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Research was conducted to predict the binding energies and geometries of benzene-BX3 and ethene-BX3 complexes using quantum mechanical ab initio calculations. Single point measurements at a much higher correlation level and larger basis sets were also performed. Results based on binding energies indicate that all the complexes were weakly bound van der Waals complexes except for the C2H4-BH3 complex. There was also a strong evidence of an unusual increase in the nucleophilicity of one of the benzene carbons in the lowest energy conformer of systems involving benzene.

Histidine state (deprotonated, neutral, and protonated) is considered an important factor influencing the structural properties and aggregation mechanisms in amyloid β-peptides (Aβ), which are associated with the pathogenesis of Alzheimer's disease. Understanding the structural properties and aggregation mechanisms is a great challenge because two forms (the N ε -H or N δ -H tautomer) can exist in the free neutral state of histidine. Here, replica-exchange molecular dynamics simulation was performed to elucidate the changes in structure and the mechanism of aggregation influenced by tautomeric behaviors of histidine in Aβ(1-40). Our results show that sheet-dominating conformations can be found in the His6(δ)-His13(δ)-His14(δ) (δδδ) isomer with significant antiparallel sheet structures between R5-D7 and L34-G38, as well as between L17-F20 and L34-G38, implying that a new aggregation mechanism may exist to promote the generation of oligomers and/or aggregates. This work is helpful in understanding the fundamental tautomeric behaviors of neutral histidine in the process of aggregation.

The aggregation of amyloid β-peptide (Aβ peptide) has been associated with the pathogenesis of Alzheimer's disease (AD). In the present study, we aimed to disclose how Zn(2+) affects the Aβ aggregation in detail. Thus, molecular dynamics simulation was implemented to elucidate the changes of structure and residual hydrophobicity upon Zn(2+) coordination. Our results show that Zn(2+) can strongly influence the structural properties of Aβ40 and Aβ42 by reducing helical formation and increasing turn formation to expose the hydrophobic regions. Furthermore, hydrophobicity of Zn(2+)-Aβ40 and Zn(2+)-Aβ42 was much higher than that of each monomer, since Zn(2+) binding can significantly influence the hydrophilic domains of Aβ. The further analyses indicate that not only four residues (H6, E11, H13, and H14) but also R5, D7, K16, K28, and terminal residues influence hydrophobicity upon Zn(2+) coordination. Importantly, R5, K16, and K28 play a crucial role to regulate solvation-free energies. This work is helpful to understand the fundamental role of Zn(2+) in aggregation, which could be useful for further development of new drugs to inhibit Zn(2+)-Aβ aggregation.

The ground-state reverse proton transfer (GSRPT) of 7-hydroxyquinoline (7HQ) along a hydrogen (H)-bonded mixed-alcohol chain made of different two alcohol molecules having dissimilar proton-donating abilities, designed as a biomimetic system of a proton wire composed of various amino acids, has been investigated in nonpolar aprotic media of n-alkanes using time-resolved transient-absorption spectroscopy with variation of alcohol combinations and medium viscosities. Solvent-inventory experiments have been carried out by varying the composition of alcohols systematically in the heterogeneous H-bonded alcohol chain to understand the molecular dynamics and the elementary mechanisms of GSRPT. Similarly to excited-state proton transfer, GSRPT takes place concertedly without accumulating any reaction intermediate but asymmetrically via a rate-determining tunneling process, and GSRPT is accelerated by the accumulated proton-donating abilities of two alcohol molecules participating in the H-bond chain by push-ahead effect. However, in the ground state, the reorganization of the H-bond bridge in a cyclic 7HQ·(alcohol)(2) complex to form an optimal precursor configuration for efficient proton tunneling takes place prior to intrinsic proton transfer, and the rate constant of GSRPT is governed mainly by configurational optimization. Consequently, the large contribution of the configurational optimization to GSRPT leads to the weaker push-ahead effect and the less-asymmetric character of GSRPT than the respective ones of excited-state proton transfer whose rate constant is determined mostly by tunneling.

A recent study (J. Phys. Chem. B 2006, 110, 5337) proposed that fullerene-porphyrin-fullerene triad (C60PC60) could be utilized as a photoinduced switch due to the difference in electron transfer directionality for the cis and trans conformer. It is found that the rotational barrier between the SS and AA conformers of C60PC60 is about 3-5 kcal/mol, which can be facilely controllable in experiment. The rotational energy barrier for the anion system is slightly higher than the neutral C60PC60, whereas the total energy of the neutral triad is decreased by about 60 kcal/mol upon electron attachment. The corresponding reorganization energy is very small. These results reveal that the C60PC60 is a potential candidate for electrochemical machinery and energy storage material.

A low-temperature scanning tunneling microscope (STM) and ab initio calculations were used to study the electric field effect on the vibration of single CO molecules in an STM junction at 13 K. The vibrational energy of CO molecules adsorbed on silver atoms, measured by STM-based inelastic electron tunneling spectroscopy, depends on the direction of the electric field applied between the STM tip and the silver species. This characteristic can be explained by the charge separation model. The electric field modifies the binding characteristics of CO on silver as a result of a change in the charged states of the species, which leads to an increase (or a decrease) of the energies of the hindered rotation and the CO stretch on silver.

Recently, the solvent power of ionic liquid (IL) has been described based on Flory-Huggins (FH) theory assuming that the volumes of the components are the same (J. Phys. Chem. B, 2006, 110, 16205). Here, we extended the FH theory to derive the solvent power in the case of different sizes (molar volumes) of the IL's components based on "polymer-like" model. Applying this model, the effect of ionic size on the solvent power of ionic liquids has been investigated. It was found that the effect of size can be characterized by introducing the effective volume (V+ and V-) of each site of the ion, and for the equivalent ionic liquid, the larger effective volume of the ionic liquid has the larger solvent power. Our results are in excellent agreement with the experimental solubility data in various ionic liquids.

The RISM-SCF and polarizable continuum model (PCM) approaches have been applied to study the conformational equilibrium of 1,2-dichloroethane (DCE) in water. Both the electron correlation effect and basis sets play an important role in the relative energies of the gauche and trans conformers in gas and solution phases. Both PCM and RISM-MP2 methods resulted in a consistent trend with the previous experimental and theoretical studies that the population of the gauche conformer increases in going from the gas phase to the aqueous solution. However, the PCM treatment could not describe the solvent effect completely in that the sign of the relative free energy of the gauche and trans forms is opposite to the most recent experimental and theoretical data, while the RISM-MP2 gives the right sign in the free energy difference. We found that the larger excess chemical potential gain (by ca. -4.1 kcal/mol) for the gauche conformer is large enough to result in the gauche preference of DCE in water, though it has to compensate for more solute reorganization energy (approximately 1.6 kcal/mol) and overcome the energy difference (approximately 1.6 kcal/mol) in the gas phase. The radial distribution functions between DCE and the nearest water shows that the electrostatic repulsion between chlorine and oxygen atoms is higher in the trans conformer than in the gauche one, while the attractive interaction between chlorine and hydrogen of water is higher in the gauche conformer.

The conformational (cis and trans) stability and electronic structures of (C(60)CHCOO)(2)-Sn(IV) porphyrin, recently synthesized as a novel fullerene-porphyrin-fullerene triad linked by metal axial coordination, have been studied by ab initio calculations. The cis conformer was found to be slightly more stable than the trans by 1.38 kcal/mol in the neutral compound. Upon the addition of an electron to the triad, the relative stability of the cis conformer was found to be higher (3.29 kcal/mol) than that in the neutral one. From the investigation of frontier molecular orbitals, for the cis conformer, it was found that the electrons are localized in HOMO of the porphyrin, while the electrons are localized in LUMO of the syn-fullerene. For the trans conformer, it was found that the electrons are localized in HOMO of the porphyrin, while the electrons are localized in LUMO of one of the two fullerene moieties, and the electrons are localized in LUMO2 of the other fullerene moiety, but the LUMO and LUMO2 have the same orbital energy. Thus, the PET may take place unidirectionally in the cis conformer from the porphyrin to the syn-fullerene, while it is bidirectional from the porphyrin to both of the fullerene moieties.

We investigate the structures, NMR chemical shifts, absorption spectra, frontier molecular orbitals, and transition density matrices of pi-stacked polyfluorenes by ab initio calculations. For F1-F4, we consider two different conformations, syn and anti. The simulated 1H NMR chemical shifts are in good agreement with the previous experiment, and the significantly upfielded chemical shifts explain that the fluorene moieties are stacked on each other. It is found that the relative stability for syn and anti conformers is almost equivalent in B3LYP calculations; however, the syn conformer becomes much more stable than the anti conformer in MP2 calculations, which is consistent with the experimental finding that only the syn conformers are relevant. The vertical detachment energy, which is linearly proportional to the ionization potential, shows the same size dependence as the previous experiment. The electron attachment energy decreases exponentially as the size increases, which implies that the electron transport would be possible even for long chains such as F3 and F4. This was evident from the frontier molecular orbitals (HOMO and LUMO). Also, it is found that the syn conformers are very favorable for electron transport through the pi-stacked fluorene moieties.