Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is a rare event sampling method of proteins, which does not rely on knowledge of the target structure. nt-PaCS-MD is an extension of targeted PaCS-MD (t-PaCS-MD). In nt-PaCS-MD, it makes use of cyclic resampling from some relevant initial structures to expand the searched conformational subspace. Reliable identification of these initial structures is the key to using nt-PaCS-MD. In the present study, we introduce the moving root-mean-square deviation (mRMSD) as a metric for identification of these statistical conformation outliers. mRMSD can be calculated for any ith geometry in the trajectory generated by short MD runs. The reference to which the mRMSD relates is the close surrounding of the ith conformation, often the (i-1) st one. Based on mRMSD, we show that it increases its effectiveness compared to the conventional MD.
To investigate the effects of forsterite structure on processes of H2O decomposition and proton diffusion, we performed molecular dynamics calculations on forsterites in glassy and crystalline states. The result shows that the decomposition rate of H2O on forsterite in the glassy state is higher than that in crystalline state in a temperature range of 200 to 400 K. Furthermore, the decomposed proton permeates into the internal part of glassy forsterite through hopping, whereas no permeation was observed for the crystalline state. These results suggest that the glassy structure of forsterite is an important factor for chemical evolution processes in interstellar spaces.
We demonstrate that accurate prediction of the crystal structures of anthracene and its derivatives is possible with the van der Waals density functional. Based on the calculated crystal structures, we investigate their electronic structures and discuss the correlation between crystal structure/molecular configuration and the electronic structure, in particular, the dispersion of the bands composed of the highest occupied molecular orbitals, which are important to discuss the charge carrier transport property.
An RNA aptamer that binds with high affinity and specificity to human immunoglobulin G (IgG) is a 24-mer single-stranded oligonucleotide containing 2′-fluoro pyrimidine nucleotides. Using X-ray crystallographic analysis, a Ca2+ ion was reported as being located near the G7 phosphate of the RNA aptamer. Surface plasmon resonance analysis showed that the RNA aptamer could not bind to IgG in a buffer without Ca2+ ions. To elucidate the role of Ca2+ ions in the binding of the RNA aptamer to IgG, we performed molecular dynamics simulation for the RNA aptamer/IgG complex with and without Ca2+ ions in a solvent. In the presence of Ca2+ ions, the RMSD of the RNA aptamer backbone remained below approximately 3.0 Å from the crystal structure during a 1,500-ns simulation. The distance between the centroids of the RNA aptamer and IgG was maintained between the centroids in the crystal structure. However, in the absence of Ca2+ ions, the RMSD increased and the structure of the RNA aptamer changed from the initial structure. These results indicate that Ca2+ ions play a role in maintaining the conformation of the RNA aptamer to the binding form.
Ferulic acid is known to have strong antioxidant properties. In the present study, we investigate the electronic structures of ferulic acid and its radical species extracting the hydrogen atom from its phenolic hydroxyl group. The relation of the results by several machine learning models using R/caret package, such as partial least squares, random forest, radial basis function kernel regularized least squares, and baysian regularized neural network, with the radical scavenging activity with the DPPH reagent, IC50, measured by Sakamoto et al. is discussed. We found all four methods gave reasonable correlation coefficients which means the possible prediction of the IC50 values with the results of the molecular orbital calculations only.
In this study, we attempted to quantify the shape of various metastable morphologies of microphase separation in block copolymers that can be observed in a computer simulation under the same condition as that for double gyroid (stable state). For the quantification, we used multifractal analysis, which is a tool to evaluate the shape having heterogeneous density inside it. Our analysis showed that the indicators relating to the multifractal analysis of metastable structures are distributed far from that of double gyroid.
Ionic liquids (ILs) are non-volatile and highly stable solvents, which consist of organic/inorganic cations and anions. ILs are attractive since they can be utilized as gas-separating materials. Using a conductor-like screening model for realistic solvation (COSMO-RS) method, in this study, Henry's law constants of 15 gases (HCN, SO2, H2O, NH3, H2S, NO2, NO, CO, N2O, CO2, C2H6, C2H4, CH4, N2, H2) in 68,775 ILs were calculated to construct an ab initio database to search for ILs which are suitable for gas separation. Based on the database, it was numerically confirmed that not only the ions' geometric structures but also electronic structures are important to predict ILs' gas absorption abilities with high accuracy.
Umbrella sampling is a method to calculate free energy by using molecular dynamics simulation. In the previous study, Free Energy Reaction Route Mapping Method (FERRMap) [5,6] is proposed, which is the method to calculate free energy reaction networks by using the umbrella integration method [1,2] and scaled hypersphere searching method [3,4]. In this study, we calculated FERNs of alanine octapeptide (Ala8) in water by using the FERRMap method on the dihedral of the Ramachandran plot, which is 12 dimensional. We found 613 equation structures and 835 transition structures on the FERN of Ala8. This FERN is too complicated to explain the folding of Ala8, we propose an effective flow analysis method. By using this method, we found the representative paths connecting the beta-strand and alpha-helix structure.
A band gap prediction model of π-conjugated polymers was constructed using aromatic/quinoid, donor/acceptor, and torsion properties to predict quantitatively the band gap of π-conjugated polymers from properties of monomers. Quinoid stabilization energy (QSE), energy difference between HOMO of donor and LUMO of acceptor, torsion angle in homo-dimer of monomers were used as descriptors of aromatic/quinoid, donor/acceptor, and torsion properties. The neural network, which was constructed by 2 hidden layers with 5 neurons per layer, quantitatively predicts (RMSD = 0.207 eV, R2 = 0.885) the band gap of the π-conjugated polymers from descriptors of monomers.
According to the current superposition law in nanoscale, the conductance gets more than doubled when the number of paths is doubled. The superposition law can be applied to the molecular graph, which is a discrete mathematical expression for a structure consisting of nodes and edges. We previously revealed that the aromatic parallel circuit i.e. benzene molecule breaks the superposition law. In this paper, we show that [4n+2] annulenes also break the current superposition law from the viewpoint of orbital interaction between two fragments in the parallel circuit.
Reaction mechanisms for the isomerization of nitrile N-oxide to isocyanate catalyzed by hydroxide ion were investigated by density functional theory calculations. In this mechanism, nitrile N-oxide first dimerizes to a six-membered ring intermediate, and then undergoes two rearrangement reactions to isomerize into two isocyanate molecules. The process with the highest activation energy as an elementary reaction was the second rearrangement reaction, with an activation free energy of 31.1 kcal/mol, which is reasonable for a reaction proceeding slowly at room temperature. This mechanism can also explain the experimental results that the oxygen atom exchanges between nitrile N-oxide molecules during the isomerization reaction.
Among ester synthesis methods, there is a method using a pyridine derivative as a catalyst, and the esterification reaction rate may be increased through a highly active acylpyridinium cation intermediate. It has been reported that the stability of acylpyridinium cations correlates with the reaction rate of esterification. In this study, we try to clarify the reason for the correlation between the reaction rate and the stability, then we investigate the relationship between the stability and structures of acylpyridinium cations. As a result, we found that the stability largely depends on the electronic donor property of the substituents, and acylpyridinium cation may act as an effective catalyst for esterification when the substituents have strong donor property at positions 3, 4, 5 of the pyridine ring.
All-atom molecular dynamics were performed on 4-heptyl-4’-cyanobiphenyl (7CB) to study the mechanism of heat conduction in the nematic liquid crystal. The non-equilibrium molecular dynamics simulation using our amended force field for 7CB has reproduced the anisotropy of the thermal conductivity in the nematic phase of 7CB. Furthermore, the calculated Phonon density of state shows that the higher thermal conductivity parallel to the director than that perpendicular to the director is due to the heat conduction derived from the stretching vibration of the well-oriented covalent bonds.
Iron–Sulfur clusters are often found in active sites of electron–transfer proteins. Their redox potentials are well controlled; however, its mechanism has not been understood well. In this study, therefore, we elucidate the effects of the protein-field, especially hydrogen bonds around the active site on the redox potential by using density functional theory (DFT) calculations. The results indicate that the ionization potentials are in proportion to the number of hydrogen bonds around the active site.
The octanol–water partition coefficient (logP) is not only an important index value of the hydrophobicity (or hydrophilicity) of a substance, but it is possible to predict the absorbability and accumulation of organic compounds in the living body, and application to the development of new drugs can be expected. In this paper, the logP values of compounds were predicted by solvation free energy calculation using packaged software, Gaussian09. In calculations of free energy in solution, we used CPCM, IEFPCM and SMD methods in the SCRF methods and compared the logP calculated by those methods with that observed by experiments. The results suggest that the SMD method gave better results than the other two.
Weathering of glass is a problem because it degrades the optical performance of the glass. The weathering occurs when the glass has been contacted with water in the long-term. In this work, a water/glass interface model was prepared and molecular dynamics simulation was performed to investigate the structure and properties near the water/glass interface. The broken surface of the glass network at near the interface was confirmed by the distribution change of the Qn species, and it suggests that the sodium ions are trapped by the destabilized glass surface structure.
In order to describe the time evolution of the electronic state, we have developed a new method, using the particle method with the Bohmian, to solve the time-dependent Schrödinger equation. The method has been applied to the time-dependent coherent state for a harmonic potential, whose analytical solutions are well-known. To evaluate this method, the ground state is evolved to estimate the excited state, and we follow the dynamic dipole moment as the linear responses of the system under externally applied perturbations in real time. From the polarizability obtained as the Fourier transform of the dipole moment, we calculate the optical strength function. As a result, a single peak is observed, which was exactly expected from the analytical solution. We recognize that the method is quite valid for the time dependent electronic structure calculation.
The surface adsorption model calculation database, which we are constructing from systematic quantum chemical calculations, is reported. The database can be utilized to analyze heterogeneous catalytic reactions. As an application, we predicted the experimental catalytic activity for the methane steam reforming reaction with this database by using the sparse modeling techniques.
We investigated the hydrogen bonding interaction between the anion and nitrogen atom of the urea derivative nPUA (n = 1, 2, 9, where n is the substituted position of the parent anthracene) to examine a proton transfer reaction in the complex in the excited state, which is known as excited-state intermolecular proton transfer (ESPT). We revealed the details of the hydrogen bonding interaction between an anthracene-urea derivative and an acetate anion in the excited state by taking advantage of TD-DFT calculation.
Aiming at developing synthetic methods of new Keggin-type polyoxometalates (POMs) that can mediate proton-conjugated multi-electron transfer reactions useful for efficient regeneration of fuels, we have investigated the reaction routes from Anderson-type POMs to Keggin-type POMs. The POM systems with various kinds of heteroatoms as their central cations were calculated using the Nudged Elastic Band (NEB) method as well as the first-principles electronic structure method. The effects of the heteroatoms on the reaction routes have been discussed.
Carbon nanotube (CNT) is conventionally expected to reinforce ceramic matrix like alumina. Previous experiments show that processing conditions such as annealing have positive effect on mechanical properties of the alumina/CNT composite. However, the reinforcing mechanism by annealing is not fully understood yet. For further improving the performance of alumina/CNT composite, this study aims to understand the reinforcing mechanism by annealing from the atomic scale with reactive molecular dynamics simulations. We conduct tensile simulations on pure alumina, non-annealed and annealed alumina/CNT composites, and then analyze the mechanical properties of the three models. Consequently, we find out that annealing enhances the interfacial interactions between alumina and CNT and reduces the interfacial slippage, so that the annealed CNT is more stretched than the non-annealed CNT, finally resulting in an improvement of the mechanical performance of composite.