Structure Of Condensed Phases Research Articles

Diserinol Isophthalamide: A Novel Reagent for Complexation with Biomolecular Anions in Electrospray Ionization Mass Spectrometry

Transferring biomolecules from solution to vacuum facilitates a detailed analysis of molecular structure and dynamics by isolating molecules of interest from a complex environment. However, inherent in the ion desolvation process is the loss of solvent hydrogen bonding partners, which are critical for the stability of a condensed-phase structure. Thus, transfer of ions to vacuum can favor structural rearrangement, especially near solvent-accessible charge sites, which tend to adopt intramolecular hydrogen bonding motifs in the absence of solvent. Complexation of monoalkylammonium moieties (e.g., lysine side chains) with crown ethers such as 18-crown-6 can disfavor structural rearrangement of protonated sites, but no equivalent ligand has been investigated for deprotonated groups. Herein we describe diserinol isophthalamide (DIP), a novel reagent for the gas-phase complexation of anionic moieties within biomolecules. Complexation is observed to the C-terminus or side chains of the small model peptides GD, GE, GG, DF-OMe, VYV, YGGFL, and EYMPME in electrospray ionization mass spectrometry (ESI-MS) studies. In addition, complexation is observed with the phosphate and carboxylate moieities of phosphoserine and phosphotyrosine. DIP performs favorably in comparison to an existing anion recognition reagent, 1,1'-(1,2-phenylene)bis(3-phenylurea), that exhibits moderate carboxylate binding in organic solvent. This improved performance in ESI-MS experiments is attributed to reduced steric constraints to complexation with carboxylate groups of larger molecules. Overall, diserinol isophthalamide is an effective complexation reagent that can be applied in future work to study retention of solution-phase structure, investigate intrinsic molecular properties, and examine solvation effects.

Tunable J-type aggregation of silicon phthalocyanines in a surface-anchored metal-organic framework thin film.

Organic chromophores and semiconductors, like anthracene, pentacene, perylene, and porphyrin, are prone to aggregation, and their packing in the solid state is often hard to predict and difficult to control. As the condensed phase structures of these chromophores and semiconductors are of crucial importance for their optoelectronic functionality, strategies to control their assembly and provide new structural motifs are important. One such approach uses metal-organic frameworks (MOFs); the organic chromophore is converted into a linker and connected by metal ions or nodes. The spatial arrangement of the organic linkers can be well-defined in a MOF, and hence optoelectronic functions can be adjusted accordingly. We have used such a strategy to assemble a phthalocyanine chromophore and illustrated that the electronic inter-phthalocyanine coupling can be rationally tuned by introducing bulky side grounds to increase steric hindrance. We have designed new phthalocyanine linkers and using a layer-by-layer liquid-phase epitaxy strategy thin films of phthalocyanine-based MOFs have been fabricated and their photophysical properties explored. It was found that increasing the steric hindrance around the phthalocyanine reduced the effect of J-aggregation in the thin film structures.

Electrofreezing of Liquid Ammonia.

Here we prove that, in addition to temperature and pressure, another important thermodynamic variable permits the exploration of the phase diagram of ammonia: the electric field. By means of (path integral) ab initio molecular dynamics simulations, we predict that, upon applying intense electric fields on ammonia, the electrofreezing phenomenon occurs, leading the liquid toward a novel ferroelectric solid phase. This study proves that electric fields can generally be exploited as the access key to otherwise-unreachable regions in phase diagrams, unveiling the existence of new condensed-phase structures. Furthermore, the reported findings have manifold practical implications, from the safe storage and transportation of ammonia to the understanding of the solid structures this compound forms in planetary contexts.

Understanding speciation and solvation of glyphosate from first principles simulations

The widespread adoption of the glyphosate (N-phosphonomethylglycine) herbicide has contributed to its increased environmental footprint. Consequently, the sequestration and degradation of excess contaminants are of significant interest, particularly in local aquatic environments. However, this inherently relies on a detailed understanding of glyphosate’s complex speciation and conformational flexibility in the condensed phase. In this work, we investigate the structure and speciation of glyphosate in the vapor and aqueous phases using first-principles simulations. Using the PBE-D3, B3LYP, and ωB97X-D functionals, we found multiple nonzwitterion and five stable zwitterion conformers in the gas phase. Ab initio molecular dynamics (AIMD) simulations in the canonical (NVT) and isothermal-isobaric (NpT) ensembles were employed using the PBE-D3 density functional. Analysis of the equilibrated trajectory allowed an understanding of condensed phase structure through the radial distribution function (RDF), hydrogen bond dynamics, and vibrational spectra. We found evidence that the phosphonate, carboxylic, and amine groups interact strongly with the solvent via hydrogen bonding leading to atypically long O-H bond length (∼ 1.1 Å) on glyphosate’s phosphonate and carboxylic functional groups. Metadynamics simulations using the PBE-D3 and optB88-vdW functionals were performed to estimate the free energy associated with the intramolecular H+ transfer separating the zwitterion and nonzwitterion conformers of glyphosate. Although both functionals confirm the stability of the zwitterion form in the aqueous phase, they differ significantly in the predicted free energy of the reaction.

Characterization of Elusive Reaction Intermediates Using Infrared Ion Spectroscopy: Application to the Experimental Characterization of Glycosyl Cations.

ConspectusA detailed understanding of the reaction mechanism(s) leading to stereoselective product formation is crucial to understanding and predicting product formation and driving the development of new synthetic methodology. One way to improve our understanding of reaction mechanisms is to characterize the reaction intermediates involved in product formation. Because these intermediates are reactive, they are often unstable and therefore difficult to characterize using experimental techniques. For example, glycosylation reactions are critical steps in the chemical synthesis of oligosaccharides and need to be stereoselective to provide the desired α- or β-diastereomer. It remains challenging to predict and control the stereochemical outcome of glycosylation reactions, and their reaction mechanisms remain a hotly debated topic. In most cases, glycosylation reactions take place via reaction mechanisms in the continuum between SN1- and SN2-like pathways. SN2-like pathways proceeding via the displacement of a contact ion pair are relatively well understood because the reaction intermediates involved can be characterized by low-temperature NMR spectroscopy. In contrast, the SN1-like pathways proceeding via the solvent-separated ion pair, also known as the glycosyl cation, are poorly understood. SN1-like pathways are more challenging to investigate because the glycosyl cation intermediates involved are highly reactive. The highly reactive nature of glycosyl cations complicates their characterization because they have a short lifetime and rapidly equilibrate with the corresponding contact ion pair. To overcome this hurdle and enable the study of glycosyl cation stability and structure, they can be generated in a mass spectrometer in the absence of a solvent and counterion in the gas phase. The ease of formation, stability, and fragmentation of glycosyl cations have been studied using mass spectrometry (MS). However, MS alone provides little information about the structure of glycosyl cations. By combining mass spectrometry (MS) with infrared ion spectroscopy (IRIS), the determination of the gas-phase structures of glycosyl cations has been achieved. IRIS enables the recording of gas-phase infrared spectra of glycosyl cations, which can be assigned by matching to reference spectra predicted from quantum chemically calculated vibrational spectra. Here, we review the experimental setups that enable IRIS of glycosyl cations and discuss the various glycosyl cations that have been characterized to date. The structure of glycosyl cations depends on the relative configuration and structure of the monosaccharide substituents, which can influence the structure through both steric and electronic effects. The scope and relevance of gas-phase glycosyl cation structures in relation to their corresponding condensed-phase structures are also discussed. We expect that the workflow reviewed here to study glycosyl cation structure and reactivity can be extended to many other reaction types involving difficult-to-characterize ionic intermediates.

Three-dimensional structure determination of protein complexes using matrix-landing mass spectrometry

Native mass spectrometry (MS) is increasingly used to provide complementary data to electron microscopy (EM) for protein structure characterization. Beyond the ability to provide mass measurements of gas-phase biomolecular ions, MS instruments offer the ability to purify, select, and precisely control the spatial location of these ions. Here we present a modified Orbitrap MS system capable of depositing a native MS ion beam onto EM grids. We further describe the use of a chemical landing matrix that preserves the structural integrity of the deposited particles. With this system we obtain a three-dimensional reconstruction of the 800 kDa protein complex GroEL from gas-phase deposited GroEL ions. These data provide direct evidence that non-covalent protein complexes can indeed retain their condensed-phase structures following ionization and vaporization. Finally, we describe how further developments of this technology could pave the way to an integrated MS-EM technology with promise to provide improved cryo-EM sample preparation over conventional plunge-freezing techniques.

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.

Structure and Reactivity of Alloxan Monohydrate in the Liquid Phase.

Alloxan is an important toxic glucose analogue used to induce diabetes in lab test animals. Once regarded as a "problem structure," the condensed-phase structure of anhydrous alloxan has largely been settled, but literature inconsistencies remain for the structure of the typically employed reagent alloxan monohydrate. Due to the criticality of structure-function relationships, we have used 1H/13C{1H} NMR, IR spectroscopy, as well as quantum mechanical (QM) calculations to probe the liquid-phase structure and reactivity of alloxan monohydrate. In protic solvents (D2O and acetic acid-d4), hydration at the C5 carbonyl of alloxan monohydrate occurs quantitatively to form the C5 gem-diol (5,5'-dihydroxybarbituric acid). In the aprotic solvent dimethyl sulfoxide (DMSO)-d6, there exists a mixture of the C5 gem-diol and planar tetraketo form of alloxan monohydrate. QM calculations explain the solvent-dependent hydration reactivity, where a solvent-assisted H-atom transfer mechanism lowers the activation energy of water addition at the C5 carbonyl by ∼16 or 27 kcal/mol in water or acetic acid, respectively, compared to the unassisted hydration reaction. Prompt recrystallization of alloxan monohydrate from boiling water does not alter the structure of the reagent. These findings probe the exact structure of alloxan monohydrate to guide future research efforts in biological sciences and in organic synthesis.

Data-driven approximations to the bridge function yield improved closures for the Ornstein-Zernike equation.

A key challenge for soft materials design and coarse-graining simulations is determining interaction potentials between components that give rise to desired condensed-phase structures. In theory, the Ornstein-Zernike equation provides an elegant framework for solving this inverse problem. Pioneering work in liquid state theory derived analytical closures for the framework. However, these analytical closures are approximations, valid only for specific classes of interaction potentials. In this work, we combine the physics of liquid state theory with machine learning to infer a closure directly from simulation data. The resulting closure is more accurate than commonly used closures across a broad range of interaction potentials.

Dimers of acetic acid in helium nanodroplets.

The structural arrangement of small carboxylic acid molecules in the liquid phase remains a controversial topic. Some studies indicate a dominance of the cyclic dimer that prevails in the gas phase, whilst other studies favor short fragments of the infinite catemer chains that are found in the crystalline phase. Furthermore, difficulties in preparing and probing size-selected catemer segments have resulted in a lack of benchmark data upon which theoretical models of the condensed phases can be built. To address these issues, we have combined infrared spectroscopy and quantum chemical calculations to explore regions of the intermolecular potential energy surface associated with the formation of metastable dimer isomers. The OH stretching region of the spectrum shows that aggregation of acetic acid molecules inside liquid helium nanodroplets yields two distinct metastable dimers, whilst negligible signal is observed from the cyclic dimer that typically overwhelms this spectral region. We deduce that the most abundant isomer in superfluid helium has one strong O-HO[double bond, length as m-dash]C and one weak C-HO[double bond, length as m-dash]C hydrogen bond. Since this bonding motif is common to the dimeric repeating unit of the catemer, it is of fundamental importance for understanding intermolecular interactions in the condensed phases of small carboxylic acids.

Gas-Phase Structural and Optical Properties of Homo- and Heterobimetallic Rhombic Dodecahedral Nanoclusters [Ag14–nCun(C≡CtBu)12X]+ (X = Cl and Br): Ion Mobility, VUV and UV Spectroscopy, and DFT Calculations

The rhombic dodecahedral nanocluster [Ag14(C≡CtBu)12Cl]+, which has been structurally characterized using X-ray crystallography, was transferred to the gas phase using electrospray ionization, where it was characterized by ion mobility (IM), vacuum ultraviolet (VUV), and ultraviolet (UV) spectroscopies in conjunction with DFT calculations. IM reveals a single peak, and modeling of the collision cross-section with the X-ray structure suggests that the cluster maintains its condensed phase structure upon transfer to the gas phase. The VUV spectra exhibit rich fragmentation, including: photoionization to give [Ag14(C≡CtBu)12Cl]2+• with an onset of 8.84 ± 0.08 eV; cluster fission fragmentation via losses of (AgC≡CtBu)n and (AgC≡CtBu)n−1(AgCl); and via reductive elimination of (tBuC≡C)2. Apart from channels associated with photoionization, similar fragment ions are observed in the UVPD spectra, although their relative intensities differ. The TDDFT absorption spectra are symmetry-allowed transitions including Au → Ag, Eu → Ag, and Eu → Eg irreducible representations. Comparing the collision cross-sections with the X-ray structures for the related clusters [Ag8Cu6(C≡CtBu)12Cl]+, [Ag14(C≡CtBu)12Br]+, and [Ag8Cu6(C≡CtBu)12Br]+ suggests that they maintain their condensed-phase structures in the gas phase. The VUV spectra of [Ag8Cu6(C≡CtBu)12Cl]+ and [Ag14(C≡CtBu)12Br]+ exhibit similar fragmentation channels and ionization onsets (8.86 ± 0.03 and 8.86 ± 0.05, respectively) compared with [Ag14(C≡CtBu)12Cl]+.

Resonance Energy Transfer Relates the Gas-Phase Structure and Pharmacological Activity of Opioid Peptides.

Enkephalins are efficient pain-relief drugs that bind to transmembrane opioid receptors. One key structural parameter that governs the pharmacological activity of these opioid peptides and is typically determined from condensed-phase structures is the distance between the aromatic rings of their Tyr and Phe residues. We use resonance energy transfer, detected by a combination of cold ion spectroscopy and mass spectrometry, to estimate the Tyr-Phe spacing for enkephalins in the gas phase. In contrast to the condensed-phase structures, these distances appear to differ substantially in enkephalins with different pharmacological efficiencies, suggesting that gas-phase structures might be a better pharmacophoric metric for ligand peptides.

Resonance Energy Transfer Relates the Gas‐Phase Structure and Pharmacological Activity of Opioid Peptides

AbstractEnkephalins are efficient pain‐relief drugs that bind to transmembrane opioid receptors. One key structural parameter that governs the pharmacological activity of these opioid peptides and is typically determined from condensed‐phase structures is the distance between the aromatic rings of their Tyr and Phe residues. We use resonance energy transfer, detected by a combination of cold ion spectroscopy and mass spectrometry, to estimate the Tyr–Phe spacing for enkephalins in the gas phase. In contrast to the condensed‐phase structures, these distances appear to differ substantially in enkephalins with different pharmacological efficiencies, suggesting that gas‐phase structures might be a better pharmacophoric metric for ligand peptides.

Living on the edge: Tuning supramolecular interactions to design two-dimensional organic crystals near the boundary of two stable structural phases.

One of the benefits of supramolecular assemblies that form at dynamic interfaces is the opportunity to develop condensed phase systems that respond to environmental stimuli. A prerequisite of this responsive behavior is that the supramolecular system be designed to sit very near the stability of two or more crystal structures. We have created such a bi-phasic system with aryl-triazole oligomers by investigating how phase morphology is controlled by the interplay between interactions that involve the oligomer's dipolar cores (Δμ = 3.5 debye), van der Waals contacts of their pendant alkyl chains (C4-C18), and close-contact hydrogen bonding. Scanning tunneling microscopy experiments conducted at the solution-graphite interface allow sub-molecular resolution of the ordered monolayers to unambiguously determine the packing and structure of two principle phases, α and β. The system is balanced very near the edge of phase stability, evidenced by co-existent phases present over short time frames and by the changes in preference between the two 2D supramolecular assemblies that occur with small modifications to the molecular structure. We demonstrate that the bi-phasic behavior can be understood as a balance between electrostatic interactions and van der Waals contacts, two variables within a larger parameter space, allowing synthetic design to move this solution-surface system across the stability boundary of different condensed-phase structures. These findings are a foundation for the development of environmentally responsive 2D supramolecular arrays.

In ESI-source H/D exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa: the role of the temperature of the desolvating capillary on H/D exchange.

Transition of proteins from the solution to the gas phase during electrospray ionization remains a challenging problem despite the large amount of attention it has received during the past few decades. One of the major questions relates to the extent to which proteins in the gas phase retain their condensed phase structures. We have used in-electrospray source hydrogen/deuterium exchange to determine the number of deuterium incorporations as a function of protein mass, charge state and temperature of the desolvating capillary where the reaction occurs. All experiments were performed on a Thermo LTQ FT Ultra equipped with a 7-T superconducting magnet. Ions were generated by an IonMax Electrospray ion source operated in the positive ESI mode. Deuterium exchange was performed by introducing a droplet of D2 O beneath the ESI capillary. We systematically investigated gas phase hydrogen/deuterium (H/D) exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa. We observed that almost all proteins demonstrate similar exchange rates for all charge states and that these rates increase exponentially with the temperature of the desolvating capillary. We did not observe any clear correlation of the number of H/D exchanges with the value of the cross section for a corresponding charge state. We have demonstrated the possibility of performing in-ESI source H/D exchange of large proteins under atmospheric pressure. The simplicity of the experimental setup makes it a useful experimental technique that can be applied for the investigation of gas phase conformations of proteins.

The hemibond as an alternative condensed phase structure for the hydroxyl radical

Despite the critical importance of the hydroxyl radical in major scientific fields, there are still open questions on the behavior of this species in the aqueous phase. In particular, there has been much debate on the existence of a hemibonded interaction between the hydroxyl radical and water molecules. While some reports indicate that the hemibonded radical might explain some experimental data, others have claimed that this interaction is simply a density functional theory (DFT) artifact. Here, we provide results from high level (basis set limit of coupled-cluster levels up to single, double, triple excitations (CCSD(T)) and beyond) ab initio calculations of different OH•(H2O)n clusters in the gas phase to accurately explore the existence of the hemibonded interaction and its energy difference with respect to other well-defined hydrogen bond interactions. Additional comparisons with second order perturbation theory (MP2) and DFT are also presented. Constrained molecular dynamics was applied to determine the free energy for the formation/disruption and ice systems. Overall, our findings confirm that the hemibond can be an alternative structure for the hydroxyl radical in the condensed phase when the formation of hydrogen bonds is impeded. These results will aid the understanding of theoretical and experimental data and help future experimental designs for the detection of this important species.

Abnormal Heat by Thermal Changing in a D-Pd Gas-Loading System

In order to explore the condensed phase whether may promote abnormal heating phenomenon and nuclear reactions occur, as well as how to construct and characterization of condensed phase structure filled with deuterium and the use of exogenous trigger transient change. Some deuterium atoms were charged into metal palladium lattice and reached a certain ratio in a D-Pd gas-solid system under the pressure of PD26J heat energy were released in 8 hours, when loading ratio of deuterium x was 0.12, current 8A, pressure 9×104Pa. Improvement of experiment, that excess heat power 41W and 79.58MJ heat energy, which was corresponding to 1.8×104eV for each palladium atom were released in 83 hours and 17 minutes, when current 7.25A, pressure 9×104Pa. An energy dispersive spectrometer (EDS) revealed that new surface topographical features with concentrations of unexpected elements Ag were detected, which implied that the excess heat might come from a nuclear transmutation reaction.

Do Charge State Signatures Guarantee Protein Conformations?

The extent to which proteins in the gas phase retain their condensed-phase structure is a hotly debated issue. Closely related to this is the degree to which the observed charge state reflects protein conformation. Evidence from electron capture dissociation, hydrogen/deuterium exchange, ion mobility, and molecular dynamics shows clearly that there is often a strong correlation between the degree of folding and charge state, with the most compact conformations observed for the lowest charge states. In this article, we address recent controversies surrounding the relationship between charge states and folding, focussing also on the manipulation of charge in solution and its effect on conformation. 'Supercharging' reagents that have been used to effect change in charge state can promote unfolding in the electrospray droplet. However for several protein complexes, supercharging does not appear to perturb the structure in that unfolding is not detected. Consequently, a higher charge state does not necessarily imply unfolding. Whilst the effect of charge manipulation on conformation remains controversial, there is strong evidence that a folded, compact state of a protein can survive in the gas phase, at least on a millisecond timescale. The exact nature of the side-chain packing and secondary structural elements in these compact states, however, remains elusive and prompts further research.

Investigating the gas phase structure of KIX with radical directed dissociation and molecular dynamics: Retention of the native structure

Evaluating protein structure in the gas phase is useful for understanding the intrinsic forces which influence protein folding and for determining the feasibility of probing condensed phase structure with gas phase interrogation. KIX is a three-helix bundle protein that has been reported previously to preserve the condensed phase structure in the gas phase. Herein, structure dependent radical directed dissociation (RDD) is used to examine the gas phase structure of KIX by establishing residue specific distance constraints which can be used to assess candidate structures obtained from molecular dynamics simulations. The data obtained by RDD is consistent with KIX structures that largely retain condensed phase structure as determined previously by NMR. There are several factors that favor retention of the KIX native fold in the gas phase. The structure is largely comprised of alpha helices, which are known to be stable in the gas phase. This is particularly true if the C-terminus of the helix is capped with a positive charge, which occurs for the two most stable helices in KIX. There are several arginine based salt bridges which link critical portions of KIX together. KIX also has an abundance of basic residues; this multiplicity increases the chance that sites which require little structural reorganization following desolvation can be charge carriers. Thus under appropriate conditions, solution phase structure can be largely retained and meaningfully examined in the gas phase.

Isolated Monohydrates of a Model Peptide Chain: Effect of a First Water Molecule on the Secondary Structure of a Capped Phenylalanine

The formation of monohydrates of capped phenylalanine model peptides, CH(3)-CO-Phe-NH(2) and CH(3)-CO-Phe-NH-CH(3), in a supersonic expansion has been investigated using laser spectroscopy and quantum chemistry methods. Conformational distributions of the monohydrates have been revealed by IR/UV double-resonance spectroscopy and their structures assigned by comparison with DFT-D calculations. A careful analysis of the final hydrate distribution together with a detailed theoretical investigation of the potential energy surface of the monohydrates demonstrates that solvation occurs from the conformational distribution of the isolated peptide monomers. The distribution of the monohydrates appears to be strongly dependent on both the initial monomer conformation (extended or folded backbone) and the solvation site initially occupied by the water molecule. The solvation processes taking place during the cooling can be categorized as follows: (a) solvation without significant structural changes of the peptide, (b) solvation inducing significant distortions of the backbone but retaining the secondary structure, and (c) solvation triggering backbone isomerizations, leading to a modification of the peptide secondary structure. It is observed that solvation by a single water molecule can fold a β-strand into a γ-turn structure (type c) or induce a significant opening of a γ-turn characterized by an elongated C(7) hydrogen bond (type b). These structural changes can be considered as a first step toward the polyproline II condensed-phase structure, illustrating the role played by the very first water molecule in the solvation process.