Real-Space Evidence of Trimeric, Tetrameric, and Pentameric Uracil Clusters Induced by Alkali Metals

Abstract

Alkali metal cations are known as the significant participants in biological processes and play the vital role in nucleic acid structures. The interactions between alkali metals and nucleobases have therefore attracted a lot of attention. As a peculiar nucleobase in RNA, uracil with its magic number clusters induced by alkali metals has attracted tremendous interest over the past decades. Here, from the interplay of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, we show the real-space evidence of the formation of trimeric, tetrameric, and pentameric uracil clusters induced by alkali metals (Li, Na, and K) on the Au(111) surface, and further investigate their specific configurations at the atomic-scale, which would be of importance for understanding the formation process of biologically relevant nanostructures involving cations in vivo.

Construction and Structural Transformation of Metal–Organic Nanostructures Induced by Alkali Metals and Alkali Metal Salts

“…In addition, four pyridyl rings from neighboring molecules formed a “four-leaf clover”. A dark protrusion could be visible at the center in a special tip state (as depicted by blue circles in Figure e) and was attributed to Na according to our previous reports, , which is also in good agreement with the situation on Ag(111) . Furthermore, additional NaCl was deposited to verify the influence of NaCl dosage on the structural diversity, which, interestingly, led to the coexistence of NaCl islands and phase I (Figure c), while no structural transformation was observed.…”

On-Surface Fabrication of Bimetallic Metal–Organic Frameworks through the Synergy and Competition among Noncovalent Interactions

“…Deposition of U molecules and Na atoms on the Au(111) surface followed by annealing at 350 K leads to the formation of a 2D-MOF as shown in Figure a. From the high-resolution STM image superimposed with the structural model (Figure d), and also a previous study, the elementary structural motif (depicted by the blue contour) is attributed to a U 4 Na 1 motif, in which U molecules interact with the central Na via electrostatic ionic bonds and the neighboring U molecules interact with each other by intermolecular hydrogen bonds that are depicted by blue dashed lines. The corresponding simulated STM image shown in Figure S1e is in good agreement with the experimental one.…”

Flexible Alkali–Halogen Bonding in Two Dimensional Alkali-Metal Organic Frameworks

“…Previous reports have shown that alkali atoms deposited on Au(111) generally lose their valence electrons to the substrates. 14,15,28 In this case, we performed the Bader charge analysis and obtained the valence of the sodium as +0.86, confirming that the sodium atoms exist in the form of Na + ions. Due to the low electron density and low height profile, Na ions has a weak contrast in conventional STM images.…”

“…Owing to the high isotropy of the alkali ion, the ortho -dibromo chelator can rotate around the alkali ion in the frame of reference of the ion, just like a ball-and-socket joint (Figure e and f). A single alkali ion can bond to multiple nucleophilic groups, − depending on the ion radius and its steric environment. Na + is a small alkali ion which can accommodate only one or two ortho -dibromo groups in a 2D plane.…”