New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study

ABSTRACT

The Bacillus subtilis chorismate mutase catalysed Claisen rearrangement of chorismate to prephenate is one of the few pericyclic processes in biology, and as such provides a rare opportunity for understanding how Nature promotes such rearrangements so successfully. The major focus of this work is on (i) Exploring the hypothesis that the mechanism of the chorismate rearrangement is the same in the gas phase, in the aqueous solution and in the enzyme; (ii) Investigating current suggestions that the enzyme lowers the barrier via transition state stabilisation rather than via space confinement; and (iii) A comparison of Nature's way of catalysing the reaction with a gold(I) catalysed chorismate rearrangement. Based the Unified Reaction Valley Approach (URVA), for the first time, a detailed one-to-one comparison of the rearrangement in the gas phase, in the aqueous solution and in the enzyme is presented. URVA confirms that the actual chemical process of CO bond breaking and CC bond forming is the same for all media and unravels the unique catalytic function of the enzyme as a combination of shortening the process of positioning the enolpyruvyl side chain over the cyclohexadienyl ring by space confinement in concert with facilitating CO cleavage by enhanced charge polarisation. The transition state does not play a signifiant role for the rearrangement. In contrast, the gold catalyst changes the chemical process. The rearrangement is split into two steps by switching between Au[I]-π and Au[I]-σ complexation, thus avoiding the energy consuming CO breakage in the first step. Suggestions are made for metalloenzyme analogues combining both strategies.     

The berth allocation problem in terminals with irregular layouts

As international trade thrives, terminals attempt to obtain higher revenue while coping with an increased complexity with regard to terminal management operations. One of the most prevalent problems such terminals face is the Berth Allocation Problem (BAP), which concerns allocating vessels to a set of berths and time slots while simultaneously minimizing objectives such as total stay time or total assignment cost. Complex layouts of real terminals introduce spatial constraints which limit the mooring and departure of vessels. Although significant research has been conducted regarding the BAP, these real-world restrictions have not been taken into account in a general way. The present work proposes both a mixed integer linear programming formulation and a heuristic, which are capable of obtaining optimal or near-optimal solutions to this novel variant of the BAP. In order to assess the quality of the heuristic, which is being employed in a real tank terminal in Belgium, it is compared against the exact approach by way of randomly-generated instances and real-world benchmark sets derived from the tank terminal.     

Effect of local toroidal flow on double-tearing modes in cylindrical geometry

The effect of local toroidal flow (LTF) on double-tearing modes (DTMs) is investigated in cylindrical geometry using the reduced magnetohydrodynamics (RMHD) model. The results indicate that the LTF between the two rational surfaces is the dominant suppression effect on DTMs. The suppression effect is enhanced with the flow width increasing, and the DTMs become more stable with the increase of the shear of the LTF between the two rational surfaces. So, in the reversed shear magnetic field configuration, the local flow is driven between the two rational surfaces, which can effectively suppress the development of DTMs and maintain the high-performance state.     

Isomorph Invariance of Higher-Order Structural Measures in Four Lennard–Jones Systems

In the condensed liquid phase, both single- and multicomponent Lennard–Jones (LJ) systems obey the “hidden-scale-invariance” symmetry to a good approximation. Defining an isomorph as a line of constant excess entropy in the thermodynamic phase diagram, the consequent approximate isomorph invariance of structure and dynamics in appropriate units is well documented. However, although all measures of the structure are predicted to be isomorph invariant, with few exceptions only the radial distribution function (RDF) has been investigated. This paper studies the variation along isomorphs of the nearest-neighbor geometry quantified by the occurrence of Voronoi structures, Frank–Kasper bonds, icosahedral local order, and bond-orientational order. Data are presented for the standard LJ system and for three binary LJ mixtures (Kob–Andersen, Wahnström, NiY2). We find that, while the nearest-neighbor geometry generally varies significantly throughout the phase diagram, good invariance is observed along the isomorphs. We conclude that higher-order structural correlations are no less isomorph invariant than is the RDF.     

Markovian modeling for dependent interrecurrence times in bladder cancer

A methodology to model a process in which repeated events occur is presented. The context is the evolution of non-muscle-invasive bladder carcinoma (NMIBC), characterized by recurrent relapses. It is based on the statistical flowgraph approach, a technique specifically suited for semi-Markov processes. A very useful feature of the flowgraph framework is that it naturally incorporates the management of censored data. However, this approach presents two difficulties with the process to be modeled. On one hand, the management of covariates is not straightforward. However, it is of great interest to know how the characteristics of a certain patient influence the evolution of the disease. On the other hand, repeated events on the same subject are generally not independent, in which case the semi-Markov framework is not sufficient because the semi-Markov assumption implies independence among waiting time distributions. We solve this issue by extending the flowgraph methodology using the Markovian arrival process (MAP), which does successfully model the dependence between events. Along the way, we provide a procedure to consider covariates and censored times in MAPs, a pending task needed in this field. In short, we have managed to extend the flowgraph methodology beyond the semi-Markovian framework, simplifying the incorporation of covariates and keeping the management of censored times. All of which has allowed us to build a multistate model of the evolution of NMIBC. The developed model allows us to compute the Survival function for any evolution of a patient with specific clinic-pathological characteristics in this primary tumor.     

Hydrogeological responses in tropical mountainous springs

This study presents a hydrogeochemical analysis of spring responses (2013–2017) in the tropical mountainous region of the Central Valley of Costa Rica. The isotopic distribution of δ¹⁸O and δ²H in rainfall resulted in a highly significant meteoric water line: δ²H?=?7.93·δ¹⁸O?+?10.37 (r^2? =?0.97). Rainfall isotopic composition exhibited a strong amount-dependent seasonality. The isotopic variation (δ¹⁸O) of two springs within the Barva aquifer was simulated using the FlowPC program to determine mean transit times (MTTs). Exponential-piston and dispersion distribution functions provided the best-fit to the observed isotopic composition at Flores and Sacramento springs, respectively. MTTs corresponded to 1.23?±?0.03 (Sacramento) and 1.42?±?0.04 (Flores) years. The greater MTT was represented by a homogeneous geochemical composition at Flores, whereas the smaller MTT at Sacramento is reflected in a more variable geochemical response. The results may be used to enhance modelling efforts in central Costa Rica, whereby scarcity of long-term data limits water resources management plans.     

分形空间中的广义预不变凸函数与相关的Hermite-Hadamard型积分不等式

在分形集R^α(0<α≤1)上定义了广义预不变凸函数, 建立了关于广义预不变凸函数的 Hermite-Hadamard积分不等式。 构建了一个与广义预不变凸函数相关的局部分数阶积分恒等式, 由此恒等式并利用广义Hölder不等式和广义幂均不等式得到了关于此类函数的几个Hermite-Hadamard型局部分数阶积分不等式。 结果推广了已有研究中的一些结论。     

Gauss–Man i n Conne ction s for Arrangements, I E igenvalues

We construct a formal connection on the Aomoto complex of an arrangement of hyperplanes, and use it to study the Gauss–Manin connection for the moduli space of the arrangement in the cohomology of a complex rank one local system. We prove that the eigenvalues of the Gauss–Manin connection are integral linear combinations of the weights which define the local system.     

ON LOCAL CONTINUITY MODULI FOR GAUSSIAN PROCESSES

ＬＵＣＨＵＡＮＲＯＮＧ（陆传荣）（ＤｅｐａｒｔｍｅｎｔｏｆＭａｔｈｅｍａｔｉｃｓ，ＨａｎｇｚｈｏｕＵｎｉｖｅｒｓｉｔｙ，Ｈａｎｇｚｈｏｕ３１００２８，Ｃｈｉｎａ）（ＴｈｉｓｗｏｒｋｉｓｓｕｐｐｏｒｔｅｄｂｙｔｈｅＮａｔｉｏｎａｌＮａｔｕｒａｌＳｃｉｅ...