Automated Exploration of Reaction Network and Mechanism via Meta-dynamics Nanoreactor

We developed an automated approach to construct the complex reaction network and explore the reaction mechanism for several reactant molecules. The nanoreactor type molecular dynamics was employed to generate possible chemical reactions, in which the meta-dynamics was taken to overcome reaction barriers and the semi-empirical GFN2-xTB method was used to reduce computational cost. The identification of reaction events from trajectories was conducted by using the hidden Markov model based on the evolution of the molecular connectivity. This provided the starting points for the further transition state searches at the more accurate electronic structure levels to obtain the reaction mechanism. Then the whole reaction network with multiply pathways was obtained. The feasibility and efficiency of this automated construction of the reaction network was examined by two examples. The first reaction under study was the HCHO + NH3 biomolecular reaction. The second example focused on the reaction network for a multi-species system composed of dozens of HCN and H2O compounds. The result indicated that the proposed approach was a valuable and effective tool for the automated exploration of reaction networks

Structures and Reactivity of Transition-Metal Compounds Featuring Metal-Ligand Multiple Bonds

This dissertation presents the results from density functional theory (DFT) calculations on three major projects I have been working on over the past several years. The first system is focused on the structure and reactivity of a novel osmium silylyne compounds featuring an Os≡Si triple bond. NMR simulation confirmed the existence of this compounds and bonding analysis like NBO and ETS-NOCV proved its triple bond character. The structures of the [2+2] cyclo-addition product from silylyne and other small molecules (PhC≡CPh and P≡C^(t)Bu) were also determined from possible isomers by energetic results and NMR simulations. The cycloaddition reactions were found to be under kinetic control and steric effects should be a major reason for that. Furthermore, the geometric and electronic structures of the osmium silylyne analogues (M≡E, M = Ru and Os; E = Si, Ge and Sn) are studied computationally and their similarities and distinctions are discussed. Both the second and third systems are related to the formation of transition metal imido compound (M=NR). In the second system a cationic oxorhenium(V) complex reacts with a series of arylazides (N_(3)Ar) to give cationic cis-rhenium(VII) oxo imido complexes. Inductive effect is found in the reaction rates but it leads to different trends for electron-donating and electron-withdrawing substituted phenyl azides. Computations found all the substituted phenyl imido products are formed through the same pathway. The reason for the different trend is due to the competitions between two major energy barriers along the reaction pathway. For the electron-withdrawing substituents, N_(2) extrusion is rate determining, while for the electron-donating substituents, the rate-determining step becomes the initial attack of the azide. The barriers for these two steps are inverted in their order with respect to the Hammett σ values; thus, the Hammett plot appears with a break in slope. In the third system a series of vanadium (III) terminal organoazides were converted to vanadium (V) imido compounds and small quantities of diazenes were found formed in the reactions. Computational studies were conducted to examine serveral possible pathways and a mechanism in which nitrene radicals released from metal-azide decompositions is supported based on two reasons: 1) The two-electron reduction on vanadium center during decomposition of azide generates two fragments both in their ground states (triplet states), which might drag the activation barrier down; 2) This conversion is spin-allowed since vanadium center and nitrene nitrogen are antiferromagnetically coupled in transition state. The ligand simplification study indicates that the bulky mesityl groups on the supporting ligand prevents the reactions from going through the direct N_(2) extrusion pathway

Realization of the Trajectory Propagation in the MM-SQC Dynamics by Using Machine Learning

The supervised machine learning (ML) approach is applied to realize the trajectory-based nonadiabatic dynamics within the framework of the symmetrical quasi-classical dynamics method based on the Meyer-Miller mapping Hamiltonian (MM-SQC). After the construction of the long short-term memory recurrent neural network (LSTM-RNN) model, it is used to perform the entire trajectory evolutions from initial sampling conditions. The proposed idea is proven to be reliable and accurate in the simulations of the dynamics of several site-exciton electron-phonon coupling models, which cover two-site and three-site systems with biased and unbiased energy levels, as well as include a few or many phonon modes. The LSTM-RNN approach also shows the powerful ability to obtain the accurate and stable results for the long-time evolutions. It indicates that the LSTM-RNN model perfectly captures of dynamical correction information in the trajectory evolution in the MM-SQC dynamics. Our work provides the possibility to employ the ML methods in the simulation of the trajectory-based nonadiabatic dynamic of complex systems with a large number of degrees of freedoms

Physiological dynamics as indicators of plant response to manganese binary effect

IntroductionHeavy metals negatively affect plant physiology. However, plants can reduce their toxicity through physiological responses. Broussonetia papyrifera is a suitable candidate tree for carrying out the phytoremediation of manganese (Mn)-contaminated soil.MethodsConsidering that Mn stress typically exerts a binary effect on plants, to reveal the dynamic characteristics of the physiological indexes of B. papyrifera to Mn stress, we conducted pot experiments with six different Mn concentrations (0, 0.25, 0.5, 1, 2, and 5 mmol/L) for 60 days. In addition to the chlorophyll content, malondialdehyde (MDA), proline (PRO), soluble sugar, superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), the absorption and transfer characteristics of Mn, and root structure were also measured.ResultsPhytoremedial potential parameters such as the bioconcentration factor (BCF) and translocation factor (TF) displayed an increasing trend with the increase of Mn concentration. At lower Mn concentrations (<0.5 mmol/L), the TF value was <1 but crossed 1 when the Mn concentration exceeded 100 mmol/L. The Mn distribution in various tissues was in the following order: leaf > stem > root. The root structure analysis revealed that low-level concentrations of Mn (1 mmol/L) promoted root development. Mn concentration and stress duration had significant effects on all measured physiological indexes, and except soluble sugar, Mn concentration and stress time displayed a significant interaction on the physiological indexes.DiscussionOur study demonstrates that the physiological indexes of B. papyrifera display dynamic characteristics under Mn stress. Thus, during the monitoring process of Mn stress, it appears to be necessary to appropriately select sampling parts according to Mn concentration

Coal Rock Breaking Simulation and Cutting Performance Analysis of Disc Cutters

The coal rock breaking ability of disc cutters directly affects the construction efficiency and safety of rescue tunnels in collapsed coal rock formations. This paper establishes the plastic constitutive relationship under the Drucker-Prager (D-P) plasticity criterion, builds up a finite-element analysis (FEA) model for the coal rock breaking with a single cutter on Abaqus FEA, and explores the influence laws of different penetrations and cutting velocities on the rock breaking performance of the cutter. The results show that: as the penetration increased from 3.0 mm to 7.0 mm, the mean vertical force of the cutter grew from 16.97 kN to 23.36 kN, and the mean rolling force rose from 1.79 kN to 3.95 kN. The increase of the cutter\u27s vertical force improves the cutting efficiency, but intensifies the vertical impact, which undermines construction safety. As the cutting velocity increased from 0.6 rad/s to 1.5 rad/s, the mean vertical force grew from 15.64 kN to 22.94 kN, and the mean rolling force rose from 1.46 kN to 4.23 kN. With the increase of cutting velocity, the cutting force grew at an increasing speed. The increase of cutting velocity can improve cutting efficiency, but an excessively fast cutting velocity will weaken the stability of the cutting operation, and add to the wear of the tool. The research method provides theoretical supports to the cutterhead design of tunnel boring machine (TBM) and tunnelling control in broken coal rock formation

CO₂/N₂ triggered switchable Pickering emulsions stabilized by alumina nanoparticles in combination with a conventional anionic surfactant

Stable n-decane-in-water Pickering emulsions were prepared using positively charged alumina nanoparticles in combination with a trace amount of the anionic surfactant sodium dodecyl sulfate (SDS) as stabilizer. Particles were hydrophobized in situ by adsorption of surfactant enhancing their surface activity. Emulsions can be readily demulsified by addition of an equal amount of a switchable surfactant, N'-dodecyl-N,N-dimethylacetamidine (DDAA), which can be transformed between a surface-active amidinium/cationic form and a surface-inactive amidine/neutral form by bubbling CO₂ or N₂, respectively. Following addition of cationic DDAA which prefers to form ion pairs with SDS, desorption of SDS from particles surfaces occurs and alumina particles are rendered hydrophilic resulting in demulsification of the emulsion. However, by bubbling N₂ into the demulsified mixture, DDAA molecules are converted to the amidine/neutral form leading to collapse of the ion pairs and re-establishment of the in situ hydrophobization of particles. Stable Pickering emulsions can be prepared again following homogenization. This simple demulsification/re-stabilization cycle can be repeated several times. Experimental evidence including measurement of the adsorption isotherm, zeta potentials, extent of particle adsorption at droplets interfaces in emulsions and microscopy is given to support the postulated mechanisms

Water level affects availability of optimal feeding habitats for threatened migratory waterbirds

Extensive ephemeral wetlands at Poyang Lake, created by dramatic seasonal changes in water level, constitute the main wintering site for migratory Anatidae in China. Reductions in wetland area during the last 15 years have led to proposals to build a Poyang Dam to retain high winter water levels within the lake. Changing the natural hydrological system will affect waterbirds dependent on water level changes for food availability and accessibility. We tracked two goose species with different feeding behaviors (greater white‐fronted geese Anser albifrons [grazing species] and swan geese Anser cygnoides [tuber‐feeding species]) during two winters with contrasting water levels (continuous recession in 2015; sustained high water in 2016, similar to those predicted post‐Poyang Dam), investigating the effects of water level change on their habitat selection based on vegetation and elevation. In 2015, white‐fronted geese extensively exploited sequentially created mudflats, feeding on short nutritious graminoid swards, while swan geese excavated substrates along the water edge for tubers. This critical dynamic ecotone successively exposes subaquatic food and supports early‐stage graminoid growth during water level recession. During sustained high water levels in 2016, both species selected mudflats, but also to a greater degree of habitats with longer established seasonal graminoid swards because access to tubers and new graminoid growth was restricted under high‐water conditions. Longer established graminoid swards offer less energetically profitable forage for both species. Substantial reduction in suitable habitat and confinement to less profitable forage by higher water levels is likely to reduce the ability of geese to accumulate sufficient fat stores for migration, with potential carryover effects on subsequent survival and reproduction. Our results suggest that high water levels in Poyang Lake should be retained during summer, but permitted to gradually recede, exposing new areas throughout winter to provide access for waterbirds from all feeding guilds

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts