Enumeration and generation of three-center valence structures

Chemical Modelling, 2000

Quarterly Journal of the Belgian, French and Italian Operations Research Societies, 2003

In the chemical community the need for representing chemical structures within a given family and of efficiently enumerating these structures suggested the use of computers and the implementation of fast enumeration algorithms. This paper considers the isomeric acyclic structures focusing on the enumeration of the alkane molecular family. For this family, Trinajstić et al.(1991) devised an enumeration algorithm which is the most widely known and utilized nowadays. Kvasnička and Pospichal (1991) have proposed an algorithmic ...

Journal of Chemical Information and Modeling, 1992

A selective generation and enumeration program for cyclic isomers, CAMGEC, is presented. The only input to this system is the molecular formula which allows for calculation of isomer characteristics such as number of rings or multiple bonds or a combination of the two. Generation could be done on one of these options or on all of them. Exhaustive generation process is based on graph theory and on a new concept of tuple notation. A filtration process, based on a decomposition-recomposition principle, for discarding repetitive structures is applied over trees specially defined for cyclic compounds that include multiple bonds and heteroatoms with multiple valencies. Selective generation could be done over one or over all of the following parameters: (a) isomer characteristics, (b) one or more selected patterns, and (c) level or degree value of the root vertex. CAMGEC'S performance shows its potential applicability in areas such as molecular design, organic synthesis, and structure elucidation.

Croatica Chemica Acta, 2001

It is required that molecules with a given graph and with covalent, coordinate-covalent, and ionic bonding contain closed-shell atoms. This requirement results in an equation for each atom, which states that the number ofvalence electrons pertaining to it before bonding, plus those made available to it in the bonding processes, close its valence shell. Solving the equations results in identifying the atoms and the bond orders of the Lewis diagrams. The algebraic procedure can identify new species. Some of them may be considered impossible (for instance, with high steric strain), or may be transitory, or may be found only under the most unusual conditions. Lists of triatomic molecules, clusters, and resonances found by solving the equations is presented. Closed-shell molecules lie on parallel planes in their chemical spaces, namely those on which isoelectronic molecules are located.

2006

After a few remarks on the history of molecular modelling we describe certain mathematical aspects of the generation of molecular structural formulae. The focus is on the automatic generation of structural formulae for the purpose of molecular structure elucidation and the examination of molecular libraries. The aim is to give a review and to point to relevant literature. We demonstrate an application in the area of quantitative structure-property/activity relationships. Then, we give a glance on ongoing research in the generation of 3Dstructures (stereoisomers and conformers), and finally we mention two problems that should be solved in the near future, the possible use of hypergraphs, and the generation of patent libraries.

Structural Chemistry, 2018

This chapter plunges into applied quantum chemistry, with various examples, ranging from elementary notions, up to rather advanced tricks of know-how and non-routine procedures of control and analysis. In the first section, the first-principles power of the ab initio techniques is illustrated by a simple example of geometry optimization, starting from random atoms, ending with a structure close to the experimental data, within various computational settings (HF, MP2, CCSD, DFT with different functionals). Besides assessing the performances of the different methods, in mutual respects and facing the experiment, we emphasize the fact that the experimental data are affected themselves by limitations, which should be judged with critical caution. The ab initio outputs offer inner consistency of datasets, sometimes superior to the available experimental information, in areas affected by instrumental margins. In general, the calculations can retrieve the experimental data only with semi-quantitative or qualitative accuracy, but this is yet sufficient for meaningful insight in underlying mechanisms, guidelines to the interpretation of experiment, and even predictive prospection in the quest of properties design. The second section focuses on HF and DFT calculations on the water molecule example, revealing the relationship with ionization potentials, electronegativity, and chemical hardness (electrorigidity) and hinting at non-routine input controls, such as the fractional tuning of populations in DFT (with the ADF code) or orbital reordering trick in HF (with the GAMESS program). Keeping the H 2 O as play pool, the orbital shapes are discussed, first in the simple conjuncture of the Kohn-Sham outcome, followed by rather advanced technicalities in handling localized orbital bases, in a Valence Bond (VB) calculation, serving to extract a heuristic perspective on the hybridization scheme. In a third section, the H 2 example forms the background for discussing the bond as spin-coupling phenomenology, constructing the Heisenberg-Dirac-van Vleck (HDvV) effective spin Hamiltonian. In continuation, other calculation procedures, such as Complete Active Space Self-Consistent Field (CASSCF) versus Broken-Symmetry (BS) approach, are illustrated, in a hands-on style, with specific input examples, interpreting the results in terms of the HDvV model parameters, mining for physical meaning in the depths of methodologies.

In information processing, in combinatorial chemistry, in structure elucidation, and in several other fields of chemistry, the computer-aided generation of all structures (constitutional formulae) within a defined structure space has become increasingly important. In this brief review the mathematical foundations of the classical molecular model and thus of the generation process are outlined, and the current state of structure generation as applied in software developed by the Bayreuth group is discussed.

Journal of Computational Methods in Sciences and Engineering, 2001

The Additive Fuzzy Density Fragmentation (AFDF) principle and the Adjustable Density Matrix Assembler (ADMA) methods are proposed for a combinatorial construction of electron density representations of a series of macromolecules, related to one another by combinatorial reassignments of constituent fragments. Some of the fundamental computational aspects of the ADMA-based Combinatorial Quantum Chemistry (ADMA-CQC) approach are discussed, with special emphasis on the constraints provided by the recently proven holographic properties of molecular electron densities.

The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering.Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.

Discrete Applied Mathematics, 1996