Accurate and Efficient Treatment of Continuous Solute Charge Density in the Mean-Field QM/MM Free Energy Calculation

QM/MM free energy calculation is computationally demanding because of the need for an excessive number of electronic structure calculations. A practical approach for reducing the computational cost is that based on mean field approximation, which calculates the QM wave function in the presence of a partially or totally averaged potential of the MM environment. For obtaining the latter potential, it is common to first represent the QM molecule in terms of point charges and then perform statistical sampling of MM molecules. However, the point charge approximation has the drawback that it tends to overestimate electrostatic (ES) interactions at short-range, which may give rise to a divergence problem in the self-consistent iterations. In this paper, we thus consider a more accurate and robust implementation of mean-field QM/MM method based on continuous QM charge density, here utilizing the following combination: (i) grid-based treatment of ES potential generated by the QM molecule, which allows for an efficient sampling of MM molecules in the presence of QM charge density, and (ii) adaptation of the QM/MM-Ewald method to the mean-field framework for eliminating cutoff errors in the long-range ES interactions. As a numerical test, we apply the obtained method to several benchmark reactions in aqueous solution, and show that the density-based method essentially eliminates the divergence problem while providing the free energy profile consistent with experiment. In addition, we test the utility of a recently proposed screened charge model for the QM charge density and show that the latter also performs well for the free energy calculation. These results suggest that explicit inclusion of charge penetration effects is beneficial for improving the accuracy and stability of the mean-field QM/MM calculation

Theoretical Study of the Solvation Effect on the Reductive Reaction of Vinylene Carbonate in the Electrolyte Solution of Lithium Ion Batteries

Carbon monoxide generation reaction of vinylene carbonate (VC) in the electrolyte solution of lithium ion batteries (ethylene carbonate (EC) and 1.0 M LiClO₄/EC) is studied using the RISM-SCF-SEDD method, a hybrid methodology of statistical mechanics for molecular liquids and quantum chemistry. The analytical treatment of the solvent and lithium salt enables us to treat the complicated composition of the solution such as the concentration of the salt which is difficult for the methods based on the molecular dynamics (MD) simulation. The free energy profile and solvation structure are discussed in order to clarify the effect of the solvent, especially lithium salt on the reaction. The lithium salt strongly stabilizes the system due to the electrostatic interaction compared with the system in which the salt does not exist. The effect of the salt is especially important for considering the ionization process of VC

Theoretical Studies on the Electronic States and Liquid Structures of Ferrocenium-Based Ionic Liquids

The solvation effects on the electronic structures and magnetic properties were computed for a series of ferrocenium cations in the ferrocenium-based ionic liquids using RISM-SCF-SEDD calculations coupled with CASSCF. The spin–orbit coupling was calculated to get insight into the spin anisotropy. The values were on the order of 100 cm^–1, exhibiting strong spin anisotropy parallel to the angular momentum. The computed results show that the magnetic properties of the ferrocenium cations are similar both in the isolated state and in ionic liquids. We also carried out molecular dynamics and RISM calculations to investigate the liquid structures. The radial and spatial distribution functions around the cations indicate that the cations are surrounded by about seven TFSA anions above and below the cyclopentadienyl rings and from the side of the ferrocenium cations. The nearest-neighbor cations exist in the oblique directions. The introduction of a butyl group to the ring disturbs the solvation structures, and butyl groups in different cations tend to attract each other like those observed in alkylimidazolium ionic liquids

Example of the analytic procedure.

<p>Sound spectrographs were displayed on a monitor, and segments suitable for analysis were selected. The octave bands sound pressure levels were calculated as the averaged value for the segments (white horizontal bars) without noise contamination (heart sounds; red arrows). Spectra in the white ellipses indicate contaminated voice sounds of another child during one respiratory phase.</p

Like-Charge Attraction of Molecular Cations in Water: Subtle Balance between Interionic Interactions and Ionic Solvation Effect

Despite strong electrostatic repulsion, like-charged ions in aqueous solution can effectively attract each other via ion–water interactions. In this paper we investigate such an effective interaction of like-charged ions in water by using the 3D-RISM-SCF method (i.e., electronic structure theory combined with three-dimensional integral equation theory for molecular solvents). Free energy profiles are calculated at the CCSD­(T) level for a series of molecular ions including guanidinium (Gdm⁺), alkyl-substituted ammonium, and aromatic amine cations. Polarizable continuum model (PCM) and mean-field QM/MM free energy calculations are also performed for comparison. The results show that the stability of like-charged ion pairs in aqueous solution is determined by a very subtle balance between interionic interactions (including dispersion and π-stacking interactions) and ionic solvation/hydrophobic effects and that the Gdm⁺ ion has a rather favorable character for like-charge association among all the cations studied. Furthermore, we investigate the like-charge pairing in Arg-Ala-Arg and Lys-Ala-Lys tripeptides in water and show that the Arg-Arg pair has a contact free-energy minimum of about −6 kcal/mol. This result indicates that arginine pairing observed on protein surfaces and interfaces is stabilized considerably by solvation effects

Comparison of right-to-left ratios (R/L ratios) of breath sound sound pressure between controls and atelectatic subjects.

<p>Comparison of right-to-left ratios (R/L ratios) of breath sound sound pressure between controls and atelectatic subjects.</p

Representative sound spectrograms in a child with right middle lobe atelectasis before and after treatment.

<p>The sound spectrograms for recordings over bilateral middle lung fields are shown. Before treatment, the inspiratory sound intensity was lower on the right than on the left. Furthermore, on the right (affected) side, the expiratory sound intensity was similar to the inspiratory sound intensity. In addition, coarse crackles (white arrows) were identified. After resolution, the right-to-left difference in inspiratory sound intensity persisted. On the other hand, the recovery of a normal pattern of inspiratory breath sound dominance over expiratory breath sound was observed and the adventitious sounds disappeared.</p

Subject characteristics.

<p>Subject characteristics.</p

Baseline breath sound sound pressure levels over the right middle lobe in the control and atelectasis subjects.

<p>Baseline breath sound sound pressure levels over the right middle lobe in the control and atelectasis subjects.</p

Echinopsacetylenes A and B, New Thiophenes from <i>Echinops transiliensis</i>

Two new polyacetylene thiophenes, echinopsacetylenes A and B (<b>1</b> and <b>2</b>), were isolated from the roots of <i>Echinops transiliensis</i>. The structures of <b>1</b> and <b>2</b> were elucidated on the basis of spectroscopic analyses and chemical transformations. Echinopsacetylenes A (<b>1</b>) is the first natural product possessing an α-terthienyl moiety covalently linked with another thiophene moiety. Echinopsacetylenes B (<b>2</b>) is the first natural thiophene conjugated with a fatty acid moiety. Echinopsacetylene A (<b>1</b>) showed toxicity against the Formosoan subterranean termite (<i>Coptotermes formosanus</i>)