pH dependence of the electronic structure of glycine

A sub-100 nm thickness flat jet for extreme ultraviolet to soft X-ray absorption spectroscopy

Experimental characterization of the structural, electronic and dynamic properties of dilute systems in aqueous solvents, such as nanoparticles, molecules and proteins, are nowadays an open challenge. X-ray absorption spectroscopy (XAS) is probably one of the most established approaches to this aim as it is element-specific. However, typical dilute systems of interest are often composed of light elements that require extreme-ultraviolet to soft X-ray photons. In this spectral regime, water and other solvents are rather opaque, thus demanding radical reduction of the solvent volume and removal of the liquid to minimize background absorption. Here, we present an experimental endstation designed to operate a liquid flat jet of sub-micrometre thickness in a vacuum environment compatible with extreme ultraviolet/soft XAS measurements in transmission geometry. The apparatus developed can be easily connected to synchrotron and free-electron-laser user-facility beamlines dedicated to XAS experiments. The conditions for stable generation and control of the liquid flat jet are analyzed and discussed. Preliminary soft XAS measurements on some test solutions are shown.

Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-dependent Density-Functional Theory

The accurate description of solvent effects on X-ray absorption spectra (XAS) is fundamental for comparing the simulated spectra with experiments in solution. Currently, few protocols exist that can efficiently reproduce the effects of the solute/solvent interactions on XAS. Here, we develop an efficient and accurate theoretical protocol for simulating the solvent effects on XAS. The protocol combines electrostatic embedding QM/MM based on electrostatic potential fitted operators for describing the solute/solvent interactions and mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for simulating accurate XAS spectra. To demonstrate the capabilities of our protocol, we compute the X-ray absorption of neutral proline in the gas phase and ionic proline in water in all relevant K-edges, showing excellent agreement with experiments. We show that states represented by core to π* transitions are almost unaffected by the interaction with water, whereas the core to σ* transitions are more impacted by the fluctuation of proline structure and the electrostatic interaction with the solvent. Finally, we reconstruct the pH-dependent XAS of proline in solution, determining that the N K-edge can be used to distinguish its three protonation states.

Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy

Near-edge X-ray absorption mass spectrometry (NEXAMS) around the nitrogen and oxygen K-edges was employed on gas-phase peptides to probe the electronic transitions related to their protonation sites, namely at basic side chains, the N-terminus and the amide oxygen. The experimental results are supported by replica exchange molecular dynamics and density-functional theory and restricted open-shell configuration with single calculations to attribute the transitions responsible for the experimentally observed resonances. We studied five tailor-made glycine-based pentapeptides, where we identified the signature of the protonation site of N-terminal proline, histidine, lysine and arginine, at 406 eV, corresponding to N 1s → σ*(NHx+) (x = 2 or 3) transitions, depending on the peptides. We compared the spectra of pentaglycine and triglycine to evaluate the sensitivity of NEXAMS to protomers. Separate resonances have been identified to distinguish two protomers in triglycine, the protonation site at the N-terminus at 406 eV and the protonation site at the amide oxygen characterized by a transition at 403.1 eV.

Role of the redox state of cerium oxide on glycine adsorption: an experimental and theoretical study

The role of the oxidation state of cerium cations in a thin oxide film in the adsorption, geometry, and thermal stability of glycine molecules was studied. The experimental study was performed for a submonolayer molecular coverage deposited in vacuum on CeO₂(111)/Cu(111) and Ce₂O₃(111)/Cu(111) films by photoelectron and soft X-ray absorption spectroscopies and supported by ab initio calculations for prediction of the adsorbate geometries, C 1s and N 1s core binding energies of glycine, and some possible products of the thermal decomposition. The molecules adsorbed on the oxide surfaces at 25 °C in the anionic form via the carboxylate oxygen atoms bound to cerium cations. A third bonding point through the amino group was observed for the glycine adlayers on CeO₂. In the course of stepwise annealing of the molecular adlayers on CeO₂ and Ce₂O₃, the surface chemistry and decomposition products were analyzed and found to relate to different reactivities of glycinate on Ce⁴⁺ and Ce³⁺ cations, observed as two dissociation channels via C-N and C-C bond scission, respectively. The oxidation state of cerium cations in the oxide was shown to be an important factor, which defines the properties, electronic structure, and thermal stability of the molecular adlayer.

A Core-Valence Separated Similarity Transformed EOM-CCSD Method for Core-Excitation Spectra

We present the theory and implementation of a core-valence separated similarity transformed EOM-CCSD (STEOM-CCSD) method for K-edge core excitation spectra. The method can select an appropriate active space using CIS natural orbitals and near "black box" to use. The second similarity transformed Hamiltonian is diagonalized in the space of single excitation. Therefore, the final diagonalization step is free from the convergence problem arising due to the coupling of the core-excited states with the continuum of doubly excited states. Convergence trouble can appear for the preceding core-ionized state calculation in STEOM-CCSD. A core-valence separation (CVS) scheme compatible with the natural orbital based active space selection (CVS-STEOM-CCSD-NO) is implemented to overcome the problem. The CVS-STEOM-CCSD-NO has a similar accuracy to that of the standard CVS-EOM-CCSD method but comes with a lower computational cost. The modification required in the CVS scheme to make use of the CIS natural orbital is highlighted. The suitability of the CVS-STEOM-CCSD-NO method for chemical application is demonstrated by simulating the K-edge spectra of glycine and thymine.

Nitrogen K-Edge X-ray Absorption Spectra of Ammonium and Ammonia in Water Solution: Assessing the Performance of Polarizable Embedding Coupled Cluster Methods

The recent development of liquid jet and liquid leaf sample delivery systems allows for accurate measurements of soft X-ray absorption spectra in transmission mode of solutes in a liquid environment. As this type of measurement becomes increasingly accessible, there is a strong need for reliable theoretical methods for assisting in the interpretation of the experimental data. Coupled cluster methods have been extensively developed over the past decade to simulate X-ray absorption in the gas phase. Their performance for solvated species, on the contrary, remains largely unexplored. Here, we investigate the current state of the art of coupled cluster modeling of nitrogen K-edge X-ray absorption of aqueous ammonia and ammonium based on quantum mechanics/molecular mechanics, where both the level of coupled cluster calculations and polarizable embedding are scrutinized. The results are compared to existing experimental data as well as simulations based on transition potential density functional theory.

Hydration of the Zwitterionic and Protonated Forms of Glycine Betaine Probed by Soft X-ray Emission Spectroscopy Coupled with Chemometrics

Soft X-ray absorption and emission spectra of glycine betaine (GB) have been measured at the O K-edge in neutral and strongly acidic solutions. The absorption spectra of the neutral solutions have a resonance peak at 532.6 eV, assigned to the transition to the π* orbital, whereas in the acidic solutions, the peak is shifted by -0.3 eV. The emission spectra taken as a function of the GB concentration have been analyzed by means of a modified classical least-squares regression method to obtain the hydration number of the solute. The analysis is successful when the emission spectra have been acquired at the energy of a slightly detuned resonance, giving 28 and 24 as the minimum values for the zwitterionic and protonated GB, respectively. The number of 28 accords with the reported values for the number of water molecules in the first hydration layer of the zwitterion and is greater than that obtained by other experimental techniques. The obtained numbers are used to discuss the hydration structure of GB with the aid of ab initio molecular orbital calculations. The hydration structure of the protonated form of GB is explored for the first time.

Local electronic structure of histidine in aqueous solution

X-Ray spectroscopy coupled with DFT calculations reveals the pH dependent electronic structure of an amino acid in an aqueous environment.

Oxygen K-edge X-ray Absorption Spectra

We review oxygen K-edge X-ray absorption spectra of both molecules and solids. We start with an overview of the main experimental aspects of oxygen K-edge X-ray absorption measurements including X-ray sources, monochromators, and detection schemes. Many recent oxygen K-edge studies combine X-ray absorption with time and spatially resolved measurements and/or operando conditions. The main theoretical and conceptual approximations for the simulation of oxygen K-edges are discussed in the Theory section. We subsequently discuss oxygen atoms and ions, binary molecules, water, and larger molecules containing oxygen, including biomolecular systems. The largest part of the review deals with the experimental results for solid oxides, starting from s- and p-electron oxides. Examples of theoretical simulations for these oxides are introduced in order to show how accurate a DFT description can be in the case of s and p electron overlap. We discuss the general analysis of the 3d transition metal oxides including discussions of the crystal field effect and the effects and trends in oxidation state and covalency. In addition to the general concepts, we give a systematic overview of the oxygen K-edges element by element, for the s-, p-, d-, and f-electron systems.

X-ray and UV Spectra of Glycine within Coupled Cluster Linear Response Theory

The coupled cluster models CCSD and CC3 are used to investigate the (core) excited states and ionization energies of glycine in the gas phase. Excited states and ionization energies in the UV spectral range are calculated using a standard coupled cluster linear response, while core-level excited states and ionization potentials are calculated using the core-valence separation approximation. The temperature dependence from different conformers is also assessed.

Local electronic structure of the peptide bond probed by resonant inelastic soft X-ray scattering

Soft X-ray emission spectroscopy and RIXS are used to determine the local electronic structure of the peptide bond.

GraftFast Surface Engineering to Improve MOF Nanoparticles Furtiveness

Controlling the outer surface of nanometric metal-organic frameworks (nanoMOFs) and further understanding the in vivo effect of the coated material are crucial for the convenient biomedical applications of MOFs. However, in most studies, the surface modification protocol is often associated with significant toxicity and/or lack of selectivity. As an alternative, how the highly selective and general grafting GraftFast method leads, through a green and simple process, to the successful attachment of multifunctional biopolymers (polyethylene glycol (PEG) and hyaluronic acid) on the external surface of nanoMOFs is reported. In particular, effectively PEGylated iron trimesate MIL-100(Fe) nanoparticles (NPs) exhibit suitable grafting stability and superior chemical and colloidal stability in different biofluids, while conserving full porosity and allowing the adsorption of bioactive molecules (cosmetic and antitumor agents). Furthermore, the nature of the MOF-PEG interaction is deeply investigated using high-resolution soft X-ray spectroscopy. Finally, a cell penetration study using the radio-labeled antitumor agent gemcitabine monophosphate (³ H-GMP)-loaded MIL-100(Fe)@PEG NPs shows reduced macrophage phagocytosis, confirming a significant in vitro PEG furtiveness.

Soft X-ray Spectroscopy of the Amine Group: Hydrogen Bond Motifs in Alkylamine/Alkylammonium Acid-Base Pairs

We use N K-edge absorption spectroscopy to explore the electronic structure of the amine group, one of the most prototypical chemical functionalities playing a key role in acid-base chemistry, electron donor-acceptor interactions, and nucleophilic substitution reactions. In this study, we focus on aliphatic amines and make use of the nitrogen 1s core electron excitations to elucidate the roles of N-H σ* and N-C σ* contributions in the unoccupied orbitals. We have measured N K-edge absorption spectra of the ethylamine bases Et _xNH_{3- x} ( x = 0...3; Et- = C₂H₅-) and the conjugate positively charged ethylammonium cation acids Et _yNH_{4- y}⁺ ( y = 0...4; Et- = C₂H₅-) dissolved in the protic solvents ethanol and water. Upon consecutive exchange of N-H for ethyl-groups, we observe a spectral shift, a systematic decrease of the N K-edge pre-edge peak, and a major contribution in the post-edge region for the ethylamine series. Instead, for the ethylammonium ions, the consecutive exchange of N-H for ethyl groups leads to an apparent reduction of pre-edge and post-edge intensities relative to the main-edge band, without significant frequency shifts. Building on findings from our previously reported study on aqueous ammonia and ammonium ions, we can rationalize these observations by comparing calculated N K-edge absorption spectra of free and hydrogen-bonded clusters. Hydrogen bonding interactions lead only to minor spectral effects in the ethylamine series, but have a large impact in the ethylammonium ion series. Visualization of the unoccupied molecular orbitals shows the consecutive change in molecular orbital character from N-H σ* to N-C σ* in these alkylamine/alkylammonium ion series. This can act as a benchmark for future studies on chemically more involved amine compounds.

Effect of amino group protonation on the carboxyl group in aqueous glycine observed by O 1s X-ray emission spectroscopy

The valence electronic structures of the amino acid glycine in aqueous solution were investigated in detail through X-ray emission spectroscopy at O 1s excitation under selective excitation conditions of the CO site in the carboxyl group.

Chitosan-coated mesoporous MIL-100(Fe) nanoparticles as improved bio-compatible oral nanocarriers

Nanometric biocompatible Metal-Organic Frameworks (nanoMOFs) are promising candidates for drug delivery. Up to now, most studies have targeted the intravenous route, related to pain and severe complications; whereas nanoMOFs for oral administration, a commonly used non-invasive and simpler route, remains however unexplored. We propose here the biofriendly preparation of a suitable oral nanocarrier based on the benchmarked biocompatible mesoporous iron(III) trimesate nanoparticles coated with the bioadhesive polysaccharide chitosan (CS). This method does not hamper the textural/structural properties and the sorption/release abilities of the nanoMOFs upon surface engineering. The interaction between the CS and the nanoparticles has been characterized through a combination of high resolution soft X-ray absorption and computing simulation, while the positive impact of the coating on the colloidal and chemical stability under oral simulated conditions is here demonstrated. Finally, the intestinal barrier bypass capability and biocompatibility of CS-coated nanoMOF have been assessed in vitro, leading to an increased intestinal permeability with respect to the non-coated material, maintaining an optimal biocompatibility. In conclusion, the preservation of the interesting physicochemical features of the CS-coated nanoMOF and their adapted colloidal stability and progressive biodegradation, together with their improved intestinal barrier bypass, make these nanoparticles a promising oral nanocarrier.

Degradation of Albumin on Plasma-Treated Polystyrene by Soft X-ray Exposure

Thin films of human serum albumin (HSA) were immobilized on polystyrene (PS) substrates previously functionalized either with polar or nonpolar functional groups. The functionalization was performed by treatment with cold gaseous plasma created in pure oxygen and tetrafluoromethane (CF₄) plasmas, respectively. Samples were examined with soft X-rays in the photon energy range of 520 to 710 eV in the ANTARES beam line at SOLEIL Synchrotron. NEXAFS spectra of O K-edge and F K-edge were collected at different spots of the sample, and measurements at each spot were repeated many times. A strong degradation of the HSA protein was observed. The weakly irradiated samples exhibited strong absorption at 531.5 eV associated with the O 1s→π*_amide transitions, and a broad non distinctive peak at 540 eV was attributed to the O 1s→σ*_C–O transitions. Both peaks decreased with increasing irradiation time until they were completely replaced by a broad non-distinctive peak at around 532 eV, indicating the destruction of the original protein conformation. The shortage of the amide groups indicated breakage of the peptide bonds.

X-ray and Electron Spectroscopy of Water

Here we present an overview of recent developments of X-ray and electron spectroscopy to probe water at different temperatures. Photon-induced ionization followed by detection of electrons from either the O 1s level or the valence band is the basis of photoelectron spectroscopy. Excitation between the O 1s and the unoccupied states or occupied states is utilized in X-ray absorption and X-ray emission spectroscopies. These techniques probe the electronic structure of the liquid phase and show sensitivity to the local hydrogen-bonding structure. Both experimental aspects related to the measurements and theoretical simulations to assist in the interpretation are discussed in detail. Different model systems are presented such as the different bulk phases of ice and various adsorbed monolayer structures on metal surfaces.

Beyond the electric-dipole approximation: A formulation and implementation of molecular response theory for the description of absorption of electromagnetic field radiation

We present a formulation of molecular response theory for the description of a quantum mechanical molecular system in the presence of a weak, monochromatic, linearly polarized electromagnetic field without introducing truncated multipolar expansions. The presentation focuses on a description of linear absorption by adopting the energy-loss approach in combination with the complex polarization propagator formulation of response theory. Going beyond the electric-dipole approximation is essential whenever studying electric-dipole-forbidden transitions, and in general, non-dipolar effects become increasingly important when addressing spectroscopies involving higher-energy photons. These two aspects are examined by our study of the near K-edge X-ray absorption fine structure of the alkaline earth metals (Mg, Ca, Sr, Ba, and Ra) as well as the trans-polyenes. In following the series of alkaline earth metals, the sizes of non-dipolar effects are probed with respect to increasing photon energies and a detailed assessment of results is made in terms of studying the pertinent transition electron densities and in particular their spatial extension in comparison with the photon wavelength. Along the series of trans-polyenes, the sizes of non-dipolar effects are probed for X-ray spectroscopies on organic molecules with respect to the spatial extension of the chromophore.

Influence of the Side Chain in the Structure and Fragmentation of Amino Acids Radical Cations

The conformational properties of ionized amino acids (Gly, Ala, Ser, Cys, Asp, Gln, Phe, Tyr, and His) have been theoretically analyzed using the hybrid B3LYP and the hybrid-meta MPWB1K functionals as well as with the post-Hartree Fock CCSD(T) level of theory. As a general trend, ionization is mainly localized at the -NH2 group, which becomes more planar and acidic, the intramolecular hydrogen bond in which -NH2 acts as proton donor being strengthened upon ionization. For this reason, the so-called conformer IV(+) becomes the most stable for nonaromatic amino acid radical cations. Aromatic amino acids do not follow this trend because ionization takes place mainly at the side chain. For these amino acids for which ionization of the side chain prevails over the -NH2 group, structures III(+) and II(+) become competitive. The Cα-X fragmentations of the ionized systems have also been studied. Among the different decompositions considered, the one that leads to the loss of COOH(•) is the most favorable one. Nevertheless, for aromatic amino acids fragmentations leading to R(•) or R(+) start being competitive. In fact, for His and Tyr, results indicate that the fragmentation leading to R(+) is the most favorable process.

Properties of aqueous nitrate and nitrite from x-ray absorption spectroscopy

Nitrate and nitrite ions are of considerable interest, both for their widespread use in commercial and research contexts and because of their central role in the global nitrogen cycle. The chemistry of atmospheric aerosols, wherein nitrate is abundant, has been found to depend on the interfacial behavior of ionic species. The interfacial behavior of ions is determined largely by their hydration properties; consequently, the study of the hydration and interfacial behavior of nitrate and nitrite comprises a significant field of study. In this work, we describe the study of aqueous solutions of sodium nitrate and nitrite via X-ray absorption spectroscopy (XAS), interpreted in light of first-principles density functional theory electronic structure calculations. Experimental and calculated spectra of the nitrogen K-edge XA spectra of bulk solutions exhibit a large 3.7 eV shift between the XA spectra of nitrate and nitrite resulting from greater stabilization of the nitrogen 1s energy level in nitrate. A similar shift is not observed in the oxygen K-edge XA spectra of NO3 (-) and NO2 (-). The hydration properties of nitrate and nitrite are found to be similar, with both anions exhibiting a similar propensity towards ion pairing.

Correlating Infrared and X-ray Absorption Energies for Molecular-Level Insight into Hydrogen Bond Making and Breaking in Solution

While ubiquitous, the making and breaking of hydrogen bonds in solution is notoriously difficult to study due to the associated complex changes of nuclear and electronic structures. With the aim to reduce the according uncertainty in correlating experimental observables and hydrogen-bond configurations, we combine the information from proximate methods to study the N-H···O hydrogen bond in solution. We investigate hydrogen-bonding of the N-H group of N-methylaniline with oxygen from liquid DMSO and acetone with infrared spectra in the N-H stretching region and X-ray absorption spectra at the N K-edge. We experimentally observe blue shifts of the infrared stretching band and an X-ray absorption pre-edge peak when going from DMSO to acetone. With ab initio molecular dynamics simulations and calculated spectra, we qualitatively reproduce the experimental observables but we do not reach quantitative agreement with experiment. The infrared spectra support the notion of weakening the N-H···O hydrogen bond from DMSO to acetone. However, we fail to theoretically reproduce the measured shift of the X-ray absorption pre-edge peak. We discuss possible shortcomings of the simulation models and spectrum calculations. Common features and distinct differences with the O-H···O hydrogen bond are highlighted, and the implications for monitoring hydrogen-bond breaking in solution are discussed.

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p-Aminobenzoic Acid

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.

Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

The global minimum of the dipeptide ArgGly is found to be in the canonical form, rather than the zwitterionic form.

Exploring Protonation and Deprotonation Effects with Auger Electron Spectroscopy

Auger electron spectroscopy is demonstrated to be a very efficient tool to probe alterations in local chemical environment due to changes in protonation states. We show that electronic and geometric structure changes induced by protonation or deprotonation are well reflected in Auger spectra through characteristic chemical shifts and spectral shape variations. We also present evidence that Auger spectra are sensitive to relative concentrations of compounds in different protonation states. Special attention is paid to the high kinetic energy spectral regions that exhibit remarkable features resulting from core ICD-like transitions in normal species and Auger transitions in deprotonated fragments. The latter contribution was so far ignored when explaining Auger spectra of species embedded in the environment. This contribution should be reconsidered, taking into account the recently discovered possibility of ultrafast dissociation of core-ionized hydrogen-bonded systems in media.

Electronic Structures of Formic Acid (HCOOH) and Formate (HCOO(-)) in Aqueous Solutions

The electronic structures of formic acid (HCOOH) and formate (HCOO(-)) have been determined in aqueous solutions over a pH range of 1.88-8.87 using a combination of X-ray photoelectron spectroscopy (XPS), partial electron-yield X-ray absorption spectroscopy (PEY XAS), and density functional theory (DFT). The carbon 1s XPS measurements reveal a binding energy shift of -1.3 eV for deprotonated HCOO(-) compared with neutral HCOOH. Such distinction between neutral HCOOH and deprotonated HCOO(-) cannot be made based solely on the respective carbon K-edge PEY XA spectra. Independent of pH, the C1s → π* state excitations occur at 288.0 eV and may lead to the incorrect conclusion that the energy levels of the π* state are the same for both species. The DFT calculations are consistent with the experimental observations and show a shift to higher energy for both the occupied C1s (lower binding energy) and unoccupied π* orbitals of deprotonated HCOO(-) compared to neutral HCOOH in aqueous solutions.

Gas-Phase Protein Inner-Shell Spectroscopy by Coupling an Ion Trap with a Soft X-ray Beamline

C, N, and O near-edge ion yield spectroscopy of 8+ selected electrosprayed cations of cytochrome c protein (12 kDa) has been performed by coupling a linear quadrupole ion trap with a soft X-ray beamline. The photoactivation tandem mass spectra were recorded as a function of the photon energy. Photoionization of the precursor, accompanied by CO2 loss, is the dominant relaxation process, showing high photoion stability following direct or resonant photoionization. The partial ion yields extracted from recorded mass spectra show significantly different behaviors for single and double ionization channels, which can be qualitatively explained by different Auger decay mechanisms. However, the single ionization spectra reveal characteristic structures when compared to existing near-edge X-ray absorption fine structure (NEXAFS) spectra from thin films of peptides and proteins. Therefore, the present experiment opens up new avenues for near-edge X-ray spectroscopy of macromolecules in the gas phase, overcoming the radiation damage issue or the environmental effects as due to the surface, intermolecular interactions, and solvent.

In situ hydrolysis of imine derivatives on Au(111) for the formation of aromatic mixed self-assembled monolayers: multitechnique analysis of this tunable surface modification

This paper presents a novel method for preparing aromatic, mixed self-assembled monolayers (SAMs) with a dilute surface fraction coverage of protonated amine via in situ hydrolysis of C═N double bond on gold surface. Two imine compounds, (4'-(4-(trifluoromethyl)benzylideneamino)biphenyl-4-yl)methanethiol (CF(3)-C(6)H(4)-CH═N-C(6)H(4)-C(6)H(4)-CH(2)-SH, TFBABPMT) and (4'-(4-cyanobenzylideneamino)biphenyl-4-yl)methanethiol (CN-C(6)H(4)-CH═N-C(6)H(4)-C(6)H(4)-CH(2)-SH, CBABPMT), self-assembled on Au(111) to form highly ordered monolayers, which was demonstrated by infrared reflection absorption spectroscopy (IRRAS) and X-ray photoelectron spectroscopy (XPS). A nearly upright molecular orientation for CF(3)- and CN-terminated SAM was detected by near edge X-ray absorption fine structure (NEXAFS) measurements. Afterward, the acidic catalyzed hydrolysis was carried out in chloroform or an aqueous solution of acetic acid (pH = 3). Systematic studies of this hydrolysis process for CN-terminated SAM in acetic acid at 25 °C were performed by NEXAFS measurements. It was found that about 30% of the imine double bonds gradually cleaved in the first 40 min. Subsequently, a larger hydrolysis rate was observed due to the freer penetration of acetic acid in the SAM and resultant more open molecular packing. Furthermore, the molecular orientation in mixed SAMs did not change during the whole hydrolysis process. This partially hydrolyzed surface contains a controlled amount of free amines/ammonium ions which can be used for further chemical modifications.

On the origins of core-electron chemical shifts of small biomolecules in aqueous solution: insights from photoemission and ab initio calculations of glycine(aq)

The local electronic structure of glycine in neutral, basic, and acidic aqueous solution is studied experimentally by X-ray photoelectron spectroscopy and theoretically by molecular dynamics simulations accompanied by first-principle electronic structure and spectrum calculations. Measured and computed nitrogen and carbon 1s binding energies are assigned to different local atomic environments, which are shown to be sensitive to the protonation/deprotonation of the amino and carboxyl functional groups at different pH values. We report the first accurate computation of core-level chemical shifts of an aqueous solute in various protonation states and explicitly show how the distributions of photoelectron binding energies (core-level peak widths) are related to the details of the hydrogen bond configurations, i.e. the geometries of the water solvation shell and the associated electronic screening. The comparison between the experiments and calculations further enables the separation of protonation-induced (covalent) and solvent-induced (electrostatic) screening contributions to the chemical shifts in the aqueous phase. The present core-level line shape analysis facilitates an accurate interpretation of photoelectron spectra from larger biomolecular solutes than glycine.

Monopeptide versus monopeptoid: insights on structure and hydration of aqueous alanine and sarcosine via X-ray absorption spectroscopy

Despite the obvious significance, the aqueous interactions of peptides remain incompletely understood. Their synthetic analogues called peptoids (poly-N-substituted glycines) have recently emerged as a promising biomimetic material, particularly due to their robust secondary structure and resistance to denaturation. We describe comparative near-edge X-ray absorption fine structure spectroscopy studies of aqueous sarcosine, the simplest peptoid, and alanine, its peptide isomer, interpreted by density functional theory calculations. The sarcosine nitrogen K-edge spectrum is blue shifted with respect to that of alanine, in agreement with our calculations; we conclude that this shift results primarily from the methyl group substitution on the nitrogen of sarcosine. Our calculations indicate that the nitrogen K-edge spectrum of alanine differs significantly between dehydrated and hydrated scenarios, while that of the sarcosine zwitterion is less affected by hydration. In contrast, the computed sarcosine spectrum is greatly impacted by conformational variations, while the alanine spectrum is not. This relates to a predicted solvent dependence for alanine, as compared to sarcosine. Additionally, we show the theoretical nitrogen K-edge spectra to be sensitive to the degree of hydration, indicating that experimental X-ray spectroscopy may be able to distinguish between bulk and partial hydration, such as found in confined environments near proteins and in reverse micelles.