Origin of Enantioselectivity in Engineered Cytochrome c-Catalyzed Carbon-Radical FePP Hydrolysis Revealed Using QM/MM (ABEEM Polarizable Force Field) and MD Simulations

The origin of highly efficient asymmetric aminohydroxylation of styrene catalyzed by engineered cytochrome c is investigated by the developed Atom-Bond Electronegativity Equalization Method polarizable force field (ABEEM PFF), which is a combined outcome of electronic and steric effects. Model molecules were used to establish the charge parameters of the ABEEM PFF, for which the bond-stretching and angle-bending parameters were obtained by using a combination of modified Seminario and scan methods. The interactions between carbon-radical Fe-porphyrin (FePP) and waters are simulated by molecular dynamics, which shows a clear preference for the pre-R over the pre-S. This preference is attributed to the hydrogen-bond between the mutated 100S and 101P residues as well as van der Waals interactions, enforcing a specific conformation of the carbon-radical FePP complex within the binding pocket. Meanwhile, the hydrogen-bond between water and the nitrogen atom in the active intermediate dictates the stereochemical outcome. Quantum mechanics/molecular mechanics (QM/MM (ABEEM PFF)) and free-energy perturbation calculations elucidate that the 3RTS is characterized by sandwich-like structure among adjacent amino acid residues, which exhibits greater stability than crowed arrangement in 3STS and enables the R enantiomer to form more favorably. Thus, this study provides mechanistic insight into the catalytic reaction of hemoproteins.

Atomic charges in molecules defined by molecular real space partition into atomic subspaces

Atomic charge (AC), which is the charge distribution of a molecule, is an important property that is closely associated with structures, reactivities, and intra- and inter-molecular interactions among molecules. Several theoretical models or methods can be used to obtain the magnitudes of AC with different characteristics. These models can be classified into fuzzy-atoms models and models partitioning a molecule into individual atoms with sharp boundaries. The first category includes Mulliken, natural population analysis (NPA), Hirshfeld, Merz-Kollman-Singh (MK), CHELPG, the electronegativity equalization method (EEM), the atom-bond electronegativity equalization method (ABEEM), and atomic polar tensor (APT). The second category is derived from quantum chemical topology (QCT) and includes the quantum theory of atoms in molecules (QTAIM) and QCT analysis based on the potential acting on one electron in a molecule (PAEMQCT). Herein, after giving a bird's-eye view of the population methods of the first category, we specifically describe some features of the second category. We only present the basic framework of QCT for obtaining ACs from QTAIM and PAEMQCT and show their important characteristics. QCT establishes the basis of the following chemical concept: a molecule is spatially partitioned into individual atoms with sharp boundaries. The ACs from QTAIM are close to the atomic valence in chemistry, and ACs from PAEMQCT may be practically suitable for modeling intra- and inter-molecular interactions.

Development of a QM/MM(ABEEM) method combined with a polarizable force field to investigate the excision reaction mechanism of damaged thymine

This paper focuses on the development of a quantum mechanics/molecular mechanics method using the ABEEM polarizable force field (QM/MM(ABEEM) method) to investigate the excision reaction mechanism of damaged thymine. This method does not simply combine the QM method with the polarizable force field. A valence electronegativity piecewise function with the distance between atoms as a variable is introduced to describe the atomic partial charges, and changes greatly during the reaction process. At the same time, the charge transfer effect is treated using the condition of local charge conservation. Compared with the traditional QM/MM method, the QM/MM(ABEEM) method can more accurately simulate the polarization effect and charge transfer effect in the reaction process. Focusing on the controversial problems of the excision of damaged bases, six reaction pathways were designed for monofunctional and difunctional deglycosylation of neutral bases and protonated bases. The results show that the QM/MM(ABEEM) method accurately simulates the polarization effect, charge transfer effect, activation energy and other properties of the reaction process. The process in which the active residue Asp activates the nucleophile H₂O to attack the protonated base is the preferred path. The average activation energy and free activation energy of the protonated base are 7.00-14.00 kcal mol^-1 lower than that of the neutral base. The study in this paper is helpful to understand the mechanism of repair enzymes in repairing bases.

Development of QM/MM (ABEEM polarizable force field) method to simulate the excision reaction mechanism of damaged cytosine

DNA damages are regarded as having harmful effects on cell. The base excision repair mechanism combats these effects by removing damaged bases. The deglycosylation mechanism of excising damaged bases by DNA glycosylase and the state of the leaving base have been controversial. The enzymatic reaction of DNA glycosylase to remove the damaged bases involves not only the formation and breaking of chemical bonds, but also complex polarization effect and charge transfer, which cannot be accurately simulated by the QM/MM method combined with the fixed charge force field. This work has developed the ABEEM fluctuating polarizable force field combining with the QM method, that is (QM/MM[ABEEM]), to accurately simulate the proton transfer, charge transfer and the charge distribution. The piecewise function is used as the valence-state electronegativity in the QM/MM (ABEEM) to realize the accurate fitting of the charge distribution in reaction. And the charge transfer is accurately simulated by the local charge conservation conditions. Four deglycosylation mechanisms including the monofunctional and difunctional mechanisms of four neutral and protonated cytosine derivatives are explored. It is confirmed that the monofunctional mechanism of Asp-activated nucleophile water is a better deglycosylation mechanism and the base is protonated before the reaction occurs. Protonization of the base reduced the activation energy by 10.00-17.00 kcal/mol. Asp provides the necessary charge for the reaction, and DNA glycosylase preferentially cleaves ɛC. This work provides a theoretical basis for the research of excising damaged bases by DNA glycosylase.

Energetics and J-coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field in vacuo and an aqueous solution

The development of an atom-bond electronegativity equalisation method at the σπ-level (ABEEM) polarisable force field (PFF) for peptides is presented. ABEEM PFF utilises a fluctuating charge model to explicitly describe...

Water-Mediated Oxidation of Guanine by a Repair Enzyme: Simulation Using the ABEEM Polarizable Force Field

The recognition mechanism of oxidative damage in organisms has long been a research hotspot. Water is an important medium in the recognition process, but its specific role remains unknown. There is a need to develop a suitable force field that can adequately describe the electrostatic, hydrogen bond, and other interactions among the molecules in the complex system of the repair enzyme and oxidized base. The developing ABEEM polarizable force field (PFF) has been used to simulate the repaired enzyme hOGG1 and oxidized DNA (PDB ID: 1EBM) in a biological environment, and the corresponding results are better than those of the fixed-charge force fields OPLS/AA and AMBER OL15. 8-Oxo-G is recognized by Gln315 of hOGG1 mainly through hydrogen bonds mediated by continuous exchange of 2 water molecules. Phe319 and Cys253 are stacked on both sides of the π planes of bases to form sandwich structures. The charge polarization effect gives an important signal to drive the exchange of water molecules and maintains the recognition of oxidation bases by enzymes. The mediated main water molecule A and mediated auxiliary water molecule B together pull Gln315 to recognize 8-oxo-G by hydrogen bond interactions. Then, the charge polarization signal of solvent water molecule C with a large absolute charge causes the absolute charge of O atoms in water molecule A or B to increase by approximately 0.2 e, and water molecule A or B leaves Gln315 and 8-oxo-G. The other water molecule and water molecule C synergistically recognize 8-oxo-G with Gln315. Even though the water molecules between Gln315 and 8-oxo-G are removed, the MD simulation results show that water molecules appear between Gln315 and 8-oxo-G in a very short time (<2 ps). The dwell time of each water molecule is approximately 60 ps. The radial distribution function and dwell time support the correctness of the above mechanism. These polarization effects and hydrogen bonding interactions cannot be simulated by a fixed-charge force field.

[Clinical study of percutaneous vertebroplasty combined with (125)I seeds implantation in the treatment of patients with thoracic metastatic tumor complicated with posterior vertebral defect]

Objective: To analyze the safety and efficacy of percutaneous vertebroplasty combined with interstitial implantation (125)I of seeds (PVPI) in the treatment of thoracic vertebroplasty with posterior vertebra defect. Methods: A retrospective analysis of the clinical data of 64 patients with thoracic spine metastases admitted to Yunnan Cancer Hospital from November 2017 to May 2019 was conducted, including 32 patients with posterior vertebra defect (experimental group) and 32 cases without (control group). Forty-two vertebral bodies of 32 patients in the experimental group were treated with improved PVPI surgery, which performed with the secondary sealing method and inclined puncture needle injection bone cement rotary filling technology, to reduce leakage. The 54 vertebral bodies of 32 patients in control group underwent PVPI. The two groups of patients were followed up on the second day, one month, three months and six months after the operation, and the short-term efficacy, long-term efficacy and safety indicators of the two groups were compared. Results: All 64 patients successfully completed the surgical treatment. The visual analogue scores and Karnofsky scores of the experimental group and the control group were improved to varying degrees on the second day, 1 month, 3 months and 6 months after the operation. There was no statistically significant difference between the two groups (P>0.05). The amount of bone cement in the experimental group and control group was (2.36±0.20) ml and (2.39±0.17) ml, and the difference was not statistically significant (P=0.482). The amount of (125)I seed implantation was (30.63±0.91) and (32.56±0.68), respectively, the difference was not statistically significant (P=0.925). The partial response rates of the study group and the control group were 81.3% and 87.5%, the stable disease rates were 12.5% and 9.4%, the differences were not statistically significant (P>0.05). The median overall survival (mOS) of the study group was 13 months, and the median progression-free survival (mPFS) was 8 months. The mOS of the control group was 14 months, and the mPFS was 8 months. The differences were not statistically significant (P>0.05). In the experimental group, 6 (14.3%) vertebral bodies had cement leakage, of which 2 (4.8%) were cement leakage at posterior vertebra, 4 (9.5%) were paravertebral cement leakage. Seven (13.0%) paravertebral cement leakage occurred in the control group. There was no significant difference in bone cement leakage between the two groups (P=0.097). Bone cement leakage in both groups did not cause serious complications such as spinal cord injury and paraplegia. Conclusion: The application of PVPI in the treatment of thoracic metastatic tumor patients with posterior vertebra defect can acquire better clinical efficacy and safety through conduction of the improved intraoperative technology and paying more attention to the control of bone cement distribution and other issues.

Dividing the Periodic Box into Subdivisions with Their Surroundings to Accelerate Molecular Dynamics Simulation with High Accuracy

A major field of current research in chemistry and biology is the development of the tools that enable in situ analysis of complex systems. However, the long-time dynamics simulation for an extremely large system in solution is almost impossible by an all-atom force field combined with an explicit solvent model. The results show that the larger the periodic box is, the closer the properties of the system are to the experimental values. Therefore, how can we carry out simulations for systems that are fast, accurate, and large enough? A method of dividing the periodic box into subdivisions with their surroundings (DBSS) is presented here, and it clearly increases the computation speed without losing accuracy and enables the simulation of extremely large systems by strongly decreasing the dimension of the charge matrix. The DBSS method divides a single periodic box or unit in an extremely large system into several subdivisions with a suitable choice according to atomic coordinates. This method ensures that these subdivisions are always changing and allows the atoms to communicate with each other. Intermolecular communication is important for molecular properties and functions but is not possible with other fragment methods. The partial charges are calculated in each subdivision with an overlapping surrounding used to take hydrogen bond interaction between the subdivisions into account. This is an iterative process because the charge population will be recalculated at intervals during the dynamics simulations. Taking a water system as an example, each subdivision is extended by 4 Å as the surrounding. The computation time scales almost linearly with the size of the system, and the slope is small. MD simulations for several properties have been performed by the ABEEM-DBSS method. The results indicate that the ABEEM-DBSS method can accurately simulate the properties of water system, and the accuracy can reach or approach that of the experimental data or of other water potentials. Interestingly, the properties become closer to the experimental data as the sizes of the periodic box increase, further validating the need for the simulation of a large system and demonstrating the value of the DBSS method.

Systematic Parameterization and Simulation of Boronic Acid-β-Lactamase Aqueous Solution in Developing the ABEEMσπ Polarizable Force Field

Boronic acid, an inhibitor of β-lactamase, has begun to be applied to the treatment of biological infections and tumors. Scientists are working to develop new and more effective boronic acid. Molecular dynamics (MD) simulation provides a powerful auxiliary tool for drug design. However, the current force fields have no boron-related parameters. In this work, an atom-bond electronegativity equalization method at the σπ level (ABEEMσπ) polarizable force field (ABEEMσπ PFF) of boronic acid and β-lactamase has been developed to determine the potential functions and parameters. The interaction between boron and serine in β-lactamase is regarded as a bonded mode. The interaction between them is simulated by the Morse potential energy function, which is close to the experimental change of the stretching potential energy in a large range. The potential energy surfaces of the bond length, bond angle, and dihedral angle of boronic acid-β-lactamase have the same stability point and change trend as M06-2X/6-311G**. For 47 boronic acid-β-lactamase training molecules, the linear correlation coefficient (R) of the charge distribution between the ABEEMσπ PFF and HF/STO-3G is greater than 0.96. Attributed to the fact that the charge distribution of the ABEEMσπ PFF can fluctuate with the change of geometry and environment, the polarization effect and charge-transfer effect are well reflected. The binding ability of different boronic acids with the same β-lactamase is different. A total of 10 boronic acid-β-lactamase model molecules and 10 boronic acid-β-lactamase and water complexes are simulated. The order of binding energy of five large model molecules calculated by the ABEEMσπ PFF is consistent with that of the MP2 method. The binding energies of boronic acid-β-lactamase and water complexes are close to those of the MP2 method. The results of MD simulation of five aqueous boronic acid-β-lactamase complexes in the NVT ensemble verify the rationality of boron-related parameters of the ABEEMσπ PFF, which have a good application prospect. This study lays a solid theoretical foundation for further study of the inhibition of boronic acid on β-lactamase.

ABEEM/MM OH- Models for OH-(H2O)n Clusters and Aqueous OH-: Structures, Charge Distributions, and Binding Energies

Based on the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), two fluctuating charge models of OH^--water system were proposed. The difference between these two models is whether there is charge transfer between OH^- and its first-shell water molecules. The structures, charge distributions, charge transfer, and binding energies of the OH^-(H₂O)_n (n = 1-8, 10, 15, 23) clusters were studied by these two ABEEM/MM models, the OPLS/AA force field, the OPLS-SMOOTH/AA force field, and the QM methods. The results demonstrate that two ABEEM/MM models can search out all stable structures just as the QM methods, and the structures and charge distributions agree well with those from the QM calculations. The structures, the charge transfer, and the strength of hydrogen bonds in the first hydration shell are closely related to the coordination number of OH^-. Molecular dynamics simulations on the aqueous OH^- solution are performed at 298 and 278 K using ABEEM/MM-I model. The MD results show that the populations of three-, four-, and five-coordinated OH^- are 29.6%, 67.1%, and 3.4% at 298 K, respectively, and those of two-, three-, four-, and five-coordinated OH^- are 10.8%, 44.9%, 39.2%, and 4.9% at 278 K, respectively; the average hydrogen bond lengths and the hydrogen bond angle in the first shell increase with the temperature decreasing.

Partitioning a Molecule into the Atomic Basins and the Resultant Atomic Charges from Quantum Chemical Topology Analysis of the Kohn-Sham Potential

Quantum chemical topology (QCT) solidifies the chemical basic concepts demonstrating how a molecular system is intrinsically partitioned into its components and what the interaction lines between them are. Here, QCT analysis using a Kohn-Sham one-electron potential (KSpot) in KS equation as a scalar function is initiated and explored, showing KSpot and its resultant electron force lines have novel spatial features which reveal that an atom in a molecule is a spatial basin governed by its nucleus as a 3D-attractor that terminates all the electron force lines defined by the negative gradient of KSpot and that a chemical bond line is just a minimum path of KSpot for the electron motion. Particularly, the atomic charges from this KSpot QCT analysis are moderate and good, having much lower dependence on basis sets chosen for computation. This may provide a platform for the study of molecular structures and properties, intra- and intermolecular electrostatic interaction, energy decomposition, and construction of force field.

Polarizable TIP7P Water Model with Perturbation Charges Evaluated from ABEEM

A polarizable version of the rigid seven-site (TIP7P) water model with the atom-bond electronegativity equalization method (ABEEM) is proposed. The model uses direct polarization, where an isolated water monomer in the equilibrium geometry is assumed as a reference state and the polarization of the monomer arises from interacting with other molecules as a perturbation of the reference state. The charge on each site of the monomer splits into reference charge and perturbation charge. The perturbation charge arises only because of other reference charges. The interaction of the perturbation charge with other perturbation charges is replaced using polarization scaling to enhance the interaction of perturbation charge with the reference charges of the sites from other molecules. The perturbation charges are updated by evaluating explicit expressions once. This direct polarization is time-reversible because the charge update is independent of the charges in previous simulation steps. A Slater-type damping function moderates the short-range electrostatics to treat charge diffusion. The Ewald method corrects the long-range electrostatics both in the nuclei movement and in electronegativity equalization to diminish the size effect. The water model is parameterized by fitting the ab initio results of water clusters and the experimental results of water monomers and thermodynamic properties for liquid water. Owing to polarizability, the model performs better than the TIP7P model in terms of vaporization enthalpy, isothermal compressibility, and shear viscosity of the liquid phase. It performs better at the melting point of ice but slightly worse under critical conditions than the TIP7P model. Direct polarization has a low time complexity of O(N) and is a good choice for ABEEM to improve its computational efficiency.

[Preparation and characterization of paclitaxel microspheres in situ gel and its antitumor efficacy by local injection]

OBJECTIVE

The current difficulties in the treatment of tumor include repeated administration and high recurrence rate after tumor resection. In order to reduce the number of doses, avoid side effects of chemotherapeutic drugs, suppress tumor growth and delay tumor recurrence after surgery, a temperature-sensitive in situ gel with paclitaxel microspheres (PTX/M gel) was prepared. PTX/M gel was administered by intratumoral injection once a month.

METHODS

First of all, paclitaxel microspheres (PTX/M) were prepared by emulsion solvent evaporation method. A laser particle size distribution analyzer was used to investigate the size, distribution, specific surface area of microspheres. Paclitaxel content was determined by high performance liquid chromatography (HPLC). Then encapsulation efficiency of paclitaxel was calculated and in vitro release characteristics were studied. Secondly, PTX/M gel was prepared by cold dissolution method. The phase transition temperature, elastic modulus, dissolution curve, correlation between dissolution and release were measured. Finally, U87 MG and 4T1 subcutaneous tumor models were established respectively to study the efficacy of PTX/M gel in suppressing tumor growth and delaying tumor recurrence after surgery.

RESULTS

The median diameter of the selected PTX/M was (32.24±1.09) μm, the specific surface area was (206.61±10.23) m²/kg, the encapsulation efficiency was 85.29%±1.34%, and the cumulative release percentage of paclitaxel from PTX/M was 33.56%±3.33% in one month. Phase transition temperature of PTX/M gel was 33 °C. The elastic modulus of PTX/M gel at 25 °C and 37 °C were 4.2×103 Pa and 18×103 Pa, respectively. The gel could stay in the body for up to 48 hours. It could be seen from the results of animal experiments that were compared with the saline group and the Taxol group, and the tumor-bearing mice of the PTX/M gel group had the slowest tumor growth (P<0.05). Similarly, in the tumor recurrence experiments, the mice of PTX/M gel group had the latest tumor recurrence after surgery.

CONCLUSION

As a local sustained-release preparation, PTX/M gel can effectively suppress tumor growth and delay postoperative recurrence of tumors. It has potential advantages in tumor treatment.

Reaction mechanism of NO with hydrolysates of NAMI-A: an MD simulation by combining the QM/MM(ABEEM) with the MD-FEP method

Nitrosylation reaction mechanisms of the hydrolysates of NAMI-A and hydrolysis reactions of ruthenium nitrosyl complexes were investigated in the triplet state and the singlet state. Activation free energies were calculated by combining the QM/MM(ABEEM) method with free energy perturbation theory, and the explicit solvent environment was simulated by an ABEEMσπ polarizable force field. Our results demonstrate that nitrosylation reactions of the hydrolysates of NAMI-A occur in both the triplet and the singlet states. The Ru-N-O angle of the triplet ruthenium nitrosyl complexes is in the range of 132.0°-138.2°. However, all the ruthenium nitrosyl complexes at the singlet state show an almost linear Ru-N-O angle. The nitrosylation reaction happens prior to the hydrolysis reaction for the first-step hydrolysates. The activation free energies of the nitrosylation reactions show that the H₂ O-NO exchange reaction of [RuCl₄ (Im)(H₂ O)] in the singlet spin sate is the most likely one. Comparing with the activation free energies of the hydrolysis reactions of the ruthenium nitrosyl complexes, the results indicate that the rate of the DMSO-H₂ O exchange reaction of [RuCl₃ (NO)(Im)(DMSO)] is faster than that of [RuCl₃ (H₂ O)(Im)(DMSO)] in both the triplet spin state and the singlet spin state. © 2018 Wiley Periodicals, Inc.

[Efficacy and safety of domestic dasatinib as second-line treatment for chronic myeloid leukemia patients in the chronic phase]

目的

探讨国产酪氨酸激酶抑制剂（TKI）达沙替尼（商品名：依尼舒）二线治疗慢性髓性白血病慢性期（CML-CP）患者的疗效及安全性。

方法

回顾性分析2016年3月至2018年7月湖北省CML协作组成员医院收治的二线服用国产达沙替尼的CML-CP患者的病例资料，统计患者治疗3、6和12个月时最佳反应率、累积完全细胞遗传学反应（CCyR）率、累积主要分子学反应（MMR）率、无进展生存（PFS）、无事件生存（EFS）情况及不良反应情况。

结果

共纳入83例CML-CP患者，中位随访时间为23（4~45）个月，达沙替尼治疗3、6、12个月最佳反应率分别为77.5%（54/71）、72.6%（61/75）、60.7%（51/69）。至随访截止，累积CCyR率、MMR率分别为65.5%（55/80）、57.1%（48/73），达CCyR和MMR的中位时间均为3个月。随访时间内，PFS率为94.0%（79/83），EFS率为77.4%（65/83）。国产达沙替尼最常见非血液学不良反应为水肿（32.5%），其次为皮疹瘙痒（18.1%）、乏力（13.3%），血液学不良反应主要有血小板减少（31.3%）、白细胞减少（19.3%）和贫血（6.0%）。

结论

国产达沙替尼二线治疗CML-CP患者具有较好的疗效及安全性，可作为CML-CP患者的治疗选择。

[A bibliometric analysis of literature on hand-transmitted vibration in China, 1990-2016]

Objective: To investigate the features of literature on hand-transmitted vibration in China, 1990-2016. Methods: In September 2017, the studies on hand-transmitted vibration in China, which were published in Chinese or English during 1990-2016, with "China" and "Taiwan" as the places where author affiliations were located, were retrieved. A bibliometric analysis was performed to investigate the type of articles, publication time, the journals in which articles were published, author affiliations, author regions, and funding. Results: A total of 205 articles on hand-transmitted vibration were retrieved. There were 7.59 articles on average published annually from 1990 to 2016. In the 205 articles, 114 (55.61%) were published in the journals indexed in one or two core journal databases. In the 64 journals, 22 (34.38%) were indexed in one or two core journal databases. The first authors were from 22 provincial regions (provinces, autonomous regions, or centrally administered municipalities) in China, with 152 articles (74.15%) by the authors in the top five regions. There were a total of 876 authors, and the co-authorship degree was 4.27 (876/205). Most of the first authors (136 articles, 66.34%) were affiliated with universities or institutes for prevention and control of occupational diseases. Among the 205 articles, 103 (50.24%) were original articles or investigations, and 72 (35.12%) were funded. Conclusion: The studies on hand-transmitted vibration fluctuated and increased from 1990 to 2016, with a relatively concentrated distribution in terms of sources, regions, and institutions. Interregional and international academic exchange should be strengthened.

The open-cubane oxo–oxyl coupling mechanism dominates photosynthetic oxygen evolution: a comprehensive DFT investigation on O–O bond formation in the S4state

How is O₂created in nature? Comprehensive DFT investigations determine the dominance of the open-cubane oxo–oxyl coupling mechanism over alternative possibilities.

How does ammonia bind to the oxygen-evolving complex in the S2state of photosynthetic water oxidation? Theoretical support and implications for the W1 substitution mechanism

The mechanistic study shows that NH₃substitutes W1 rather than O5 of the OEC in the S₂state and leaves in the S₄′ state.

Magnetism-Driven Ferroelectricity in Double Perovskite Y₂NiMnO₆

We report the discovery of multiferroic behavior in double perovskite Y2NiMnO6. X-ray diffraction shows that the material has a centrosymmetric crystal structure of space group P2(1)/n with Ni(2+)/Mn(4+) ordering. This result is further confirmed by aberration-corrected scanning transmission electron microscopy combined with atomic resolution electron energy loss spectroscopy. The appearance of ferroelectric polarization coincides with the magnetic phase transition (∼67 K), which indicates that the ferroelectricity is driven by magnetism, and this is further confirmed by its strong magnetoelectric (ME) effect. We proposed the origin of the ferroelectricity is associated with the combination of Ni(2+)/Mn(4+) charge ordering and the ↑↑↓↓ spin ordering. When compared with other known magnetic multiferroics, Y2NiMnO6 displays several attractive multiferroic properties, including high polarization (∼145 μC/m(2)), a high multiferroic transition temperature (∼67 K), and strong ME coupling (∼21%).

Polycyclic aromatic hydrocarbons in deposited bedroom dust collected from Xinxiang, a fast developing city in North China

To investigate the contamination levels of polycyclic aromatic hydrocarbons (PAHs) in the indoor environment, 16 PAHs were measured in 20 deposited bedroom dust (DBD) samples collected from four residential areas in Xinxiang City. The total PAH concentrations (∑PAHs, defined as the sum of 16 PAHs) in 20 DBD samples ranged from 1.47 to 21.8 μg/g dry weight. PAH ratios indicated that main sources of PAHs in most DBD samples were coal, grasses, and wood combustion. Correlation analysis showed that there were no significant positive correlations between ∑PAH concentrations in DBD and the number of family members or duration of residence. Analysis using the t test revealed that tobacco smoke was a source of PAHs in DBD and that an unattached kitchen may be a significant influencing factor related to PAHs in DBD collected from residential areas in Xinxiang City. Our results showed that the kitchen exhaust fan or hood had no significant influence on total PAHs in DBD, and there was no significant difference in ∑PAH concentrations in DBD in homes which used liquefied petroleum gas and those which used natural gas.

Investigation of the distinction between van der Waals interaction and chemical bonding based on the PAEM-MO diagram

In recent years, the basic problem of understanding chemical bonding, nonbonded, and/or van der Waals interactions has been intensively debated in terms of various theoretical methods. We propose and construct the potential acting on one electron in a molecule-molecular orbital (PAEM-MO) diagram, which draws the PAEM inserted the MO energy levels with their major atomic orbital components. PAEM-MO diagram is able to show clear distinction of chemical bonding from nonbonded and/or vdW interactions. The rule for this is as follows. Along the line connecting two atoms in a molecule or a complex, the existence of chemical bonding between these two atoms needs to satisfy two conditions: (a) a critical point of PAEM exists and (b) PAEM barrier between the two atoms is lower in energy than the occupied major valence-shell bonding MO which contains in-phase atomic components (positive overlap) of the two considered atoms. In contrast to the chemical bonding, for a nonbonded interaction or van der Waals interaction between two atoms, both conditions (a) and (b) do not be satisfied at the same time. This is demonstrated and discussed by various typical cases, particularly those related to helium atom and H-H bonding in phenanthrene. There are helium bonds in HHeF and HeBeO molecules, whereas no H-H bonding in phenanthrene. The validity and limitation for this rule is demonstrated through the investigations of the curves of the PAEM barrier top and MO energies versus the internuclear distances for He2 , H2 , and He2 (+) systems.

Morphological transition difference of linear and cyclic block copolymer with polymer blending in a selective solvent by combining dissipative particle dynamics and all-atom molecular dynamics simulations based on the ABEEM polarizable force field

AAMD based on ABEEM PFF were performed to obtain reliable DPD parameters for morphological transition.

Occurrence of higher chlorinated benzenes in livers of grass carp and common carp collected from markets of Xinxiang, China

Five higher chlorinated benzenes (including hexachlorobenzene (HCB), pentachlorobenzene (PeCB) and three isomers of tetrachlorobenzens) were measured in the livers of grass carp and common carp collected from five markets in Xinxiang city, China. HCB and PeCB were detected in all samples. The major component of the higher CBs residue was HCB and significant correlations existed between HCB and PeCB in both grass carp and common carp livers. The ratio range of HCB/PeCB in grass carp and common carp were 3.4-6.2 and 4.9-7.7, respectively, which implied the sources of higher CBs originate mainly from the revolatilization of industrial HCB with a minor impact from PeCB.

Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system

The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.

Atom-Bond Electronegativity Equalization Method and its Applications Based on Density Functional Theory

The atom-bond electronegativity equalization method (ABEEM) and its applications for predicting intrinsic properties of large molecules, such as the charge distribution, the molecular energy, the local softness and the Fukui function, the regio- and stereo-selectivity of Diels–Alder reactions, the linear response function, and the charge polarization normal modes have been formulated. The examples show that there is a very good agreement of the ABEEM results with those of the corresponding ab initio quantum chemical calculations, demonstrating the reasonable and possible ABEEM's applications to the large molecular systems.

4,6-Dichloro-5-(2-meth-oxy-phen-oxy)-2,2'-bipyrimidine

In the title compound, C₁₅H₁₀Cl₂N₄O₂, the dichloro­pyrimidine and meth­oxy­phen­oxy parts are approximately perpendicular [dihedral angle = 89.9 (9)°]. The dihedral angle between the two pyrimidine rings is 36.3 (4)° In the crystal, there are no hydrogen bonds but the mol­ecules are held together by short inter­molecular C⋯N [3.206 (3) Å] contacts and C—H⋯π inter­actions.

Special distribution of polybrominated diphenyl ethers in brain tissues of free-range domestic hens and ducks from a village near an electronic waste recycling site in South China

The rural village, Taizhou of Zhejiang Province, had been exposed to e-waste recycling for years, the polybrominated diphenyl ether (PBDE) levels in hens and ducks were high. The concentration of ∑PBDEs in the brain was the lowest among tissues of individual hens and ducks after correction for the respective lipid content. Also, the concentration ratio of BDE-153 versus BDE-154 (153/154) of brain was the highest among tissues of individual hens and ducks. Our results indicate that the hindrance of blood-brain barrier to compounds, such as high molecular weight and non-planar conformation (steric hindrance), contributed to the low concentration of PBDEs in the brain tissue of hens and ducks, especially in cases exposed to high levels of PBDE.

Distribution and characterization of higher chlorinated benzenes in outdoor dust collected from a fast developing city in North China

Five higher chlorinated benzenes (CBs), include hexachlorobenzene (HCB), pentachlorobenzene (PeCB) and three isomers of tetrachlorobenzens, were analyzed in 20 outdoor dust samples collected from a fast developing city, Xinxiang. Only HCB was detected in all outdoor dust samples. The dominate part of the CBs residue in most samples was HCB and the mean HCB concentration (4.13 ng/g dry weight) in this study was in the range of global background soil HCB levels (ranging from 0.010 to 5.20 ng/g dry weight). The higher ratios of HCB/PeCB in the outdoor dust samples in the present study indicate that pesticide application may be an important source of HCB in China.

Investigation of the molecular surface area and volume: Defined and calculated by the molecular face theory

Based on the molecular face (MF) theory, the molecular face surface area (MFSA) and molecular face volume (MFV) are defined. For a variety of organic molecules and several inorganic molecules, the MFSA and MFV have been studied and calculated in terms of an algorithm of our own via the Matlab package. The MFV shows a very good linear relationship with the experimentally measured critical molar volume. It is also found that the MFSA and MFV have significant linear correlations with those of the commonly used hard-sphere model and the electron density isosurface.