A comparison of three DFT exchange-correlation functionals and two basis sets for the prediction of the conformation distribution of hydrated polyglycine

Dipole Cooperativity and Polarization Frustration Determine the Secondary Structure Distribution of Short Alanine Peptides in Water

The physical driving forces for secondary structure preferences of hydrated alanine peptide are investigated with B3LYP-D3(BJ) and the adaptive force matching (AFM) method. The AFM fit to the DFT surface, ALA2022, provides excellent agreement with the nuclear magnetic resonance scalar coupling constants from experiments. In turn, the model is used to gain insight into the physical driving forces behind secondary structure preferences of hydrated peptides. DFT calculations with and without the Conductor-like Screening Model (COSMO) show that the α helix is stabilized by solvent polarization due to dipole cooperativity. The two adjacent amide groups in β strand form a near-planar trapezoid that is not much larger than the size of water molecules. When the finite size of a water molecule is considered, the stabilization from solvent polarization for such a trapezoid is frustrated. Water molecules cannot find orientations to properly stabilize all four polar regions close to each other with such an awkward arrangement. This leads to quite substantial reduction in polarization stabilization. Although the polyproline II (PP-II) conformation is very similar to the β strand, the small twist in the backbone angles allowed much improved polarization stabilization. The improved polarization, when combined with favorable intrapeptide interactions, leads to the PP-II to be lowest in free energy. Other factors, such as the entropic TΔS and the ϕ, ψ coupling terms, are also studied but are found to play only a minor role. The insight shown in this work helps to better understand the structure of globular and intrinsic disordered proteins and facilitate future force field development.

Accurate Geometry and Non-Covalent Interactions in 1-Phenylethanol and Its Monohydrate: A Rotational Study

The pure rotational spectra of 1-phenylethanol and its monohydrate were measured by using a pulsed jet Fourier transform microwave spectrometer. One conformer of the 1-phenylethanol monomer with the trans form was observed in the pulsed jet. The experimental values of rotational constants of ten isotopologues, including eight mono-substituted ¹³ C and one D isotopologues, allow an accurate structure determination of the skeleton of 1-phenylethanol. For its monohydrate, only one isomer has been observed, of which 1-phenylethanol adopts the trans form and binds with water through an O-H⋅⋅⋅O_w and an O_w -H⋅⋅⋅π hydrogen bond. Each rotational transition displays a doublet with a relative intensity ratio of 1 : 3, due to a hindered internal rotation of water around its C₂ axis. This study provides the information on accurate geometry of 1-phenylethanol (PE) and large amplitude motion of water in the PE monohydrate.

Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching

A fragmentation approach referred to as a simple overlapping region method for force matching (SORForM) is presented. SORForM is designed to enable efficient computation of quantum mechanical (QM) forces for large molecules and is validated in the framework of adaptive force matching (AFM) to develop solute models in water. The SORForM method divides a molecule into overlapping QM regions with each region containing a gradient zone and a buffer zone. The buffer zone ensures that the atoms in the gradient zone have their surroundings unchanged with fragmentation. The performance of the method is validated with mefenamic acid and linalyl acetate by comparing the hydration free energies of AFM models developed with and without SORForM. The AFM hydration free energies are also compared with that of the experiments. The models developed with B3LYP-D3(BJ) and def2-TZVP are in excellent agreement with experiments. Our work shows that PBE-D3(BJ) provides less satisfactory results when compared to B3LYP-D3(BJ). The def2-TZVP basis set is found to greatly improve the agreement with experiments when compared to a double-zeta quality basis set.

The Exchange-Correlation Effects on the Electronic Bands of Hybrid Armchair Single-Walled Carbon Boron Nitride Nanostructure

This study investigates the effect of exchange-correlation on the electronic properties of hybridized hetero-structured nanomaterials, called single-walled carbon boron nitride nanotubes (SWCBNNT). A first principles (ab initio) method implemented in Quantum ESPRESSO codes, together with different parametrizations (local density approximation (LDA) formulated by Perdew Zunga (PZ) and the generalized gradient approximation (GGA) proposed by Perdew–Burke–Ernzerhof (PBE) and Perdew–Wang 91 (PW91)), were used in this study. It has been observed that the disappearance of interface states in the band gap was due to the discontinuity of the π–π bonds in some segments of SWCNT, which resulted in the asymmetric distribution in the two segments. This work has successfully created a band gap in SWCBNNT, where the PBE exchange-correlation functional provides a well-agreed band gap value of 1.8713 eV. Effects of orbitals on electronic properties have also been studied elaborately. It has been identified that the Py orbital gives the largest contribution to the electrical properties of our new hybrid SWCBNNT nanostructures. This study may open a new avenue for tailoring bandgap in the hybrid heterostructured nanomaterials towards practical applications with next-generation optoelectronic devices, especially in LED nanoscience and nanotechnology.