Gas-Phase IR Spectroscopy of Nucleobases

Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials

Rare tautomeric forms of nucleobases can lead to Watson-Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guanine-thymine (G-T) mispairs; however, the mechanism of proton transfer and the degree to which nuclear quantum effects play a role are unclear. We use a B-DNA helix exhibiting a wGT mispair as a model system to study tautomerization reactions. We perform ab initio (PBE0/6-31G*) quantum mechanical/molecular mechanical (QM/MM) simulations to examine the free energy surface for tautomerization. We demonstrate that while the ab initio QM/MM simulations are accurate, considerable sampling is required to achieve high precision in the free energy barriers. To address this problem, we develop a QM/MM machine learning potential correction (QM/MM-ΔMLP) that is able to improve the computational efficiency, greatly extend the accessible time scales of the simulations, and enable practical application of path integral molecular dynamics to examine nuclear quantum effects. We find that the inclusion of nuclear quantum effects has only a modest effect on the mechanistic pathway but leads to a considerable lowering of the free energy barrier for the GT*⇌G*T equilibrium. Our results enable a rationalization of observed experimental data and the prediction of populations of rare tautomeric forms of nucleobases and rates of their interconversion in B-DNA.

Conformational Mapping, Interactions, and Fluorine Impact by Combined Spectroscopic Approaches and Quantum Chemical Calculations

Noncovalent interactions and their careful variation can be crucial in understanding molecular structures, conformational topographies, and properties. Here, we examine the fluorination impact on the structure and conformational behavior of 2-(2-fluorophenyl)ethyl alcohol (2-FPEAL) by monitoring the first individual ionization-loss-stimulated Raman spectra of the jet-cooled molecule. The comparison of two different broad-range spectra and predicted equivalents discloses two distinct structures. One possesses a folded side chain (gauche) and the other an extended chain (anti) with the terminal hydrogen atom pointing opposite or toward the fluorine side, indicating the improper previous tentative assignment of the latter. These conformers resemble and differ from the nonfluorinated analogue structures. Theoretical analyses reveal interconversion pathways of 2-FPEAL conformers during expansion and the delicate balance between attractive (C-H···F and O-H···π) and repulsive interactions. These findings show the achievements of our integrated approach, suggesting its potential for overcoming future structural challenges.

Experimental/Computational Study on the Impact of Fluorine on the Structure and Noncovalent Interactions in the Monohydrated Cluster of ortho-Fluorinated 2-Phenylethylamine

Fluorine-containing medicinal compounds frequently allow modulation of physical-chemical properties. Here, we address the effect of fluorine, near the ethylamino side chain, on conformational flexibility and noncovalent interactions (NCIs) of the selected jet-cooled monohydrated cluster of 2-(2-fluoro-phenyl)-ethylamine (2-FPEA) by mass-selected resonance-enhanced two-photon ionization and ionization-loss stimulated Raman spectroscopies. Our results show that Raman spectral signatures of the 2-FPEA-H₂O cluster match the scaled harmonic vibrational Raman frequencies, resulting from density functional theory calculations of the most stable 2-FPEA gauche conformer hydrogen-bonded (HB) to water, confirming the three-dimensional cluster structure. This predicted electronic structure, together with NCI analysis, allows visualization and assessment of the attractive and repulsive interactions. The comparison of the NCIs and revealed red (O-H and N-H stretches) and blue shifts (C-H stretches and CH₂ out-of-plane bends) of the cluster to other class members confirm O-H···N, N-H···π, C-H···O, and C-H···F HB formation and their contribution to structure stabilization, uncovering the potential of the approach.

Revealing the Structure and Noncovalent Interactions of Isolated Molecules by Laser-Desorption/Ionization-Loss Stimulated Raman Spectroscopy and Quantum Calculations

The structural and dynamical characteristics of isolated molecules are essential, yet obtaining this information is difficult. We demonstrate laser-desorption jet-cooling/ionization-loss stimulated Raman spectroscopy to obtain Raman spectral signatures of nonvolatile molecules in the gas phase. The vibrational features of a test substance, the most abundant conformer of tryptamine, are compared and found to match those resulting from the scaled harmonic Raman spectrum obtained by density functional theory calculations. The vibrational signatures serve to identify the most prominent gauche conformer and evaluate its predicted electronic structure. These findings, together with noncovalent interaction (NCI) analysis, provide new insights into electron densities and reduced density gradients, assessing the hydrogen bonds (N-H···π and C-H···H-C) and interplay between attractive and repulsive NCIs affecting the structure. This approach accesses vibrational signatures of isolated nonvolatile molecules by tabletop lasers at uniform resolution and in a broad frequency range, promising great benefit to future studies.

Guanine Tautomerism in Ionic Complexes with Ag+ Investigated by IRMPD Spectroscopy and Mass Spectrometry

In this paper, we present the IRMPD spectra of three ionic complexes between guanine (G) and silver (Ag⁺): [GAg-H₂O]⁺, [GAgG]⁺ produced in the electrospray ionization source of the mass spectrometer, and [GAg]⁺ produced by collision induced dissociation of the [GAgG]⁺ complex. On the basis of the comparison of theoretically calculated IR spectra, we show that there are two isomers of each complex containing two different keto-amino (KA) tautomers of G (GKA(1,9) and GKA(1,7)). The observed isomers are the most stable structures in aqueous solution, and their experimentally estimated relative populations are in better agreement with the calculated relative populations in solution than in the gas phase, both at 298 K. We concluded that these observations suggest that GKA(1,9) and GKA(1,7) coexist in solution according to previous theoretical reports (Colominas, C.; et al. J. Am. Chem. Soc. 1996, 118, 6811). We were unable to find any evidence of the presence of the GEA(9), GKA(3,7), GKA(3,9), or GKA(7,9), whose relative stabilities in solution are strongly dependent on the theoretical method used to account for the solvent effect (Hanus, M.; et al. J. Am. Chem. Soc. 2003, 125, 7678).

In Silico Infrared Characterization of Synthetic Cannabinoids by Quantum Chemistry and Chemometrics

The concept of forensic sciences as mere trace analysis has been modified by the idea of forensic intelligence, which entails applying data to make decisions within the investigative process. Many countries are engaged in combating drug trafficking and drug use because they are related to public health and safety issues. Prohibiting the consumption of traditional drugs has led new psychoactive substances (NPSs) to emerge. NPSs consist of compounds that resemble the initially banned substance and which aim to mimic the traditional drug recreational effects while circumventing drug legislation. For example, synthetic cannabinoids are sprayed on herbal products to reproduce the cannabis recreational effects. According to the United Nations Office on Drugs and Crime (UNODC), the toxic effects of synthetic cannabis types are unknown, and harm and fatalities associated with the use of these drugs have been reported. Information on the characterization related to these species is lacking. The rate at which NPSs appear poses a significant challenge because employing conventional methods to understand the characteristics of these compounds may require time and be costly. This work uses in silico practices as an alternative to understand how NPSs related to cannabis behave. We apply quantum chemistry methods to evaluate several synthetic cannabinoids recognized in forensic samples. More specifically, we generate infrared spectra that can be employed as a benchmark for NPSs. We apply a multivariate classification to evaluate the results. We conclude that in silico methods are an alternative that provide information about the spectra of undetected substances. This information can help to identify new drugs, to increase knowledge about them, and to feed information procedures.

DNA Polymerase λ Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study

Human DNA polymerase λ is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase λ, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an unexpected Watson-Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thymine in the DNA or guanine in the deoxyguanosine triphosphate analogue may spend a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the polymerase λ mutant. The experiments do not determine particular forms of the nucleobases that contribute to this mutagenic mispair. Thus, we investigate the thermodynamics of formation of various mispairs between guanine and thymine in the ternary complex at a neutral pH using classical molecular dynamics simulations and the free energy perturbation method. Our free energy calculations, as well as a comparison of the experimental and computed structures of mispairs, indicate that the Watson-Crick-like mispair between the enol tautomer of guanine and the keto tautomer of thymine is dominant. The wobble mispair between the keto forms of guanine and thymine and the Watson-Crick-like mispair between the keto tautomer of guanine and the enol tautomer of thymine are less prevalent, and mispairs that involve deprotonated guanine or thymine are thermodynamically unlikely. These findings are consistent with the experiment and relevant for understanding mechanisms of spontaneous mutagenesis.