Artificial intelligence driven molecule adsorption prediction (AIMAP) applied to chirality recognition of amino acid adsorption on metals.

Predicting the adsorption structure of molecules has long been a challenging topic given the coupled complexity of surface binding sites and molecule flexibility. Here, we develop AIMAP, an Artificial Intelligence Driven Molecule Adsorption Prediction tool, to achieve the general-purpose end-to-end prediction of molecule adsorption structures. AIMAP features efficient exploration of the global potential energy surface of the adsorption system based on global neural network (G-NN) potential, by rapidly screening qualified adsorption patterns and fine searching using stochastic surface walking (SSW) global optimization. We demonstrate the AIMAP efficiency in constructing the Cu-HCNO6 adsorption database, encompassing 1 182 351 distinct adsorption configurations of 9592 molecules on three copper surfaces. AIMAP is then utilized to identify the best adsorption structure for 18 amino acids (AAs) on achiral Cu surfaces and the chiral Cu(3,1,17) S surface. We find that AAs chemisorb on copper surfaces in their highest deprotonated state, through both the carboxylate-amino skeleton and side groups. The chiral recognition is identified for the d-preference of Asp, Glu, and Tyr, and l-preference for His. The physical origin for the enantiospecific adsorption is thus rationalized, pointing to the critical role of the competitive adsorption between functional side groups and the carboxylate-amino skeleton at surface low-coordination sites.

Interpretation of genotype-environment-sowing date/plant density interaction in sorghum [Sorghum bicolor (L.) Moench] in early mature regions of China.

Sorghum [Sorghum bicolor (L.) Moench] is an important crop for food security in semiarid and arid regions due to its high tolerance to abiotic and biotic stresses and its good performance in marginal lands with relatively low fertility. To deeply understand the interrelationship among sorghum genotype, environment, sowing dates, and densities in the spring sowing early maturing (SSEM) areas of China, and to provide a basis for specifying scientific and reasonable cultural practices, a two-year field experiment was conducted with six popular varieties at six locations. Combined ANOVA showed that the yield difference between years was significant (P<0.05); the yield differences among locations, varieties, sowing dates, and densities were all highly significant (P<0.01). The variety effect was mainly influenced by location, year, sowing dates and their interactions. The sowing effect was mainly influenced by the location, year, variety and their interactions The plant density effect was significantly influenced by location and location-year interaction. Of the contributions of various test factors to yield variance, the location was the largest one (38.18%), followed by variety (12.31%), sowing date (1.53%), density (0.54%), and year (0.09%), with all these single factors accounting for 52.65%. The total contribution of all two-factor interactions accounted for 14.24%, among which the greatest contributor was location-hybrid interaction (8.07%). The total contribution of all three-factor interactions accounted for 14.58%, of which year-location-hybrid interaction was the largest contributor (9.02%). Sowing dates significantly affected model of sorghum growth and development, especially during the late period. The key climatic factors affecting yield were different among the six locations. Weather factors during the grain filling stages contributed much more than those during the early stage to grain yield. Mid-maturing varieties are recommended other than early maturing varieties for the SSEM areas even when late sowing occurs. Sowing as early as possible is recommended for areas with very short frost-free period (Harbin, Tongliao, and Datong). Proper delayed sowing is recommended for areas with a relative long frost-free period (Gongzhuling, Baicheng and Zhangjiakou). This research will provide a conducive reference for sorghum production in similar areas.

Direct diabatization and analytic representation of coupled potential energy surfaces and couplings for the reactive quenching of the excited 2Σ+ state of OH by molecular hydrogen.

We have employed extended multiconfiguration quasidegenerate perturbation theory, fourfold-way diabatic molecular orbitals, and configurational uniformity to develop a global three-state diabatic representation of the potential energy surfaces and their couplings for the electronically nonadiabatic reaction OH* + H2 → H2O + H, where * denotes electronic excitation to the A 2Σ+ state. To achieve sign consistency of the computed diabatic couplings, we developed a graphics processing unit-accelerated algorithm called the cluster-growing algorithm. Having obtained consistent signs of the diabatic couplings, we fit the diabatic matrix elements (which consist of the diabatic potentials and the diabatic couplings) to analytic representations. Adiabatic potential energy surfaces are generated by diagonalizing the 3 × 3 diabatic potential energy matrix. The comparisons between the fitted and computed diabatic matrix elements and between the originally computed adiabatic potential energy surfaces and those generated from the fits indicate that the current fit is accurate enough for dynamical studies, and it may be used for quantal or semiclassical dynamics calculations.

[Significance of Th1/Th17 Imbalance in Mice with Acute Graft-versus-Host Disease].

OBJECTIVE: To investigate the effects of Th1/Th17 cell imbalance on the pathogenesis of acute graft-versus-host disease (GVHD) in mice. METHODS: In a murine GVHD model of C57BL/6 (H-2(b)), a low dose of halofuginone (HF) was applied for treating the recipients in order to result in Th1/Th17 imbalance. Rechipient mice were divided into GVHD group (without HF intervention) and GVHD plus HF group (treated by HF). The recipients were monitored for survival rate, clinical scores of acute GVHD, contents of circulatory Th1 and Th17 cells, Th1/Th17 ratio and serum level of IFN-γ and IL-17A. Expression levels of IFN-γ and IL-17A in target organs were analyzed by using real-time PCR, and the target organs were delivered for histological examinations. RESULTS: Recipients treated with HF showed that all the mortality, circulatory Th1/Th17 ratio and clinical score were higher than those in the mice without HF intervention (P < 0.05). Circulatory Th1/Th17 ratio positively correlates with clinical score (P < 0.001). HF administration reduces the expression level of intestinal IL-17A and increases intrahepatic and intestinal IFN-γ level (P < 0.05), HF treatment aggravates GVHD in liver and small intestine with augmented hepatic and intestinal inflammation. CONCLUSION: Th1/Th17 imbalance contributes to the pathogenesis of acute GVHD.

Extended Energy Divide-and-Conquer Method Based on Charge Conservation.

The divide-and-conquer (DC) scheme, the most popular linear-scaling method, is very important in the quantum mechanics computation of large systems. However, when a chemical system is divided into subsystems, its covalent bonds are often broken and then capped by complementary atoms/groups. In this paper, we show that the charge transfer between subsystems and the complementary atoms/groups causes the nonconservation of the total charge of the whole system, and this is the main source of error for the computed total energy. On the basis of this finding, an extension of the many-body expansion method (energy-based divide-and-conquer, EDC) utilizing charge conservation (E-EDC) is proposed. In the E-EDC method, initially the total energies of the whole system at different many-body correction levels are computed according to the EDC scheme. The total charges of the whole system, that is, the sum of the charges of the subsystems without cap atoms/groups at different many-body correction levels, are also computed. Then the total energy is extrapolated to the value at which the net charge of the whole system equals to the real value. Other properties such as atomic forces can also be extrapolated in a similar way. In the test of 24 and 32 glycine oligomers, this scheme reduces the error of the total energy by about 40-70%, but the computational cost is almost the same as that of the EDC scheme.

[Recovery of vascular niche in bone marrow by donor derived endothelial progenitor cells after allogeneic bone marrow transplantation in mice].

OBJECTIVE: To investigate the role of endothelial progenitor cell (EPC) injection in the restoration of vascular niche in bone marrow (BM) after allo-BMT in mice, and to observe its role on hematopoietic reconstitution. METHODS: 6-8 weeks old female BALB/c (H-2(d)) were randomized to BMT (allo-BMT) group and combined EPC transplant (allo-BMT + EPC) group. For allo-BMT group, female BALB/c mice were lethally irradiated with 60Co source, and then were injected intravenously with 5×10(6) BM cells from donor mice. In allo-BMT + EPC group, recipient mice were injected intravenously with 5×10(6) BM cells and 5×10(5) EPC from donor mice. The recipients were monitored for histological changes of endothelial cells (EC) in BM. The recovery of hematopoiesis was determined by white blood cell counts and the proportion of reticulocytes in circulation and the proportion of hematopoietic stem cells (HSC) in BM. The histology of hematopoiesis in BM was also detected. RESULTS: The in vitro induced EPC successfully homed to the bone marrow of recipients. The ECs of allo-BMT recipients were destructed severely, while the structures of ECs were restored in EPC treated recipients. 10 and 15 days after allo-BMT, the amount of Lin-c-kit(+)Sca-1(+) cells in the BM of the EPC treated group were (20.31 ± 2.65)×10(3) per mouse and (10.26 ± 2.19)×10(3) per mouse, while the allo-BMT group's were (9.61 ± 0.98)×10(3) per mouse and (4.09 ± 1.34)×10(3) per mouse; and 15 days after allo-BMT, the amount of white blood cell counts and proportion of reticulocytes of the EPC treated group were (1.20 ± 0.11)×10(9)/L and (2.35 ± 0.30)% comparing to the allo-BMT group which were (0.65 ± 0.10)×10(9)/L and (1.63 ± 0.20)%. CONCLUSION: Co-transfer of donor EPC restores the ECs of bone marrow, which consequently promotes hematopoietic reconstitution in murine allo-BMT.

[An absence of donor TH17 differentiation ameliorates dermal tissue damage].

OBJECTIVE: To explore the functions of TH17 cell in cutaneous graft-versus-host disease (GVHD). METHODS: A model of acute GVHD (aGVHD) was established with a major histocompatibility complex class I/II-disparate allogeneic bone marrow transplantation (BMT). Bone marrow monocytes and splenic T cells from donor C57/BL6 were enriched. The recipient BABL mice were irradiated ((60)Co source) with 7.5 Gy total body irradiation (TBI) and injected with 5 × 10(6) marrow monocytes and 5 × 10(5) T cells. The experimental mice were divided into 3 groups: lethal total body irradiation (TBI); allogeneic bone marrow transplantation (BMT) and recipients of halofuginone (HF). The symptoms of aGVHD were observed daily and detailed histopathologic analyses of recipient skin were performed at Day 6 post-transplantation. And Tri-color flow cytometry (FCM) was performed at Day 6 post-transplantation to measure the levels of interleukin (IL)-17, interferon (IFN)-γ and TH1/TH17. RESULTS: Clinical GVHD symptoms were observed in recipient mice. The administration of HF to lethally irradiated recipients led to very modest GVHD-induced cutaneous changes manifested predominantly by fur loss. However, the experimental animals receiving only allogeneic BMT showed significant fur loss and pathologic skin conditions. Consistent with the clinical evaluations, the histopathologic results demonstrated significantly increased pathologic cutaneous lesions in recipients undergoing only BMT. The median ratios of TH1/TH17 cells were 17.57 and 5.31 in the HF and BMT groups respectively. The difference had statistical significance (P < 0.05). The serum levels of IL-17 were(1.47 ± 0.18) and (2.81 ± 0.19) pg/ml in the TBI and BMT groups respectively (P < 0.05). But IL-17 could not be detected in the HF group. The serum levels of IFN-γ were (3.86 ± 0.32), (42.97 ± 0.42) and (9.89 ± 0.51) pg/ml in the TBI, BMT and HF groups respectively. The inter-group differences had statistical significance (P < 0.05). CONCLUSION: An absence of TH17 cell may alleviate the cutaneous GVHD but exacerbate the systemic GVHD.

[The role of Th17 cells in early onset of mice acute graft versus host disease].

OBJECTIVE: To explore the role of Th17 cells in early onset of acute graft-versus-host disease (aGVHD) and its mechanism. METHODS: Mice aGVHD model was established by irradiated BABL/c mice inoculated with mixed suspension of C57BL/6 bone marrow cells and splenocytes. The mice were divided into 4 groups: (1) normal control, (2) irradiated group, (3) allo-BMT + DMSO group, (4) allo-BMT + halofuginone (HF) group. HF was given intraperitoneally at 5 µg per mouse from -1 d to +10 d after allogeneic bone marrow transplantation(allo-BMT).Mice aGVHD symptoms and survival were observed. Th1/Th17 cells ratio was evaluated by flow cytometry. RESULTS: All the experimental groups (3) and (4) developed aGVHD after transplantation. More severe aGVHD was observed in group (4) than in group (3). HF prevented cutaneous aGVHD in all the mice, but augmented hepatic and small intestine GVHD. The percentage of Th17 cells and the ratio of Th1/Th17 were significantly higher while the percentage of Th1 cells was significantly lower in group (4) at day +6 (P < 0.05). CONCLUSION: Early blockage of Th17 cell results in increase of Th1 cell percentage, which exacerbates aGVHD.

Local Hybrid Divide-and-Conquer Method for the Computation of Medium and Large Molecules.

A local hybrid divide-and-conquer method (LHDC) which combines the high accuracy of sophisticated wave function theory (WFT) methods and the low cost of density functional theory (DFT) has been proposed for computational studies of medium and large molecules. In the method, a large system is divided into small subsystems for which the coefficients of the exchange functional in a hybrid functional are first optimized according to the energy calculated by an accurate WFT method. The hybrid coefficients are then used to evaluate the energy of the whole system. The method not only can reproduce the total energies of the chosen WFT method in good accuracy but also provides electronic structure information for the entire system.

Accurate prediction of heat of formation by combining Hartree-Fock/density functional theory calculation with linear regression correction approach.

A linear regression correction approach has been developed successfully to account for the electron correlation energy missing in Hartree-Fock calculation and to reduce the calculation errors of density functional theory. The numbers of lone-pair electrons, bonding electrons and inner layer electrons in molecules, and the number of unpaired electrons in the composing atoms in their ground states are chosen to be the most important physical descriptors to determine the correlation energy unaccounted by Hartree-Fock method or to improve the results calculated by B3LYP density functional theory method. As a demonstration, this proposed linear regression correction approach has been applied to evaluate the standard heats of formation DeltaH(f) (Theta) of 180 small-sized to medium-sized organic molecules at 298.15 K. Upon correction, the mean absolute deviation for the 150 molecules in the training set decreases from 351.0 to 4.6 kcal/mol and 360.9 to 4.6 kcal/mol for HF/6-31G(d) and HF/6-311+G(d,p) methods, respectively. For B3LYP method, the mean absolute deviations are reduced from 9.2 and 18.2 kcal/mol to 2.7 and 2.4 kcal/mol for 6-31G(d) and 6-311+G(d,p) basis sets, respectively.