Direct ab-initio MD study on the diffusion of lithium ion on the Nano-Carbon Materials

The diffusion dynamics of the Li^+ ion on carbon materials such as graphene and fullerene (C_) have been investigated by means of direct molecular orbital-molecular dynamics (MO-MD) method. Simulation temperatures were chosen in the ranges 10-1200 K. The dynamics calculations showed that the diffusion coefficients for the Li^+ ion on the C_ surface are larger than those of the graphite surface at low temperature (below 300 K). Those of both C_ and graphene surface were almost equivalent at medium temperatures around 300 K. At higher temperatures (T > 300K), the coefficients for graphene surface were significantly larger than those of C_. On the basis of theoretical results, we designed an ion switching molecular device composed of C_ and graphite sheet.Nagasaki Symposium on Nano-Dynamics 2008 (NSND2008) 平成20年1月29日(火)於長崎大学 Poster Presentatio

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl

Reaction dynamics for a microsolvated SN2 reaction OH–(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25 kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl–+H2O: denoted by channel I), (2) a solvation channel (the products are Cl–(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OHH2O+Cl–: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results. ©2006 American Institute of Physic

SN2 and SN2' reaction dynamics of cyclopropenyl chloride with halide ion : A direct ab initio molecular dynamics (MD) study

Direct ab initio molecular dynamics (MD) calculations have been carried out for the reaction of cyclopropenyl chloride with halide ion (F–) (F– + (CH)3Cl → F(CH)3 + Cl–) in gas phase. Both SN2 and SN2′ channels were found as product channels. These channels are strongly dependent on the collision angle of F– to the target (CH)3Cl molecule. The collision at one of the carbon atoms of the C=C double bond leads to the SN2′ reaction channel; whereas the collision at the methylene carbon atom leads to the SN2 reaction channel. The reactions proceed via a direct mechanism without long-lived complexes. The reaction mechanism is discussed on the basis of the theoretical results

Effects of single water molecule on proton transfer reaction in uracil dimer cation

Ionizing radiation to DNA induces sometimes the DNA damage. In this report, the ionization dynamics of uracil dimer (U)(2) and its water complex (U)(2)-H2O have been investigated by means of direct ab initio molecular dynamics (AIMD) method in order to elucidate the effects of single water molecule on the reaction rate of proton transfer (PT) in DNA model base pair. The (U)(2) dimer is widely used as a simplified mimetic model of Watson-Crick base pair. The static ab initio calculation showed that two conformers exist as neutral complex of (U)(2)-H2O. The direct AIMD calculation of ionization process of (U)(2)-H2O showed that the rate of PT is affected even by a single water molecule, while it was dependent on the position of H2O around (U)(2). The interaction of water molecule with (U)(2) affected the potential energy curve for PT. Especially, the activation barrier along the PT coordinate was significantly changed by the interaction with one H2O molecule. The effects of one H2O molecule on the PT process were discussed on the basis of theoretical results

Electron hydration dynamics in water clusters: A direct ab initio molecular dynamics approach

Electron attachment dynamics of excess electron in water cluster (H2O)n (n=2 and 3) have been investigated by means of full-dimensional direct ab initio molecular dynamics (MD) method at the MP2/6-311++G(d,p) level. It was found that the hydrogen bond breaking due to the excess electron is an important process in the first stage of electron capture in water trimer. Time scale of electron localization and hydrogen bond breaking were determined by the direct ab initio MD simulation. The initial process of hydration in water cluster is clearly visualized in the present study. In n=3, an excess electron is first trapped around the cyclic water trimer with a triangular form, where the excess electron is equivalently distributed on the three water molecules at time zero. After 50 fs, the excess electron is concentrated into two water molecules, while the potential energy of the system decreases by –1.5 kcal/mol from the vertical point. After 100 fs, the excess electron is localized in one of the water molecules and the potential energy decreases by –5.3 kcal/mol, but the triangular form still remained. After that, one of the hydrogen bonds in the triangular form is gradually broken by the excess electron, while the structure becomes linear at 100–300 fs after electron capture. The time scale of hydrogen bond breaking due to the excess electron is calculated to be about 300 fs. Finally, a dipole bound state is formed by the linear form of three water molecules. In the case of n=2, the dipole bound anion is formed directly. The mechanism of electron hydration dynamics was discussed on the basis of theoretical results. ©2006 American Institute of Physic

Alkali metal mediated C-C bond coupling reaction

Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)(2), have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)(2), the structure of [ Li(Bz)(2)](-) was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C-1-C-1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results. (C) 2015 AIP Publishing LLC

Reaction dynamics following electron capture of chlorofluorocarbon adsorbed on water cluster : a direct density functional theory molecular dynamics study

The electron capture dynamics of halocarbon and its water complex have been investigated by means of the full dimensional direct density functional theory molecular dynamics method in order to shed light on the mechanism of electron capture of a halocarbon adsorbed on the ice surface. The CF2Cl2 molecule and a cyclic water trimer (H2O)3 were used as halocarbon and water cluster, respectively. The dynamics calculation of CF2Cl2 showed that both C–Cl bonds are largely elongated after the electron capture, while one of the Cl atoms is dissociated from CF2Cl as a Cl− ion. Almost all total available energy was transferred into the internal modes of the parent CF2Cl radical on the product state, while the relative translational energy of Cl− was significantly low due to the elongation of two C–Cl bonds. In the case of a halocarbon-water cluster system, the geometry optimization of neutral complex CF2Cl2(H2O)3 showed that one of the Cl atoms interacts with n orbital of water molecules of trimer and the other Cl atom existed as a dangling Cl atom. After the electron capture, only one C–Cl bond (dangling Cl atom) was rapidly elongated, whereas the other C–Cl bond is silent during the reaction. The dangling Cl atom was directly dissociated from CF2Cl(H2O)3 as Cl−. The fast Cl− ion was generated from CF2Cl(H2O)3 on the water cluster. The mechanism of the electron capture of halocarbon on water ice was discussed on the basis of the theoretical results. ©2007 American Institute of Physic

Ionization dynamics of the branched water cluster: A long-lived non-proton-transferred intermediate

The proton transfer (PT) reaction after water cluster ionization is known to be a very fast process occurring on the 10-30 fs time scale. In the present study, the ionization dynamics of the branched water tetramer (H2O)(4) were investigated by means of a direct ab initio molecular dynamics (AIMD) method to elucidate the time scale of PT in the water cluster cation. A long-lived non-proton-transferred intermediate was found to exist after the ionization of the branched-type water cluster. The lifetimes of the intermediate were calculated to be ca. 100-150 fs. PT occurred after the formation of the intermediate. The structure of the intermediate was composed of a symmetric cation core: H2O-H2O+-H2O. The broken symmetry of the structure led to PT from the intermediate. The reaction mechanism is discussed based on the theoretical results. (C) 2016 Elsevier B.V. All rights reserved