MPI/OpenMP hybrid parallel algorithm for resolution of identity second‐order Møller–Plesset perturbation calculation of analytical energy gradient for massively parallel multicore supercomputers

A massively parallel algorithm of the analytical energy gradient calculations based the resolution of identity Møller–Plesset perturbation (RI‐MP2) method from the restricted Hartree–Fock reference is presented for geometry optimization calculations and one‐electron property calculations of large molecules. This algorithm is designed for massively parallel computation on multicore supercomputers applying the Message Passing Interface (MPI) and Open Multi‐Processing (OpenMP) hybrid parallel programming model. In this algorithm, the two‐dimensional hierarchical MP2 parallelization scheme is applied using a huge number of MPI processes (more than 1000 MPI processes) for acceleration of the computationally demanding O (N ⁵) step such as calculations of occupied–occupied and virtual–virtual blocks of MP2 one‐particle density matrix and MP2 two‐particle density matrices. The new parallel algorithm performance is assessed using test calculations of several large molecules such as buckycatcher C₆₀@C₆₀H₂₈ (144 atoms, 1820 atomic orbitals (AOs) for def2‐SVP basis set, and 3888 AOs for def2‐TZVP), nanographene dimer (C₉₆H₂₄)₂ (240 atoms, 2928 AOs for def2‐SVP, and 6432 AOs for cc‐pVTZ), and trp‐cage protein 1L2Y (304 atoms and 2906 AOs for def2‐SVP) using up to 32,768 nodes and 262,144 central processing unit (CPU) cores of the K computer. The results of geometry optimization calculations of trp‐cage protein 1L2Y at the RI‐MP2/def2‐SVP level using the 3072 nodes and 24,576 cores of the K computer are presented and discussed to assess the efficiency of the proposed algorithm. © 2017 Wiley Periodicals, Inc.     

Chemical composition of Helietta parvifolia and its in vitro anticholinesterase activity

The chemical composition of the essential oil and the n-hexane (Hex), Ethyl Acetate (EtOAc) and butanol (BuOH) extracts from the leaves of Helietta parvifolia were determined by detailed GC-MS analysis, spectroscopic and spectrometric data. Eighty-four compounds were identified, revealing a furoquinoline alkaloid-rich composition. The phytochemical analysis of the extracts allowed the isolation of eigth furoquinoline alkaloids. Retention indices in GC-MS for six of this alkaloids are reported for the first time. Furoquinoline alkaloids are acethylcholinesterase inhibitors. Thus, the essential oil and extracts were submitted to this in vitro assay. The EtOAc and BuOH extracts showed potent activity, with IC₅₀ of 9.7 and 12.9 μg mL^?1, respectively. Additionaly, a correlation of their chemical constituents, established by principal component analysis (PCA) demostrated a similar profile and a high content of alkaloids. It is for these reasons that we can assume that the alkaloid content in these extracts could be responsible for their anticholinesterase activity.     

GC-MS联用技术结合化学计量学方法分析枳实枳壳挥发油成分

利用水蒸气蒸馏法提取四川枳实和山西枳壳的挥发油成分,采用GC-MS联用技术结合化学计量学方法(直观推导式演进特征投影法和选择性离子检测法)进行分析,同时结合程序升温保留指数辅助定性。定量分析采用峰面积归一化法。结果从枳实中35种化合物,占相对总面积含量的83.07%;枳壳中鉴定出37种化合物,占相对总面积含量的97.74%。二者共有组分20种,主要为D-Limonene,枳实中为50.87%,枳壳中为64.41%。研究表明,将化学计量学方法用于中药挥发油成分的定性定量分析可提高分析结果的准确性。     

IR-UV联合法测定固相微萃取涂层中单体含量

合成了作为固相微萃取涂层的苯乙烯-丙烯酸丁酯-乙烯基三乙氧基硅氧烷三元共聚物。采用红外光谱(IR)和紫外光谱(UV)相结合的方法测定了聚合物中苯乙烯和丙烯酸丁酯的含量。由IR法测得样品中二者的摩尔比。采用双波长紫外光谱法测得苯乙烯的含量。由苯乙烯与丙烯酸丁酯的摩尔比及苯乙烯的含量得出样品中丙烯酸丁酯含量,进而得出乙烯基三乙氧基硅氧烷的含量。苯乙烯与丙烯酸丁酯的摩尔比测定的外标曲线方程为A_r=0.114m_r+0.032,相关系数r2=0.999 3;苯乙烯含量测定的标准曲线方程为ΔA=0.078 6c+0.081 2,相关系数r2=0.998 9。苯乙烯含量测定的相对标准偏差(RSD)为0.41%,加标回收率为97.8%～104.0%;丙烯酸丁酯含量测定的相对标准偏差(RSD)为0.39%,加标回收率为97.1%～99.6%。     

Characterisation of polymers by size exclusion chromatography using multiple detection. Investigations on the determination of structural differences of hydroxyethyl starches

Summary An aqueous size exclusion chromatography system is outlined using dual detection by a multi-angel laser light scattering photometer (MALLS) and a concentration detector (RI). This system makes possible the determination of the molecular weight distribution of water soluble polymers in conjunction with the radius of gyration. The differences in the radii of gyration at the same molecular weights of two hydroxyethyl starches with different molecular structure are presented qualitatively. The determination of the Mark-Houwink relation for these polymers leads to a qualitatively similar result.     

Neutron and Alpha Structure in Neutron Deficient Nuclei in Astrophysics

The paper includes discussions on the important role of neutron and alpha configurations in proton-rich nuclei in nuclear astrophysics in terms of nucleosynthesis under extremely high-temperature hydrogenburning conditions. The p-process, which is supposed to take place at the very early epoch of type II supernovae, has considerable neutrons and alphas together with protons. The alpha-induced reactions on proton-rich unstable nuclei in the light mass regions is expected to play a crucial role, but very few of them were investigated well yet because of the experimental difficulties. Specifically, I report our recent experimental effort for the breakout process from the pp-chain region, 7Be(α ,γ )11C(α ,p)14N under the p-process. The neutron-induced reactions on proton-rich nuclei, which is even more a challenging subject, were investigated previously for very few nuclei. One possible experimental method is the Trojan Horse Method (THM). We successfully have applied THM to the 18F(n, )14N reaction study with an unstable beam of 18F.     

HPLC-RI法快速准确测定大豆磷脂酰胆碱含量

用HPLC -RI法和HPLC -UV法对大豆卵磷脂样品中的磷脂酰胆碱含量进行分析 ,并与二维TLC -P法(AOCSJa7-86)作比较。以WatersSpherisorbS5W(5μmSilica)4.6×250mm硅胶柱为固定相 ,正己烷 -异丙醇 -水 (体积比1∶4∶1)为流动相。色谱条件 :流速0.8mL·min -1,进样量10μL,柱温35℃ ,RI检测器温度35℃。由外标法得出其中磷脂酰胆碱的含量 ,分别采用大豆磷脂酰胆碱标样和蛋黄磷脂酰胆碱标样作为外标物。结果表明HPLC -RI法受标样来源影响小 ,分析结果准确 ,分析过程简便、快速 ,适合作为常规分析方法     

Efficient linear algebra routines for symmetric matrices stored in packed form

Quantum chemistry methods require various linear algebra routines for symmetric matrices, for example, diagonalization or Cholesky decomposition for positive matrices. We present a small set of these basic routines that are efficient and minimize memory requirements.