Does the interaction with enviroment change the geometry of a molecule ? for example in H2O the angle betwen H-O-H is 104.5 degrees. Does this angle change for example if the molecule of water is near to a molecule of HCL where electrostatic interactions will take place ?
Does the interaction with enviroment change the geometry of a molecule?
Yes. Water is a simple example. Since interactions can remove an H from an H$_2$O molecule (as is constantly happening and un-happening in a cup of pure water), we should expect interactions to affect the geometry. The magnitude of the effect depends on the circumstances. For example, according to the following website, the bond angles are different in an isolated molecule, liquid water, and ice:
- "Water Molecule Structure", http://www1.lsbu.ac.uk/water/water_molecule.html
There is some uncertainty in the values, but ab initio calculations and measurements both indicate that the bond angle depends (slightly) on the molecule's environment. The values quoted in the cited website range from $\sim 104.5^\circ$ to $\sim 108.4^\circ$, with a larger angle in ice than in an isolated molecule. (Some of this variation may be attributed to uncertainty in the calculations/measurements.)
By the way, water has several different solid phases. The bond angles may be slightly different in these different phases, but I don't know if this has been confirmed.
H$_2$O has vibrational modes, including a "bending mode," often depicted as a time-varying angle between the two bonds, as shown in
- "Water Absorption Spectrum", http://www1.lsbu.ac.uk/water/water_vibrational_spectrum.html
Since the molecule can vibrate in this way, we again expect that the bond angle should be affected to some degree by the molecule's environment.
(A more accurate picture of the bending mode, much harder to draw, would involve a wavefunction in which the three atoms do not have sharply-defined positions, much like an electron in an isolated hydrogen atom is better described as a delocalized entity in a static orbital rather than a classical pointlike particle revolving around the nucleus.)
For larger molecules, such as protein molecules or DNA, the geometry tends to be even more affected by the environment. According to excerpts from Molecular Biology of the Cell given in https://www.ncbi.nlm.nih.gov/books/NBK26830,
A protein can be unfolded, or denatured, by treatment with certain solvents, which disrupt the noncovalent interactions holding the folded chain together. This treatment converts the protein into a flexible polypeptide chain that has lost its natural shape. When the denaturing solvent is removed, the protein often refolds spontaneously, or renatures, into its original conformation...