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.

Case Report: Rare Acute Abdomen: Focal Nodular Hyperplasia With Spontaneous Rupture

Focal nodular hyperplasia (FNH) of the liver is a benign lesion characterized by hypertrophic nodules with central star-shaped fibrous scars. The etiology and pathogenesis of FNH are not completely understood. A 43-year-old man was hospitalized because of acute abdominal pain. Emergency computed tomography(CT) showed hepatic tumor rupture and bleeding. The patient’s condition improved following arteriographic embolization to stop bleeding. Laparotomy confirmed spontaneous rupture and hemorrhage of focal hyperplasia and the patient remains asymptomatic after an uneventful recovery. FNH with spontaneous rupture and bleeding is extremely rare. Currently, there is no unified management standard for FNH and most previous studies recommend observation and follow-up. We recommend consideration of surgical treatment of cases with spontaneous rupture and bleeding.

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.

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.

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.

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.

[Long-term outcomes after cataract surgery in infants with congenital cataract]

Objective: To observe the long-term outcomes after congenital cataract surgery performed prior to 36 months of age. Methods: A retrospective case study was conducted. Thirty-two cases (57 eyes) of congenital cataract were included from January 2004 to January 2012. All patients received intraocular lens (IOL) implantation with posterior continuous curvilinear capsulorhexies and anterior vitrectomy after cataract extraction and were followed up. At the last visit, the best corrected visual acuity (BCVA) was determined and postoperative complications were evaluated during follow-up with a longest time of 13 years. Non-normal distribution showed in median M (minimum and maximum). Data were analyzed by Kruskal Wallis single factor variance analysis and multiple comparison. The independent Mann-Witney U test was used to analyze non-normal distribution data. Results: There were thirty-two cases (57 eyes) of congenital cataract including 7 unilateral cases and 25 bilateral cases. The median age at cataract extraction was 6.0months; the median IOL implantation age was 28.0 months and the median duration of follow-up after cataract extraction was 67.0 months. The median postoperative BCVA was (LogMAR) 0.52. Unilateral and bilateral cataract postoperative BCVA difference had no statistical significance (U=107, P>0.05). Patients received cataract surgery in 2 to 4 months, the postoperative BCVA was better than in 5 to 8 months. The difference was statistical significance (H=-15.33, P<0.05). BCVA after IOL implantation before 24 months were significantly better than after 30 months. The difference had statistical significance(H=-20.61,-20.78, P<0.05). Postoperative complications were posterior capsular opacity (5 eyes; 8.77%), glaucoma (2 eyes; 3.51%), strabismus (17 eyes; 29.82%) and nystagmus (30 eyes; 52.63%). Conclusions: Most infantile cataract surgeries performed prior to 36 mouths of life together with the implantation of IOL can achieve good visual acuity. No serious complications occurred. (Chin J Ophthalmol, 2017, 53: 266-273).

[Preliminary analysis of lung function of population with biofuel smoke exposure]

Objective: To analyse the impaired lung functions of people with biofuel smoke exposure. Methods: Nonsmokers with biofuel smoke exposure were selected as research objects in a mountainous area of northern Guangdong where the families used biofuels as main energies and the nonsmokers without biofuel smoke exposure in the same area as control. Questionnaire interviews and spirometry tests were performed on all subjects. To analyse the differences of lung functions in both. Results: Seventy hundred and seventeen subjects were enro1led in this study.There were 530 nonsmokers with biofuel smoke exposure(observation group) including 442 women and 88 men, average age 54±10. There were 187 nonsmokers without biofuel smoke exposure(control group) including 141 women and 46 men, average age 54±10. There was no significant difference between two groups in age, height, weight, BMI, waist circumference, hip circumference and waist/hip ratio(P>0.05). The pulmonary ventilation function index(FEV(1)%Pred, FEV(1)/FVC) in the observation group was significantly less than that in control group [(100±18) vs.(106±25); (80±10) vs.(83±6) respectively, P<0.05]. Small airway function index(PEF25, PEF50, PEF75, MMPEF and MMPEF%Pred) was significantly less than that in control group(P<0.01). According to the univariate regression analysis and multivariate regression analysis, regression coefficients between BIOFUEL-INDEX and FEV/FVC was -0.1, 95%CI(-0.1, -0.1, P<0.01). According to the threshold analysis, the vertice of BIOFUEL-INDEX was 46.0, where the predicted Y value was 81.76, 95%CI (80.2, 83.33). When BIOFUEL-INDEX<46.0, the regression coefficient was 0, 95%CI (-0.1, 0.0)(P>0.05); when BIOFUEL-INDEX> 46.0, the regression coefficient 2 was -0.1, 95%CI (-0.2, -0.1)(P<0.01). The difference between coefficient 2 and 1 was -0.1, 95%CI (-0.2, 0.0), which was statistically significant (P<0.05). The Log-Likelihood ratio between Model I and Model Ⅱ had statistical significance (P=0.019). Conclusions: The biofuel smokes exposure causes damages in lung function.

[Bibliometric analysis of scientific articles on epidemiological study of burns in China]

Objective: To analyze the current status of epidemiological study of burns in China, and to explore the related strategies. Methods: Retrospective or cross-sectional scientific articles in Chinese or English on epidemiological study of burns in China published from January 2005 to December 2015 were systemically retrieved from 4 databases. The databases include PubMed, Embase, China Biology Medicine disc, and Chinese Journals Full-text Database. From the results retrieved, data with regard to publication year, journal distribution, number of institutions participated in the study, affiliation of the first author and its location, and admission time span and age of patients in all the scientific articles were collected. Furthermore, the definition of age range and the grouping method of age of pediatric patients in English articles on epidemiological study of pediatric burns of China were recorded. Data were processed with descriptive statistical analysis. Results: A total of 256 scientific articles conforming to the study criteria were retrieved, among which 214 (83.59%) articles were in Chinese, and 42 (16.41%) articles were in English; 242 (94.53%) articles were retrospective studies, and 14 (5.47%) articles were cross-sectional studies. During the 11 years, the number of the relevant articles was fluctuant on the whole. The scientific articles were published in 130 journals, with 42 English articles in source journals for SCIENCE CITATION INDEX EXPANDED-JOURNAL LIST, accounting for 16.41%, and 116 Chinese articles in Source Journal for Chinese Scientific and Technical Papers, accounting for 45.31%. Totally 215 (83.98%) articles were single-center studies, and 29 (11.33%) articles were multicenter studies which were conducted by three or more centers. The number of affiliations of the first author of articles was 161 in total. The top 10 institutions regarding the article publishing number published 58 articles, accounting for 22.66%. Scientific articles on epidemiological study of burns were retrieved with location of affiliation of the first author in 31 provinces, autonomous regions, and municipalities directly under the Central Government in Mainland China, and also in Taiwan Province and Hong Kong Special Administrative Region, among which Shanghai ranked first with 24 (9.38%) articles published. The admission time span of patients in the articles ranged from 3 months to 47 years, with 120 (46.87%) articles from 3 months to 5 years, 79 (30.86%) articles from 6 to 10 years, and 57 (22.27%) articles more than 10 years, respectively. Regarding the age of patients in the study, 123 articles were on epidemiological study of pediatric burns, and 16 articles on epidemiological study of elderly burns, accounting for 48.05% and 6.25%, respectively. Further analysis of articles on epidemiological study of pediatric burns in English showed that there was no standard definition of age range or unified grouping method of age for pediatric burn patients. Conclusions: The epidemiological study of burns in China has been carried out nationwide, but the number of institutions conducted relevant study is not that much, and multicenter epidemiological studies remain scanty. The quality of the articles needs to be further improved. The epidemiological study of elderly burns is relatively deficient and calls for more attention. The epidemiological study of burns in China lacks regularity or continuity in time scope. There is an urgent need for the guideline on classification method for items of epidemiological study of burns in China so as to standardize the related research.

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.

Antitussive, expectorant, and anti-inflammatory activities of four caffeoylquinic acids isolated from Tussilago farfara

CONTEXT

The flower bud of Tussilago farfara L. (Compositae) (FTF) is one of the traditional Chinese medicinal herbs used to treat cough, phlegm, bronchitic, and asthmatic conditions.

OBJECTIVE

The objective of this study is to isolate four caffeoylquinic acids from the ethyl acetate extract (EtE) of FTF and to evaluate their antitussive, expectorant, and anti-inflammatory activities.

MATERIALS AND METHODS

The structures of compounds 1-4 isolated from EtE were determined by spectral analysis. Mice were orally treated with these compounds and their mixture (in a ratio of 5:28:41:26 as in EtE) at doses of 10 and 20 mg/kg once daily for 3 d. The antitussive and expectorant activities were evaluated separately with the ammonia liquor-induced model and the phenol red secretion model. The anti-inflammation activity was evaluated using leukocyte count in the bronchoalveolar lavage fluid after ammonia liquor-induced acute airway inflammation.

RESULTS

The four compounds were identified as chlorogenic acid (1), 3,5-dicaffeoylquinic acid (2), 3,4-dicaffeoylquinic acid (3), and 4,5-dicaffeoylquinic acid (4). All compounds, especially compound 4 (58.0% inhibition in cough frequency), showed a significant antitussive effect. However, the mixture was the most effective to inhibit the cough frequency by 61.7%. All compounds also showed a significant expectorant effect, while compound 2 was the most potent to enhance the phenol red secretion by 35.7%. All compounds significantly alleviated inflammation, but compound 4 showed the strongest effect to inhibit the leukocytosis by 49.7%.

DISCUSSION AND CONCLUSION

The caffeoylquinic acids and their mixture, exhibiting significant antitussive, expectorant, and anti-inflammatory effects, could be considered as the main effective ingredients of FTF, and they may act in a collective and synergistic way.

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.

Akirin2 expression in response to vaccine-induced immunity in chicken

Akirin2 is a nuclear factor that plays an important role in the development and regulation of innate immune response. In this study, akirin2 gene expression in several primary immune organs (liver, thymus, and bursa) of Hi-Line Brown chicken administered with the LoSota vaccine was analyzed during the various stages of increase in Newcastle disease virus antibody titer. The results revealed that akirin2 expression was significantly higher in the liver (P < 0.01) and bursa (P < 0.05) of vaccinated chicken 7 and 14 days post-immunization, respectively. These results could serve as a foundation for further studies on the functions of akirin2 in immune response.

Molecular characterization of a cytosolic manganese superoxide dismutase from the Chinese mitten crab, Eriocheir sinensis

A cytosolic manganese superoxide dismutase gene (Es-cMnSOD) was cloned from the Chinese mitten crab Eriocheir sinensis, using reverse transcription-polymerase chain reaction and the rapid amplification of cDNA ends. The open reading frame of Es-cMnSOD is 867 bp in length and encodes a 288-amino acid protein without a signal peptide. The calculated molecular mass of the translated protein of Es-cMnSOD is 31.43 kDa, with an estimated isoelectric point of 6.30. The deduced amino acid sequence of Es-cMnSOD has similarities of 90, 89, 84, 87, and 81% to those of white shrimp Litopenaeus vannamei MnSOD, black tiger shrimp Penaeus monodon MnSOD, giant freshwater prawn Macrobrachium rosenbergii MnSOD, blue crab Callinectes sapidus MnSOD, and red swamp crayfish Procambarus clarkii MnSOD, respectively. Es-cMnSOD contains a manganese superoxide dismutase domain (DVWEHAYY) and 4 conserved amino acids responsible for binding manganese. Es-cMnSOD was expressed in the hemocytes, eyestalk, muscle, intestine, gill, and hepatopancreas. Es-cMnSOD transcripts in hemocytes of E. sinensis increased at 1.5 and 48 h after injection of Aeromonas hydrophila, indicating that the induction of the SOD system response occurred within a short period of time. This study suggests that MnSOD may play a critical role in crab immunity, allowing efficient activation of an early innate immune response in the crab.

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.

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.

The synthesis and optical properties of ZnO nanocombs

The ZnO nanocombs were synthesized by chemical vapor deposition method, which the uniform and dense nanotips were along one side of the comb ribbon. The growth mechanism was described as free catalyst self-assembled and vapor-solid model. The optical properties related with the surface states were investigated by Raman and PL spectra. The large redshift of 1LO phonon peak was attributed to the surface and interface states. The normalized PL spectra showed that the deep-level emission decreased for the sample to be annealed in O2 ambient at 500 degrees C. On the contrary, the deep-level emission increased while for the annealed sample in O2 ambient at 600 degrees C. The deep-level emission was attributed to the transition from the shallow donor to the deep acceptor. The XPS analysis showed the existence of oxygen rich and Zn deficient in the ZnO nanocombs annealed at 600 degrees C. The abnormal temperature dependence of integrated PL intensity was attributed to the abundant surface states.

Optical properties of ZnMgO nanowalls grown by plasma-assisted molecular beam epitaxy

ZnMgO nanowalls were prepared by plasma-assisted molecular beam epitaxy without a catalyst on c-Al2O3 substrate. The obtained nanowalls have preferred orientation along c axis. The nanowalls are about 10 to 20 nm in thickness and about 50 nm in height. Only Zn, Mg, O and Al signals are detected in the nanowalls from the energy dispersive spectroscopy (EDS). The Mg content is about 3% in ZnMgO nanowalls. The room temperature photoluminescence (PL) spectra shows the emission peak of the ZnMgO nanowalls at 3.346 eV. The origin of the ultraviolet emission is discussed with the help of temperature-dependent PL spectra. The ultraviolet emission band is free exiton recombination observed in the low temperature PL spectra (at 81 K). We also observe the free-to-acceptor (FA) emission of the ZnMgO nanowalls. The acceptor binding energy obtained from photoluminescence studies is about 123 meV. The results show that Mg doping leads to an increase of the acceptor binding energy. The possible growth mechanism of the ZnMgO nanowall networks was discussed.

Insight into mechanism of formation of c8 adducts in carcinogenic reactions of arylnitrenium ions with purine nucleosides

For the most important arylnitrenium ion-guanosine C8 adducts in the reactions involving arylamine-initiated carcinogenesis, a detailed mechanism of their formation still remains unclear. In this paper, we employ quantum chemistry methods to explore this issue. Our study indicates that formation of these C8 adducts proceeds directly by additions of arylnitrenium ions to C8 position of nucleoside bases in DNA. The good agreements of theoretical rate constants, pK(a) value, and NMR chemical shifts of C8 intermediate with experimental data support this theoretical finding. Excitingly, predictions of what adducts can be observed in reactions of arylnitrenium ions with guanine and hypoxanthine are in fair agreement with experimental observations. This study answers an important question, in carcinogenesis researches, of what is the mechanism for formation of C8 adducts.