- [id] => 305
- [recorddate] => 2017:08:29:13:55:49
- [lastupdate] => 2017:08:29:13:55:49
- [type] => conference
- [place] => Cluj-Napoca, Romania
- [subject] => chemistry - computational; informatics - numerical optimization; mathematics - modeling; mathematics - optimization
- [relatedworks] =>
- 4 (some):
- A new method for mobile phase optimization in high-performance thin-layer chromatography (HPTLC), ?id=2
- A new mathematical model for the optimization of the mobile phase composition in HPTLC and the comparison with other models, ?id=3
- Informational entropy of b-ary trees after a vertex cut, ?id=175
- Linear regression modeling and validation strategies for structure-activity relationships, ?id=275
- Extending characteristic polynomial from graphs to molecules, ?id=303

- 4 (some):
- [file] => ?f=305
- [mime] => application/pdf
- [size] => 781583
- [pubname] => Bio-Nano-Math-Chem 2017
- [pubinfo] => European Society of Mathematical Chemistry
- [workinfo] => June 28-30, 2017, Oral presentation, (Thursday) June 29, 9
^{00}‐9^{30} - [year] => 2017
- [title] => Geometry optimization of nC24 cyclic polyyne cluster [presentation]
- [authors] => Lorentz JÄNTSCHI
- [abstract] =>

Background. In a previous study were investigated the optimal size of polyynes to form rings (and was found to be 24) as well were investigated the conformation of a cluster of 4 crossing C24 cyclic polyynes. Geometry optimization of molecular clusters is slightly different than the geometry optimization of molecules since at clusters the degrees of freedom no longer represents the atoms positions itself but the molecules positions. Aim. Here are reported a study regarding the developing of an geometry optimization (energy minimization) program at molecular mechanics theory level designed to provide a good profile for the conformation of crossed nC24 polyynes by the pattern previously found - each cyclic polyyne is crossed by another 3. Material. Clusters of nC24 were designed by the pattern by involving successive geometrical 3D rotations and translations and replications of the C24 cyclic polyyne as well as of its cluster. The resulted cluster was subjected to energy minimization and a program was developed to do this. Method and algorithm. Several tricks were found and implemented during the program development. A molecule (C24) position was characterized by its center (three Cartesian coordinates) and its direction (three angular coordinates). Thus, the subject of optimization was 6∙n variables corresponding to the degrees of freedom of the molecules positions in the cluster. Since all atoms are Carbon, and all atoms have the same constrains (a single and a triple bond) supplementary coefficients or constants other than the distance parameterizing interaction were not necessary. The optimization objective which was found to be suitable is the sum of the inverses of the fourth power of the distance between atoms to minimum. Other trick is how to keep the molecules together since the tendency of the optimization score is to depart the molecules one to any other. Program and results. A FreePascal program was developed and parameterized correspondingly to be used for any value of the n to do the geometrical optimization of the nC24 cluster. Program has been tested for n = 4, n = 10 and n = 22 and it works. In order to keep the molecules together, a module identifying the crosses was developed and used as constrain during the optimization. The crosses of each molecule to another are actually the second topology level of the cluster, if the bonds between the atoms are considered to be the first. Conclusion. The study revealed that the developed program performs very well in the optimization of the geometry of the cluster. - [keywords] => Software for cluster modeling; Cyclic polyyne clusters; Geometry optimization (energy minimization)