Ten stationary points on the water dimer potential energy surface have been characterized with the coupled-cluster technique which includes all single and double excitations as well as a perturbative approximation of triple excitations [CCSD(T)]. Using a triple-ζ basis set with two sets of polarization functions augmented with higher angular momentum and diffuse functions $[\mathrm{TZ2P}\mathrm{(f,d)+}\mathrm{dif}\mathrm{],}$ the fully optimized geometries and harmonic vibrational frequencies of these ten stationary points were determined at the CCSD(T) theoretical level. In agreement with other ab initio investigations, only one of these ten stationary points is a true minimum. Of the other nine structures, three are transition structures, and the remaining are higher order saddle points. These high-level ab initio results indicate that the lowest lying transition state involved in hydrogen interchange is chiral, of $C_1$ symmetry rather than $C_s$ as suggested by recently developed 6D potential energy surfaces. The one- and n-particle limits of the electronic energies of these ten stationary points were probed by systematic variation of the atomic orbital basis sets and the treatment of electron correlation within the framework of the focal-point analysis of Allen and co-workers. The one-particle limit was approached via extrapolation of electronic energies computed with the augmented correlation consistent basis sets $(\mathrm{aug-cc-p}\mathrm{V}X\mathrm{Z},$ $\text{X=D−6),}$ and, independently, by estimating the basis set incompleteness effect with the explicitly-correlated second-order Møller-Plesset method (MP2-R12). Electron correlation was evaluated at levels as high as the Brueckner coupled cluster method with double excitations and perturbatively treated triple and quadruple excitations [BD(TQ)]. Core correlation and relativistic effects were also assessed. Consideration of the aforementioned electronic effects as well as basis set superposition error leads to an estimate of 21.0 kJ mol⁻¹ for the electronic dissociation energy of $({\mathrm{H}}_{\mathrm{2}}{\mathrm{O)}}_{\mathrm{2}}.$

DNA sequences with the potential to form secondary structures such as i-motifs (iMs) and G-quadruplexes (G4s) are abundant in the promoters of several oncogenes and, in some instances, are known to regulate gene expression. Recently, iM-forming DNA strands have also been employed as functional units in nanodevices, ranging from drug delivery systems to nanocircuitry. To understand both the mechanism of gene regulation by iMs and how to use them more efficiently in nanotechnological applications, it is essential to have a thorough knowledge of factors that govern their conformational states and stabilities. Most of the prior work to characterize the conformational dynamics of iMs have been done with iM-forming synthetic constructs like tandem (CCT)_n repeats and in standard dilute buffer systems. Here, we present a systematic study on the consequences of epigenetic modifications, molecular crowding, and degree of hydration on the stabilities of an iM-forming sequence from the promoter of the c-myc gene. Our results indicate that 5-hydroxymethylation of cytosines destabilized the iMs against thermal and pH-dependent melting; contrarily, 5-methylcytosine modification stabilized the iMs. Under molecular crowding conditions (PEG-300, 40% w/v), the thermal stability of iMs increased by ∼10 °C, and the pK_a was raised from 6.1 ± 0.1 to 7.0 ± 0.1. Lastly, the iM’s stability at varying degrees of hydration in 1,2-dimethoxyethane, 2-methoxyethanol, ethylene glycol, 1,3-propanediol, and glycerol cosolvents indicated that the iMs are stabilized by dehydration because of the release of water molecules when folded. Our results highlight the importance of considering the effects of epigenetic modifications, molecular crowding, and the degree of hydration on iM structural dynamics. For example, the incorporation of 5-methylycytosines and 5-hydroxymethlycytosines in iMs could be useful for fine-tuning the pH- or temperature-dependent folding/unfolding of an iM. Variations in the degree of hydration of iMs may also provide an additional control of the folded/unfolded state of iMs without having to change the pH of the surrounding matrix.

Infrared cavity ringdown laser absorption spectroscopy has been used to study the O–H stretching vibrations of jet-cooled methanol clusters in direct absorption. Rovibrational bands for (CH3OH)2, (CH3OH)3, and (CH3OH)4 have been measured. Both bonded and free O–H stretches were measured for the dimer, indicating that its structure is linear. Five bands were assigned to the methanol trimer, indicating the presence of a second cyclic isomer in the molecular beam. A detailed study of the free O–H stretching region shows that methanol clusters larger than dimer must exist in cyclic ring configurations. In order to facilitate spectral assignment, harmonic frequencies and infrared intensities were calculated for the methanol monomer, dimer, and trimer with second order Mo/ller–Plesset perturbation theory. Using the theoretical infrared intensities and measured vibrational band absorptions, absolute cluster concentrations were calculated. Results agree with previous experimental and theoretical work.

The atomic electron affinities of the eight first row (H,Li,…,F) atoms as well as the adiabatic electron affinities of 12 first row diatomic and 15 first row triatomic molecules were determined using six different density functional or hybrid Hartree–Fock/density functional methods. The 35 species were selected for having relatively well-established experimental electron affinities. Harmonic zero-point vibrational energy corrected electron affinities are also reported for the diatomic and triatomic molecules. Equilibrium geometries and harmonic vibrational frequencies are given for the 27 molecules and their anions as determined with each density functional method. Discussion focuses on comparison of theoretical and experimental electron affinities. For the atomic, diatomic, and triatomic electron affinities the average absolute error is reported for each exchange–correlation functional. Since many of the molecular anion structures and vibrational frequencies are unknown, the work suggests new experimental directions.