PolaBer: a program to calculate and visualize distributed atomic polarizabilities based on electron density partitioning

Abstract

This paper describes the program PolaBer, which calculates atomic polarizability tensors from electric field perturbations of a partitioned electron density distribution. Among many possible partitioning schemes, PolaBer is currently using the quantum theory of atoms in molecules and it is interfaced to programs that apply such a partitioning. The calculation of the atomic tensors follows the idea suggested by Keith [The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design, (2007), edited by C. F. Matta & R. J. Boyd. Weinheim: Wiley‐VCH], which enables the removal of the intrinsic origin dependence of the atomic charge contributions to the molecular dipole moment. This scheme allows the export, within chemically equivalent functional groups, of properties calculated from atomic dipoles, such as for example the atomic polarizabilities. The software permits visualization of the tensors and calculation of straightforward optical properties of a molecule (like the molar refractive index) or a crystal (assuming the molecule in a given crystal lattice).

Hirshfeld‐based intrinsic polarizability density representations as a tool to analyze molecular polarizability

“…On the one hand, the latter was designed to specifically use the FF approach, instead of showing a general definition considering both analytical and FF approaches. On the other hand, it uses a response of molecular fragment approach explained by Keith in a part of the calculation, which is inherently ill‐defined, when “the program requires the atomic charges, polarization dipoles, and critical points of the electron density calculated from external programs, with and without an applied electric field.” This cannot ensure all QTAIM basins are kept constant in the process. Hence, as observed in the QTAIM condensed Fukui indices, one is putting at risk the reliability of the calculation because of this fact.…”

The Role of Hydrogen Bond in Designing Molecular Optical Materials

“…In this respect, we observe that RLFT substantially improves over the oriented-gas, but still underperforms the periodic first-principles calculation. Interestingly, the electric susceptibility tensor and refractive indices of crystalline urea have been estimated from a variety of approaches [13]. Among them, RLFT resulted in values very close to the periodic first-principles methods, as well as to the experimental values extrapolated to zero frequency.…”

“…modified and implemented in a program called PolaBer [13], used to calculate the distributed polarizability tensors reported in this paper (for details of the implementation, as well as for the methodological procedures used in this work, see Supporting Information). The total, molecular or crystal polarizability can be straightforwardly obtained through summation of the atomic counterparts, as typical for any molecular property estimated using QTAIM.…”

Distributed Atomic Polarizabilities of Amino Acids and their Hydrogen-Bonded Aggregates

“…27 It was slightly modified and implemented by some of us in the PolaBer software. 28 The static first-order dipole polarizability tensor of a molecular system, , is the gradient of the electric dipole moment with respect to an external, uniform, and time-independent electric field :…”

“…26 Subsequently, Keith 27 generalized Bader's method, within the "atomic response theory", recently modified and implemented in a program (PolaBer) by some of us. 28 The main advantage is the removal of origin-dependent terms, which are particularly disadvantageous for the transferability of atomic or group quantities. PolaBer extends the quantities computed from the atomic polarizabilities, including bond polarizabilities and evaluation of refractive indices in crystals.…”