The de novo design of median molecules within a property range of interest

Summary In this paper an application is presented of the median molecule workflow to the de novo design of novel molecular entities with a property profile of interest. Median molecules are structures that are optimised to be similar to a set of existing molecules of interest as an approach for lead exploration and hopping. An overview of this workflow is provided together with an example of an instance using the similarity to camphor and menthol as objectives. The methodology of the experiments is defined and the workflow is applied to designing novel molecules for two physical property datasets: mean molecular polarisability and aqueous solubility. This paper concludes with a discussion of the characteristics of this method.     

Error in an approximate wave function and an error minimization scheme

An estimate of error in an approximate wave function for a stationary state is put forward that does not require any information about the exact state. The measure is sensitive and direct. Parameters embedded in a trial wave function can be varied to minimize this error as well, leading to a variational principle. Such a scheme works nicely for bound states and the more so for Siegert states, for which the standard energy minimization principle does not apply. Pilot calculations on the anharmonic oscillator system and the radial Stark effect in the hydrogen atom reveal the worth of the endeavor. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Theoretical study and rate constant calculation for the reactions of SH (SD) with Cl2, Br2, and BrCl

The mechanisms of the SH (SD) radicals with Cl2 (R1), Br2 (R2), and BrCl (R3) are investigated theoretically, and the rate constants are calculated using a dual-level direct dynamics method. The optimized geometries and frequencies of the stationary points are calculated at the MP2/6-311G(d,p) and MPW1K/6-311G(d,p) levels. Higher-level energies are obtained at the approximate QCISD(T)/6-311++G(3df, 2pd) level using the MP2 geometries as well as by the multicoefficient correlation method based on QCISD (MC-QCISD) using the MPW1K geometries. Complexes with energies less than those of the reactants or products are located at the entrance or the exit channels of these reactions, which indicate that the reactions may proceed via an indirect mechanism. The enthalpies of formation for the species XSH/XSD (X = Cl and Br) are evaluated using hydrogenation working reactions method. By canonical variational transition-state theory (CVT), the rate constants of SH and SD radicals with Cl2, Br2, and BrCl are calculated over a wide temperature range of 200-2000 K at the a-QCISD(T)/6-311++G(3df, 2pd)//MP2/6-311G(d, p) level. Good agreement between the calculated and experimental rate constants is obtained in the measured temperature range. Our calculations show that for SH (SD) + BrCl reaction bromine abstraction (R3a or R3a') leading to the formation of BrSH (BrSD) + Cl in a barrierless process dominants the reaction with the branching ratios for channels 3a and 3a' of 99% at 298 K, which is quite different from the experimental result of k3a'/k3' = 54 +/- 10%. Negative activation energies are found at the higher level for the SH + Br2 and SH + BrCl (Br-abstraction) reactions; as a result, the rate constants show a slightly negative temperature dependence, which is consistent with the determination in the literature. The kinetic isotope effects for the three reactions are "inverse". The values of kH/kD are 0.88, 0.91, and 0.69 at room temperature, respectively, and they increase as the temperature increases.     

Fast Marching Method for Calculating Reactive Trajectories for Chemical Reactions

We present a method for computing classical Newtonian trajectories that minimize the path length or transit time from reactant to product. Our approach is based on a generalization of the fast-marching method, which allows us to construct the solution of the Hamilton-Jacobi equation for the action that optimizes the desired quantity. The resulting “reactive paths” can be interpreted as reaction coordinates but, unlike more conventional choices, they contain dynamical information about the chemical system of interest.     

Two Hamiltonian cycles

If the line graph of a graph G decomposes into Hamiltonian cycles, what is G? We answer this question for decomposition into two cycles.     

Hamilton cycles in line graphs of 3-hypergraphs

We prove that every 52-connected line graph of a rank 3 hypergraph is Hamiltonian. This is the first result of this type for hypergraphs of bounded rank other than ordinary graphs.     

基于简化的应变梯度理论下Kirchhoff板模型边值问题的提法及其应用北大核心CSCD

考虑应变梯度和速度梯度的影响,建立薄板控制微分方程及给出其边值问题的提法,修正了前人给出的薄板角点条件.采用Levy法,给出受分布力作用下简支板的挠度及自由振动频率的解析解.通过与文献中分子动力学数据对比,验证了该文模型的有效性并提出校核材料参数的一种方法.研究结果表明,增大弹性地基和应变梯度参数可以有效提高板的等效刚度,而速度梯度参数则相反.该文提出的板的边值问题为研究薄板在复杂支撑边界及外荷载等条件提供了理论依据.同时,有望为其有限元法、有限差分法和基于能量原理的Galerkin法等数值方法提供理论依据.     

Minimax principles for elliptic mixed hemivariational–variational inequalities

In this paper, minimax principles are explored for elliptic mixed hemivariational–variational inequalities. Under certain conditions, a saddle-point formulation is shown to be equivalent to a mixed hemivariational–variational inequality. While the minimax principle is of independent interest, it is employed in this paper to provide an elementary proof of the solution existence of the mixed hemivariational–variational inequality. Theoretical results are illustrated in the applications of two contact problems.     

Maximum principle at infinity for complete minimal surfaces in flat 3-manifolds

The main result of this paper is the following maximum principle at infinity:Theorem.Let M ₁ and M ₂ be two disjoint properly embedded complete minimal surfaces with nonempty boundaries, that are stable in a complete flat 3-manifold. Then dist(M ₁,M ₂)=min(dist(M ₁,M ₂), dist(M ₂,M ₁)).In case one boundary is empty, e.g. M ₁,then dist(M ₁,M ₂)=dist(M ₂,M ₁).If both boundaries are empty, then M ₁ and M ₂ are flat.     

Large deviation analysis of the single server queue

We establish the large deviation principle (LDP) for the virtual waiting time and queue length processes in the GI/GI/1 queue. The rate functions are found explicitly. As an application, we obtain the logarithmic asymptotics of the probabilities that the virtual waiting time and queue length exceed high levels at large times. Additional new results deal with the LDP for renewal processes and with the derivation of unconditional LDPs for conditional ones. Our approach applies in large deviations ideas and methods of weak convergence theory.This work was supported in part by AT&T Bell Labs.