Cyclic Hydrogen Bonding in Indole Carboxylic Acid Clusters

Abstract

Monolayers of indole-2-carboxylic acid and indole-3-carboxylic acid on gold are studied using ultrahigh-vacuum scanning tunneling microscopy. Both molecules form symmetric, cyclic, hydrogen-bonded pentamers, a structure that is stabilized by the presence of a weak hydrogen-bond donor (NH or CH) adjacent to the carboxylic acid on the five-membered ring. In addition to pentamers, indole-2-carboxylic acid forms hexamers and catemer chains, while indole-3-carboxylic acid monolayers are generally disordered. Density functional theory calculations show that pentamers and hexamers have stability comparable to dimers or short catemers. The coexistence of all of these structures likely arises from the nonequilibrium conditions present in solution during pulse deposition of the monolayer.

Non-intuitive clustering of 9,10-phenanthrenequinone on Au(111)

“…Instead, we propose the explanation that tetramers initially form in solution, either in the rapidly evaporating droplet in transit or a rapidly evaporating film at the Au(111) surface. Given past studies that have observed both direct [ 30 ] and indirect [ 13 – 14 19 ] evidence of the formation of metastable clusters in solution during pulse deposition, we think that this mechanism is a plausible one for the formation of these tetramers.…”

“…Pulse deposition usually results in a heterogeneous surface, most likely due to the fact that any cluster formation that occurs in the rapidly evaporating droplet will proceed under non-equilibrium conditions and thus can produce kinetic intermediates [ 13 – 14 19 , 27 – 30 ]. For 9,10-phenanthrenequinone we observe three broad categories of assembly: disordered molecules, rectangular tetramers, and ordered linear rows, as seen in Fig.…”

“…Some hydrogen-bonding organic molecules have a common feature in that C–H···O bonding plays a critical role in stabilizing metastable clusters [ 13 – 14 19 – 20 ]. This makes 9,10-phenanthrenequinone ( Fig.…”

Hydrogen-Bonded Tetramers of Carbamazepine

“…Solution deposition has been known to result in metastable configurations, as compared to vapor-deposited monolayers of the same molecule. 18,19 In addition, because there is less thermal energy available at 78 K than at room temperature, adsorbate molecules have less energy to re-organize into a lower energy configuration, and the resulting trimer structure may be a metastable configuration that at higher temperature, could reorganize into a different configuration, in this case, tetramers.…”

Strong C H/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size

“…In addition, it was shown that if the hydrogen atom is attached to a polarized carbon atom, it can form hydrogen bonds as strong as those formed by regular hydrogen-donating atoms [3,4]. Today it is generally accepted that C-H/O interactions represent true hydrogen bonds [5][6][7] and that they play significant role in the stability of nucleic acid and protein structures, enzymatic activity and crystal packing [8][9][10][11]. C-H/O interactions are essential for stabilization of protein structures since it was shown that they make up to 25% of all hydrogen bonds in the structure of proteins [12,13].…”