Towards a reliable prediction of the infrared spectra of cosmic fullerenes and their derivatives in the JWST era

Fullerenes, including C60, C70, and C60+, are widespread in space through their characteristic infrared vibrational features (C60+ also reveals its presence in the interstellar medium through its electronic transitions) and offer great insights into the carbon chemistry and stellar evolution. The potential existence of fullerene-related species in space has long been speculated and recently put forward by a set of laboratory experiments of C60+, C60H+, C60O+, C60OH+, C70H+, and [C60-Metal]+ complexes. The advent of the James Webb Space Telescope (JWST) provides a unique opportunity to search for these fullerene-related species in space. To facilitate JWST search, analysis, and interpretation, an accurate knowledge of their vibrational properties is essential. Here, we compile a VibFullerene database and conduct a systematic theoretical study on those species. We derive a set of range-specific scaling factors for vibrational frequencies, to account for the deficiency of density functional theory calculations in predicting the accurate frequencies. Scaling factors with low root-mean-square and median errors for the frequencies are obtained, and their performance is evaluated, from which the best-performing methods are recommended for calculating the infrared spectra of fullerene derivatives which balance the accuracy and computational cost. Finally, the recommended vibrational frequencies and intensities of fullerene derivatives are presented for future JWST detection.Comment: 19 pages, 8 figures, 5 tables. Accepted for publication in MNRA

Pentagon, Hexagon, or Bridge? Identifying the Location of a Single Vanadium Cation on Buckminsterfullerene Surface

Buckminsterfullerene C60 has received extensive research interest ever since its discovery. In addition to its interesting intrinsic properties of exceptional stability and electron-accepting ability, the broad chemical tunability by decoration or substitution on the C60-fullerene surface makes it a fascinating molecule. However, to date there is uncertainty about the binding location of such decorations on the C60 surface, even for a single adsorbed metal atom. In this work, we report the gas-phase synthesis of the C60V+ complex and its in-situ characterization by mass spectrometry and in-frared spectroscopy with the help of quantum chemical calculations and molecular dynamics simulations. We identify the most probable binding position of a vanadium cation on C60 above a pentagon center in eta5-fashion, demonstrate a high thermal stability for this complex, and explore the bonding nature between C60 and the vanadium cation, reveal-ing that large orbital and electrostatic interactions lie at the origin of the stability of the eta5-C60V+ complex.Comment: 29 pages (11 pages for main text and 17 pages for the supporting information

Spontaneous breaking and re-making of the RS-Au-SR staple in self-assembled ethylthiolate/Au(111) interface

The stability of the self-assembled RS–Au–SR (R = CH₂CH₃)/Au­(111) interface at room temperature has been investigated using scanning tunneling microscopy (STM) in conjunction with density functional theory (DFT) and MD calculations. The RS–Au–SR staple, also known as Au-adatom-dithiolate, assembles into staple rows along the [112̅] direction. STM imaging reveals that while the staple rows are able to maintain a static global structure, individual staples within the row are subjected to constant breaking and remaking of the Au–SR bond. The C₂S–Au–SC₂/Au­(111) interface is under a dynamic equilibrium and it is far from rigid. DFT/MD calculations show that a transient RS–Au–Au–SR complex can be formed when a free Au atom is added to the RS–Au–SR staple. The relatively high reactivity of the RS–Au–SR staple at room temperature could explain the reactivity of thiolate-protected Au nanoclusters, such as their ability to participate in ligand exchange and intercluster reactions

Bridge-bonded methylthiolate on Au(111) observed with the scanning tunneling microscope

We report the discovery of bridge-bonded methylthiolate, SCH3, along the step edges of the Au(111) surface. Real-space imaging with a scanning tunnelling microscope reveals the presence of bridge-bonded SCH3 along both the [1[1 with combining macron]0] and the [11[2 with combining macron]] oriented step edges. The nearest neighbour distances of SCH3 along these steps are 2a and Image ID:c8cp03684e-t1.gif, respectively. The Au(111) terrace is covered with the usual CH3SAuSCH3 staples. The bridge-bonded alkanethiolate is expected to play a rather significant role in the formation of thiol-passivated Au nanoclusters because of the high fraction of atoms in similar low-coordination sites

Why Is the Correlation between Gene Importance and Gene Evolutionary Rate So Weak?

One of the few commonly believed principles of molecular evolution is that functionally more important genes (or DNA sequences) evolve more slowly than less important ones. This principle is widely used by molecular biologists in daily practice. However, recent genomic analysis of a diverse array of organisms found only weak, negative correlations between the evolutionary rate of a gene and its functional importance, typically measured under a single benign lab condition. A frequently suggested cause of the above finding is that gene importance determined in the lab differs from that in an organism's natural environment. Here, we test this hypothesis in yeast using gene importance values experimentally determined in 418 lab conditions or computationally predicted for 10,000 nutritional conditions. In no single condition or combination of conditions did we find a much stronger negative correlation, which is explainable by our subsequent finding that always-essential (enzyme) genes do not evolve significantly more slowly than sometimes-essential or always-nonessential ones. Furthermore, we verified that functional density, approximated by the fraction of amino acid sites within protein domains, is uncorrelated with gene importance. Thus, neither the lab-nature mismatch nor a potentially biased among-gene distribution of functional density explains the observed weakness of the correlation between gene importance and evolutionary rate. We conclude that the weakness is factual, rather than artifactual. In addition to being weakened by population genetic reasons, the correlation is likely to have been further weakened by the presence of multiple nontrivial rate determinants that are independent from gene importance. These findings notwithstanding, we show that the principle of slower evolution of more important genes does have some predictive power when genes with vastly different evolutionary rates are compared, explaining why the principle can be practically useful despite the weakness of the correlation

The Use of Orthologous Sequences to Predict the Impact of Amino Acid Substitutions on Protein Function

Computational predictions of the functional impact of genetic variation play a critical role in human genetics research. For nonsynonymous coding variants, most prediction algorithms make use of patterns of amino acid substitutions observed among homologous proteins at a given site. In particular, substitutions observed in orthologous proteins from other species are often assumed to be tolerated in the human protein as well. We examined this assumption by evaluating a panel of nonsynonymous mutants of a prototypical human enzyme, methylenetetrahydrofolate reductase (MTHFR), in a yeast cell-based functional assay. As expected, substitutions in human MTHFR at sites that are well-conserved across distant orthologs result in an impaired enzyme, while substitutions present in recently diverged sequences (including a 9-site mutant that “resurrects” the human-macaque ancestor) result in a functional enzyme. We also interrogated 30 sites with varying degrees of conservation by creating substitutions in the human enzyme that are accepted in at least one ortholog of MTHFR. Quite surprisingly, most of these substitutions were deleterious to the human enzyme. The results suggest that selective constraints vary between phylogenetic lineages such that inclusion of distant orthologs to infer selective pressures on the human enzyme may be misleading. We propose that homologous proteins are best used to reconstruct ancestral sequences and infer amino acid conservation among only direct lineal ancestors of a particular protein. We show that such an “ancestral site preservation” measure outperforms other prediction methods, not only in our selected set for MTHFR, but also in an exhaustive set of E. coli LacI mutants