LInk organic, inorganic, & physical chemistry
~ from molecular interactions to chemical reactions ~
Module A : Fundamentals of molecular interaction
Understanding molecular interaction is an important chemical issue for molecular design. For example, boiling points of matter strongly relate to the molecular interaction of their constituents (Fig. A-1). You might also know that drugs perform their functions by properly interacting with target biomolecules such as proteins causing diseases (Fig. A-2).
Fig. A-1 Water has an unusually high boiling point of 100°C (1atm), which supports abundant life on Earth. This is because H2O molecules build hydrogen-bonding interaction.
Fig. A-2 An image of a pharmacologically active molecule interacting with a disease-causing protein
In this Module A, you will learn how to evaluate molecular interactions, which are essential for controlling the functions of various materials using quantum chemistry calculation. While it is hard to observe molecular interactions in a direct manner, the quantum chemical interaction analysis is not only easy to perform but also provides information on the "origin" of these interactions, which cannot be evaluated experimentally.
Module A-1: hydrogen- and halogen-bonding interactions
It is widely known that hydrogen bonding interaction governs the properties of matter. Similarly, there are examples where specific elements can intervene to develop specific intermolecular interactions and give a substance with a special chemical function. This module presents one such example, halogen bonding interactions.
The electrostatic potentials of HCl, a molecule well known to exhibit hydrogen bonding, and its analog, the ClF molecule, are shown (Fig. A-3). The electrostatic potential map obtained from a simple quantum chemical calculation shows that the Cl atoms have completely different electrostatic potentials depending on the combination of elements, i.e., in the ClF molecule, the Cl atom has a positively charged region in the bond axis direction.
Fig. A-3 Electrostatic potential of HCl & ClF.
In this module A-1, we calculate the bond angle dependence of the interaction potentials for the formaldehyde-M (M=HCl, ClF) 1:1 complexes in the gas phase. The former forms hydrogen-bonding and the latter forms halogen-bonding complexes. You will compare their interaction potentials and discuss differences in the interaction strength and angular dependency.
Exercise
In which configuration are the hydrogen- and halogen-bonding interaction the most stable?
Which interaction component does dominate the configurations? Use NEDA.
Input sample
Download Gaussian Inputs for Module A-1
Module A-2: Application of quantum chemistry calculation to spectroscopy and structural chemistry
In the early 2000s, Mori et al. performed experiments in which p-aminophenol interacted with CO and N2 molecules under gas-phase conditions; CO and N2 are isoelectronic systems but differ in that they either have a slight dipole moment or are completely nonpolar.
In this module A-2, you will attribute the vibrational spectra of p-aminophenol and its CO complexes measured by the ab initio method, which can precisely estimate weak intermolecular interactions.
Exercise
Which configuration is the most stable?
Compare the calculated vibration spectrum with the experimental observation.
