A parallelized integral-direct second-order Møller–Plesset perturbation theory method with a fragment molecular orbital scheme

We propose a parallelized integral-direct algorithm of the second-order Møller–Plesset perturbation theory (MP2) as a size-consistent correlated method. The algorithm is a modification of the recipe by Mochizuki et al. [(1996) Theor Chim Acta 93:211]. There is no need to communicate the bulky data of integrals across worker processes, keeping the formal fifth-power dependence on the number of basis functions. A multiple integral screening procedure is incorporated to reduce the operation costs effectively. An approximate MP2 density matrix can also be directly calculated through the integral contraction with orbital energies. We implement the MP2 code by accepting Kitauras fragment molecular orbital (FMO) scheme as in the program ABINIT-MP developed by Nakano et al. [(2002) Chem Phys Lett 351:475]. The error in the FMO–MP2 energies is found to be within the order of the chemical accuracy. Timing and parallel acceleration results are shown for test molecules.     

Synthesis and nematicidal evaluation of 1,2,3-benzotriazin-4-one derivatives containing piperazine as linker against Meloidogyne incognita

To explore new skeleton with nematicidal activity, a series of novel 1,2,3-benzotriazin-4-one derivatives containing piperazine as linker were synthesized and varied fragments were also introduced to increase structure diversity of thenew skeleton.     

Efficient deep blue OLEDs with extremely low efficiency roll-off at high brightness based on phenanthroimidazole derivatives

Local emissions located on the PI moiety and anthracene moiety play a key role in alleviating efficiency roll-off at high Brightness in non-doped and doped devices.     

Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations

Polyglutamine (polyQ) diseases, including Huntington’s disease (HD), are caused by expansion of polyQ-encoding repeats within otherwise unrelated gene products. The aggregation mechanism of polyQ diseases, the inhibition mechanism of Congo red, and the alleviation mechanism of trehalose were proposed here based on quantum chemical calculations and molecular dynamics simulations. The calculations and simulations revealed the following. The effective molecular bonding is between glutamine (Gln) and Gln (Gln + Gln), between Gln and Congo red (Gln + Congo red), and between Gln and trehalose (Gln + trehalose). The bonding strength is −13.1 kcal/mol for Gln + Gln, −24.4 kcal/mol for Gln + Congo red, and −12.0 kcal/mol for Gln + trehalose. In the polyQ region, both the number of intermolecular Gln + Gln formations and the total calories generated by the Gln + Gln formation are proportional to the number of repetitions of Gln. We propose an aggregation mechanism whose heat generated by the intermolecular Gln + Gln formation causes the pathogeny of polyQ disease. In our aggregation mechanism, this generated heat collapses the host protein and promotes fibrillogenesis. Without contradiction, our mechanism can explain all the experimental results reported to date. Our mechanism can also explain the inhibition mechanism by Congo red as an inhibitor of polyglutamine-induced protein aggregation and the alleviation mechanism by trehalose as an alleviator of that aggregation. The inhibition mechanism by Congo red is explained by the strong interaction with Gln and by the characteristic structure of Congo red.     

定域片断轨道基组的对称化

片断的UHF运算不能保证每个片断轨道具有确切的电子占据数,故Kost定域化是必需的.当片断产生于多键断裂时,在确保目标轨道单占据性的同时,Kost定域破坏了轨道基组的对称性.为此,在Kost定域化后,必须对单占据轨道作2×2对称化旋转后,再作有条件的RHF运算.以乙烯基片断CHCH(波二烯分子中的一个片断)为例,详述了对称化的方法、原理和计算程序.以C-H片断为例,细述三单键片断轨道基组对称化的特殊性.介绍C-HR参考键长选择的判据,探讨键长与选择Gaussian基组大小的关系.     

Some properties of contraction-critical 5-connected graphs

Let k be a positive integer and let G be a k-connected graph. An edge of G is called k-contractible if its contraction still results in a k-connected graph. A non-complete k-connected graph G is called contraction-critical if G has no k-contractible edge. Let G be a contraction-critical 5-connected graph, Su proved in [J. Su, Vertices of degree 5 in contraction-critical 5-connected graphs, J. Guangxi Normal Univ. 17 (3) (1997) 12-16 (in Chinese)] that each vertex of G is adjacent to at least two vertices of degree 5, and thus G has at least vertices of degree 5. In this paper, we further study the properties of contraction-critical 5-connected graph. In the process, we investigate the structure of the subgraph induced by the vertices of degree 5 of G. As a result, we prove that a contraction-critical 5-connected graph G has at least vertices of degree 5.     

Characterization of the chemical composition of white chrysanthemum flowers of Hangzhou by using high‐performance ion trap mass spectrometry

In this study, high‐performance liquid chromatography coupled with amaZon SL high‐performance ion trap mass spectrometry was used to analyze the target components in white chrysanthemum flowers of Hangzhou. Twenty‐one components were detected and identified in both white chrysanthemum flowers of Hangzhou samples by using target compound analysis. Furthermore, seven new compounds in white chrysanthemum flowers of Hangzhou were found and identified by analyzing the fragment ion behavior in the mass spectra. The established method can be expedient for the global quality investigation of complex components in herbal medicines and food.     

Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

We have developed a parallelized integral-direct code of the perturbative doubles correction for configuration interaction with singles, proposed as CIS(D) by Head-Gordon et al. (Chem Phys Lett 219:21, 1994). The CIS(D) method provides the energy corrections both of the relaxation and differential correlation for the respective CIS excited states. The implementation of CIS(D) is based on our original algorithm for the second-order Møller–Plesset perturbation (MP2) calculations (Mochizuki et al. in Theor Chem Acc 112:442, 2004). There is no need to communicate bulky intermediate data among worker processes of the parallelized execution. This CIS(D) code is then incorporated into a developer version of ABINIT-MP program, in order to improve the overestimation in excitation energies calculated by the CIS method in conjunction with the multilayer fragment molecular orbital scheme (MLFMO-CIS) (Mochizuki et al. in Chem Phys Lett 406:283, 2005). The MLFMO-CIS(D) method is first used in evaluating the lowest n\(\pi^{*}\) excitation energy of the hydrated formaldehyde. The photoactive yellow protein (PYP) is the second target of MLFMO-CIS(D) calculation. Through these applications, it is shown that the CIS(D) correction improves the CIS results favorably.     

Multiple ligand detection and affinity measurement by ultrafiltration and mass spectrometry analysis applied to fragment mixture screening

Binding affinity of a small molecule drug candidate to a therapeutically relevant biomolecular target is regarded the first determinant of the candidate's efficacy. Although the ultrafiltration-LC/MS (UF-LC/MS) assay enables efficient ligand discovery for a specific target from a mixed pool of compounds, most previous analysis allowed for relative affinity ranking of different ligands. Moreover, the reliability of affinity measurement for multiple ligands with UF-LC/MS has hardly been strictly evaluated. In this study, we examined the accuracy of K_d determination through UF-LC/MS by comparison with classical ITC measurement. A single-point K_d calculation method was found to be suitable for affinity measurement of multiple ligands bound to the same target when binding competition is minimized. A second workflow based on analysis of the unbound fraction of compounds was then developed, which simplified sample preparation as well as warranted reliable ligand discovery. The new workflow implemented in a fragment mixture screen afforded rapid and sensitive detection of low-affinity ligands selectively bound to the RNA polymerase NS5B of hepatitis C virus. More importantly, ligand identification and affinity measurement for mixture-based fragment screens by UF-LC/MS were in good accordance with single ligand evaluation by conventional SPR analysis. This new approach is expected to become a valuable addition to the arsenal of high-throughput screening techniques for fragment-based drug discovery.