotide. Comparison is made with adenine alkylation reaction in water performed by the smallest of these compounds (NBOC?DSA). The MD calculations suggest that, in noncovalent complexes, (i) drug binding causes a partial dehydration of the minor groove, without inducing a significant conformational changes, and (ii) DSA and DSI occupy a more favorable position for nucleophilic attack than NBOC?DSA, consistently with the lower reactivity of the latter. The QM/MM calculations, which are used to investigate the first step of the alkylation reaction, turn out to provide strongly underestimated free energy barriers. Within these approximations, our calculations suggest that an important ingredient for the experimentally observed DNA catalytic power is the polarization of the drug by the biomolecular scaffold.
Article Reference Dynamical Nonplanarity of Benzene. Evidences from the Car–Parrinello Molecular Dynamics Study
Car–Parrinello molecular dynamics simulation of an isolated benzene molecule unextectedly revealed very low population of a planar geometry of the ring (less than 10%) despite the ideal aromatic character of a cyclic conjugated system. Analysis of nonplanar conformations of benzene in terms of puckering parameters demonstrates that benzene in the gas phase exists mainly as a mixture of two mirror-symmetrical families of flattened boat and twist boat conformations with a total population of more than 70%. The average conformation of the ring is nonplanar with values of endocyclic torsion angles of 6.7°.
Article Reference Elucidating the Origin of Diastereoselectivity in a Self-Replicating System: Selfishness versus Altruism
We have investigated a diastereoselective self-replicating system based on a cycloaddition of a fulvene derivative and a maleimide using a two-pronged approach of combining NMR spectroscopy with computational modelling. Two diastereomers are formed with identical rates in the absence of replication. When replication is enabled, one diastereomer takes over the resources as a “selfish” autocatalyst, while exploiting the competitor as a weak “altruist”, resulting in a diastereoselectivity of 16:1. We applied 1D and 2D NMR spectroscopic techniques supported by ab initio chemical shifts as well as ab initio molecular dynamics simulations to study the structure and dynamics of the underlying network. This powerful combination allowed us to decipher the energetic and structural rationale behind the observed behaviour, while static computational methods currently used in the field did not.
Article Reference Energetics and electronic structure of encapsulated single-stranded DNA in carbon nanotubes
We report total-energy electronic-structure calculations based on density functional theory performed on single-stranded DNA (ssDNA) encapsulated in single-walled carbon nanotubes (SWCNTs). We find that the encapsulation reaction is exothermic for nanotubes with diameters greater than 1.33 nm. The energy gain is calculated to be in the range of 0.8-1.5 eV/nm, depending on tube diameter, base sequences, and ssDNA structure. In optimal ssDNA-SWCNT hybrid-system geometries, the polar groups of ssDNA, i.e. the POH moiety in its backbone, are located adjacent to the wall of the nanotube. The electronic structure of the hybrid system is qualitatively similar to a simple sum of those of an isolated ssDNA molecule and an empty SWCNT. However, detailed analysis of the electronic structure of the hybrid system reveals that the encapsulation of ssDNA into a SWCNT affects the electronic structures of both the ssDNA and the SWCNT.
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