Glycine on Cu(001) is used as an example to illustrate the critical role of molecular polarity and finite temperature effect in self-assembly of biomolecules at a metal surface. A unified picture for glycine self-assembly on Cu(001) is derived based
on full polarity compensation considerations, implemented as a generic rule. Temperature plays a non-trivial role: the ground-state structure at 0 K is absent at room temperature, where intermolecular hydrogen bonding overweighs competing molecule-substrate interactions. The unique p(2X4) structure from the rule is proved as the most stable one by ab initio molecular dynamics at room temperature, and its STM images and anisotropic free-electron-like dispersion are in excellent agreement with experiments. Moreover, the rich self-assembling patterns including the heterochiral and homochiral phases, and their interrelationships are entirely governed by the same mechanism.
The recently discovered FeAs-based superconductors show intriguing behavior and unusual dynamics of electrons and holes which occupy the Fe $d$-orbitals and As $4s$ and $4p$ orbitals. Starting from the atomic limit, we carry out a strong coupling exp
ansion to derive an effective hamiltonian that describes the electron and hole behavior. The hopping and the hybridization parameters between the Fe $d$ and As $s$ and $p$-orbitals are obtained by fitting the results of our density-functional-theory calculations to a tight-binding model with nearest-neighbor interactions and a minimal orbital basis. We find that the effective hamiltonian, in the strong on-site Coulomb repulsion limit, operates on three distinct sub-spaces coupled through Hunds rule. The three sub-spaces describe different components (or subsystems): (a) one spanned by the $d_{x^2-y^2}$ Fe orbital; (b) one spanned by the degenerate atomic Fe orbitals $d_{xz}$ and $d_{yz}$; and (c) one spanned by the atomic Fe orbitals $d_{xy}$ and $d_{z^2}$. Each of these Hamiltonians is an extended t-t-J-J model and is characterized by different coupling constants and filling factors. For the case of the undoped material the second subspace alone prefers a ground state characterized by a spin-density-wave order similar to that observed in recent experimental studies, while the other two subspaces prefer an antiferromagnetic order. We argue that the observed spin-density-wave order minimizes the ground state energy of the total hamiltonian.
