Correcting PCR amplification errors in unique molecular identifiers to generate accurate numbers of sequencing molecules.

Unique molecular identifiers are random oligonucleotide sequences that remove PCR amplification biases. However, the impact that PCR associated sequencing errors have on the accuracy of generating absolute counts of RNA molecules is underappreciated. We show that PCR errors are a source of inaccuracy in both bulk and single-cell sequencing data, and synthesizing unique molecular identifiers using homotrimeric nucleotide blocks provides an error-correcting solution that allows absolute counting of sequenced molecules.

Correction: Terahertz spectroscopy of the helium endofullerene He@C60.

Correction for 'Terahertz spectroscopy of the helium endofullerene He@C60' by Tanzeeha Jafari et al., Phys. Chem. Chem. Phys., 2022, 24, 9943-9952, https://doi.org/10.1039/D2CP00515H.

Ne, Ar, and Kr oscillators in the molecular cavity of fullerene C60.

We used THz (terahertz) and INS (inelastic neutron scattering) spectroscopies to study the interaction between an endohedral noble gas atom and the C60 molecular cage. The THz absorption spectra of powdered A@C60 samples (A = Ar, Ne, Kr) were measured in the energy range from 0.6 to 75 meV for a series of temperatures between 5 and 300 K. The INS measurements were carried out at liquid helium temperature in the energy transfer range from 0.78 to 54.6 meV. The THz spectra are dominated by one line, between 7 and 12 meV, at low temperatures for three noble gas atoms studied. The line shifts to higher energy and broadens as the temperature is increased. Using a spherical oscillator model, with a temperature-independent parameterized potential function and an atom-displacement-induced dipole moment, we show that the change of the THz spectrum shape with temperature is caused by the anharmonicity of the potential function. We find good agreement between experimentally determined potential energy functions and functions calculated with Lennard-Jones additive pair-wise potentials with parameters taken from the work of Pang and Brisse, J. Chem. Phys. 97, 8562 (1993).

A combined inelastic neutron scattering and simulation study of the 3He@C60 endofullerene.

The 3He@C60 endofullerene consists of a single 3He atom entrapped inside a C60 fullerene cage. The confining potential, arising from the non-covalent interaction between the enclosed He atom and the C atoms of the cage, is investigated by inelastic neutron scattering. These measurements allow us to obtain information in both energy (ω) and momentum (Q) transfers in the form of the dynamical structure factor S (Q, ω). Simulations of the S (Q, ω) maps are performed for a spherical anharmonic oscillator model. Good agreement between the experimental and simulated data sets is achieved.

Synthesis and 83Kr NMR spectroscopy of Kr@C60.

Synthesis of Kr@C60 is achieved by quantitative high-pressure encapsulation of the noble gas into an open-fullerene, and subsequent cage closure. Krypton is the largest noble gas entrapped in C60 using 'molecular surgery' and Kr@C60 is prepared with >99.4% incorporation of the endohedral atom, in ca. 4% yield from C60. Encapsulation in C60 causes a shift of the 83Kr resonance by -39.5 ppm with respect to free 83Kr in solution. The 83Kr spin-lattice relaxation time T1 is approximately 36 times longer for Kr encapsulated in C60 than for free Kr in solution. This is the first characterisation of a stable Kr compound by 83Kr NMR.

Terahertz spectroscopy of the helium endofullerene He@C60.

We studied the quantized translational motion of single He atoms encapsulated in molecular cages by terahertz absorption. The temperature dependence of the THz absorption spectra of 3He@C60 and 4He@C60 crystal powder samples was measured between 5 and 220 K. At 5 K there is an absorption line at 96.8 cm-1 (2.90 THz) in 3He@C60 and at 81.4 cm (2.44 THz) in 4He@C60, while additional absorption lines appear at higher temperature. An anharmonic spherical oscillator model with a displacement-induced dipole moment was used to model the absorption spectra. Potential energy terms with powers of two, four and six and induced dipole moment terms with powers one and three in the helium atom displacement from the fullerene cage center were sufficient to describe the experimental results. Excellent agreement is found between potential energy functions derived from measurements on the 3He and 4He isotopes. One absorption line corresponds to a three-quantum transition in 4He@C60, allowed by the anharmonicity of the potential function and by the non-linearity of the dipole moment in He atom displacement. The potential energy function of icosahedral symmetry does not explain the fine structure observed in the low temperature spectra.

Experimental determination of the interaction potential between a helium atom and the interior surface of a C60 fullerene molecule.

The interactions between atoms and molecules may be described by a potential energy function of the nuclear coordinates. Nonbonded interactions between neutral atoms or molecules are dominated by repulsive forces at a short range and attractive dispersion forces at a medium range. Experimental data on the detailed interaction potentials for nonbonded interatomic and intermolecular forces are scarce. Here, we use terahertz spectroscopy and inelastic neutron scattering to determine the potential energy function for the nonbonded interaction between single He atoms and encapsulating C60 fullerene cages in the helium endofullerenes 3He@C60 and 4He@C60, synthesized by molecular surgery techniques. The experimentally derived potential is compared to estimates from quantum chemistry calculations and from sums of empirical two-body potentials.

A Solid-State Intramolecular Wittig Reaction Enables Efficient Synthesis of Endofullerenes Including Ne@C60 , 3 He@C60 , and HD@C60.

An open-cage fullerene incorporating phosphorous ylid and carbonyl group moieties on the rim of the orifice can be filled with gases (H2 , He, Ne) in the solid state, and the cage opening then contracted in situ by raising the temperature to complete an intramolecular Wittig reaction, trapping the atom or molecule inside. Known transformations complete conversion of the product fullerene to C60 containing the endohedral species. As well as providing an improved synthesis of large quantities of 4 He@C60 , H2 @C60 , and D2 @C60 , the method allows the efficient incorporation of expensive gases such as HD and 3 He, to prepare HD@C60 and 3 He@C60 . The method also enables the first synthesis of Ne@C60 by molecular surgery, and its characterization by crystallography and 13 C NMR spectroscopy.

Rotational coherence of encapsulated ortho and para water in fullerene-C60 revealed by time-domain terahertz spectroscopy.

We resolve the real-time coherent rotational motion of isolated water molecules encapsulated in fullerene-C60 cages by time-domain terahertz (THz) spectroscopy. We employ single-cycle THz pulses to excite the low-frequency rotational motion of water and measure the subsequent coherent emission of electromagnetic waves by water molecules. At temperatures below ~ 100 K, C60 lattice vibrational damping is mitigated and the quantum dynamics of confined water are resolved with a markedly long rotational coherence, extended beyond 10 ps. The observed rotational transitions agree well with low-frequency rotational dynamics of single water molecules in the gas phase. However, some additional spectral features with their major contribution at ~2.26 THz are also observed which may indicate interaction between water rotation and the C60 lattice phonons. We also resolve the real-time change of the emission pattern of water after a sudden cooling to 4 K, signifying the conversion of ortho-water to para-water over the course of 10s hours. The observed long coherent rotational dynamics of isolated water molecules confined in C60 makes this system an attractive candidate for future quantum technology.

An Internuclear J-Coupling of 3He Induced by Molecular Confinement.

The solution-state 13C NMR spectrum of the endofullerene 3He@C60 displays a doublet structure due to a J-coupling of magnitude 77.5 ± 0.2 mHz at 340 K between the 3He nucleus and a 13C nucleus of the enclosing carbon surface. The J-coupling increases in magnitude with increasing temperature. Quantum chemistry calculations successfully predict the approximate magnitude of the coupling. This observation shows that the mutual proximity of molecular or atomic species is sufficient to induce a finite scalar nuclear spin-spin coupling, providing that translational motion is restricted by confinement. The phenomenon may have applications to the study of surface interactions and to mechanically bound species.

Synthesis of Ar@C60 using molecular surgery.

Synthesis of Ar@C60 is described, using a route in which high-pressure argon filling of an open-fullerene and photochemical desulfinylation are the key steps for >95% encapsulation of the noble gas. Enrichment by recycling HPLC leads to quantitative incorporation of argon in the product endofullerene, with a mass recovery of tens of milligrams, allowing the first characterisation of fine structure in the solution 13C NMR spectrum.

Fine structure in the solution state 13C-NMR spectrum of C60 and its endofullerene derivatives.

The 13C NMR spectrum of fullerene C60 in solution displays two small "side peaks" on the shielding side of the main 13C peak, with integrated intensities of 1.63% and 0.81% of the main peak. The two side peaks are shifted by -12.6 ppb and -20.0 ppb with respect to the main peak. The side peaks are also observed in the 13C NMR spectra of endofullerenes, but with slightly different shifts relative to the main peak. We ascribe the small additional peaks to minor isotopomers of C60 containing two adjacent 13C nuclei. The shifts of the additional peaks are due to a secondary isotope shift of the 13C resonance caused by the substitution of a 12C neighbour by 13C. Two peaks are observed since the C60 structure contains two different classes of carbon-carbon bonds with different vibrational characteristics. The 2 : 1 ratio of the side peak intensities is consistent with the known structure of C60. The origin and intensities of the 13C side peaks are discussed, together with an analysis of the 13C solution NMR spectrum of a 13C-enriched sample of C60, which displays a relatively broad 13C NMR peak due to a statistical distribution of 13C isotopes. The spectrum of 13C-enriched C60 is analyzed by a Monte Carlo simulation technique, using a theorem for the second moment of the NMR spectrum generated by J-coupled spin clusters.