Enumeration and generation of three-center valence structures

A novel software product STRGEN-2D for generation of 2D chemical structures from a gross formula is implemented. It is based on an approach developed by one of the authors (IB). Various functionalities and options of the program are discussed. The output of STRGEN-2D software is compared with the generated structures by MOLGEN software. The generation efficiency and correctness of obtained structure sets are proved.

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.

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.

Acta Crystallographica Section B-structural Science, 2006

A method to describe, analyze and even predict the coordination geometries of metal complexes is proposed, based on previous well established concepts such as bond valence and valence-shell electron-pair repulsion (VSEPR). The idea behind the method is the generalization of the scalar bond-valence concept into a vector quantity, the bond-valence vector (BVV), with the innovation that the multidentate ligands are represented by their resultant BVVs. Complex nligand coordination spheres (frequently indescribable at the atomic level) reduce to much simpler ones when analyzed in BVV space, with the bonus of a better applicability of the VSEPR predictions. The geometrical implications of the BVV description are analyzed for the cases of n = 2 and 3 (n = number of ligands), and the validity of its predictions, checked for a large number of metal complexes.

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 2001

Theoretical calculations (B3LYP/6±311+ +G**) were performed on a series of formally hypervalent compounds showing linear three-center geometries. The bonding nature was analyzed by the electron density, q(r), and electron-localization function (ELF) topologies, including calculations of the AIM charges and NMR chemical shifts (GIAO method). In addition, a quantitative analysis was also performed of the localization and delocalization indexes, obtained from the electron-pair density in conjunction with the de-®nition of an atom in a molecule. Furthermore, the populations and¯uctuations in the ELF basins were also evaluated. The compounds studied presented linear (1± 5), T-shaped (6±9), and bipyramidal structures (10±15). Our results support the 3c-4e model for the linear (1±5) structures, but reveal for the T-shaped (6±9) structures only a small contribution from this model. In addition, there is no evidence to support the 3c-4e bond scheme for the bipyramidal compounds (10±15).

The Journal of Physical Chemistry A, 2004

have been studied using valence bond theory (VB). The classic three-structure VB picture changes slightly to account for the increased importance of the VB configuration with both electrons on the donor fragment. When the effects of geometric distortion upon molecule formation are removed, the expected trends in bond energies emerge. Addition of electron-withdrawing (F) substitutents increases bond energy in H 3 N-BF 3 and decreases bond energy in F 3 N-BH 3 . Likewise, addition of electron-donating methyl groups (Me) decreases bond energy in H 3 N-BMe 3 and increases bond energy in Me 3 N-BH 3 . In addition, the effects of adding fluorines stepwise in the series H 3 N-BH 3 , H 3 N-BH 2 F, H 3 N-BHF 2 , H 3 N-BF 3 has been determined. Bond energies are due to the opposing factors of electron withdrawal due to the high fluorine electronegativity and donation into the N-B bonding region by F p lone pairs. VB weights obtained by the method of Chirgwin and Coulson were unstable for coordinate covalently bonded molecules whereas no such problems were found for inverse overlap weights. VB weights in conjunction with bond energy partitioning show that the coordinate covalent bonds studied herein are predominantly charge shift bonds which owe their stability to VB structure mixing rather than any one structure alone. †

Lecture Notes in Computer Science, 2020

Benzenoids are a subfamily of hydrocarbons (molecules that are only made of hydrogen and carbon atoms) whose carbon atoms form hexagons. These molecules are widely studied in theoretical chemistry and have a lot of concrete applications. Therefore, generating benzenoids which have certain structural properties (e.g. having a given number of hexagons or having a particular structure from a graph viewpoint) is an interesting and important problem. It constitutes a preliminary step for studying their chemical properties. In this paper, we show that modeling this problem in Choco Solver and just letting its search engine generate the solutions is a fast enough and very flexible approach. It can allow to generate many different kinds of benzenoids with predefined structural properties by posting new constraints, saving the efforts of developing bespoke algorithmic methods for each kind of benzenoids.

Computers & Chemical Engineering, 1998

The problem of designing molecules or compounds with desired properties is complex primarily because it is combinatorial. A novel approach is proposed here by resorting to a combinatorial analysis of the problem. It is supposed that the set of functional groups is available and that the intervals of values of the desired properties of the molecule or compound to be designed are known. The desired properties constitute constraints on the integer variables assigned to the functional groups. The feasible region defined by such constraints is determined by an algorithm involving a branching strategy. This algorithm generates those collections of the functional groups that can constitute structurally feasible molecules or compounds satisfying the constraints on the given properties. The efficacy of the approach has been demonstrated with several examples.

Journal of Computational Chemistry, 2009

An efficient algorithm for energy gradients in valence bond theory with nonorthogonal orbitals is presented. A general Hartree‐Fock‐like expression for the Hamiltonian matrix element between valence bond (VB) determinants is derived by introducing a transition density matrix. Analytical expressions for the energy gradients with respect to the orbital coefficients are obtained explicitly, whose scaling for computational cost is m4, where m is the number of basis functions, and is thus approximately the same as in HF method. Compared with other existing approaches, the present algorithm has lower scaling, and thus is much more efficient. Furthermore, the expression for the energy gradient with respect to the nuclear coordinates is also presented, and it provides an effective algorithm for the geometry optimization and the evaluation of various molecular properties in VB theory. Test applications show that our new algorithm runs faster than other methods. © 2008 Wiley Periodicals, Inc....

2005

The generation of molecular graphs by computer programs has undergone some changes. The development is reported with focus on various mathematical methods that are created and employed in this process. No attempt has been made to explicitely state and prove the theorems but this overview contains hints to the relevant literature. In particular, a new generator MOLGEN 4.0 is described that aims at highest flexibility in using constraints during the generation process and, thus, meeting the needs of practical applications.