Hi,

what is the best method or algorithm or where could I find information for, given a certain molecule, know what bonds are not rigid ? For instance in Ph-CH2-Ph, the CH2 carbon would you consider as rigid or as flexible ?

Thanks

Hi horacioemilio -

Since my expertise lies within the fields of micro- and molecular biology, I asked one of the chemists at my facility to respond to your question.


Here is his answer....


The bond energy for each C-H bond is 438kJ/mol. If there is sufficient energy absorbed into that molecule, the molecule will transmit. Thats the deal for any organic molecule. The transmittance energies for alkyl groups will be:


IR 2850 2960cm-1 (should be moderate to sharp)

13C NMR singlet around 40PPM

1H NMR singlet around 4PPM


As to the rigid or flexible question, the carbon is what I would call rigid. The sp3 hydrogens are what I call flexible. Blast ANYTHING with enough energy and itll dance. The bonds around the carbon are what tell you whats what.




Hope this helps! Let me know if you need further clarification.

thanks a lot for your answer

I meant in normal conditions in solution

Hello again horacioemilio!


Here are a few references that you might want to look up. There might be some information within their research which could help answer you question...


A. P. Giddy, M. T. Dove, G. S. Pawley and V. Heine. The determination of rigid-unit modes as potential soft modes for displacive phase transitions in framework crystal structures. Acta Cryst. (1993). A49, 697-703 doi:10.1107/S0108767393002545

Abstract:
his paper describes a computational method for the determination of all possible phonon modes in framework crystal structures that leave the fundamental structural units (tetrahedra and octahedra) undistorted. Such rigid-unit modes (RUMs) are prime candidates as soft modes for displacive phase transitions, such as in the perovskite structure, and this computational method can be used to rationalize the phase transitions in any framework structure. The method has been programmed for general use. The RUM approach is illustrated by consideration of the perovskite, quartz and cristobalite structures.


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D. Bellert and W. H. Breckenridge. A spectroscopic determination of the bond length of the LiOLi molecule: Strong ionic bonding. J. Chem. Phys. -- February 15, 2001 -- Volume 114, Issue 7, pp. 2871-2874

Abstract:
The short bond length of the linear ground state of the 7Li16O7Li molecule has been accurately determined to be 1.606±0.008 by analysis of the rotational structure of several bands assigned to transitions from the jet-cooled 1Sigma+ vibronic ground state to a bent 1B1 excited state. This value is in good agreement with, but more accurate than, other experimental and ab initio bond-length estimates for the prototypical ionically bound triatomic molecule Li + O2Li +.


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D. René Rasmussen, Stuart McKernan, and C. Barry Carter. Rigid-body translation and bonding across {110} antiphase boundaries in GaAs . Phys. Rev. Lett. 66, 2629 - 2632 (1991)
DOI: 10.1103/PhysRevLett.66.2629

Abstract:
A transmission-electron-microscope strong-beam technique is used to investigate the rigid-body translation across {110} antiphase boundaries in GaAs. The results show a translation in the 〈001〉 direction parallel to the plane of the boundary. The magnitude of the translation is determined, and the antisite bond lengths are discussed in terms of the tetrahedral radii of Ga and As. Given this knowledge of the rigid-body translation, the absolute polarity of a GaAs grain can be determined immediately from a bright-field image of the {110} antiphase boundary.


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William J. Wedemeyer, Carol A. Rohl and Harold A. Scheraga. Exact solutions for chemical bond orientations from residual dipolar couplings. Journal of Biomolecular NMR. Volume 22, Number 2 / February, 2002. 137-151
DOI: 10.1023/A:1014206617752

Abstract:
New methods for determining chemical structures from residual dipolar couplings are presented. The fundamental dipolar coupling equation is converted to an elliptical equation in the principal alignment frame. This elliptical equation is then combined with other angular or dipolar coupling constraints to form simple polynomial equations that define discrete solutions for the unit vector(s). The methods are illustrated with residual dipolar coupling data on ubiquitin taken in a single anisotropic medium. The protein backbone is divided into its rigid groups (namely, its peptide planes and Cagr frames), which may be solved for independently. A simple procedure for recombining these independent solutions results in backbone dihedral angles phgr and psgr that resemble those of the known native structure. Subsequent refinement of these phgr-psgr angles by the ROSETTA program produces a structure of ubiquitin that agrees with the known native structure to 1.1 Cagr rmsd.


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Yegor D. Smurnyy, Michail E. Elyashberg, Kirill A. Blinov, Brent A. Lefebvre, Gary E. Martin and Antony J. Williams. Computer-aided determination of relative stereochemistry and 3D models of complex organic molecules from 2D NMR spectra. Tetrahedron. Volume 61, Issue 42, 17 October 2005, Pages 9980-9989
doi:10.1016/j.tet.2005.08.022

Abstract:
A method for elucidation of the relative stereoconfiguration of natural product molecular structures and their 3D models based on NOE data and the application of a genetic algorithm is described. The method is applicable mainly for rigid polycyclic structures commonly encountered in natural products. It is demonstrated that the technique of simulated annealing cannot be easily used when dealing with low-weight fused ring molecules but the application of a genetic algorithm is proven successful. Examples of a typical genetic algorithm workflow and the optimization of the algorithmic parameters are discussed. The efficiency of the approach developed here is demonstrated on the complex natural products of both Taxol (C47H51NO14) and brevetoxin B (C50H70O14).

The X-ray crystal structure of brevetoxin B (yellow) and the 3D model of the best stereoisomer (blue) from a stereochemistry determination system are superimposed. Small differences in the bond angles of some of the more flexible rings are present, but all stereocenters have been properly oriented.


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Let me know which of these references were of any help. If so, maybe I can re-define my search to help direct you to more specific references...

Good luck!