Evaluation of PM3(tm) as a Geometry Generator in Theoretical Studies of Transition-Metal-Based Catalysts for Polymerizing Olefins

The PM3(tm) method has been applied to several systems of relevance to catalytic polymerization of olefins, for catalysts containing Ti, Zr or Cr. With some exceptions, PM3(tm) calculations reproduce experimental geometries of stable, closed-shell, precursors well. For stationary points along the path of monomer insertion into a metal-alkyl bond, the comparison is made to structures obtained by optimization using various first-principle methods. Large errors are uncovered for the transient structures, in particular pertaining to metal-ethylene coordination and agostic interactions. The energy profiles for four insertion reactions are computed by gradient-corrected density functional (DFTG) methods, using molecular structures taken from PM3(tm) and first-principle geometry optimizations, respectively. The chromium case is promising, giving values for the barrier to monomer insertion of 11 and 9 kcal/mol based on PM3(tm) and DFTG geometries, respectively. The Ti- and Zr-based systems are predicted to proceed downhill based on PM3(tm) structures, whereas small barriers are found when using first-principle structures. A hybrid PM3(tm)-DFTG procedure is suggested for geometry optimization, which facilitates an accurate estimate of the barrier when applied to one of the zirconium systems.     

Benchmark of different charges for prediction of the partitioning coefficient through the hydrophilic/lipophilic index

A few different theoretical methods for assigning the partial atomic charges were benchmarked for calculation of the hydrophilic/lipophilic index (HLI). The coefficients were selected to produce the best correlation of the HLI values with the experimental octanol-water partition. Different parameters were checked in calculations of partial charges to get the best performance of the HLI values obtained. Thus, four partitioning schemes (Coulson, Mulliken, Merz-Kollman, Ford-Wang) were benchmarked for calculations of atomic charges with six semiempirical methods (AM1, PM3, RM1, PM6, PM6-D3H4, PM7). Moreover, five distinct types of partial atomic charges (Mulliken, Hirshfeld, Löwdin, CHELPG, NPA), obtained at the Hartree–Fock and DFT levels of theory with three basis sets, were tested for their ability to produce the HLI values with the best correlation to experimental logP coefficients of 50 mono-charged organic anions. In the case of the semiempirical methods, the best correlation between the HLI and logP values (the correlation coefficient r?=?0.9216) was obtained with the AM1 Ford–Wang parametric electrostatic potential charges. The Mulliken and Coulson charges calculated with the PM7 method can be used as an alternative to AM1, with the r values of 0.9107 and 0.8984, respectively. In the case of the DFT, the PBE/def2-TZVP natural population analysis charges produce the best correlation (r?=?0.9220). Nevertheless, in spite of a marginally lower performance (r?=?0.9159), the NPA charges computed at the PBE/def2-SVP level are more robust and can be regarded as the optimum choice for calculating the HLI values.

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Graphical abstract The hydrophilic/lipophilic index (HLI)

     

On the performance of semiempirical MO theory for dipole moments of dye molecules

The dipole moments of a set of 71 simple dye molecules calculated at the ab initio, DFT, and semiempirical levels have been compared. The DFT dipole moments are on average 16% larger than those obtained by MP2/6-31G**. AM1 and PM3 modified with an empirical correction procedure yield dipole moments essentially at the same level of accuracy as the results of non-empirical calculations. INDO/S and CNDO/S are considerably less accurate. Among different versions of spectral methods, the CISD scheme gives the best performance.Electronic Supplementary Material available.     

Performance assessment of semiempirical molecular orbital methods in the structural prediction of Sb(III) and Bi(III) complexes

In this paper we carried out a systematic study in order to assess the quality of some semiempirical methods (AM1, PM3 and PM6), comparing predicted structural properties of many Sb(III) and Bi(III) complexes with the corresponding experimental data, indicating which one is more appropriate to describe the structure of such compounds. Root-mean squared deviation (RMSD) and unsigned mean error (UME) were used to evaluate the accuracy of the semiempirical methods to predict the ground state geometries of complexes with many ligand types. Our results have shown that, in general, PM3 predicts more accurately the geometry of Sb(III) complexes, being considered by us as the method of choice to study Sb(III) complexes with a great variety of ligands. PM6 is indicated as the method of choice to study Bi(III) complexes with many types of ligands and also to study Sb(III) thiocompounds, even though PM6 showed an inability to reproduce Sb-N bonds for complexes with flexible ligands, presenting an average deviation of 71.5 % compared the X-ray data.     

A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation

Hydrogen bonding and polar interactions play a key role in identification of protein-inhibitor binding specificity. Quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations combined with DFT and semi-empirical Hamiltonian (AM1d, RM1, PM3, and PM6) methods were performed to study the hydrogen bonding and polar interactions of two inhibitors BEN and BEN1 with trypsin. The results show that the accuracy of treating the hydrogen bonding and polar interactions using QM/MM MD simulation of PM6 can reach the one obtained by the DFT QM/MM MD simulation. Quantum mechanics/molecular mechanics generalized Born surface area (QM/MM-GBSA) method was applied to calculate binding affinities of inhibitors to trypsin and the results suggest that the accuracy of binding affinity prediction can be significantly affected by the accurate treatment of the hydrogen bonding and polar interactions. In addition, the calculated results also reveal the binding specificity of trypsin: (1) the amidinium groups of two inhibitors generate favorable salt bridge interaction with Asp189 and form hydrogen bonding interactions with Ser190 and Gly214, (2) the phenyl of inhibitors can produce favorable van der Waals interactions with the residues His58, Cys191, Gln192, Trp211, Gly212, and Cys215. This systematic and comparative study can provide guidance for the choice of QM/MM MD methods and the designs of new potent inhibitors targeting trypsin.     

Benchmarking of ONIOM method for the study of NH<Subscript>3</Subscript> dissociation at open ends of BNNTs

The reliability of ONIOM approach have been examined in calculations of adsorption energies, transition structures, change of HOMO-LUMO energy gaps and equilibrium geometries of the interaction between NH₃ and N-enriched (A) or B-enriched (B) open ended boron nitride nanotubes. To these ends, four models of the A or B, with different inner and outer layers have been studied. In addition, various low-levels including, AM1, PM3, MNDO and UFF have been examined, applying B3LYP/6-31 G* in all high-levels. It was shown, that in the case of A, (choosing two atom layers of the tube open-end as inner layer) the results of ONIOM approach are in best agreement with those of the pure density functional theory (DFT) calculations, while their results significantly differ from those of DFT in the case of B in same conditions. All above and population analysis demonstrate that the ONIOM may be a reliable scheme in the study of weak interactions while it is a controversial approach and should be applied cautiously in the case of strong interactions. We also probed the effect of tube length and diameter on the consistency between ONIOM and DFT results, showing that this consistency is independent of the mentioned parameters.     

Aminequinone-hydroxylquinoneimine tautomeric equilibrium revisited: molecular modeling study of the tautomeric equilibrium and substituent effects in 4-(4-R-phenylamino)naphthalene-1,2-diones

Semi-empirical (AM1 and PM3) and DFT (B3LYP/6-31G(d)) calculations were employed to study the tautomeric equilibrium between the aminequinone A and hydroxylquinoneimine B forms of 4-(4-R-phenylamino)naphthalene-1,2-diones. Substituent effects on the tautomeric equilibrium as well as on geometric and electronic parameters were also determined. In the gas phase the hydroxylquinoneimine B form is the most stable, whereas in water the aminequinone A form becomes more stable. The substituents do not modify the relative energies of the two tautomers. These results are in accordance with experimental data reported in the literature.     

Theoretical and experimental studies on the inhibition potentials of aromatic oxaldehydes for the corrosion of mild steel in 0.1 M HCl

Experimental aspect of the inhibition of the corrosion of mild steel by oxaldehydes was carried out using gravimetric, gasometric and thermometric methods while the theoretical studies were carried out using quantum chemical principle and quantitative structure activity relation (QSAR) approaches. The results obtained indicated that the studied oxaldehydes are good inhibitors for the corrosion of mild steel in HCl solutions. The adsorption of the inhibitors on mild steel surface is spontaneous, exothermic and is consistent with the assumptions of Langmuir adsorption isotherm. Excellent correlations were found between the calculated quantum chemical parameters and experimental inhibition efficiencies of the studied compounds. Correlations between theoretical and experimental inhibition efficiencies (for the different Hamiltonians, namely, PM6, PM3, AM1, RM1 and MNDO) were very close to unity. Condensed Fukui function and condensed softness have been used to determine the sites for electrophilic and nucleophilic attacks on each of the inhibitors.     

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol⁻¹. For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol⁻¹. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6–31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6–31G*: 7.4, and AM1: 10.0 kcal mol⁻¹. Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction of geometries. Figure Calculated structure of the complex ion [Ta₆Cl₁₂]²⁺ (footnote): Reference value in parenthesis Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A Comparative Semiempirical, Ab initio and DFT Study of Decarbonylation of Cyclic Ketones Part 1: Thermal Fragmentation of Cyclopropanone

Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G^** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol^-1, mainly localized around 37±2 kcal·mol^-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol^-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol^-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [_2s + _2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.     

Nonlinear optical properties of some substituted biphenyls

A series of donor-acceptor substituted biphenyls is examined using semiempirical SCF-MO methods. The geometries, dipole moments and first hyperpolarizabilities are obtained from AM1, MNDO and PM3 calculations. The finite-field method is used to calculate the polarizabilities. The properties of the substituents and the torsion angle between the phenyl rings are of fundamental importance for the hyperpolarizabilities. Among the three methods, AM1 leads to torsion angles closest to the experimental data. For each molecule, the HOMO is found to be localized on the donor part to some extent, whereas the LUMO is more concentrated on the acceptor part. The spectroscopic properties of the molecules are investigated using the ZINDO model. For all the molecules considered, the transition from the HOMO to the LUMO is found to be the most important for charge transfer, and this transition has been used in a two-state model to compute the first hyperpolarizability.     

THE HAMSTER CLOCK PHASE-RESPONSE CURVE FROM SUMMERLIKE LIGHT:DARK CYCLES AND ITS ROLE IN DAILY AND SEASONAL TIMEKEEPING

We address the subject of entrainment of the hamster clock by the day:night cycle in summer when the sun sets after 6 PM and rises before 6 AM (nights<12 h). Summer day:night cycles were simulated by 6 light:dark (LD) cycles with D<12 h (summerlike, SLD) ranging from SLD 12.5h:11.5h (D, 6:15 PM–5:45 AM) to 18h:6h (D, 9 PM–3 AM). These are the near limiting SLDs for constant PM timing (entrainment) of behavioral estrus and wheel running in hamsters. The onset of estrus was observed every 4 d in the same hamsters as a phase marker of their 24h clock. On the day before an experimental estrus, preceded and followed by control onsets, a dark period was imposed to cover a putative 6 PM–6 AM light-sensitive period (LSP). This was scanned with a light pulse (and periodic 5sec bell alarms) lasting 5–240 min. Shifts in onset of estrus on the next day were plotted vs. the end of the light pulse for PM times (“dusk”) and its onset for AM times (“dawn”). The resulting phase shifts from the six SLDs were similar, permitting their combination into a single phase-response curve (PRC) of 1605 shifts. This SLD composite PRC rose at 10:15 PM, peaked at 2 AM (81min advanced shift), fell linearly to 5:55 AM, and then abruptly to normal at 6 AM (no shift). Peak shift was unaffected by light pulse duration or intensity, or hamster age. The SLD composite PRC lacked the 6 PM–9 PM curve of delayed shifts present in reported PRCs from LD 12h:12h and DD. However, a two-pulse experiment showed that all light from 6 PM to L-off was needed to block (balance) the advancing action of a 5min morning light pulse, thereby maintaining entrainment. A working hypothesis to explain daily entrainment and seasonal fertility in the golden hamster is illustrated. A nomenclature for labeling the phases of the hamster clock (circadian time) is proposed.     

In vivo and in vitro activation of alveolar macrophages by recombinant interferon-gamma

In vivo administration of recombinant interferon-gamma (rIFN-gamma) was previously shown to result in activation of the microbicidal activities of peritoneal macrophages (PM phi). Because macrophages at different anatomical sites vary in their functional capacities, we considered it of interest to determine whether administration of murine rIFN-gamma, either in vitro or in vivo, can enhance the microbicidal activity of resident alveolar macrophages (AM phi) and to compare the effects of rIFN-gamma on AM phi and PM phi. After incubation in vitro with rIFN-gamma, the antimicrobial activities of both murine AM phi and PM phi were enhanced, as assessed by their ability to inhibit replication of the intracellular parasite, Toxoplasma gondii. This effect was dose dependent for AM phi over a range of 0.1 to 1 U/ml and for PM phi over a range of 0.5 to 1000 U/ml. In this assay, the minimum dosage required for in vitro activation of AM phi was one-half that required for activation of PM phi, suggesting a greater sensitivity of AM phi to the in vitro activity of rIFN-gamma. Macrophages from both anatomical sites were also activated when rIFN-gamma was administered in vivo. This effect was dose dependent over a range of 10(3) to 10(5) U/mouse. Freshly harvested AM phi and PM phi from mice injected 24 hr earlier with 10(4) U rIFN-gamma by either the i.v. or i.p. routes markedly inhibited intracellular multiplication of Toxoplasma. In contrast, AM phi and PM phi from control mice permitted fourfold to ninefold increases in numbers of intracellular Toxoplasma. The anti-toxoplasma activity of AM phi and PM phi gradually diminished over a period of 3 days when assayed at successive 24 hr periods after a single i.v. injection of rIFN-gamma. At 3 days after injection, a substantial loss of anti-toxoplasma activity was observed with PM phi as compared with controls; residual anti-toxoplasma activity was still demonstrable in AM phi at 3 days. These results demonstrate that in vitro as well as in vivo treatment with rIFN-gamma confers on AM phi an enhanced antimicrobial activity. These findings provide a rationale for evaluating rIFN-gamma in the treatment of pulmonary infections, especially those due to opportunistic pathogens against which AM phi play a major role in host defense.     

The hamster clock phase-response curve from summerlike light:dark cycles and its role in daily and seasonal timekeeping

We address the subject of entrainment of the hamster clock by the day:night cycle in summer when the sun sets after 6 PM and rises before 6 AM (nights < 12 h). Summer day:night cycles were simulated by 6 light:dark (LD) cycles with D < 12 h (summerlike, SLD) ranging from SLD 12.5 h:11.5 h (D, 6:15 PM-5:45 AM) to 18 h:6 h (D, 9 PM-3 AM). These are the near limiting SLDs for constant PM timing (entrainment) of behavioral estrus and wheel running in hamsters. The onset of estrus was observed every 4 d in the same hamsters as a phase marker of their 24 h clock. On the day before an experimental estrus, preceded and followed by control onsets, a dark period was imposed to cover a putative 6 PM-6 AM light-sensitive period (LSP). This was scanned with a light pulse (and periodic 5 sec bell alarms) lasting 5-240 min. Shifts in onset of estrus on the next day were plotted vs. the end of the light pulse for PM times ("dusk") and its onset for AM times ("dawn"). The resulting phase shifts from the six SLDs were similar, permitting their combination into a single phase-response curve (PRC) of 1605 shifts. This SLD composite PRC rose at 10:15 PM, peaked at 2 AM (81 min advanced shift), fell linearly to 5:55 AM, and then abruptly to normal at 6 AM (no shift). Peak shift was unaffected by light pulse duration or intensity, or hamster age. The SLD composite PRC lacked the 6 PM-9 PM curve of delayed shifts present in reported PRCs from LD 12 h:12 h and DD. However, a two-pulse experiment showed that all light from 6 PM to L-off was needed to block (balance) the advancing action of a 5 min morning light pulse, thereby maintaining entrainment. A working hypothesis to explain daily entrainment and seasonal fertility in the golden hamster is illustrated. A nomenclature for labeling the phases of the hamster clock (circadian time) is proposed.     

Aminopyrimidines and Derivatives. 19 1. Reaction of 1, 6-Dihydro-4-Beta; D (2, 3, 4, 6-Tetra-0-Acetyl)Glucopyranosylamino-1-Methyl-Z-Methoxy-6-Oxo Pyrimidine with Choracetyl Chloride

Abstract

Reaction between 1, 6-dihydro-4-β-D(2, 3, 4, 6-tetra-O-acetyl) glucopyranosylamino-l-methyl-2-methoxy-6-oxo pyrimidine and chloracetyl chloride yields the corresponding 5-α-chloracetyl derivative and 2,6-di oxo-4-β -D (2,3,4,6-tetra-0-acetyl) glucopyranosylamino-l-methyl-1,2,3,6 tetrahdro pyrimidine. The first compund has been cyclized to the corresponding 7-β-D-glucopyranosyl-pyrrolo 2, 3-d pyrimidine and the second one to 3-βD-glucopyranosyl-vic-triazolo 4,5-d pyrimidine.     

一年生和多年生豆禾混播草地超产与多样性效应的比较

为了测度一年生和多年生豆禾混播草地的超产效应与植物多样性效应的关系, 明确一年生和多年生混播草地的高产优势, 探索豆禾混播草地多样性效应和超产效应对其生态功能的响应机制, 于2013-2015年在新疆伊犁地区昭苏盆地开展了3年的牧草产量观测试验。该试验设置3种牧草混播种类和混播比例, 分别为一年生豆禾混播草地(2种牧草混播, AM2)和多年生豆禾混播草地(2种牧草混播, PM2; 4种牧草混播, PM4; 6种牧草混播, PM6), 豆禾混播比例分别为6:4、5:5和4:6。结果表明: 1) 2013、2014年和3年平均值AM2的超产幅度小于PM2和PM6, 2015年AM2的超产幅度大于PM2、PM4和PM6; 混播群落生产力与群落组分中生产力最高产物种单产以及各组分种平均单产的差值表现出相似的规律。2) 2013、2014年和3年平均值AM2的互补效应大于PM2、PM4和PM6, AM2的选择效应则远小于互补效应, PM2、PM4和PM6的互补效应则比较稳定。3)物种丰富度和物种均匀度与牧草产量(群落生产力)大部分情况下呈单峰的“饱和上升型”模式, 分别在4种牧草混播和豆禾混播比例为5:5时, 具有较高生产力。4)多年生豆禾混播草地的互补效应、选择效应和多样性净效应均随生长年限的延长而呈下降趋势, 也导致了超产幅度、超产效应及其稳定性的下降。由此可见, 在建植初期, 互补效应和选择效应共同主导了多年生豆禾混播草地的超产效应, 而随着生长年限的延长, 选择效应则成为主要影响因素; 一年生豆禾混播草地的超产效应则一直受互补效应的影响。     

Contribution of IL-1 beta and TNF-alpha to the initiation of the peripheral lung response to atmospheric particulates (PM10)

Alveolar macrophages (AM) play a key role in clearing atmospheric particulates from the lung surface and stimulating epithelial cells to produce proinflammatory mediators. The present study examines the role of "acute response" cytokines TNF-alpha and IL-1 beta released by AM exposed to ambient particulate matter with a diameter of <10 microm (PM(10)) in amplifying the proinflammatory mediator expression by A549 cells and human bronchial epithelial cells (HBEC). The results showed that supernatants from human AM incubated 24 h with PM(10) (100 microg/ml) contained more TNF-alpha, IL-1 beta, granulocyte-macrophage colony stimulating factor, IL-6, and IL-8 than nonexposed AM supernatants. The 3-h treatment of A549 cells with PM(10)-exposed AM supernatants increased TNF-alpha, IL-1 beta, IL-8, regulated on activation normal T-cells expressed and secreted (RANTES), and leukemia inhibitory factor mRNA compared with the treatment with nonexposed AM supernatants and, compared with untreated A549 cells, additionally increased ICAM-1 and monocyte chemotactic protein-1 mRNA. Preincubating PM(10)-exposed AM supernatants with anti-IL-1 beta antibodies reduced all the above mediators as well as VEGF mRNA expression (P < 0.05), while anti-TNF-alpha antibodies were less effective (P > 0.05), and the combination of the two antibodies most effective. When HBEC were treated similarly, anti-TNF-alpha antibodies had the greatest effect. In A549 cells PM(10)-exposed AM supernatants increased NF-kappa B, activator protein (AP)-1 and specificity protein 1 binding, while anti-TNF-alpha and anti-IL-1 beta antibodies reduced NF-kappa B and AP-1 binding. We conclude that AM-derived TNF-alpha and IL-1 beta provide a major stimulus for the production of proinflammatory mediators by lung epithelial cells and that their relative importance may depend on the type of epithelial cell target.     

Vibrational spectroscopy of hydroxy-heterobiaryls. IR-active modes of [2,2'-bipyridyl]-3,3'-diol.

All observed IR-active vibrational modes of [2,2'-bipyridyl]-3,3'-diol (BP(OH)2) and its two isotopomers, BP(OD)2 and BP(OH)2-d6 have been assigned on the basis of the comparison of experimental results with predictions obtained from DFT (B3LYP/6-31G(d,p)) calculations. The sensitivity of the vibrational transitions to the environment has been studied by comparing the spectra recorded in vapour, different solutions, KBr pellets, and cryogenic argon matrices. The results may be useful for the quantum control of excited state single or double proton transfer in BP(OH)2.