ABSTRACT
Low-energy spectra of single-molecule magnets (SMMs) are often described by Heisenberg Hamiltonians. Within this formalism, exchange interactions between magnetic centers determine the ground-state multiplicity and energy separation between the ground and excited states. In this contribution, we extract exchange coupling constants (J) for a set of iron (III) binuclear and tetranuclear complexes from all-electron calculations using non-collinear spin-flip time-dependent density functional theory (NC-SF-TDDFT). For 12 binuclear complexes with J-values ranging from -6 to -132 cm-1 , our benchmark calculations using the short-range hybrid ωPBEh functional and 6-31G(d,p) basis set agree well with the experimentally derived values (mean absolute error of 4.7 cm-1 ). For the tetranuclear SMMs, the computed J constants are within 6 cm-1 from the experimentally derived values. We explore the range of applicability of the Heisenberg model by analyzing bonding patterns in these Fe(III) complexes using natural orbitals (NO), their occupations, and the number of effectively unpaired electrons. The results illustrate the efficiency of the spin-flip protocol for computing the exchange couplings and the utility of the NO analysis in assessing the validity of effective spin Hamiltonians.
ABSTRACT
We present a new implementation for computing spin-orbit couplings (SOCs) within a time-dependent density-functional theory (TD-DFT) framework in the standard spin-conserving formulation as well in the spin-flip variant (SF-TD-DFT). This approach employs the Breit-Pauli Hamiltonian and Wigner-Eckart's theorem applied to the reduced one-particle transition density matrices, together with the spin-orbit mean-field treatment of the two-electron contributions. We use a state-interaction procedure and compute the SOC matrix elements using zero-order non-relativistic states. Benchmark calculations using several closed-shell organic molecules, diradicals, and a single-molecule magnet illustrate the efficiency of the SOC protocol. The results for organic molecules (described by standard TD-DFT) show that SOCs are insensitive to the choice of the functional or basis sets, as long as the states of the same characters are compared. In contrast, the SF-TD-DFT results for small diradicals (CH2, NH2 +, SiH2, and PH2 +) show strong functional dependence. The spin-reversal energy barrier in a Fe(III) single-molecule magnet computed using non-collinear SF-TD-DFT (PBE0, ωPBEh/cc-pVDZ) agrees well with the experimental estimate.
ABSTRACT
Stabilization of a G-quadruplex (G4) DNA structure in the proto-oncogene c-MYC using small molecule ligands has emerged as an attractive strategy for the development of anticancer therapeutics. To understand the subtle structural changes in the G4 structure upon ligand binding, molecular dynamics (MD) simulations of c-MYC G4 DNA were carried out in a complex with six different potent ligands: 3AQN, 6AQN, 3APN, 360A, Nap-Et, and Nap-Pr. The results show that the ligands 3AQN, 6AQN, 3APN, and 360A stabilize the G4 structure by making stacking interactions with the top quartet. On the other hand, Nap-Et and Nap-Pr bind at the groove of the G4 structure. These groove binding ligands make crucial H-bond contacts with the guanines and electrostatic interactions with the phosphate backbone. Two-dimensional dynamic correlation maps unraveled the ligand-induced correlated motions between the guanines in the quartet and a di-nucleotide present in the propeller loop-2 of the G4 structure. Cluster analysis and ONIOM calculations revealed the structural dynamics in the loop of the quadruplex upon ligand binding. Overall, the results from the present study suggest that engineering specific contacts with the propeller loop can be an efficient way to design c-MYC G4-specific ligands.