Answers of Referee queries:

Also it is important that the multi-thiophene systems clarified. What is the relative orientation of the rings are maintained in plane by constraining planarity? are they

In our model, we have used thiophene molecular wire consisting of multiple rings aligned and maintained in the plane, but for simplicity we have used the word multi-thiophene systems. Yes, the rings are maintained in a plane by constraining planarity, but for each calculation, we optimized the molecular system using Gaussian as well as Atomistix Tool Kit along with its graphical user interface Virtual Nano Lab. There is discussion on thermal activation and temperature dependence of the conductance. From what I see all the calculations are performed at the electronic structure level with no consideration of phonon coupling effects. How are thermal effects on the electronic transmission included? Here we utilized ab-initio Density Function Theory combined with the non-equilibrium Greens function method (NEGF) to calculate (i) relaxed geometries, (ii) elastic transport properties, (iii) vibrational frequencies, (iv) coupling of vibrational modes to electrons (electron-phonon coupling) and the VNL simulation packages are used for the DFT/NEGF calculations presented here. To obtain geometries of the molecules bonded to gold surfaces, geometry relaxation is performed for the atomic coordinates of the molecule as well as the surface gold atoms, i.e., the vibrational region in Figure 1. Periodic boundary conditions are utilized in the calculations on unit cells consisting of one molecule together with 54 Au atoms (six layers of 3 X 3) to represent the Au(111) surfaces. The geometry optimization has been repeated for different lengths of the unit cell in the direction perpendicular to the surface to find (local) energy minima. Vibrational frequencies are calculated using finite differences. The dynamical matrix (Hessian) for the finite vibrational region (Figure 1) is found from the forces induced by displacing each of the atoms in all three directions by a factor of 0.02.

The electron-phonon couplings (M()) are obtained from the vibrational modes (v()) and the derivative of the Hamiltonian (H)1
( )

( )

where *| +is the basis set, is the mass of the atom corresponding to the nuclear coordinate , and is the angular frequency of mode . The derivatives of the Hamiltonian are calculated by a finite difference method2. To limit the range of the electronphonon coupling, the interaction is assumed to be negligible outside the device subspace (Figure 1); i.e., the coupling is assumed to be limited to the molecule and the first two layers of gold atoms in the surface.

The current is calculated using the NEGF method in the lowest order expansion (LOE) approximation described in refs 2, and 3. This approximation relies on two assumptions: (i) expansion to lowest order in the electron-phonon coupling and (ii) constant density of states in the device and contacts close to the Fermi energy. For the molecules considered here, the first approximation is well justified since the electrons only interact weakly with vibrations. It is more difficult to rigorously justify the second approximation since the calculated transmission function varies around the Fermi energy for the molecules considered here. Our calculations include heating effects of the vibrational modes. To obtain the number of vibrational quanta in each mode, we impose the condition that the net power exchange between electrons and vibrational modes is zero for each vibration; i.e., the emission processes are balanced by creation of electron-hole pairs (electron-hole damping)4. To simplify the discussion, we consider the low-temperature limit (our numerical results use the full temperature dependent solution from ref 4) and solve for the number of vibrational quanta n as a function of bias voltage (V) ( ) | | { } ( ) | | | | ( ) ( ) where [ ( ) ] is the electron-hole damping rate and the vibration ( ) ( ) ( ) emission constant [ ] is expressed in terms of the electron( ) phonon coupling ( ), the spectral densities resulting from the two contacts A1 and A2, and the elastic spectral function A = A1 + A2 .
It seems that three layers have been used in the cluster model. Are these the three first layer onto which the SE are projected on? Please take care of using the terms "surface" and "layers" more carefully. A layer would be the 3x3 plane of Au atoms. The surface would be the last repeating unit of 3 layers on which the SE is project to and which are included in the central region. Namely, your discussion of Figure 1 has to be made clear.

The thiophene molecule is connected to surface which would be the last repeating unit of three layers on which the SE is projected to and which is included in the central region as shown in given figure.
The electronic structure calculation used in the DFT-NEGF is not clarified sufficiently. Were plane waves or atomic basis sets used in these calculations? If basis set were used was periodicity added as well on the cluster model?

The electronic properties of closed and open quantum systems have been based on DFTNEGF using numerical basis sets. The key parameter in the self-consistent loop is the density matrix. For open systems, the density matrix is calculated using NEGF, while for closed or periodic systems it is calculated by using diagonals from the Kohn-Sham Hamiltonian. The Density Matrix defines the electron density, and the electron density sets up an effective potential known as the Hartree exchange-correlation potential. From the effective potential, we can obtain the Kohn-Sham Hamiltonian. In DFT, the electronic structure of the system is described in terms of the one-electron Kohn-Sham Hamiltonian

Here the first term describes the kinetic energy of the electron, while second term describes an effective potential energy of the electron moving in the mean field from the other electrons, where the other electrons are described in terms of the total electron density n. We find the one-electron eigenstates of the Kohn-Sham Hamiltonian by solving the one-electron Schrdinger equation To solve this differential equation we expand the wave functions in a set of basis functions

This modifies the differential equation into a matrix equation for determining

The Hamiltonian matrix, and overlap matrix are given by 3D integrals over the basis functions. The occupied eigenstates defines the electron density of the system

Where is the Fermi function, the Fermi energy, and the electron temperature. The density is conveniently represented in terms of the density matrix

And the density matrix is given by basis set expansion coefficients

For Semi-Empirical (SE) cases, the non-self-consistent part of the tight-binding Hamiltonian is parametrized using a two-centre approximation, i.e. the matrix elements only depend on the distance between two atoms, and is independent of the position of the other atoms. In the extended Hckel theory model, the matrix elements are described in terms of overlaps between Slater orbitals on each site. In this way, the matrix elements can be defined by very few parameters. In the Slater-Koster model, the distance-dependence of the matrix elements is given as a numerical function; which gives not only higher flexibility, but also makes the fitting procedure more difficult. The self-consistent part of the calculation is identical for both SE models. The density matrix is calculated from the Hamiltonian using non-equilibrium Green's functions for device systems, while for molecules and crystals, it is calculated by diagonalization. The density matrix defines the real-space electron density, and consequently the Hartree potential can be obtained by solving the Poisson equation. The following equation describes the details of the mathematical formalism behind the implementation. The Hamiltonian is expanded in a basis of local atomic orbitals (an LCAO expansion) Here is a spherical harmonic and is a radial function. Typically, the atomic orbitals used in the LCAO expansion, has a close resemblance to the atomic eigen functions. With this form of the basis set, the onsite elements are given by

Here is an adjustable parameter, which often is close to the atomic eigen energy. The central object in the extended Hckel model is the overlap matrix,

To calculate this integral, the form of the basis functions must be specified. In the extended Hckel model, the basis functions are parametrized using Slater orbitals

The LCAO basis is described by the adjustable parameters , and . These parameters must be defined for each angular shell of valence orbitals, for each element. The overlap matrix defines the Hamiltonian

Where

is the onsite orbital energy and

is a Hckel fitting parameter

In the self-consistent semi-empirical models, the electron density is computed using the tightbinding model as described above. The density gives rise to a Hartree potential and this Hartree potential is included through an additional term in the Hamiltonian

The electron density is given by the occupied eigen-functions

Here temperature, and orbital basis as

is the Fermi function, the Fermi energy, the electron the energy of eigenstate . Next write the eigen states in the Slater

and see that the total number of electrons,

is given by

where

is the density matrix.

We have used atomic basis sets in our calculation.