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Pinnick

2013

High-pressure Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline adenosine at 295 K by evaluating the logarithmic derivative of the vibrational frequency with respect to pressure: [Formula: see text]. Crystalline samples of molecular materials such as adenosine will have vibrational modes that are localized within a molecular unit ("internal" modes) as well as modes in which the molecular units vibrate against each other ("external" modes). The value of the logarithmic derivative is found to be a diagnostic probe of the nature of the eigenvector of the vibrational modes. Stretching modes which are predominantly internal to the molecule have low logarithmic derivatives while external modes have higher logarithmic derivatives. Particular interest is paid to the low-frequency (≤150 cm(-1)) modes. Based on the pressure dependence of its logarithmic derivative, a mode near 49 cm(-1) is identified as internal mode. The other modes below 400 cm(-1) have pressure dependences of their logarithmic derivatives consistent with being either (1) modes which are mainly external, meaning that the molecules of the unit cell vibrate against each other in translational or librational motions (or linear combinations thereof), or (2) torsional or bending modes involving a large number of atoms, mainly within a molecule. The modes above 400 cm(-1) all have pressure dependences of their logarithmic derivatives consistent with being mainly internal modes.

A study of the eigenvectors of the low-frequency vibrational modes in crystalline adenosine via high pressure Raman spectroscopy

Pinnick

2013

A study of the eigenvectors of the vibrational modes in crystalline cytidine via high-pressure Raman spectroscopy

Pinnick

2014

Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline cytidine at 295 K and high pressures by evaluating the logarithmic derivative of the vibrational frequency ω with respect to pressure P: [Formula: see text]. Crystalline samples of molecular materials have strong intramolecular bonds and weak intermolecular bonds. This hierarchy of bonding strengths causes the vibrational optical modes localized within a molecular unit ("internal" modes) to be relatively high in frequency while the modes in which the molecular units vibrate against each other ("external" modes) have relatively low frequencies. The value of the logarithmic derivative is a useful diagnostic probe of the nature of the eigenvector of the vibrational modes because stretching modes (which are predominantly internal to the molecule) have low logarithmic derivatives while external modes have higher logarithmic derivatives. In crystalline cytidine, the modes at 85.8, 101.4, and 110.6 cm(-1) are external in which the molecules of the unit cell vibrate against each other in either translational or librational motions (or some linear combination thereof). All of the modes above 320 cm(-1) are predominantly internal stretching modes. The remaining modes below 320 cm(-1) include external modes and internal modes, mostly involving either torsional or bending motions of groups of atoms within a molecule.

A high pressure study of the eigenvectors of the infra-red active vibrational modes of crystalline adenosine

Starkey

2015

High-pressure infrared spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline adenosine at 298 K by evaluating the logarithmic derivative of the vibrational frequency with respect to pressure: [Formula: see text]. Crystalline samples of molecular materials such as adenosine have vibrational modes that are localized within a molecular unit ("internal" modes) as well as modes in which the molecular units vibrate against each other ("external" modes). The value of the logarithmic derivative is that it is a diagnostic probe of the nature of the eigenvector of these vibrational modes. Stretching modes, which are predominantly internal to the molecule, have low logarithmic derivatives while external modes have higher logarithmic derivatives. Particular attention is paid to modes in the 800-1000 cm(-1) range since modes in that region of the vibrational spectrum are found to be sensitive to the conformation of double-helical DNA. Since the sugar pucker is different for the various conformations of DNA, this fact suggests that these modes involve the motion of atoms in the sugar group. The vibrations of the hydrogen atoms are also of interest to study since the vibrational frequency of hydrogen atoms involved in hydrogen bonds has a negative pressure derivative. Such behavior clearly shows which hydrogen atoms are involved in hydrogen bonding.