Multiple isomers of uracil–water complexes: infrared spectroscopy in helium nanodroplets

Uracil-water interaction revisited - in search of single H-bonded secondary minima

Monohydrated uracil (UW) complexes are stabilized by both O⋯HO and NH⋯O hydrogen bonds (H-bonds), simultaneously participating in forming three stable cyclic structures. The role and contribution of these individual H-bonds (O⋯HO and NH⋯O) to the stability of the three UW complexes are still not understood, because of the technical problems in obtaining their optimized structures by standard geometry optimization. The present study explores a non-standard approach to identify three single H-bonded local minima structures without imaginary frequency using DFT (M06-2X, B3LYP and B3LYP-D3), MP2 and CCSD(T) theories and Dunning's correlation-consistent aug-cc-pVTZ basis set, in both vacuum and aqueous media (CPCM method). The results reveal that these new structures are very shallow secondary minima between two deep wells or next to a deep well of primary minima (double H-bonded structures) in the potential energy surface. The H-bond energy of these single H-bonded complexes is found to be less sensitive to a wide range (about 15-20 degrees) of O⋯HO and NH⋯O angles, and the linearity is preferred in the stable three single H-bonded structures. The technical method used to locate such a shallow minimum is described in detail and may be useful for identifying local minima in other cases where consecutive multiple H-bonded structures are global minima. Energy decomposition (using symmetry adapted perturbation theory (SAPT)) of interaction energy, electron redistribution, and relevant vibrational modes are discussed.

Exploration of the theobromine-water dimer: comparison with DNA microhydration

Understanding the molecular basis of the appearance of life on Earth is an exciting research field. Many factors may have influenced the election of the molecules used by living beings and evolution may have modified those original compounds. In an attempt to understand the role played by intermolecular interactions in the election of CGAT as the alphabet of life, we present here a thorough experimental and computational study on the interaction of theobromine with water. Theobromine is a xanthine derivative, structurally related to the nucleobases, and also present in many living beings. The experimental results demonstrate that the most stable isomer of theobromine-water was formed and detected in supersonic expansions. This isomer very well resembles the structure of the dimers between nucleobases and water, offering similar values of binding energy. A comparison between the results obtained for theobromine-water with those reported in the literature for monohydrates of nucleobases is also offered.

Clustering of Uracil Molecules on Ice Nanoparticles

We generate a molecular beam of ice nanoparticles (H₂O)_N, N̅ ≈ 130-220, which picks up several individual gas phase uracil (U) or 5-bromouracil (BrU) molecules. The mass spectra of the doped nanoparticles prove that the uracil and bromouracil molecules coagulate to clusters on the ice nanoparticles. Calculations of U and BrU monomers and dimers on the ice nanoparticles provide theoretical support for the cluster formation. The (U)_mH⁺ and (BrU)_mH⁺ intensity dependencies on m extracted from the mass spectra suggest a smaller tendency of BrU to coagulate compared to U, which is substantiated by a lower mobility of bromouracil on the ice surface. The hydrated U_m·(H₂O)_nH⁺ series are also reported and discussed. On the basis of comparison with the previous experiments, we suggest that the observed propensity for aggregation on ice nanoparticles is a more general trend for biomolecules forming strong hydrogen bonds. This, together with their mobility, leads to their coagulation on ice nanoparticles which is an important aspect for astrochemistry.

Conformational structures of jet-cooled acetaminophen-water clusters: a gas phase spectroscopic and computational study

Jet-cooled acetaminophen (AAP)-water clusters, AAP-(H₂O)₁, were investigated by mass-selected resonant two-photon ionization (R2PI), ultraviolet-ultraviolet hole-burning (UV-UV HB), infrared-dip (IR-dip), and infrared-ultraviolet hole-burning (IR-UV HB) spectroscopy. Each syn- and anti-AAP rotamer has three distinctive binding sites (-OH, >CO, and >NH) for a water molecule, thus 6 different AAP-(H₂O)₁ conformers are expected to exist in the molecular beam. The origin bands of the AAP(OH)-(H₂O)₁ and AAP(CO)-(H₂O)₁ conformers (including their syn- and anti-conformers) in the R2PI spectrum are shifted to red and blue compared to those of the AAP monomer, respectively. These frequency shifts upon complexation between a water molecule and a specific binding site of AAP are also predicted by theoretical calculations. The spectral assignments of the origin bands in the R2PI spectra and the IR vibrational bands in the IR-dip spectra of the four lowest-energy conformers of AAP-(H₂O)₁, [syn- and anti-AAP(OH)-(H₂O)₁ and syn- and anti-AAP(CO)-(H₂O)₁], are aided by ab initio and time-dependent density functional theory (TDDFT) calculations. Further investigation of the IR-dip spectra has revealed a hydrogen-bonded NH stretching mode, supporting the presence of the syn-AAP(NH)-(H₂O)₁ conformer. Moreover, by employing IR-UV HB spectroscopy, we have reconfirmed the existence of the syn-AAP(NH)-(H₂O)₁ conformer, which happened to be buried underneath the broad background contributed by the AAP(OH)-(H₂O)₁ conformers. These observations have led us to conclude that all of the possible conformers of AAP-(H₂O)₁ have been found in this study.

Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases

The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C=O stretchings, face unexpected difficulties when dealing with N-H stretchings. On these grounds, a linear regression for N-H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N-H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine-uracil, adenine-thymine, guanine-cytosine and adenine-4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm(-1)), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.

Microsolvation of 2-thiouracil: molecular structure and spectroscopic parameters of the thiouracil-water complex

State-of-the-art quantum-chemical computations have been employed to accurately determine the equilibrium structure and interaction energy of the 2-thiouracil-water complex, thus extending available reference data for biomolecule solvation patterns. The coupled-cluster level of theory in conjunction with a triple-ζ basis set has been considered together with extrapolation to the basis set limit, performed by employing second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections. On the basis of the comparison of experiment and theory for 2-thiouracil [ Puzzarini et al. Phys. Chem. Chem. Phys. 2013 , 15 , 16965 - 16975 ], structural changes due to water complexation have been pointed out. Molecular and spectroscopic properties of the 2-thiouracil-water complex have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the accurate determination of the molecular dipole moment and of the spectroscopic parameters required for predicting the rotational spectrum.

Specific photodynamics in thymine clusters: the role of hydrogen bonding

A photoionization detected IR study of thymine and 1-methylthymine monohydrates and of their homodimers was carried out to shed some light on the structure of the thymine clusters whose complex photodynamics has recently been the subject of great interest. Under supersonic jet conditions, thymine forms doubly H-bonded cyclic clusters with water or another base preferentially via its N1-H group and the adjacent carbonyl group. This hydrate is of no biological relevance since the N1-H group is the sugar binding site in thymidine. On the other hand, 1-methylthymine forms the donor H-bonds only via the N3-H group. Hence, properties of the N1-H and the N3-H bound clusters of thymine can be studied using thymine and 1-methylthymine molecules, respectively. No biologically relevant conformations of the dimers and hydrates of thymine, contrary to those of 1-methylthymine, are observed under supersonic jet conditions. Thymine homodimer, which extensively fragments upon UV ionization by formation of a protonated monomer, exhibits two N1-H···O═C2 hydrogen bonds. The photodynamics of hydrated thymines is found to be extremely sensitive to the hydration site: ranging from an ultrafast relaxation in less than 100 fs up to formation of a dark state with the lifetime on the microsecond time scale.

Electronic polarization spectroscopy of metal phthalocyanine chloride compounds in superfluid helium droplets

We report the electronic polarization spectroscopy of two metal phthalocyanine chloride compounds (MPcCl, M=Al,Ga) embedded in superfluid helium droplets and oriented in a dc electric field. For both compounds, the laser induced fluorescence spectra show preference for perpendicular excitation relative to the orientation field. This result indicates that the permanent dipoles of both compounds are predominantly perpendicular to the transition dipole. Since the permanent dipole derives from the metal chloride, while the transition dipole derives from the phthalocyanine chromophore, in the plane of phthalocyanine, this qualitative result is not surprising. However, quantitative modeling reveals that this intuitive model is inadequate and that the transition dipole might have tilted away from the molecular plane of phthalocyanine. The out of plane component of the transition dipole amounts to approximately 10% if the permanent dipole is assumed to be approximately 4 debye. The origin for this tilt is puzzling, and we tentatively attribute it to the transition of nonbonding orbitals, either from the chlorine atom or from the bridge nitrogen atom, to the pi* orbitals of the phthalocyanine chromophore. On the other hand, although unlikely, we cannot completely exclude the possibility that both our high level density functional theory calculation and ab initio results severely deviate from reality. The droplet matrix induces redshifts in the origin of the electronic transition and produces discrete phonon wings. Nevertheless, in dc electric fields, all phonon wings and the zero phonon line demonstrate the same dependence on the polarization direction of the excitation laser. Although electronic excitation does couple to the superfluid helium matrix and the resulting phonon wings add complications to the electronic spectrum, this coupling does not affect the direction of the electronic transition dipole. Electronic polarization spectroscopy in superfluid helium droplets is thus still informative in revealing the permanent dipole and its relation relative to the transition dipole.

Effects of Microsolvation on the Adenine−Uracil Base Pair and Its Radical Anion: Adenine−Uracil Mono- and Dihydrates

Microhydration effects upon the adenine-uracil (AU) base pair and its radical anion have been investigated by explicitly considering various structures of their mono- and dihydrates at the B3LYP/DZP++ level of theory. For the neutral AU base pair, 5 structures were found for the monohydrate and 14 structures for the dihydrate. In the lowest-energy structures of the neutral mono- and dihydrates, one and two water molecules bind to the AU base pair through a cyclic hydrogen bond via the N(9)-H and N(3) atoms of the adenine moiety, while the lowest-lying anionic mono- and dihydrates have a water molecule which is involved in noncyclic hydrogen bonding via the O4 atom of the uracil unit. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of the AU base pair are predicted to increase upon hydration. While the VDE and AEA of the unhydrated AU pair are 0.96 and 0.40 eV, respectively, the corresponding predictions for the lowest-lying anionic dihydrates are 1.36 and 0.75 eV, respectively. Because uracil has a greater electron affinity than adenine, an excess electron attached to the AU base pair occupies the pi* orbital of the uracil moiety. When the uracil moiety participates in hydrogen bonding as a hydrogen bond acceptor (e.g., the N(6)-H(6a)...O(4) hydrogen bond between the adenine and uracil bases and the O(w)-H(w)...N and O(w)-H(w)...O hydrogen bonds between the AU pair and the water molecules), the transfer of the negative charge density from the uracil moiety to either the adenine or water molecules efficiently stabilizes the system. In addition, anionic structures which have C-H...O(w) contacts are energetically more favorable than those with N-H...O(w) hydrogen bonds, because the C-H...O(w) contacts do not allow the unfavorable electron density donation from the water to the uracil moiety. This delocalization effect makes the energetic ordering for the anionic hydrates very different from that for the corresponding neutrals.

Vibrational Spectroscopy of Protonated Imidazole and its Complexes with Water Molecules: Ab Initio Anharmonic Calculations and Experiments

The results of anharmonic frequency calculations on neutral imidazole (C3N2H4, Im), protonated imidazole (ImH+), and its complexes with water (ImH+)(H2O)n, are presented and compared to gas phase infrared photodissociation spectroscopy (IRPD) data. Anharmonic frequencies are obtained via ab initio vibrational self-consistent field (VSCF) calculations taking into account pairwise interactions between the normal modes. The key results are: (1) Prediction of anharmonic vibrational frequencies on an MP2 ab initio potential energy surface show excellent agreement with experiment and outstanding improvement over the harmonic frequencies. For example, the ab initio calculated anharmonic frequency for (ImH+)(H2O)N2 exhibits an overall average percentage error of 0.6% from experiment. (2) Anharmonic vibrational frequencies calculated on a semiempirical potential energy surface fitted to ab initio harmonic data represents spectroscopy well, particularly for water complexes. As an example, anharmonic frequencies for (ImH+)H2O and (ImH+)(H2O)2 show an overall average deviation of 1.02% and 1.05% from experiment, respectively. This agreement between theory and experiment also supports the validity and use of the pairwise approximation used in the calculations. (3) Anharmonic coupling due to hydration effects is found to significantly reduce the vibrational frequencies for the NH stretch modes. The frequency of the NH stretch is observed to increase with the removal of a water molecule or replacement of water with N2. This result also indicates the ability of the VSCF method to predict accurate frequencies in a matrix environment. The calculation provides insights into the nature of anharmonic effects in the potential surface. Analysis of percentage anharmoncity in neutral Im and ImH+ shows a higher percentage anharmonicity in the NH and CH stretch modes of neutral Im. Also, we observe that anharmonicity in the NH stretch modes of ImH+ have some contribution from coupling effects, while that of neutral Im has no contribution whatsoever from mode-mode coupling. It is concluded that the incorporation of anharmonic effects in the calculation brings theory and experiment into much closer agreement for these systems.

Infrared Laser Spectroscopy of Uracil and Thymine in Helium Nanodroplets: Vibrational Transition Moment Angle Study

Vibrational spectra are reported in the N-H stretching region for uracil and thymine monomers in helium nanodroplets. Each monomer shows only a single isomer, the global minimum, in agreement with previous experimental and theoretical studies. The assignment of the infrared vibrational bands in the spectra is aided by the measurement of the corresponding vibrational transition moment angles (VTMAs) and ab initio frequency calculations. The ambiguity in the VTMA assignment of the N3H band for the uracil monomer is explained by the presence of dimer bands, which are overlapped with the monomer band.

Dissociative electron attachment to hydrated single DNA strands

The present experiments concern electron interactions with a film of short single strands of DNA covered by 3 monolayers of water, which corresponds to 5.25 water molecules per nucleotide. We report on the desorption of H{-}, O{-}, OH{-} from this target induced by 3-20 eV electrons. Below 15 eV, these anions emanate principally from a new type of dissociative core-excited transient anions formed via electron capture by a DNA- H2O complex. A smaller portion of the H{-} desorption signal arises from weakly bonded H2O molecules. The overall anion yield from DNA is increased by a factor of 1.6 owing to the presence of water.

Resonant infrared multiphoton dissociation spectroscopy of gas-phase protonated peptides. Experiments and Car–Parrinello dynamics at 300 K

The gas-phase structures of protonated peptides are studied by means of resonant infrared multiphoton dissociation spectroscopy (R-IRMPD) performed with a free electron laser. The peptide structures and protonation sites are obtained through comparison between experimental IR spectra and their prediction from quantum chemistry calculations. Two different analyses are conducted. It is first supposed that only well-defined conformations, sufficiently populated according to a Boltzmann distribution, contribute to the observed spectra. On the contrary, DFT-based Car-Parrinello molecular dynamics simulations show that at 300 K protonated peptides no longer possess well-defined structures, but rather dynamically explore the set of conformations considered in the first conventional approach.

Formation and properties of metal clusters isolated in helium droplets

The unique conditions forming atomic and molecular complexes and clusters using superfluid helium nanodroplets have opened up an innovative route for studying the physical and chemical properties of matter on the nanoscale. This review summarizes the specific characteristics of the formation of atomic clusters partly generated far from equilibrium in the helium environment. Special emphasis is on the optical response, electronic properties as well as dynamical processes which are mostly affected by the surrounding quantum matrix. Experiments include the optical induced response of isolated cluster systems in helium under quite different excitation conditions ranging from the linear regime up to the violent interaction with a strong laser field leading to Coulomb explosion and the generation of highly charged atomic fragments. The variety of results on the outstanding properties in the quantum size regime highlights the peculiar capabilities of helium nanodroplet isolation spectroscopy.

Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.

Infrared Laser Spectroscopy of Imidazole Complexes in Helium Nanodroplets: Monomer, Dimer, and Binary Water Complexes

Infrared laser spectroscopy has been used to characterize imidazole (IM), imidazole dimer (IMD), and imidazole-water (IMW) binary systems formed in helium nanodroplets. The experimental results are compared with ab initio calculations reported here. Vibrational transition moment angles provide conclusive assignments for the various complexes studied here, including IM, one isomer of IMD, and two isomers of the IMW binary complexes.