The borazine dimer: the case of a dihydrogen bond competing with a classical hydrogen bond

Insight into the interaction between amino acids and SO2: Detailed bonding modes

CONTEXT

Amino acids are a highly effective and environmentally friendly adsorbent for SO2. However, there has been no comprehensive study of the binding modes between amino acids and SO2 at the molecular level. In this paper, the binding modes of three amino acids (Asp, Lys, and Val) with SO2 are studied comprehensively and in detail using quantum chemical calculations. The results indicate that each amino acid has multiple binding modes: 22 for Asp, 49 for Lys, and 10 for Val. Both the amino and carboxyl groups in amino acids, as well as those in side chains, can serve as binding sites for chalcogen bonds. The binding energies range from - 6.42 to - 1.06 kcal/mol for Asp, - 12.43 to - 1.63 kcal/mol for Lys, and - 7.42 to - 0.60 kcal/mol for Val. Chalcogen and hydrogen bonds play a crucial role in the stronger binding modes. The chalcogen bond is the strongest when interacting with an amino group, with an adiabatic force constant of 0.475 mDyn/Å. Energy decomposition analysis indicates that the interaction is primarily electrostatic attraction, with the orbital and dispersive interactions dependent on the binding mode.

METHODS

Amino acids and complexes of amino acids with SO2 were used to do semi-empirical MD using Molclus combined with xtb at the GFN2 level. Optimization and frequency calculations of the structures were conducted using density-functional theory (DFT) B3LYP/6-311G* (with DFT-D3 correction). Single-point energy calculations were performed for all structures using DLPNO-CCSD(T)/aug-cc-pVTZ with tightPNO. Further analysis of the structures was conducted using ESP, AIM, IGMH, and sob-EDA to gain a deeper understanding of the interactions between amino acids and SO2.

Theory of Borazine-Derived Nanothreads: Enumeration, Reaction Pathways, and Piezoelectricity

Nanothreads are one-dimensional macromolecules formed by pressure-induced polymerization along stacks of multiply unsaturated (or highly strained) molecules such as benzene (or cubane). Borazine is isoelectronic to benzene yet with substantial bond polarity, thus motivating a theoretical examination of borazine-derived nanothreads with degrees of saturation of 2, 4, and 6 (defined as the number of four-coordinated boron and nitrogen atoms per borazine formula unit). The energy increases upon going from molecular borazine to degree-2 borazine-derived threads and then decreases for degree-4 and degree-6 nanothreads as more σ bonds are formed. With the constraint of no more than two borazine formula units within the repeat unit of the framework's bonding topology, there are only 13 fully saturated (i.e., degree-6) borazine-derived nanothreads that avoid energetically costly homopolar bonds (as compared to more than 50 such candidates for benzene-derived threads). Only two of these are more stable than borazine. Hypothetical pathways from molecular borazine to these two degree-6 borazine-derived nanothreads are discussed. This relative paucity of outcomes may assist in kinetic control of reaction products. Beyond the high mechanical strength also predicted for carbon-based threads, properties such as piezoelectricity and flexoelectricity may be accessible to the polar lattice of borazine-derived nanothreads, with intriguing prospects for expression in these extremely thin yet rigid objects.

Unraveling hydridic-to-protonic dihydrogen bond predominance in monohydrated dodecaborate clusters

Hydridic-to-protonic dihydrogen bonds (DHBs) are involved in comprehensive structural and energetic evolution, and significantly affect reactivity and selectivity in solution and solid states. Grand challenges exist in understanding DHBs' bonding nature and strength, and how to harness DHBs. Herein we launched a combined photoelectron spectroscopy and multiscale theoretical investigation using monohydrated closo-dodecaborate clusters B12X12 2-·H2O (X = H, F, I) to address such challenges. For the first time, a consistent and unambiguous picture is unraveled demonstrating that B-H⋯H-O DHBs are superior to the conventional B-X⋯H-O HBs, being 1.15 and 4.61 kcal mol-1 stronger than those with X = F and I, respectively. Energy decomposition analyses reveal that induction and dispersion terms make pronounced contributions resulting in a stronger B-H⋯H-O DHB. These findings call out more attention to the prominent roles of DHBs in water environments and pave the way for efficient and eco-friendly catalytic dihydrogen production based on optimized hydridic-to-protonic interactions.

Homo pair formations of thiobarbituric acid: DFT calculations and QTAIM analysis

Homo pair formations of thiobarbituric acid (TBA) were investigated in this work by performing density functional theory (DFT) calculations and the quantum theory of atoms in molecule (QTAIM) analysis. Different types of interactions including N–H . . . O, N–H . . . S, C–H . . . O, and C–H . . . S were involved in formations of five models of homo pair of TBA. In this regard, the results of energy strength and QTAIM features indicated that the model with two N–H . . . O interacting bond (D1) was placed at the highest stability and the model with one N–H . . . O and one C–H . . . S interacting bonds (D5) was placed at the lowest stability. Existence of hydrogen bond (HB) interactions in the models were confirmed based on the obtained results. As a consequence, self-interaction of TBA, as an initiator of pharmaceutical compounds production, was investigated in this work in addition to recognition of existence of different types of interactions.

Stacking interactions of borazine: important stacking at large horizontal displacements and dihydrogen bonding governed by electrostatic potentials of borazine

Potential energy surfaces of borazine-benzene and borazine-borazine stacking interactions were studied by performing DFT, CCSD(T)/CBS and SAPT calculations. The strongest borazine-benzene stacking was found in a parallel-displaced geometry, with a CCSD(T)/CBS interaction energy of -3.46 kcal mol-1. The strongest borazine-borazine stacking has a sandwich geometry, with a CCSD(T)/CBS interaction energy of -3.57 kcal mol-1. The study showed that borazine forms significant stacking interactions at large horizontal displacements (over 4.5 Å), with energies of -2.20 kcal mol-1 for the borazine-benzene and -1.96 kcal mol-1 for the borazine-borazine system. The strength of interactions and their geometrical preferences can be rationalized by observing the electrostatic potentials of borazine and benzene, which is in agreement with SAPT analysis showing that electrostatics is the most important energy component for borazine stacking. All the interactions found in crystal structures of borazine and related compounds were identified either as potential curve minima or the geometries obtained from their optimizations. We also report a new dihydrogen bonding dimer with a CCSD(T)/CBS interaction energy of -2.37 kcal mol-1, which is encountered in the borazine crystal structures and enables the formation of additional simultaneous interactions that contribute to the overall stability of the crystals.

Noble gas inserted compounds of borazine and its derivative B3N3R6: structures and bonding

Quantum chemistry computations were performed at the MP2 and B3LYP levels of theory using the basis sets aug-cc-pVDZ and def2-TZVPPD to study the noble gas (Ng) compounds formed by insertion of a Ng atom (Kr, Xe, Rn) into the B-H/F and N-H/F bonds of inorganic benzene B₃N₃H₆ and its fluorine derivative B₃N₃F₆. The geometrical structures were optimized and vibrational analysis was carried out to demonstrate these structures being local minima on the potential energy surface. The thermodynamic properties of the formation process of Ng compounds were calculated. A series of theoretical methods based on the wavefunction analysis, including NBO, AIM and ELF methods and energy decomposition analysis, was used to investigate the bonding nature of the noble gas atoms and the properties of the Ng compounds. The N-Ng bond was found to be stronger than the B-Ng bond, but the B-Ng bond is of typical covalent character and σ-donation from the Ng atom to the ring B atom makes the predominant contribution towards stability of the B-Ng bond. NICS calculation shows that these Ng-containing compounds are of weak π-aromaticity.