*From*: <buyong -8 at 8- ibmnla.chem.uga.edu>*Subject*: comparison betweem EXP and Compuation*Date*: Thu, 28 Aug 1997 10:18:05 -0400 (EDT)

On Thu, 28 Aug 1997, Dr. Adel El-Azhary wrote: > Dear CCL members: > > I sent an e-mail to ccl yesterday but it looks like that it was not received. > So my apologies if you receive it twice. My question is that I am doing some > calculation on some small molecules for which effective, substituted, average > or equilibrium experimental geometries are available. So which of these is the > best to be comapred to the calculated geometry. This is a good question. Too often, we compare computed molecular structure with experimental value without concerning whether they are comparable. First of all, WHAT IS A MOLECULE? (see, Gribov, L. A. J. Mol. Struc. 1993,300,415). There is one quite accuarte definition: it is the smallest particle of the substance made up of eletrons and nuclei of a definit mass. This definition can be expressed mathematically by the schrodinger equation. However, we must reduce to classical expresions if we want to compare calculated structure with a real experiment. We have to use classic models, different models for different experiments. Let us start from several experimental procedures obtaining the information of molecular structure. Two kinds of operational bond lengths R(0) and R(s) may be derived directly from rotational and rotation-vibrational spectroscopy. The R(0) structure is derived from the ground state rotational constants B(0) directly, or more usually with assumptions about some of the structural parameters. When the rotational constants for various isotopic species are observed, the substituted structure R(s) can be determined by Kraitchman method. When vibrational (both harmonic and anharmonic) properties are recorded, one may obtained equilibrium structure R(e) with some approximation. Only is the R(e) really comparable with the value from quantum mechanical calculations, which give the distance between equilibrium nuclear position R(e). X-ray or neutron diffraction experiments give the average nuclear positions at thermal equilibrium, and from which the average nuclear position the internuclear distance R(alpha) is defined. When we refer to the structure at 0 K, we get R(z) structure, which may derived from rotational and rotation-vibrational spectroscopy. Gas phase electron diffraction experiments give the thermal average value of internuclear distance: R(g) structure. The relationship and interconversion of those strcutures may be formulated by classical approximation (see reference cited in the end of this message). MM3(96) version will print out all those structures. If you are using molecular mechanical method, MM3(96) is a good option. you can compare your calculated results with comparable experimental data. Other molecular mechanical packages, as I know, do not realized the difference. If you are talking about QM calculation, of course, experimental equilibrium structure is first choice. However, if it is not available, R(s) structure is close to R(e). I have derived a formula R(s) =[R(z) + R(e)]/2 . R(z) comes third, then R(alpha), and finally R(g). Note that QM results are base sets and correlation dependent, and convergence should be considered in the comparison. Refernce: a) Kuchitus, K. in Accurated Molecular Structures, Ed Domenicano, A et al. Oxford Science Publication, 1992. b) Ma, B.; et al. J. Physical chem. 1996, 100, 8763. J. Am. Chem. Soc. 1997, 119, 2570. J. Mol. Struc. In press ( the issure dedicated to Dr. Kuchitsu). ================================================================= Dr. Buyong Ma buyong -8 at 8- ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 =================================================================