Two new flexible-monomer two-body ab initio potential energy surfaces (PESs) for the neon and krypton van der Waals complexes with carbon dioxide were developed, extending our previous work on the Ar–CO2 molecule. The accuracy of the PESs was validated by their agreement with the vibrational spectrum of the rare-gas complexes. The intermolecular and intramolecular vibrational excitation energies were computed at the vibrational self-consistent field and vibrational configuration interaction levels of theory. Overall, the agreement between theory and experiment is excellent throughout the vibrational spectra. The observed slight splitting of the bending modes, resulting from their nondegeneracy in the complexes, is confirmed by our computations, and the results qualitatively agree with the experiment. The splitting increases with increasing polarizability of the rare-gas atom. Additionally, we explain a discrepancy in the mode assignment in the intermolecular region of the neon complex with our VCI character assignment.
more »
« less
Proton NMR relaxation from molecular dynamics: intramolecular and intermolecular contributions in water and acetonitrile
NMR relaxation rates for protons in liquid water and neat acetonitrile were computed based on ab initio molecular dynamics (aiMD) with forces from Kohn–Sham (KS) theory as well as force-field (FF) based classical dynamics. Intra- and intermolecular dipole–dipole contributions were separated, and nearly quantitative agreement with experiment was obtained for water. Spin-rotation (SR) contributions to the intramolecular relaxation rate in acetonitrile were computed using nuclear SR coupling tensors obtained from KS theory. Their inclusion improved the total computed intramolecular rate to within a factor of two of experiment. Insufficient sampling of rare short-time collision events between neighboring acetonitrile molecules in the simulations is hypothesized as a major source of error in the intermolecular contributions.
more »
« less
- Award ID(s):
- 1855470
- PAR ID:
- 10162285
- Date Published:
- Journal Name:
- Physical Chemistry Chemical Physics
- Volume:
- 21
- Issue:
- 48
- ISSN:
- 1463-9076
- Page Range / eLocation ID:
- 26621 to 26629
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Two-dimensional infrared (2D IR) spectroscopy, infrared pump–infrared probe spectroscopy, and density functional theory calculations were used to study vibrational relaxation by ring and carbonyl stretching modes in a series of methylated xanthine derivatives in acetonitrile and deuterium oxide (heavy water). Isotropic signals from the excited symmetric and asymmetric carbonyl stretch modes decay biexponentially in both solvents. Coherent energy transfer between the symmetric and asymmetric carbonyl stretching modes gives rise to a quantum beat in the time-dependent anisotropy signals. The damping time of the coherent oscillation agrees with the fast decay component of the carbonyl bleach recovery signals, indicating that this time constant reflects intramolecular vibrational redistribution (IVR) to other solute modes. Despite their similar frequencies, the excited ring modes decay monoexponentially with a time constant that matches the slow decay component of the carbonyl modes. The slow decay times, which are faster in heavy water than in acetonitrile, approximately match the ones observed in previous UV pump–IR probe measurements on the same compounds. The slow component is assigned to intermolecular energy transfer to solvent bath modes from low-frequency solute modes, which are populated by IVR and are anharmonically coupled to the carbonyl and ring stretch modes. 2D IR measurements indicate that the carbonyl stretching modes are weakly coupled to the delocalized ring modes, resulting in slow exchange that cannot explain the common solvent-dependence. IVR is suggested to occur at different rates for the carbonyl vs ring modes due to differences in mode-specific couplings and not to differences in the density of accessible states.more » « less
-
Nuclear spin relaxation mechanisms are often difficult to isolate and identify, especially in molecules with internal flexibility. Here we combine experimental work with computation in order to determine the major mechanisms responsible for 31 P spin–lattice and singlet order (SO) relaxation in pyrophosphate, a physiologically relevant molecule. Using field-shuttling relaxation measurements (from 2 μT to 9.4 T) and rates calculated from molecular dynamics (MD) trajectories, we identified chemical shift anisotropy (CSA) and spin–rotation as the major mechanisms, with minor contributions from intra- and intermolecular coupling. The significant spin–rotation interaction is a consequence of the relatively rapid rotation of the –PO 3 2− entities around the bridging P–O bonds, and is treated by a combination of MD simulations and quantum chemistry calculations. Spin–lattice relaxation was predicted well without adjustable parameters, and for SO relaxation one parameter was extracted from the comparison between experiment and computation (a correlation coefficient between the rotational motion of the groups).more » « less
-
Abstract Hydrogen bonding is a central concept in chemistry and biochemistry, and so it continues to attract intense study. Here, we examine hydrogen bonding in the H2S dimer, in comparison with the well-studied water dimer, in unprecedented detail. We record a mass-selected IR spectrum of the H2S dimer in superfluid helium nanodroplets. We are able to resolve a rotational substructure in each of the three distinct bands and, based on it, assign these to vibration-rotation-tunneling transitions of a single intramolecular vibration. With the use of high-level potential and dipole-moment surfaces we compute the vibration-rotation-tunneling dynamics and far-infrared spectrum with rigorous quantum methods. Intramolecular mode Vibrational Self-Consistent-Field and Configuration-Interaction calculations provide the frequencies and intensities of the four SH-stretch modes, with a focus on the most intense, the donor bound SH mode which yields the experimentally observed bands. We show that the intermolecular modes in the H2S dimer are substantially more delocalized and more strongly mixed than in the water dimer. The less directional nature of the hydrogen bonding can be quantified in terms of weaker electrostatic and more important dispersion interactions. The present study reconciles all previous spectroscopic data, and serves as a sensitive test for the potential and dipole-moment surfaces.more » « less
-
Abstract 2’‐Deoxy‐5‐formylcytidine (5fdCyd), a naturally occurring nucleoside found in mammalian DNA and mitochondrial RNA, exhibits important epigenetic functionality in biological processes. Because it efficiently generates triplet excited states, it is an endogenous photosensitizer capable of damaging DNA, but the intersystem crossing (ISC) mechanism responsible for ultrafast triplet state generation is poorly understood. In this study, time‐resolved mid‐IR spectroscopy and quantum mechanical calculations reveal the distinct ultrafast ISC mechanisms of 5fdCyd in water versus acetonitrile. Our experiment indicates that in water, ISC to triplet states occurs within 1 ps after 285 nm excitation. PCM‐TD‐DFT computations suggest that this ultrafast ISC is mediated by a singlet state with significant cytosine‐to‐formyl charge‐transfer (CT) character. In contrast, ISC in acetonitrile proceeds via a dark1nπ* state with a lifetime of ∼3 ps. CT‐induced ISC is not favored in acetonitrile because reaching the minimum of the gateway CT state is hampered by intramolecular hydrogen bonding, which enforces planarity between the aldehyde group and the aromatic group. Our study provides a comprehensive picture of the non‐radiative decay of 5fdCyd in solution and new insights into the factors governing ISC in biomolecules. We propose that the intramolecular CT state observed here is a key to the excited‐state dynamics of epigenetic nucleosides with modified exocyclic functional groups, paving the way to study their effects in DNA strands.more » « less
An official website of the United States government

