Journal of Computational Chemistry

A new approach (PICVib) to compute selected vibrational frequencies at high levels or of large systems is presented by Marcus V. P. dos Santos, Eduardo C. Aguiar, João Bosco P. da Silva, and Ricardo L. Longo on page 611. The image illustrates this approach applied to the water dimer where the green circles represent the selected vibration and the arrows the harmonically displaced structures along the corresponding normal mode. Only single-point calculations are used to accurately predict the vibrational frequency. Thus, high level methods, including coupled-cluster, can be employed and large systems can be viably treated, as represented in the background by many interacting molecules.

A new geometric-flow based approach is used to self-consistently solve the Poisson equation and determine the dielectric profile around the small molecule glycerol triacetate, as presented by Dennis G. Thomas, Jaehun Chun, Zhan Chen, Guowei Wei, and Nathan A. Baker on page 687. This approach is applied to a set of small molecules and produces solvation energy results that are in good agreement with experimental measurements. More importantly, the self-consistent nature of the geometric flow method removes the ambiguity associated with the functional form of the solute-solvent interface, a source of confusion and error in many implicit solvent electrostatics calculations.

A new approach (PICVib) was developed to provide vibrational frequencies of selected modes using only the structure and energy calculations at a more demanding computational level. The approach has an excellent performance at only a small fraction of the computational demand required for a complete analytical calculation. It is general, robust and was validated for a wide range of frequency values (20–4800 cm⁻¹) and large systems.

A new type of the Hamiltonian replica-exchange method was proposed for molecular dynamics and Monte Carlo simulations, referred to as the Coulomb replica-exchange method. In this method, electrostatic charge parameters are exchanged among replicas. This method was applied to a fragment of an amyloid-β peptide in an explicit water solvent. β-Helix, α-helix, 3₁₀-helix, β-hairpin, and β-sheet structures were obtained, and the conformational transition pathways among these structures from the free-energy landscape were deduced.

A new umbrella sampling method was developed to calculate free energies of helical transitions. With this method, the free energy landscape as a function of the helical radius and pitch was calculated for four peptides using the AMBER and CHARMM force fields.

The main atmospheric degradation pathway for aromatic pollutants like fluorobenzene is initiated by hydroxyl radical due to its high oxidation potential. The transition state for the formation of prereaction complex was determined for the first time. G3 calculations correctly predicted that atmospheric oxidation of fluorobenzene is dominated by the ortho and para reaction channels. The experimental reaction rates and their unusual temperature dependence were successfully reproduced by RRKM theory in the temperature range of environmental concern.

Computationally predicted closo-tricarbaboranes C₃B_n–3H_n⁺ (n = 5, 6, 7, 10, 12) are further analyzed in terms of computing their ¹¹B and ¹³C chemical shifts. The data obtained for these potentially weakly coordinating cations do not show any substantial deviations from known values of chemical shifts in the area of boron cluster chemistry, and on that basis their experimental availability is possible.

Electrophilic (Δ⁺h(k)) and nucleophilic (Δ⁻h(k)) hardness potential [h (r)] can address the N-dependence problem of the local hardness descriptor and at the same time can, in principle, explain the intermolecular and intramolecular reactivities toward nucleophilic and electrophilic attacks on systems, where the electronic factor plays the deciding role of reactivity.

The intermolecular potential energy surface (PES) of argon–ethane was studied. The PES of argon–ethane was characterized by a global minimum at a near T-shaped configuration, and a second minimum at a collinear configuration. An augmented correlation-consistent basis set with a set of bond functions can effectively produce results equivalent to the next larger augmented correlation-consistent basis set. The use of bond functions improved the PES, resulting in accurate potential anisotropy.

The Bader's quantum theory of atoms in molecules (QTAIM) was used in a wide range of applications from solid state physics and X-ray crystallography to drug design and biochemistry. However, it has not always been feasible to apply QTAIM to large systems due to its computational cost. This article presents a vectorized and parallel algorithm for computing the QTAIM topology of the electron density that scales linearly with the system size and quasi-linearly with the number of processors. The method is applied to a series of representative molecules.

A geometric flow implicit solvent model with a self-consistent treatment of polar and nonpolar energetics was used to study properties of a series of small molecules. The graphical abstract figure illustrates the solute–solvent interface obtained from this implicit solvent model.

Electron-donating and weakly electron-accepting substituents affect H-bond strengths (and related properties) more strongly than electron-accepting ones.