The color space of a graph

If k is a prime power, and G is a graph with n vertices, then a k‐coloring of G may be considered as a vector in $\mathbb{GF}$(k)ⁿ. We prove that the subspace of $\mathbb{GF}$(3)ⁿ spanned by all 3‐colorings of a planar triangle‐free graph with n vertices has dimension n. In particular, any such graph has at least n − 1 nonequivalent 3‐colorings, and the addition of any edge or any vertex of degree 3 results in a 3‐colorable graph. © 2000 John Wiley & Sons, Inc. J Graph Theory 34: 234–245, 2000     

Numerical analysis of breaking waves using the moving particle semi-implicit method

The numerical method used in this study is the moving particle semi-implicit (MPS) method, which is based on particles and their interactions. The particle number density is implicitly required to be constant to satisfy incompressibility. A semi-implicit algorithm is used for two-dimensional incompressible non-viscous flow analysis. The particles whose particle number densities are below a set point are considered as on the free surface. Grids are not necessary in any calculation steps. It is estimated that most of computation time is used in generation of the list of neighboring particles in a large problem. An algorithm to enhance the computation speed is proposed. The MPS method is applied to numerical simulation of breaking waves on slopes. Two types of breaking waves, plunging and spilling breakers, are observed in the calculation results. The breaker types are classified by using the minimum angular momentum at the wave front. The surf similarity parameter which separates the types agrees well with references. Breaking waves are also calculated with a passively moving float which is modelled by particles. Artificial friction due to the disturbed motion of particles causes errors in the flow velocity distribution which is shown in comparison with the theoretical solution of a cnoidal wave. © 1998 John Wiley & Sons, Ltd.     

Theoretical approach to the pharmacophoric pattern of GABAB analogs

In order to determine the structural requirements that are important for GABA_B binding affinity, a quantum-chemical-based conformational study has been performed, followed by a similarity analysis which includes 12 GABA_B analogs. Due to the flexibility of the structures, a semigrid GABA_B analog [2RS-(5,5-dimethyl) morpholinyl-acetic acid] has been used as a template for the amonium moiety in order to help to identify the active conformation. Both in vacuo, and solvent-simulated calculations, for the physiological media modeled as water molecules, have been compared, for this analog, at ab initio (G94, 6-31+G(d,p)) and semiempirical (PM3) levels, respectively. On the basis of this comparison, the results of in vacuo PM3 calculations have been chosen for the similarity analysis. We have included, in the calculations, a group of molecules heterogeneous enough to become representative of the different families that can bind to the GABA_B receptor site. Following their comparison we report the leading characteristics that can be related to their binding capability and define a pharmacophoric pattern for GABA_B analogs. The latter is compared with the one previously found for the binding affinity at the GABA_A receptor site. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1195–1208, 1998     

Ring currents in condensed ring systems

We have studied magnetism and aromaticity of polycyclic ring systems by analyzing ring currents for different circulations in these molecules. The technique employed for calculating ring currents uses correction vectors which implicitly includes all the eigenstates of the Hamiltonian in the space of the chosen configurations. We have employed the Pariser–Parr–Pople Hamiltonian and have carried out full configuration interaction (CI) calculations for small systems and approximate CI calculations for large systems. The systems studied include polyacenes, nonaromatic ring systems including the C₆₀ fragments pyracylene, fluoranthene, and corannulene, and heteroatomic systems with upto two six-membered rings. We find that in polyacenes, the aromaticity of the extreme phenyl rings reduces with increasing number of phenyl rings in the system, and it saturates at ≈⅔ the benzene value. In systems containing nonaromatic rings, we find paramagnetic or diamagnetic behavior for different circulations depending upon the number of atoms in the chosen ring cycle, in agreement with the 4n+2 rule. In corannulene, the largest fragment of C₆₀ we have studied, the five-membered ring is weakly diamagnetic while the six-membered ring is more diamagnetic, although much less than in isolated benzene. The ring structures with heteroatoms studied are pyridine, pyrimidine, and its isomers, s-triazine, quinoline and its isomer, and quinazoline and its isomers. All these have similar ring currents as in their purely carbon counterparts, although ions of these molecules show interesting behavior. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 503–513, 1998     

基于Gibbs矢量估计卫星轨道姿态的滤波算法研究

针对“矢量观测 陀螺”这种典型的三轴稳定卫星姿态确定系统模式,引入具有四元数优越性的Gibbs矢量作为姿态参数,提出了一种新的具有良好实时性能的轨道姿态估计方案。在方案设计中,为描述卫星轨道姿态的Gibbs矢量,推导出了基于四元数的运动学方程,并将QUEST法作为处理多矢量观测信息的压缩技术引入估计器,使得滤波修正算法得以简化。另外,针对单矢量观测情况,给出了能够加快状态估值收敛速度的改进协方差修正算法。仿真结果验证,新方案的姿态估计精度与传统的欧拉角估计法相当,而运算效率却明显高于欧拉角估计法。     

ELECT++: Faster conformational search method for docking flexible molecules using molecular similarity

We have developed a program, ELECT++ (Effective LEssening of Conformations by Template molecules in C++), to speed up the conformational search for small flexible molecules using the similar property principle. We apply this principle to molecular shape and, importantly, to molecular flexibility. After molecules in a database are clustered according to flexibility and shape (FCLUST++), additional reagents are generated to screen the conformational space of molecules in each cluster (TEMPLATE++). We call these representative reagents of each cluster template reagents. Template reagents and clustered reagents produce, after reaction, template molecules and clustered molecules, respectively (tREACT++). The conformations of a template molecule are searched in the context of a macromolecular target. Acceptable conformational choices are then applied to all molecules in its cluster, thus effectively biasing conformational space to speed up conformational searches (tSEARCH++). In our incremental search method, it is necessary to calculate the root-mean-square deviations (RMSD) matrix of distances between different conformations of the same molecule to reduce the number of conformations. Instead of calculating the RMSD matrix for all molecules in a cluster, the RMSD matrix of a template molecule is chosen as a reference and applied to all the molecules in its cluster. We demonstrate that FCLUST++ clusters the primary amine reagents from the Available Chemicals Directory (ACD) successfully. The program tSEARCH++ was applied to dihydrofolate reductase with virtual molecules generated by tREACT++ using clustered primary amine reagents. The conformational search by the program tSEARCH++ was about 4.8 times faster than by SEARCH++, with an acceptable range of errors. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1834–1852, 1998     

Vibrational projection analysis: New tool for quantitatively comparing vibrational normal modes of similar molecules

A new method for quantitatively comparing calculated vibrational modes is described that relies on projecting the vectors describing the normal modes of one molecule onto those of a basis molecule. The procedure virtually automates the assignment of vibrational modes from one molecule to a second, structurally similar one. We illustrate the concept by using the classical Wilson modes of benzene as a basis for describing normal modes of the monosubstituted benzene derivatives phenol, phenol-d5, and phenol radical cation. These examples demonstrate the method's power for accurately assigning and comparing the normal modes of molecules perturbed by chemical substitution, isotopic substitution, or oxidation state. The vibrational projection analysis method—a special case of vector projection analysis—is compared and contrasted with total energy distribution analysis, perhaps the most commonly used technique for quantitatively comparing vibrational modes, and is found superior in each case when comparing normal modes. Vibrational projection analysis need not be limited to single molecules and quantum calculations, because normal modes may be obtained for much larger systems using molecular mechanics or molecular dynamics techniques. The method should therefore prove useful for interpreting the normal modes of ordered periodic solids and structures perturbed by noncovalent contacts, including proteins and polymers. The method may also prove useful in evaluating new computational methods by allowing direct, quantitative comparison of the vibrational modes obtained from different techniques. The power of this technique will make vibrational projection analysis a valuable tool for computational chemists as well as those using calculations to complement vibrational spectroscopic measurements. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1663–1674, 1998     

Quantum similarity measures under atomic shell approximation: First order density fitting using elementary Jacobi rotations

The elementary Jacobi rotations technique is proposed as a useful tool to obtain fitted electronic density functions expressed as linear combinations of atomic spherical shells, with the additional constraint that all coefficients are kept positive. Moreover, a Newton algorithm has been implemented to optimize atomic shell exponents, minimizing the quadratic error integral function between ab initio and fitted electronic density functions. Although the procedure is completely general, as an application example both techniques have been used to compute a 1S-type Gaussian basis for atoms H through Kr, fitted from a 3-21G basis set. Subsequently, molecular electronic densities are modeled in a promolecular approximation, as a simple sum of parameterized atomic contributions. This simple molecular approximation has been employed to show, in practice, its usefulness to some computational examples in the field of molecular quantum similarity measures. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2023–2039, 1997