Some dimension problems in molecular databases

Molecular databases obtained either by combinatorial chemistry tools or by more traditional methods are usually organized according to a set of molecular properties. A database may be regarded as a multidimensional collection of points within a space spanned by the various molecular properties of interest, the property space. Some properties are likely to be more important than others, those considered important form the essential dimensions of the molecular database. How many properties are essential, this depends on the molecular problem addressed, however, the search in property space is usually limited to a few dimensions. Two types of search strategies are related either to search by property or search by lead compound. The first case corresponds to a lattice model, where the search is based on sets of adjacent blocks, usually hypercubes in property space, whereas lead-based searches in databases can be regarded as search around a center in property space. A natural model for lead-based searches involves a hyperspherical model. In this contribution a theoretical optimum dimension is determined that enhances the effectiveness of lead-based searches in property space of molecular databases.     

A dynamic theory of the transition state in the phase space: Application to isomerization in the LiNC-LiCN molecule

A theoretical method for systematic calculations of all the periodic orbits resulting in isomerization in the LiNC → LiCN system was suggested. Calculations used the property of hyperbolic orbits at the saddle point separating isomers in the configuration space. These orbits formed invariant stable and unstable manifolds in the phase space, which served as guides in fairly entangled and usually chaotic molecular dynamics. Manifold intersections result in the formation of so-called homoclinic orbits, which, in turn, form infinite families of bifurcation orbits constituting the structural framework of the phase space of the system. This approach allows isomerization reactions in the LiNC-LiCN molecular system to be described in terms of a roadmap determining the transfer of classical density from one local minimum to another.     

Two alternative criteria for labelling approximate treatments for molecules as “fully quantal” ones

If the confinement of a trial wavefunction on a subspace of the full Hilbert space of a systems is taken as a “constraint” that prevents an approximate method to be labelled as a “fully quantum” one, then it can be shown that practically all known molecular approximate method are not rigorously quantal ones. Another weaker (and already known) criterion used by nuclear physicists for such a labelling is discussed and illustrated for the generator coordinate method (in this case a quantum approach) and Hartree—Fock method (a semiclassical approach. On the other hand, although Lathouwers' treatment of molecular spectra may be labelled “fully quantum” (for certain molecules at least) under this softer criterion, it will be remarked that the loss of the variational upper-bound property attenuates much of its theoretical attractiveness.     

六方硫化钒晶体的空间群推演

晶体空间群推演是晶体结构描述和表达的关键环节,也是理论印证实验晶体结构的手段。因涉及数学方法、物理技术和图形软件,所以不仅是晶体结构教学的重点也是难点。本文基于六方硫化钒晶体结构测定的基本结构数据,用自编晶体学程序cryst 2015在图形软件上再现硫化钒的晶体结构。在点空间和三维实向量空间中,由线性映射表达平移和非平移对称操作,得到硫化钒的空间群和对应的矩阵表示群。由生成元的幂次连乘导出空间群群元素的生成顺序,以及由空间群导致的晶体学分类。这种借助实例的连贯推演方法,有助于建立晶体学知识结构框架,尤其能帮助初学者理解晶体学的科学思想体系。     

Designing molecules with optimal properties using the linear combination of atomic potentials approach in an AM1 semiempirical framework

The linear combination of atomic potentials (LCAP) approach is implemented in the AM1 semiempirical framework and is used to design molecular structures with optimized properties. The optimization procedure uses property derivative information to search molecular space and thus avoid direct enumeration and evaluation of each molecule in a library. Two tests are described: the optimization of first hyperpolarizabilities of substituted aromatics and the optimization of a figure of merit for n-type organic semiconductors.     

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.