广义sine-Gordon方程高精度隐式紧致差分方法

本文研究一类二维非线性的广义sine-Gordon(简称SG)方程的有限差分格式.首先构造三层时间的紧致交替方向隐式差分格式,并用能量分析法证明格式具有二阶时间精度和四阶空间精度.然后应用改进的Richardson外推算法将时间精度提高到四阶.最后,数值算例证实改进后的算法在空间和时间上均达到四阶精度.     

Matching energy of unicyclic and bicyclic graphs with a given diameter

Gutman and Wagner proposed the concept of matching energy (ME) and pointed out that the chemical applications of ME go back to the 1970s. Let G be a simple graph of order n and be the roots of its matching polynomial. The ME of G is defined to be the sum of the absolute values of . In this article, we characterize the graphs with minimal ME among all unicyclic and bicyclic graphs with a given diameter d. © 2014 Wiley Periodicals, Inc. Complexity 21: 224–238, 2015     

Lipase mediated separation of triterpene structural isomers, α- and β-amyrin

Pentacyclic triterpenoids α- and β-amyrin possess a wide range of biological and pharmacological activities. High structural similarity between these two structural isomers makes their chromatographic separation an ineffective and tedious choice. In this study, Candida rugosa lipase catalyzed separation protocol for the isolation of individual isomers has been developed. In the presence of vinyl acetate as the acyl donor, Candida rugosa lipase carried out acetylation of β-amyrin more efficiently as compared to α-amyrin leading to a kinetic separation. The conditions of transesterification reaction were optimized systematically, which was utilized to separate α- and β-amyrin from a mixture obtained from the latex of Plumeria obtusa.     

Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules

A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. © 2013 Wiley Periodicals, Inc.     

Novel tri-carbazole modified fluorene host material for highly efficient solution-processed blue and green electrophosphorescent devices

A series of novel solution-processable small-molecule host materials: 2DPF-TCz, 2SBF-TCz, 27DPF-TCz, and 27SBF-TCz comprising a fluorene monomer as the rigid core and tri-carbazole as the periphery have been designed and synthesized, and their optical, electrochemical, and thermal properties have been fully characterized. The host materials exhibit high glass-transition temperatures (231–310 °C) and high triplet energy levels (2.61–2.73 eV). High-quality amorphous thin films can be obtained by spin-coating the host materials from solutions. It is found that the HOMO level of the host materials can be tuned by linking the tri-carbazole unit to the 2,7 positions of the fluorine core, resulting in appropriate HOMO energy levels (−5.36 to −5.23 eV) for improved hole-injection in the device. Solution-processed blue and green electrophosphorescent devices bases on the developed host materials exhibit high efficiencies of 21.2 and 34.8 cd A⁻¹, respectively.     

Ultraviolet light absorber with low surface energy: synthesis and characterization

Novel fluorine-containing ultraviolet absorbers (FBPs) with low surface energy were successfully synthesized based on 2,4-dihydroxy benzophenone (BP-1), and their structures were characterized by ¹H NMR, ¹³C NMR, FTIR, and HRMS. UV absorption of FBPs was studied in 10⁻⁴ M dichloromethane (CH₂Cl₂), which demonstrated the superior UV absorption capability of FBPs (ca. ?=1.7×10⁴ to 2.2×10⁴ at λ_max) over the matrix (?=1.7×10⁴ at λ_max). Quantum chemistry calculation was performed to investigate the stable structure and UV electronic absorption bands of FBPs. The surface chemistry information of high-chlorinated polyethylene (HCPE) coating films embedded with ultraviolet absorbers (UVAs) was given by X-ray photoelectron spectroscopy (XPS) and contact angle measurement. The results show that the surface enrichment capability of FBPs is remarkably better than traditional UVAs (including BP-1, BP-3, BP-12) because of the low surface energy properties of FBPs.     

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

The Poisson–Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N‐ and C‐terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Characterization of the potential energy surfaces of two small but challenging noncovalent dimers: (P2)2 and (PCCP)2

This work characterizes eight stationary points of the P₂ dimer and six stationary points of the PCCP dimer, including a newly identified minimum on both potential energy surfaces. Full geometry optimizations and corresponding harmonic vibrational frequencies were computed with the second‐order Møller–Plesset (MP2) electronic structure method and six different basis sets: aug‐cc‐pVXZ, aug‐cc‐pV(X+d)Z, and aug‐cc‐pCVXZ where X = T, Q. A new L‐shaped structure with C₂ symmetry is the only minimum for the P₂ dimer at the MP2 level of theory with these basis sets. The previously reported parallel‐slipped structure with C_2h symmetry and a newly identified cross configuration with D₂ symmetry are the only minima for the PCCP dimer. Single point energies were also computed using the canonical MP2 and CCSD(T) methods as well as the explicitly correlated MP2‐F12 and CCSD(T)‐F12 methods and the aug‐cc‐pVXZ (X = D, T, Q, 5) basis sets. The energetics obtained with the explicitly correlated methods were very similar to the canonical results for the larger basis sets. Extrapolations were performed to estimate the complete basis set (CBS) limit MP2 and CCSD(T) binding energies. MP2 and MP2‐F12 significantly overbind the P₂ and PCCP dimers relative to the CCSD(T) and CCSD(T)‐F12 binding energies by as much as 1.5 kcal mol^?1 for the former and 5.0 kcal mol^?1 for the latter at the CBS limit. The dominant attractive component of the interaction energy for each dimer configuration was dispersion according to several symmetry‐adapted perturbation theory analyses. © 2014 Wiley Periodicals, Inc.     

A general,recursive, and open‐ended response code

We present a new implementation of a recent open‐ended response theory formulation for time‐ and perturbation‐dependent basis sets (Thorvaldsen et al., J. Chem. Phys. 2008, 129, 214108) at the Hartree–Fock and density functional levels of theory. A novel feature of the new implementation is the use of recursive programming techniques, making it possible to write highly compact code for the analytic calculation of any response property at any valid choice of rule for the order of perturbation at which to include perturbed density matrices. The formalism is expressed in terms of the density matrix in the atomic orbital basis, allowing the recursive scheme presented here to be used in linear‐scaling formulations of response theory as well as with two‐ and four‐component relativistic wave functions. To demonstrate the new code, we present calculations of the third geometrical derivatives of the frequency‐dependent second hyperpolarizability for HSOH at the Hartree–Fock level of theory, a seventh‐order energy derivative involving basis sets that are both time and perturbation dependent. © 2014 Wiley Periodicals, Inc.