Water-Induced Folding of 1,7-Diammoniumheptane

A Computational Analysis of the Proton Affinity and the Hydration of TEMPO and Its Piperidine Analogs

The study investigated the impact of protonation and hydration on the geometry of nitroxide radicals using B3LYP and M06-2X methods. Results indicated that TEMPO exhibited the highest proton affinity in comparison to TEMPOL and TEMPONE. Two pathways contribute to hydrated protonated molecules. TEMPO shows lower first enthalpies of hydration (ΔH1-M), indicating stronger H-bonding interactions, while TEMPONE shows higher values, indicating weaker interactions with H2O. Solvent effects affect charge distribution by decreasing their atomic charge. Spin density (SD) is primarily concentrated in the NO segment, with minimal water molecule contamination. Protonation increases SD on N-atom, while hydration causes a more pronounced redistribution for water molecules. The stability of the dipolar structure (>N⋅+-O-) is evident in SD redistributions. The frontier molecular orbital (FMO) analysis of TEMPONE reveals a minimum EHOMO-LUMO gap (EH-L), enhancing the piperidine ring's reactivity. TEMPO is the most nucleophilic species, while TEMPONE exhibits strong electrophilicity. Transitioning from NO radicals to protonated forms increases the EH-L gap, indicating protonation stabilizes FMOs. Increased water molecules make the molecule less reactive, while increasing hydration decreases this energy gap, making the molecule more reactive. A smaller EH-L gap indicates the compound becomes softer and more prone to electron density and reactivity changes.

Probing microhydration-induced effects on carbonyl compounds

Characterizing the microhydration of organic molecules is a crucial step in understanding many phenomena relevant to atmospheric, biological, and industrial applications. However, its precise experimental and theoretical description remains a challenge. For four organic solutes containing a CO bond, and included in the recent HyDRA challenge [T. L. Fischer, M. Bödecker, A. Zehnacker-Rentien, R. A. Mata and M. A. Suhm, Phys. Chem. Chem. Phys., 2022, 24, 11442-11454.], we performed a detailed study of different monohydrate isomers and their properties; these were cyclooctanone (CON), 1,3-dimethyl-2-imidazolidinon (DMI), methyl lactate (MLA), and 2,2,2-trifluoroacetophenone (TPH) molecules. As reported in the literature, the O-H elongation shift of the water molecule appears to be a good candidate for characterizing complexation-induced effects. We also show that CO elongation shift and UV-vis spectroscopy can be successfully used for these purposes. Besides, we present a comparative analysis of the strengths of non-covalent interactions within these monohydrated complexes based on interpretative tools of quantum chemistry, including topological analysis of electron density (ρ), topological analysis of electron pairing function, and analysis of the core-valence bifurcation index (CVBI), which exhibits a close linear dependency on ρ. Accordingly, a classification of intermolecular water-solute interactions is proposed.

A Rule for Response Sensitivity of Structural-Color Photonic Colloids

To mimic natural photonic crystals having color regulation capacities dynamically responsive to the surrounding environment, periodic assembly structures have been widely constructed with response materials. Beyond monocomponent materials with stimulus responses, binary and multiphase systems generally offer extended color space and complex functionality. Constructing a rule for predicting response sensitivity can provide great benefits for the tailored design of intelligently responsive photonic materials. Here, we elucidate mathematical relationships between the response sensitivity of dynamically structural-color changes and the location distances of photonic co-phases in three-dimensional Hansen space that can empirically express the strength of their interaction forces, including dispersion force, polarity force, and hydrogen bonding. Such an empirical rule is proven to be applicable for some typical alcohols, acetone, and acetic acid regardless of their molecular structures, as verified by angle resolution spectroscopy, in situ infrared spectroscopy, and molecular simulation. The theoretical method we demonstrate provides rational access to custom-designed responsive structural coloration.

Investigation of Charge-State-Dependent Compaction of Protein Ions with Native Ion Mobility-Mass Spectrometry and Theory

The precise relationship between native gas-phase protein ion structure, charge, desolvation, and activation remains elusive. Much evidence supports the Charge Residue Model for native protein ions formed by electrospray ionization, but scaling laws derived from it relate only to overall ion size. Closer examination of drift tube CCSs across individual native protein ion charge state distributions (CSDs) reveals deviations from global trends. To investigate whether this is due to structure variation across CSDs or contributions of long-range charge-dipole interactions, we performed in vacuo force field molecular dynamics (MD) simulations of multiple charge conformers of three proteins representing a variety of physical and structural features: β-lactoglobulin, concanavalin A, and glutamate dehydrogenase. Results from these simulated ions indicate subtle structure variation across their native CSDs, although effects of these structural differences and long-range charge-dependent interactions on CCS are small. The structure and CCS of smaller proteins may be more sensitive to charge due to their low surface-to-volume ratios and reduced capacity to compact. Secondary and higher order structure from condensed-phase structures is largely retained in these simulations, supporting the use of the term "native-like" to describe results from native ion mobility-mass spectrometry experiments, although, notably, the most compact structure can be the most different from the condensed-phase structure. Collapse of surface side chains to self-solvate through formation of new hydrogen bonds is a major feature of gas-phase compaction and likely occurs during the desolvation process. Results from these MD simulations provide new insight into the relationship of gas-phase protein ion structure, charge, and CCS.

Effects of Hydration on the Conformational Behavior of Flexible Molecules with Two Charge Centers

The hydration behavior of alkyl-diammonium di-cations and alkyl-dicarboxylate di-anions, of varying alkyl chain length, was examined using basin-hopping (BH) global optimization techniques. For every di-ion investigated, a conformational transition from linear to folded is observed at a critical hydration number, n*, specific to each di-ion. A stepwise hydration study has been undertaken for alkyl-dicarboxylate di-anions in finite water clusters containing 1-12 water molecules, and low-energy structures have been examined for larger water clusters. An even number of carbons in the alkyl chain gives rise to more stable conformations in unhydrated, implicitly solvated, and explicitly solvated conditions. This work provides valuable information on how the hydration of ammonium and carboxylate ions influence larger biomolecules' conformations.

Effect of Basicity and Structure on the Hydration of Protonated Molecules, Proton-Bound Dimer and Cluster Formation: An Ion Mobility-Time of Flight Mass Spectrometry and Theoretical Study

Protonation, hydration, and cluster formation of ammonia, formaldehyde, formic acid, acetone, butanone, 2-ocatanone, 2-nonanone, acetophenone, ethanol, pyridine, and its derivatives were studied by IMS-TOFMS technique equipped with a corona discharge ion source. It was found that tendency of the protonated molecules, MH⁺, to participate in hydration or cluster formation depends on the basicity of M. The molecules with higher basicity were hydrated less than those with lower basicity. The mass spectra of the low basic molecules such as formaldehyde exhibited larger clusters of M_nH⁺(H₂O)_n, while for compounds with high basicity such as pyridine, only MH⁺ and MH⁺M peaks were observed. The results of DFT calculations show that enthalpies of hydrations and cluster formation decrease as basicities of the molecules increases. Using comparison of mass spectra of formic acid, formaldehyde, and ethanol, effect of structure on the cluster formation was also investigated. Formation of symmetric (MH⁺M) and asymmetric proton-bound dimers (MH⁺N) was studied by ion mobility and mass spectrometry techniques. Both theoretical and experimental results show that asymmetric dimers are formed more easily between molecules (M and N) with comparable basicity. As the basicity difference between M and N increases, the enthalpy of MH⁺N formation decreases.

Hydration of Guanidinium Ions: An Experimental Search for Like-Charged Ion Pairs

Guanidinium ions (GdmH⁺) are reported to form stable complexes (GdmH⁺/GdmH⁺) in aqueous solution despite strong repulsive interactions between the like-charged centers. These complexes are thought to play important roles in protein folding, membrane penetration, and formation of protein dimers. Although GdmH⁺ ions are weakly hydrated, semiempirical calculations provide evidence that these like-charged complexes are stabilized by water molecules, which serve important structural and energetic roles. Specifically, water molecules bridge between the GdmH⁺ ions of GdmH⁺/GdmH⁺ complexes as well as complexes involving the guanidinium side chains of arginine. Potential biological significances of like-charged complexes have been largely confirmed by ab initio molecular dynamics simulations and indirect experimental evidence. We report cryo-ion mobility-mass spectrometry results for the GdmH⁺/GdmH⁺ ion pair confined in a nanodroplet- the first direct experimental observation of this like-charged complex. A second like-charged complex, described as a water-mediated complex involving GdmH⁺ and H₃O⁺, was also observed.

Probing the geometry reorganization from solution to gas-phase in putrescine derivatives by IRMPD, 1H-NMR and theoretical calculations

Geometry reorganization of ESI formed ions are demonstrated and explicit calculations of the solution phase are shown to be relevant.

Pulsed Nano-ESI Atmospheric-Pressure Ion Mobility Mass Spectrometry with Enhanced Ion Sampling

Ion mobility-mass spectrometry (IM-MS) has gained considerable attention for detection of clusters and weakly bound species created by electrospray ionization (ESI). Atmospheric-pressure (AP) IM-MS offers an advantage in these studies compared to its low-pressure counterpart, owing to soft introduction of ions into the mobility cell with minimal ion activation. Here, we report new approaches to improve the sensitivity and soft ion introduction in AP-IM-MS. For the former, we demonstrate enhanced aerodynamic sampling of ions from the mobility cell into the MS using pulsed-field sampling. In this approach, ions are driven toward the MS, and the field is shut down once the ions reach the vicinity of the MS inlet orifice. The pulsed-field operation provides arrival times without the need for an exit ion gate in the mobility cell and leads to improvements in sensitivity of up to 1 order of magnitude. For soft ion generation, we report a pulsed nano-ESI source to introduce a packet of ions into the room-temperature mobility cell without induced desolvation. Further, we demonstrate the application of the pulsed nano-ESI AP-IM-MS with enhanced ion sampling for detection of solvent clusters of amines and peptide aggregates.

Water-Mediated Dimerization of Ubiquitin Ions Captured by Cryogenic Ion Mobility-Mass Spectrometry

The dynamics, structures, and functions of most biological molecules are strongly influenced by the nature of the peptide's or protein's interaction with water. Here, cryogenic ion mobility-mass spectrometry studies of ubiquitin have directly captured a water-mediated protein-protein binding event involving hydrated, noncovalently bound dimer ions in solution, and this interaction has potential relevance to one of the most important protein-protein interactions in nature. As solvent is removed, dimer ions, viz. [2 M + 14H](14+), can be stabilized by only a few attached water molecules prior to dissociation into individual monomeric ions. The hydrophobic patch of ubiquitin formed by the side chains of Leu-8, Ile-44, and Val-70 meet all the necessary conditions for a protein-protein binding "hot spot," including the requirement for occlusion of water to nearby hydrophilic sites, and it is suggested that this interaction is responsible for formation of the hydrated noncovalent ubiquitin dimer.

Microhydration of Protonated Nα-Acetylhistidine: A Theoretical Approach

Extensive exploration of the potential energy surfaces of protonated Nα-acetylhistidine hydrated by 0-3 molecules of water was performed. The methodology combined hierarchical and genealogical (Darwin family tree) approaches using polarizable AMOEBA force field and M06 functional. It is demonstrated that this mixed approach allows recovering a larger number of conformers than the number recovered by using any one of the two methods alone. Hydration enthalpies of protonated Nα-acetylhistidine and of model compounds have been computed using higher theoretical methods, up to the G4MP2 procedure. Excellent agreement with experiment is observed for successive hydration of methylamonium and imidazolium cations using MP2/6-311++G(2d,2p)//M06/6-311++G(d,p) and G4MP2 methods, thereby validating the theory levels used for hydrated protonated Nα-acetylhistidine. It is found that the first hydration enthalpy of protonated Nα-acetylhistidine is ca. 10 kJ mol(-1) lower than that of imidazolium, a result explained by the local environment of the positively charged imidazolium moiety.

Diphenylalanine self assembly: novel ion mobility methods showing the essential role of water

The mechanism and driving forces behind the formation of diphenylalanine (FF) nanotubes have attracted much attention in the past decades. The hollow structure of the nanotubes suggests a role for water during the self-assembly process. Here, we use novel ion-mobility mass spectrometry methods to probe the early oligomers formed by diphenylalanine peptides. Interestingly, water-bound oligomers are observed in nano-electrospray ionization (ESI) mass spectra in the absence of bulk solvent. In addition, ligated water clusters transit the ion mobility cell but (often) dissociate before detection. These water molecules are shown to be essential for the formation of diphenylalanine oligomers larger than the dimer. The ligated water molecules exist in the solvent free environment either as neutral water or as protonated water clusters, depending on the composition of solvent from which they are sprayed. Water adduction helps stabilize conformers that are otherwise energetically unstable ultimately leading to the assembly of FF nanotubes.

Hydration of gaseous m-aminobenzoic acid: ionic vs neutral hydrogen bonding and water bridges

Hydration of a protonated amine and a neutral carboxylic acid were investigated for protonated m-aminobenzoic acid (MABAH(+)) with up to 15 water molecules attached using infrared photodissociation spectroscopy, laser-induced dissociation kinetics, and computational chemistry. A free COO-H stretch in the spectra of MABAH(+)·(H2O)1-5 indicates that water does not bind to the carboxylic acid H atom. This band is absent in the spectrum of MABAH(+) with six or more water molecules attached, and there is a hydrogen-bonded (HB) COO-H stretch indicating that water hydrogen bonds to the carboxylic acid H atom for these larger clusters. Photodissociation kinetic data for MABAH(+)·(H2O)6 indicate that greater than 74 ± 13% of the ion population consists of the HB COO-H isomer, consistent with this isomer being ≥0.5 kJ mol(-1) lower in energy than isomers where the carboxylic acid H atom does not donate a hydrogen bond. Calculations at the B3LYP/6-31+G** and MP2/6-31+G**//B3LYP/6-31+G** levels of theory indicate that this energy difference is 3-5 kJ mol(-1), in agreement with the experimental results. Lower effective ion heating rates, either by attenuation of the laser power or irradiation of the ions at a lower frequency, result in more time for interconversion between the free and HB COO-H isomers. These data suggest that the barrier to dissociation for the free COO-H isomer is less than that for the HB COO-H isomer but greater than the barrier for interconversion between the two isomers. These results show the competition between hydration of a primary protonated amine vs that of a neutral carboxylic acid and the effect of water bridging between the two functional groups, which provide valuable insight into the hydration of protonated amino acids and establish rigorous benchmarks for theoretical modeling of water-biomolecule interactions.

Host-guest chemistry in the gas phase: complex formation of cucurbit[6]uril with proton-bound water dimer

The hydration of cucurbit[6]uril (CB[6]) in the gas phase is investigated using electrospray ionization traveling wave ion mobility mass spectrometry (ESI-TWIM-MS). Highly abundant dihydrated and tetrahydrated species of diprotonated CB[6] are found in the ESI-TWIM-MS spectrum. The hydration patterns of the CB[6] ion and the dissociation patterns of the hydrated CB[6] ion indicate that two water molecules are bound to each other, forming a water dimer in the CB[6] complex. Ion mobility studies combined with the structures calculated by density functional theory suggest that the proton-bound water dimer is present as a Zundel-like structure in the CB[6] portal, forming a hydrogen bond network with carbonyl groups of the CB[6]. When a large guest molecule is bound to a CB[6] portal, water molecules cannot bind to the portal. In addition, the strong binding energy of the water dimer blocks the portal, hindering the insertion of the long alkyl chain of the guest molecule into the CB[6] cavity. With small alkali metal cations, such as Li(+) and Na(+), a single water molecule interacts with the CB[6] portal, forming hydrogen bonds with the carbonyl groups of CB[6]. A highly stable Zundel-like structure of the proton-bound water dimer or a metal-bound water molecule at the CB[6] portal is suggested as an initial hydration process for CB[6], which is only dissolved in aqueous solution with acid or alkali metal ions.

Solvent-mediated folding of dicarboxylate dianions: aliphatic chain length dependence and origin of the IR intensity quenching

We combine infrared photodissociation spectroscopy with quantum chemical calculations to characterize the hydration behavior of microsolvated dicarboxylate dianions, (CH2)m(COO(-))2·(H2O)n, as a function of the aliphatic chain length m. We find evidence for solvent-mediated folding transitions, signaled by the intensity quenching of the symmetric carboxylate stretching modes, for all three species studied (m = 2, 4, 8). The number of water molecules required to induce folding increases monotonically with the chain length and is n = 9-12, n = 13, and n = 18-19 for succinate (m = 2), adipate (m = 4), and sebacate (m = 8), respectively. In the special case of succinate, the structural transition is complicated by the possibility of bridging water molecules that bind to both carboxylates with merely minimal chain deformation. On the basis of vibrational calculations on a set of model systems, we identify the factors responsible for intensity quenching. In particular, we find that the effect of hydrogen bonds on the carboxylate stretching mode intensities is strongly orientation dependent.

Locating protonated amines in clathrates

The structures and inherent stabilities of hydrated, protonated ammonia, select protonated primary, secondary, and tertiary amines as well as tetramethylammonium with 19-21 water molecules were investigated using infrared photodissociation (IRPD) spectroscopy and blackbody infrared radiative dissociation (BIRD) at 133 K. Magic number clusters (MNCs) with 20 water molecules were observed for all ions except tetramethylammonium, and the BIRD results indicate that these clusters have stable structures, which are relatively unaffected by addition of one water molecule but are disrupted in clusters with one less water molecule. IRPD spectra in the water free O-H stretch region are consistent with clathrate structures for the MNCs with 20 water molecules, whereas nonclathrate structures are indicated for tetramethylammonium as well as ions at the other cluster sizes. The locations of protonated ammonia and the protonated primary amines either in the interior or at the surface of a clathrate were determined by comparing IRPD spectra of these ions to those of reference ions; Rb(+) and protonated tert-butylammonia with 20 water molecules were used as references for an ion in the interior and at the surface of a clathrate, respectively. These results indicate that protonated ammonia is in the interior of the clathrate, whereas protonated methyl- and n-heptylamine are at the surface. Calculations suggest that the number of hydrogen bonds in these clusters does not directly correlate with structural stability, indicating that both the number and orientation of the hydrogen bonds are important. These experimental results should serve as benchmarks for computational studies aimed at elucidating ion effects on the hydrogen-bonding network of water molecules and the surface activity of ions.

The Ionic Hydrogen/Deuterium Bonds between Diammoniumalkane Dications and Halide Anions

Halide-anion binding to 1,12-dodecanediammonium, tetramethyl-1,12-dodecanediammmonium, and tetramethyl-1,7-heptanediammonium has been investigated with infrared multiple-photon dissociation (IRMPD) spectroscopy in the 1000-2250 cm^-1 spectral region and with theory. Both charged ammonium groups in these diammonium compounds interact with the halide anion resulting in an ionic hydrogen bond (IHB) stretching frequency outside of the spectral frequency range that can be measured with the free-electron laser (FEL). This frequency is shifted into the spectral range upon exchanging all of the labile hydrogen atoms with deuterium atoms, thus making measurement of the ionic deuterium bond (IDB) stretching frequency possible. The IDB stretching frequency shifts to higher values with increasing halide-anion size, methylation of the ammonium groups, and alkane chain length, consistent with the halide-anion-deuterium bond strength decreasing with decreasing gas-phase basicity of the halide anion and the increasing gas-phase basicity of the ammonium groups. The IDB stretching frequency also depends on the alkane chain length owing to constraints on the angle of the bonds between the halide anion and the two ammonium groups. There are additional bands in the IDB stretching feature in the IRMPD spectra, which are attributed to Fermi resonances and arise from coupling with overtone or combination bands that can be identified from theory and depend on the halide-anion identity and alkane chain length.