Modeling the Dimeric Structure of Partly Deprotonated Trimesic Acid Molecules

Abstract

We propose a model and determine the formation conditions of the deprotonated dimeric structure, which is known to substitute the honeycomb (HON) phase in a trimeric acid (TMA) molecular assembly subjected to temperature or electric field effect. The model demonstrates that the dimeric phase occurs in a system of singly deprotonated molecules (deprotonation level, DPL = 1) bonded by neutral and ionic H-bond interactions, as well as in a 1:1 mixture of singly deprotonated and intact molecules (DPL = 0.5). We use density functional theory (DFT) to estimate the interactions between the intact and deprotonated molecules. The ground-state analysis and Monte Carlo (MC) modeling at DPL = 1 define the interaction parameters' space (including those calculated by DFT), where the dimeric phase is more stable than other structures, the HON phase and its higher-order homologue. With a decrease of DPL, the TMA−TMA dimers with ionic H-bonds are gradually replaced by usual dimers with neutral double Hbond interactions, but the dimeric geometry is fully preserved down to DPL = 0.5. At DPL ≈ 0.4, both dimeric and HON phases are equally favorable, as confirmed by their coexistence in MC simulations. For DPL < 0.3, the molecular system shows a clear preference for the HON phase.

Modeling of Close-Packed Patterns of Intact and Partially Deprotonated TPTC Molecules

“…15,16,18 A combined DFT and MC approach was employed to model the emergence of deprotonated structures of TMA and BTB. 19,20,37 This work is an extension of these studies for CP arrays of intact and partially deprotonated TPTC molecules at DP = 0 and DP = 1. We used DFT to study the finite TPTC molecular clusters and the building blocks of different structures and calculated the intermolecular pair interaction potentials, which consequently allowed us to evaluate the energies of the most stable structures.…”

“…This type of trio bonding is found in the partially deprotonated TMA system and it is very strong (≈−54 to −56 kcal/mol). 15,16,19 The requirement of trio bonding eliminates the HONG and CP structures from consideration at DP = 1. The honeycomb structure, and the double hydrogen bond in particular, are known to be unstable upon deprotonation.…”

Modeling of Different Ordering Schemes for Halogen-Functionalized Molecules with Triazine and Benzene Core

“…Density functional theory (DFT) methods are often used to determine the possible geometries and energies of interactions in supramolecular networks. − Molecular dynamics and Monte Carlo (MC) modeling has been performed to find the most stable phases of triangular, ,− linear, cross-shaped, V-shaped, and other , molecules with various functional groups.…”

Deprotonation-Induced Phase Transitions in the Self-Assembled Structure of Prochiral Carboxyl Derivatives

“…In addition, annealing in an ultrahigh vacuum (UHV) could lead to the deprotonation − and decarboxylation − of carboxylic acids to form carboxylates and polymers, respectively, as the reaction barrier is significantly reduced on the transition-metal substrate. The carboxylate groups can not only form stronger ionic hydrogen bonds to other atoms and molecules , but also interact strongly with metal surfaces. − As a result, the adjustment of the noncovalent interaction can inevitably lead to a restructuring of the self-assembled structure. , …”