Perspective: intrinsic interactions of metal ions with biological molecules as studied by threshold collision-induced dissociation and infrared multiple photon dissociation

In this perspective, gas-phase studies of group 1 monocations and group 12 dications with amino acids and small peptides are highlighted. Although the focus is on two experimental techniques, threshold collision-induced dissociation and infrared multiple photon dissociation action spectroscopy, these methods as well as complementary approaches are summarized. The synergistic interplay with theory, made particularly powerful by the small sizes of the systems explored and the absence of solvent and support, is also elucidated. Importantly, these gas-phase methods permit quantitative insight into the structures and thermodynamics of metal cations interacting with biological molecules. Periodic trends in how these interactions vary as the metal cations get heavier are discussed as are quantitative trends with changes in the amino acid side chain and effects of hydration. Such trends allow these results to transcend the limitations associated with the biomimetic model systems.

Intermolecular hydrogen bonding in DNA base pairs interacting with different numbers of bare and hydrated Li+: NBO, QTAIM, and computational spectroscopic studies

In this study, the effect of different numbers of Li+ interacting with various sites of DNA base pairs (adenine-thymine (AT) and cytosine-guanine (GC)) on the base pair structures, the strength of hydrogen bonding between the bases, and spectroscopic properties (IR and absorption spectra) of the base pairs was investigated. Two quantum computational analyses, the natural bonding orbitals (NBO) and the quantum theory of atoms in molecules (QTAIM), were used to follow the change in the strength of hydrogen bonds between the bases in each pair. The type of base pair's site interacting with Li+ showed different effects on the change in the strength of the hydrogen bonds between the bases. The IR and absorption spectra of the lithiated base pairs were calculated and compared with those of bare base pairs. This comparison provided the changes in the spectra as a fingerprint for the structural identification of different lithiated base pairs. Also, the determination of the change in the strength of hydrogen bonds in the lithiated base pairs compared to their bare base pairs. In the other part of this study, the effect of the hydration of the attached Li+ in the structure of lithiated base pairs on the strength of their hydrogen bonds and spectra was investigated.

Generation of an accurate CCSD(T)/CBS data set and assessment of DFT methods for the binding strengths of group I metal-nucleic acid complexes

Accurate information about interactions between group I metals and nucleic acids is required to understand the roles these metals play in basic cellular functions, disease progression, and pharmaceuticals, as well as to aid the design of new energy storage materials and nucleic acid sensors that target metal contaminants, among other applications. From this perspective, this work generates a complete CCSD(T)/CBS data set of the binding energies for 64 complexes involving each group I metal (Li+, Na+, K+, Rb+, or Cs+) directly coordinated to various sites in each nucleic acid component (A, C, G, T, U, or dimethylphosphate). This data have otherwise been challenging to determine experimentally, with highly accurate information missing for many group I metal-nucleic acid combinations and no data available for the (charged) phosphate moiety. Subsequently, the performance of 61 DFT methods in combination with def2-TZVPP is tested against the newly generated CCSD(T)/CBS reference values. Detailed analysis of the results reveals that functional performance is dependent on the identity of the metal (with increased errors as group I is descended) and nucleic acid binding site (with larger errors for select purine coordination sites). Over all complexes considered, the best methods include the mPW2-PLYP double-hybrid and ωB97M-V RSH functionals (≤1.6% MPE; <1.0 kcal/mol MUE). If more computationally efficient approaches are required, the TPSS and revTPSS local meta-GGA functionals are reasonable alternatives (≤2.0% MPE; <1.0 kcal/mol MUE). Inclusion of counterpoise corrections to account for basis set superposition error only marginally improves the computed binding energies, suggesting that these corrections can be neglected with little loss in accuracy when using larger models that are necessary for describing biosystems and biomaterials. Overall, the most accurate functionals identified in this study will permit future works geared towards uncovering the impact of group I metals on the environment and human biology, designing new ways to selectively sense harmful metals, engineering modern biomaterials, and developing improved computational methods to more broadly study group I metal-nucleic acid interactions.

A vibrational spectroscopic and computational study of gaseous protonated and alkali metal cationized G-C base pairs

The structures and properties of metal cationized complexes of 9-ethylguanine (9eG) and 1-methylcytosine (1mC), (9eG:1mC)M⁺, where M⁺ = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ as well as the protonated complex, (9eG:1mC)H⁺, have been studied using a combination of IRMPD spectroscopy and computational methods. For (9eG:1mC)H⁺, the dominant structure is a Hoogsteen type complex with the proton covalently bound to N3 of 1mC despite this being the third best protonation site of the two bases; based on proton affinities N7 of 9eG should be protonated. However, this structural oddity can be explained considering both the number of hydrogen bonds that can be formed when N3 of 1mC is protonated as well as the strong ion-induced dipole interaction that exists between an N3 protonated 1mC and 9eG due to the higher polarizability of 9eG. The anomalous dissociation of (9eG:1mC)H⁺, forming much more (1mC)H⁺ than would be predicted based on the computed thermochemistry, can be explained as being due to the structural oddity of the protonation site and that the barrier to proton transfer from N3 of 1mC to N7 of 9eG grows dramatically as the base pair begins to dissociate. For the (9eG:1mC)M⁺; M = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ complexes, single unique structures could not be assigned. However, the experimental spectra were consistent with the computed spectra. For (9eG:1mC)Li⁺, the lowest energy structure is one in which Li⁺ is bound to O6 of 9eG and both O2 and N3 of 1mC; there is also an interbase hydrogen bond from the amine of 1mC to N7 of 9eG. For Na⁺, K⁺, and Rb⁺, similar binding of the metal cation to 1mC is calculated but, unlike Li⁺, the lowest energy structure is one in which the metal cation is bound to N7 of 9eG; there is also an interbase hydrogen bond between the amine of 1mC and the carbonyl of 9eG. The lowest energy structure for the Cs complex is the Watson-Crick type base pairing with Cs⁺ binding only to 9eG through O6 and N7 and with three hydrogen bonds between 9eG and 1mC. It also interesting to note that the Watson-Crick base pairing structure gets lower in Gibbs energy relative to the lowest energy complexes as the metal gets larger. This indicates that the smaller, more densely charged cations have a greater propensity to interfere with Watson-Crick base pairing than do the larger, less densely charged metal cations.

Structures and Infrared Spectra of [M(CO2)7]+ (M = V, Cr, and Mn) Complexes

Gas-phase infrared photodissociation spectra of [V(CO₂) _n]⁺ complexes revealed three new vibrational bands at 1140, 1800, and 3008 cm^-1 at n = 7, the features of which are retained in the larger clusters (Ricks, A. M.; Brathwaite, A. D.; Duncan, M. A. J. Phys. Chem. A 2013, 117, 11490-11498). However, structural assignment of this intriguing feature remains open. Herein, quantum chemical calculations on [V(CO₂)₇]⁺ were carried out to identify the structure of the low-lying isomers and to assign the observed spectral features. The comparison of calculated infrared spectra of [V(CO₂)₇]⁺ with experimental infrared spectra identified the formation of a bent CO₂^- species, suggesting the ligand-induced activation of CO₂ by the vanadium cation. The structures and infrared spectra of [Cr(CO₂)₇]⁺ and [Mn(CO₂)₇]⁺ were also predicted and discussed.

Understanding proton capture and cation-induced dimerization of [Ag29(BDT)12]3−clusters by ion mobility mass spectrometry

We present a unique reaction of [Ag₂₉(BDT)₁₂]³⁻cluster with protons and dimerization of the cluster induced by alkali metal ions.

Photoelectron spectroscopy of solvated dicarboxylate and alkali metal ion clusters, M+[O2C(CH2)2CO2]2− [H2O]n (M = Na, K; n = 1–6)

We present results of combined experimental photoelectron spectroscopy and theoretical modeling studies of solvated dicarboxylate species (⁻O₂C(CH₂)₂CO₂⁻) in complex with Na⁺ and K⁺ metal cations.

Directionality of Cation/Molecule Bonding in Lewis Bases Containing the Carbonyl Group

Relationship between the C═O-X⁺ (X = H, Li, Na, K, Al, Cu) angle and covalent characteristic of the X⁺-M (M = CH₂O, CH₃CHO, acetone, imidazol-2-one (C₂H₂N₂O), cytosine, γ-butyrolactone) was investigated, theoretically. The calculated electron densities ρ at the bond critical points revealed that the covalency of the M-X⁺ interaction depended on the nature of the cation and varied as H⁺ > Cu⁺ > Al⁺ > Li⁺ > Na⁺ > K⁺. The alkali cations tended to participate in electrostatic interactions and aligned with the direction of the molecule dipole or local dipole of C═O group to form linear C═O-X geometries. Because of overlapping with lone-pair electrons of the sp² carbonyl oxygen, the H⁺ and Cu⁺ formed a bent C═O-X angle. Al⁺ displayed an intermediate behavior; the C═O-Al angle was 180° in [CH₂O/Al]⁺ (mainly electrostatic), but when the angle was bent (146°) under the effect of local dipole of an adjacent imine group in cytosine, the covalency of the CO-Al⁺ interaction increased. The C═O-X angles in M/X⁺ adduct ions were scanned in different O-X bond lengths. It was found that the most favorable C═O-X angle depended on the O-X bond length. This dependency was attributed to variation of covalent and electrostatic contributions with O-X distance. In addition, the structures of [CH₂S/X]⁺ and [CH₂Se/X]⁺ were studied, and only bent C═S-X and C═Se-X angles were obtained for all cations, although the dipole vectors of CH₂S and CH₂Se coincide with the C═S and C═Se bonds. The bending of the C═S-X and C═Se-X angles was attributed to the covalent characteristic of S-X and Se-X interactions due to high polarizability of S and Se atoms.

Cationic Noncovalent Interactions: Energetics and Periodic Trends

In this review, noncovalent interactions of ions with neutral molecules are discussed. After defining the scope of the article, which excludes anionic and most protonated systems, methods associated with measuring thermodynamic information for such systems are briefly recounted. An extensive set of tables detailing available thermodynamic information for the noncovalent interactions of metal cations with a host of ligands is provided. Ligands include small molecules (H2, NH3, CO, CS, H2O, CH3CN, and others), organic ligands (O- and N-donors, crown ethers and related molecules, MALDI matrix molecules), π-ligands (alkenes, alkynes, benzene, and substituted benzenes), miscellaneous inorganic ligands, and biological systems (amino acids, peptides, sugars, nucleobases, nucleosides, and nucleotides). Hydration of metalated biological systems is also included along with selected proton-based systems: 18-crown-6 polyether with protonated peptides and base-pairing energies of nucleobases. In all cases, the literature thermochemistry is evaluated and, in many cases, reanchored or adjusted to 0 K bond dissociation energies. Trends in these values are discussed and related to a variety of simple molecular concepts.

Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals

The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.

Capturing Transient Endoperoxide in the Singlet Oxygen Oxidation of Guanine

The chemistry of singlet O2 toward the guanine base of DNA is highly relevant to DNA lesion, mutation, cell death, and pathological conditions. This oxidative damage is initiated by the formation of a transient endoperoxide through the Diels-Alder cycloaddition of singlet O2 to the guanine imidazole ring. However, no endoperoxide formation was directly detected in native guanine or guanosine, even at -100 °C. Herein, gas-phase ion-molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with singlet O2 at ambient temperature. Corroborated by results from potential energy surface exploration, kinetic modeling, and dynamics simulations, various aspects of endoperoxide formation and transformation (including its dependence on guanine ionization and hydration states, as well as on collision energy) were determined. This work has pieced together reaction mechanisms, kinetics, and dynamics data concerning the early stage of singlet O2 induced guanine oxidation, which is missing from conventional condensed-phase studies.

Probing the early stages of solvation of cis-pinate dianions by water, acetonitrile, and methanol: a photoelectron spectroscopy and theoretical study

Photoelectron spectroscopy and theoretical studies indicate the coexistence of symmetric and asymmetric solvated clusters for cis-pinate dianions.

Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif

(CCG)(n)•(CGG)(n) trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)(n)•(CGG)(n) repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C(+)•C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo- and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.