Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level

IR spectrum of SiH3OH2+SiH4: cationic OH⋯HSi dihydrogen bond versus charge-inverted SiH⋯Si hydrogen bond

The low electronegativity of Si gives rise to a variety of nonconventional intermolecular interactions in clusters of silanes and their derivatives, which have not been well characterized yet. Herein, we characterize the structures of various isomers of bare and Ar-tagged SiH3OH2+SiH4 dimers composed of protonated silanol and silane by infrared photodissociation (IRPD) of mass-selected ions and dispersion-corrected density functional calculations (B3LYP-D3/aug-cc-pVTZ). The analysis of the IRPD spectra recorded in the OH stretch range reveals the competition between two types of nonconventional hydrogen bonds (H-bonds). The first one represents a OH⋯HSi ionic dihydrogen bond (DHB), in which SiH4 interacts with the H2O moiety of SiH3OH2+. The second one represents a charge-inverted SiH⋯Si ionic H-bond (CIHB), in which the SiH4 ligand interacts with the SiH3 moiety of SiH3OH2+. The latter may also be considered as a weak three-centre two-electron (3c-2e) bond. Although both types of H-bonds are computed to have comparable interaction strengths for SiH3OH2+SiH4 (D0 ≈ 35-40 kJ mol-1), DHB isomers dominate the population in the supersonic plasma expansion, while the abundance of CIHB isomers is roughly one order of magnitude lower, probably as a result of entropic factors.

Internal Energy Dependence of the Pyrrole Dimer Cation Structures Formed in a Supersonic Plasma Expansion: Charge-Resonance and Hydrogen-Bonded Isomers

The structures of the pyrrole dimer cation (Py2+) formed in an electron-ionization-driven supersonic plasma expansion of Py seeded in Ar or N2 are probed as a function of its internal energy by infrared photodissociation (IRPD) spectroscopy in a tandem mass spectrometer. The IRPD spectra recorded in the CH and NH stretch ranges are analyzed by dispersion-corrected density functional theory (DFT) calculations at the B3LYP-D3/aug-cc-pVTZ level. The spectra of the cold Ar/N2-tagged Py2+ clusters, Py2+Ln (n = 1-5 for Ar, n = 1 for N2), indicate the exclusive formation of the most stable antiparallel π-stacked Py2+ structure under cold conditions, which is stabilized by charge-resonance interaction. The bare Py2+ dimers produced in the ion source have higher internal energy, and the observation of additional transitions in their IRPD spectra suggests a minor population of less stable hydrogen-bonded isomers composed of heterocyclic Py/Py+ structures formed after intramolecular H atom transfer and ring opening. These intermolecular isomers differ from the chemically bonded structures proposed earlier in the analysis of IRPD spectra of Py2+ generated by VUV ionization of neutral Pyn clusters.

Molecular Structure of Salicylic Acid and Its Hydrates: A Rotational Spectroscopy Study

We present a study of salicylic acid and its hydrates, with up to four water molecules, done by employing chirped-pulse Fourier transform microwave spectroscopy. We employed the spectral data set of the parent, 13C, and 2H isotopologues to determine the molecular structure and characterize the intra- and intermolecular interactions of salicylic acid and its monohydrate. Complementary theoretical calculations were done to support the analysis of the experimental results. For the monomer, we analyzed structural properties, such as the angular-group-induced bond alternation (AGIBA) effect. In the microsolvates, we analyzed their main structural features dominated by the interaction of water with the carboxylic acid group. This work contributes to seeding information on how water molecules accumulate around this group. Moreover, we discussed the role of cooperative effects further stabilizing the observed inter- and intramolecular hydrogen bond interactions.

Conformational Mapping, Interactions, and Fluorine Impact by Combined Spectroscopic Approaches and Quantum Chemical Calculations

Noncovalent interactions and their careful variation can be crucial in understanding molecular structures, conformational topographies, and properties. Here, we examine the fluorination impact on the structure and conformational behavior of 2-(2-fluorophenyl)ethyl alcohol (2-FPEAL) by monitoring the first individual ionization-loss-stimulated Raman spectra of the jet-cooled molecule. The comparison of two different broad-range spectra and predicted equivalents discloses two distinct structures. One possesses a folded side chain (gauche) and the other an extended chain (anti) with the terminal hydrogen atom pointing opposite or toward the fluorine side, indicating the improper previous tentative assignment of the latter. These conformers resemble and differ from the nonfluorinated analogue structures. Theoretical analyses reveal interconversion pathways of 2-FPEAL conformers during expansion and the delicate balance between attractive (C-H···F and O-H···π) and repulsive interactions. These findings show the achievements of our integrated approach, suggesting its potential for overcoming future structural challenges.

Electronic and vibrational spectroscopies of aromatic clusters with He in a supersonic jet: The case of neutral and cationic phenol-Hen (n = 1 and 2)

Van der Waals clusters composed of He and aromatic molecules provide fundamental information about intermolecular interactions in weakly bound systems. In this study, phenol-helium clusters (PhOH-Hen with n ≤ 2) are characterized for the first time by UV and IR spectroscopies. The S1 ← S0 origin and ionization energy both show small but additive shifts, suggesting π-bound structures of these clusters, a conclusion supported by rotational contour analyses of the S1 origin bands. The OH stretching vibrations of the PhOH moiety in the clusters match with those of bare PhOH in both the S0 and D0 states, illustrating the negligible perturbation of the He atoms on the molecular vibration. Matrix shifts induced by He attachment are discussed based on the observed band positions with the help of complementary quantum chemical calculations. For comparison, the UV and ionization spectra of PhOH-Ne are reported as well.

Synergistic Spectroscopic and Computational Characterization Evidencing the Preservation or Flipping of the Hydroxyl Group of 2-Phenylethyl Alcohol upon Single and Double Hydration

Even apparently simple, obtaining and analyzing observations on molecules and clusters and unambiguously assigning their structures is challenging. We report here the first ionization-loss Raman spectra compared to quantum chemical predictions for establishing the structural preferences of hydrates of the neurotransmitters hydroxy analogue, 2-phenylethyl alcohol (PEAL). The spectra encode two monohydrates and two previously unnoticed dihydrates, consequences of water insertion and sidewise attachment to the O-H group of gauche PEALs, in PEAL-H2O and PEAL-(H2O)2, or the higher-energy gauche-trans PEAL in the latter. The electronic structures retain the stable PEAL or flip its O-H to convert the gauche-trans PEAL conformer to the global minimum-energy dihydrate. We disclose conventional and bifurcated hydrogen bonds and electron steric repulsions by noncovalent interaction analysis and correlations between the experimental O-H stretching vibrational frequencies and the O-H and H···X bond lengths and electron densities, pointing to implications on hydrate forms and our approach virtue.

Microhydration of the Pyrrole Cation (Py+) Revealed by IR Spectroscopy: Ionization-Induced Rearrangement of the Hydrogen-Bonded Network of Py+(H2O)2

Microhydration of heterocyclic aromatic molecules can be an appropriate fundamental model to shed light on intermolecular interactions and functions of macromolecules and biomolecules. We characterize herein the microhydration process of the pyrrole cation (Py⁺) by infrared photodissociation (IRPD) spectroscopy and dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). Analysis of IRPD spectra of mass-selected Py⁺(H₂O)₂ and its cold Ar-tagged cluster in the NH and OH stretch range combined with geometric parameters of intermolecular structures, binding energies, and natural atomic charge distribution provides a clear picture of the growth of the hydration shell and cooperativity effects. Py⁺(H₂O)₂ is formed by stepwise hydration of the acidic NH group of Py⁺ by a hydrogen-bonded (H₂O)₂ chain with NH···OH···OH configuration. In this linear H-bonded hydration chain, strong cooperativity, mainly arising from the positive charge, strengthens both the NH···O and OH···O H-bonds with respect to those of Py⁺H₂O and (H₂O)₂, respectively. The linear chain structure of the Py⁺(H₂O)₂ cation is discussed in terms of the ionization-induced rearrangement of the hydration shell of the neutral Py(H₂O)₂ global minimum characterized by the so-called "σ-π bridge structure" featuring a cyclic NH···OH···OH···π H-bonded network. Emission of the π electron from Py by ionization generates a repulsive interaction between the positive π site of Py⁺ and the π-bonded OH hydrogen of (H₂O)₂, thereby breaking this OH···π hydrogen bond and driving the hydration structure toward the linear chain motif of the global minimum on the cation potential.

Ionization energies and ionization-induced structural changes in 2-phenylethylamine and its monohydrate

We report the resonance-enhanced two-photon ionization combined with various detection approaches and quantum chemical calculations of biologically relevant neurotransmitter prototypes, the most stable conformer of 2-phenylethylamine (PEA), and its monohydrate, PEA-H₂O, to reveal the possible interactions between the phenyl ring and amino group in the neutral and ionic species. Extracting the ionization energies (IEs) and appearance energy was achieved by measuring the photoionization and photodissociation efficiency curves of the PEA parent and photofragment ions, together with velocity and kinetic energy-broadened spatial map images of photoelectrons. We obtained coinciding upper bounds for the IEs for PEA and PEA-H₂O of 8.63 ± 0.03 and 8.62 ± 0.04 eV, within the range predicted by quantum calculations. The computed electrostatic potential maps show charge separation, corresponding to a negative charge on phenyl and a positive charge on the ethylamino side chain in the neutral PEA and its monohydrate; in the cations, the charge distributions naturally become positive. The significant changes in geometries upon ionization include switching of the amino group orientation from pyramidal to nearly planar in the monomer but not in the monohydrate, lengthening of the N-H⋯π hydrogen bond (HB) in both species, C_α-C_β bond in the side chain of the PEA⁺ monomer, and the intermolecular O-H⋯N HB in PEA-H₂O cations, leading to distinct exit channels.

Surface or Internal Hydration - Does It Really Matter?

The precise location of an ion or electron, whether it is internally solvated or residing on the surface of a water cluster, remains an intriguing question. Subtle differences in the hydrogen bonding network may lead to a preference for one or the other. Here we discuss spectroscopic probes of the structure of gas-phase hydrated ions in combination with quantum chemistry, as well as H/D exchange as a means of structure elucidation. With the help of nanocalorimetry, we look for thermochemical signatures of surface vs internal solvation. Examples of strongly size-dependent reactivity are reviewed which illustrate the influence of surface vs internal solvation on unimolecular rearrangements of the cluster, as well as on the rate and product distribution of ion-molecule reactions.

Microhydrated clusters of a pharmaceutical drug: infrared spectra and structures of amantadineH+(H2O)n

Solvation of pharmaceutical drugs has an important effect on their structure and function. Analysis of infrared photodissociation spectra of amantadineH⁺(H₂O)_n=1-4 clusters in the sensitive OH, NH, and CH stretch range by quantum chemical calculations (B3LYP-D3/cc-pVTZ) provides a first impression of the interaction of this pharmaceutically active cation with water at the molecular level. The size-dependent frequency shifts reveal detailed information about the acidity of the protons of the NH₃⁺ group of N-protonated amantadineH⁺ (AmaH⁺) and the strength of the NH⋯O and OH⋯O hydrogen bonds (H-bonds) of the hydration network. The preferred cluster growth begins with sequential hydration of the NH₃⁺ group by NH⋯O ionic H-bonds (n = 1-3), followed by the extension of the solvent network through OH⋯O H-bonds. However, smaller populations of cluster isomers with an H-bonded solvent network and free N-H bonds are already observed for n ≥ 2, indicating the subtle competition between noncooperative ion hydration and cooperative H-bonding. Interestingly, cyclic water ring structures are identified for n ≥ 3, each with two NH⋯O and two OH⋯O H-bonds. Despite the increasing destabilization of the N-H proton donor bonds upon gradual hydration, no proton transfer to the (H₂O)_n solvent cluster is observed up to n = 4. In addition to ammonium cluster ions, a small population of microhydrated iminium isomers is also detected, which is substantially lower for the hydrophilic H₂O than for the hydrophobic Ar environment.

Stepwise hydrations of anhydride tuned by hydrogen bonds: rotational study on maleic anhydride-(H2O)1-3

The rotational spectra of maleic anhydride-(H₂O)_1-3 have been investigated for the first time by using pulsed jet Fourier transform microwave spectroscopy with complementary computational analyses. The experimental evidence points out that water tends to self-aggregate with hydrogen bonds and form homodromic cycles. Differences in bond lengths and charge distribution between the two carbonyl sites have been observed upon stepwise hydrations, which might further introduce a selectivity on the nucleophilic attack sites of hydrolysis. This study provides an important insight into the incipient solvation process (microsolvation) of maleic anhydride in water by understanding the cooperation and rearrangement of intermolecular hydrogen bonds in its stepwise hydrates.

Ultrafast Dynamics of Solute Molecules Probed by Resonant Optical Kerr Effect Spectroscopy

Ultrafast molecular dynamics in fluids is of great importance in many biological and chemical systems. Although such dynamics in bulk liquids has been explored by various methods, experimental tools that unveil the dynamics of solvated solutes are limited. In this work, we have developed resonant optical Kerr effect spectroscopy (ROKE), which is an analogue of optical Kerr effect spectroscopy that measures the reorientational relaxation of a dilute solute in solution. By adjusting the pump and probe wavelengths at the resonant absorption band of a solute, the time response of the solute was distinguished easily from the negligible signal of the solvent. The heterodyne detection of ROKE enables the determination of reorientational relaxation time constants with an accuracy of 2.6%. The signal-to-noise ratio was high enough (average ∼26.7) to obtain an adequate signal from even a 10 μM solution. Thus, ROKE is a powerful tool to study solute dynamics with high sensitivity in a broad range of applications.

A combined theoretical and experimental study of small anthracene-water clusters

Water-cluster interactions with polycyclic aromatic hydrocarbons (PAHs) are of paramount interest in many chemical and biological processes. We report a study of anthracene monomers and dimers with water (up to four)-cluster systems utilizing molecular beam vacuum-UV photoionization mass spectrometry and density functional calculations. Structural loss in photoionization efficiency curves when adding water indicates that various isomers are generated, while theory indicates only a slight shift in energy in photoionization states of different isomers. Calculations reveal that the energetic tendency of water is to remain clustered and not to disperse around the PAH. Theoretically, we observe water confinement exclusively in the case of four water clusters and only when the anthracenes are in a cross configuration due to optimal OH⋯π interactions, indicating dependence on the size and structure of the PAH. Furthermore theory sheds light on the structural changes that occur in water upon ionization of anthracene, due to the optimal interactions of the resulting hole and water hydrogen atoms.

Opening of the Diamondoid Cage upon Ionization Probed by Infrared Spectra of the Amantadine Cation Solvated by Ar, N2 , and H2 O

Radical cations of diamondoids, a fundamental class of very stable cyclic hydrocarbon molecules, play an important role in their functionalization reactions and the chemistry of the interstellar medium. Herein, we characterize the structure, energy, and intermolecular interaction of clusters of the amantadine radical cation (Ama⁺, 1‐aminoadamantane) with solvent molecules of different interaction strength by infrared photodissociation (IRPD) spectroscopy of mass‐selected Ama⁺L_n clusters, with L=Ar (n≤3) and L=N₂ and H₂O (n=1), and dispersion‐corrected density functional theory calculations (B3LYP−D3/cc‐pVTZ). Three isomers of Ama⁺ generated by electron ionization are identified by the vibrational properties of their rather different NH₂ groups. The ligands bind preferentially to the acidic NH₂ protons, and the strength of the NH…L ionic H‐bonds are probed by the solvation‐induced red‐shifts in the NH stretch modes. The three Ama⁺ isomers include the most abundant canonical cage isomer (I) produced by vertical ionization, which is separated by appreciable barriers from two bicyclic distonic iminium ions obtained from cage‐opening (primary radical II) and subsequent 1,2 H‐shift (tertiary radical III), the latter of which is the global minimum on the Ama⁺ potential energy surface. The effect of solvation on the energetics of the potential energy profile revealed by the calculations is consistent with the observed relative abundance of the three isomers. Comparison to the adamantane cation indicates that substitution of H by the electron‐donating NH₂ group substantially lowers the barriers for the isomerization reaction.

Selective desolvation in two-step nucleation mechanism steers crystal structure formation

The two-step nucleation (TSN) theory and crystal structure prediction (CSP) techniques are two disjointed yet popular methods to predict nucleation rate and crystal structure, respectively. The TSN theory is a well-established mechanism to describe the nucleation of a wide range of crystalline materials in different solvents. However, it has never been expanded to predict the crystal structure or polymorphism. On the contrary, the existing CSP techniques only empirically account for the solvent effects. As a result, the TSN theory and CSP techniques continue to evolve as separate methods to predict two essential attributes of nucleation - rate and structure. Here we bridge this gap and show for the first time how a crystal structure is formed within the framework of TSN theory. A sequential desolvation mechanism is proposed in TSN, where the first step involves partial desolvation to form dense clusters followed by selective desolvation of functional groups directing the formation of crystal structure. We investigate the effect of the specific interaction on the degree of solvation around different functional groups of glutamic acid molecules using molecular simulations. The simulated energy landscape and activation barriers at increasing supersaturations suggest sequential and selective desolvation. We validate computationally and experimentally that the crystal structure formation and polymorph selection are due to a previously unrecognized consequence of supersaturation-driven asymmetric desolvation of molecules.

Reaction dynamics studied via femtosecond X-ray liquidography at X-ray free-electron lasers

X-ray free-electron lasers (XFELs) provide femtosecond X-ray pulses suitable for pump–probe time-resolved studies with a femtosecond time resolution. Since the advent of the first XFEL in 2009, recent years have witnessed a great number of applications with various pump–probe techniques at XFELs. Among these, time-resolved X-ray liquidography (TRXL) is a powerful method for visualizing structural dynamics in the liquid solution phase. Here, we classify various chemical and biological molecular systems studied via femtosecond TRXL (fs-TRXL) at XFELs, depending on the focus of the studied process, into (i) bond cleavage and formation, (ii) charge distribution and electron transfer, (iii) orientational dynamics, (iv) solvation dynamics, (v) coherent nuclear wavepacket dynamics, and (vi) protein structural dynamics, and provide a brief review on each category. We also lay out a plausible roadmap for future fs-TRXL studies for areas that have not been explored yet.

Femtosecond X-ray liquidography using X-ray free-electron lasers (XFELs) visualizes various aspects of reaction dynamics.

Isomer-Selective Spectroscopy and Dynamics of Phenol-Arn (n ≤ 5) Clusters

Structures and ionization-induced solvation dynamics of phenol-(argon)_n clusters, PhOH-Ar_n (n ≤ 5), were studied by using a variety of isomer-selective photoionization and vibrational spectroscopic techniques. Several higher-energy isomers were found and assigned for the first time by systematically controlling the experimental conditions of the supersonic expansion. This behavior is also confirmed for the PhOH-Kr₂ cluster. Solvation structures are elucidated by evaluating systematic shifts in the S₁ ← S₀ origin and ionization energies obtained by resonance-enhanced photoionization, in addition to the OH stretching frequency obtained by IR photodissociation. Isomer-selective picosecond time-resolved IR spectroscopy for the n = 2 clusters revealed that the dynamics for the ionization-induced intermolecular π → H site-switching reaction strongly depends on the initial isomeric structure. In particular, the reaction time for the (1|1) isomer is 7 ps, while that for (2|0) is <3 ps. This difference shows that the switching time is determined by the distance of the reaction coordinate between the initial π-site and the final OH-site.

Real-time observation of photoionization-induced water migration dynamics in 4-methylformanilide-water by picosecond time-resolved infrared spectroscopy and ab initio molecular dynamics simulations

A novel time-resolved pump-probe spectroscopic approach that enables to keep high resolution in both the time and energy domain, nanosecond excitation-picosecond ionization-picosecond infrared probe (ns-ps-ps TRIR) spectroscopy, has been applied to the trans-4-methylformanilide-water (4MetFA-W) cluster. Water migration dynamics from the CO to the NH binding site in a peptide linkage triggered by photoionization of 4MetFA-W is directly monitored by the ps time evolution of IR spectra, and the presence of an intermediate state is revealed. The time evolution is analyzed by rate equations based on a four-state model of the migration dynamics. Time constants for the initial to the intermediate and hot product and to the final product are obtained. The acceleration of the dynamics by methyl substitution and the strong contribution of intracluster vibrational energy redistribution in the termination of the solvation dynamics is suggested. This picture is well confirmed by the ab initio on-the-fly molecular dynamics simulations. Vibrational assignments of 4MetFA and 4MetFA-W in the neutral (S₀ and S₁) and ionic (D₀) electronic states measured by ns IR dip and electron-impact IR photodissociation spectroscopy are also discussed prior to the results of time-resolved spectroscopy.

Advances in Magnetic Nanoparticles Engineering for Biomedical Applications-A Review

Magnetic iron oxide nanoparticles (MNPs) have been developed and applied for a broad range of biomedical applications, such as diagnostic imaging, magnetic fluid hyperthermia, targeted drug delivery, gene therapy and tissue repair. As one key element, reproducible synthesis routes of MNPs are capable of controlling and adjusting structure, size, shape and magnetic properties are mandatory. In this review, we discuss advanced methods for engineering and utilizing MNPs, such as continuous synthesis approaches using microtechnologies and the biosynthesis of magnetosomes, biotechnological synthesized iron oxide nanoparticles from bacteria. We compare the technologies and resulting MNPs with conventional synthetic routes. Prominent biomedical applications of the MNPs such as diagnostic imaging, magnetic fluid hyperthermia, targeted drug delivery and magnetic actuation in micro/nanorobots will be presented.

Solution and Solid-State Photophysical Properties of Positional Isomeric Acrylonitrile Derivatives with Core Pyridine and Phenyl Moieties: Experimental and DFT Studies

The compounds I (Z)-2-(phenyl)-3-(2,4,5-trimethoxyphenyl)acrylonitrile with one side (2,4,5-MeO-), one symmetrical (2Z,2'Z)-2,2'-(1,4-phenylene)bis(3-(2,4,5-trimethoxyphenyl)acrylonitrile), II (both sides with (2,4,5-MeO-), and three positional isomers with pyridine (Z)-2-(pyridin-2- 3, or 4-yl)-3-(2,4,5-trimethoxyphenyl)acrylonitrile, III-V were synthetized and characterized by UV-Vis, fluorescence, IR, H1-NMR, and EI mass spectrometry as well as single crystal X-ray diffraction (SCXRD). The optical properties were strongly influenced by the solvent (hyperchromic and hypochromic shift), which were compared with the solid state. According to the solvatochromism theory, the excited-state (μe) and ground-state (μg) dipole moments were calculated based on the variation of Stokes shift with the solvent's relative permittivity, refractive index, and polarity parameters. SCXRD analyses revealed that the compounds I and II crystallized in the monoclinic system with the space group, P21/n and P21/c, respectively, and with Z = 4 and 2. III, IV, and V crystallized in space groups: orthorhombic, Pbca; triclinic, P-1; and monoclinic, P21 with Z = 1, 2, and 2, respectively. The intermolecular interactions for compounds I-V were investigated using the CCDC Mercury software and their energies were quantified using PIXEL. The density of states (DOS), molecular electrostatic potential surfaces (MEPS), and natural bond orbitals (NBO) of the compounds were determined to evaluate the photophysical properties.

Experimental observation of the unique solvation process along multiple solvation coordinates of photodissociated products

Chemical reaction dynamics in solution are closely related to solvation dynamics, and understanding solvent responses remains a crucial issue in chemistry and chemical biology. In this study, we experimentally and computationally investigated the solvation dynamics along different solvation coordinates of the same molecule: the electronically excited state and ground state of the p-aminophenylthiyl radical generated by the photodissociation of bis(p-aminophenyl)disulfide. Time profiles of the peak shifts from the transient absorption and emission spectra after photodissociation were extracted to discuss the solvent reorganization process in various ionic liquids (ILs) with different viscosities. The absorption peak position of the radical followed common solvation dynamics, shifting to a lower energy with time due to reorganization of the surrounding solvent molecules in response to the charge redistribution and molecular volume change caused by photodissociation. On the other hand, the emission band of the radical did not show a meaningful spectral shift with time. It was also found that the solvation time in the ground state was not strongly dependent on the solvent viscosity. These experimental results deviate from the conventional dynamic Stokes shift theory. To discuss the experimental results, non-equilibrium molecular dynamics simulations were conducted. The spectral shift obtained by MD simulations indicated the existence of a large solvation energy change and solvation dynamics around the radical after the photodissociation. On the other hand, the electronic excitation of the radical brought about a relatively smaller solvation energy change, especially at the long delay time after the photodissociation. These differences might be one of the reasons for the unique experimentally observed solvation dynamics.

Tuning Local Hydration Enables a Deeper Understanding of Protein-Ligand Binding: The PP1-Src Kinase Case

Water plays a key role in biomolecular recognition and binding. Despite the development of several computational and experimental approaches, it is still challenging to comprehensively characterize water-mediated effects on the binding process. Here, we investigate how water affects the binding of Src kinase to one of its inhibitors, PP1. Src kinase is a target for treating several diseases, including cancer. We use biased molecular dynamics simulations, where the hydration of predetermined regions is tuned at will. This computational technique efficiently accelerates the SRC-PP1 binding simulation and allows us to identify several key and yet unexplored aspects of the solvent's role. This study provides a further perspective on the binding phenomenon, which may advance the current drug design approaches for the development of new kinase inhibitors.

Microhydration of substituted diamondoid radical cations of biological relevance: infrared spectra of amantadine+-(H2O)n = 1-3 clusters

Hydration of biomolecules and pharmaceutical compounds has a strong impact on their structure, reactivity, and function. Herein, we explore the microhydration structure around the radical cation of the widespread pharmaceutical drug amantadine (C16H15NH2, Ama) by infrared photodissociation (IRPD) spectroscopy of mass-selected Ama+Wn = 1-3 clusters (W = H2O) recorded in the NH, CH, and OH stretch range of the cation ground electronic state. Analysis of the size-dependent frequency shifts by dispersion-corrected density functional theory calculations (B3LYP-D3/cc-pVTZ) provides detailed information about the acidity of the protons of the NH2 group of Ama+ and the structure and strength of the NHO and OHO hydrogen bonds (H-bonds) of the hydration network. The preferred sequential cluster growth begins with hydration of the two acidic NH protons of the NH2 group (n = 1-2) and continues with an extension of the H-bonded hydration network by forming an OHO H-bond of the third W to one ligand in the first hydration subshell (n = 3), like in the W2 dimer. For n = 2, a minor population corresponds to Ama+W2 structures with a W2 unit attached to Ama+via a NHW2 H-bond. Although the N-H proton donor bonds are progressively destabilized by gradual microhydration, no proton transfer to the Wn solvent cluster is observed in the investigated size range (n ≤ 3). Besides the microhydration structure, we also obtain a first impression of the structure and IR spectrum of bare Ama+, as well as the effects of both ionization and hydration on the structure of the adamantyl cage. Comparison of Ama+ with aliphatic and aromatic primary amine radical cations reveals differences in the acidity of the NH2 group and the resulting interaction with W caused by substitution of the cycloalkyl cage.

Molecule-Based Transistors: From Macroscale to Single Molecule

Molecule-based field-effect transistors (FETs) are of great significance as they have a wide range of application prospects, such as logic operations, information storage and sensor monitoring. This account mainly introduces and reviews our recent work in molecular FETs. Specifically, through molecular and device design, we have systematically investigated the construction and performance of FETs from macroscale to nanoscale and even single molecule. In particular, we have proposed the broad concept of molecular FETs, whose functions can be achieved through various external controls, such as light stimulation, and other physical, chemical or biological interactions. In the end, we tend to focus the discussion on the development challenges of single-molecule FETs, and propose prospects for further breakthroughs in this field.

Gas-Phase Synthesis and Characterization of the Methyl-2,2-dicyanoacetate Anion Using Photoelectron Imaging and Dipole-Bound State Autodetachment

The methyl-2,2-dicyanoacetate anion is synthesized in an electrospray ionization source through a gas-phase reaction involving tetracyanoethylene and methanol. Photoelectron imaging is used to determine the isomeric form of the product. The photoelectron spectra and angular distributions are consistent with only a single isomer. Additionally, mode-specific vibrational autodetachment is observed. This can be correlated with the emission from a photoexcited dipole-bound state by considering the IR spectrum of the neutral molecule, adding further confirmation of the isomeric form and providing a binding energy of the dipole-bound state. Our experiments show how conventional photoelectron imaging can be used to determine detailed information about gas-phase reaction products.

Microhydration of protonated biomolecular building blocks: protonated pyrimidine

Protonation and hydration of biomolecules govern their structure, conformation, and function. Herein, we explore the microhydration structure in mass-selected protonated pyrimidine-water clusters (H⁺Pym-W_n, n = 1-4) by a combination of infrared photodissociation spectroscopy (IRPD) between 2450 and 3900 cm^-1 and density functional theory (DFT) calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level. We further present the IR spectrum of H⁺Pym-N₂ to evaluate the effect of solvent polarity on the intrinsic molecular parameters of H⁺Pym. Our combined spectroscopic and computational approach unequivocally shows that protonation of Pym occurs at one of the two equivalent basic ring N atoms and that the ligands in H⁺Pym-L (L = N₂ or W) preferentially form linear H-bonds to the resulting acidic NH group. Successive addition of water ligands results in the formation of a H-bonded solvent network which increasingly weakens the NH group. Despite substantial activation of the N-H bond upon microhydration, no intracluster proton transfer occurs up to n = 4 because of the balance of relative proton affinities of Pym and W_n and the involved solvation energies. Comparison to neutral Pym-W_n clusters reveals the drastic effects of protonation on microhydration with respect to both structure and interaction strength.

From atoms to aerosols: probing clusters and nanoparticles with synchrotron based mass spectrometry and X-ray spectroscopy

Synchrotron radiation provides insight into spectroscopy and dynamics in clusters and nanoparticles.

Oxygen K-shell spectroscopy of isolated progressively solvated peptide

X-ray spectroscopy of an isolated controllably hydrated peptide: core excitation of the first solvation shell enhances peptide backbone fragmentation.

Ionization-Induced π → H Site Switching in Resorcinol-Arn (n = 1 and 2) Clusters Probed by Infrared Spectroscopy

Infrared (IR) spectra of resorcinol (Rs)-Ar_n clusters (n = 1 and 2) have been measured in the neutral and cationic ground states (S₀ and D₀) by IR dip and resonance-enhanced multiphoton ionization (REMPI)-IR spectroscopy. The OH stretching vibrations in S₀ keep their frequency regardless of the number of Ar atoms and the conformation of the OH groups in Rs (rotamers RsI and RsII), demonstrating that the Ar atoms are attached to the aromatic π-ring (π-bound structure) in S₀. In the D₀ state, the IR spectra of Rs⁺-Ar_n reflect the difference in the Rs conformations (RsI⁺ and RsII⁺). For n = 1, the IR spectra of both rotamers are almost the same as those of the corresponding monomer cations, indicating that Ar ligands essentially remain π-bonded after ionization. In contrast, the IR spectra of Rs⁺-Ar₂ show hydrogen-bonded and free OH stretching vibrations, demonstrating that for a significant fraction of the clusters, the Ar atoms migrate from the π-bound site to the OH groups. The ionization-induced π → H migration yields are not unity for both rotamers RsI⁺-Ar₂ and RsII⁺-Ar₂. This result is in sharp contrast to phenol⁺-Ar₂, in which one of the Ar atoms migrates to the OH site with 100% yield. The mechanism leading to the nonunity yield in Rs⁺-Ar₂ is discussed in terms of the number of OH binding sites and Franck-Condon factors. The ionization excess energy dependence of the IR spectra of Rs⁺-Ar₂ and its Rs⁺-Ar fragments is discussed in terms of the Ar binding energies estimated from the photoionization and photodissociation efficiency spectra.

Probing the Solute-Solvent Interaction of an Azo-Bonded Prodrug in Neat and Binary Media: Combined Experimental and Computational Study

Preferential solvation has significant importance in interpreting the molecular physicochemical properties of wide spectrum of materials in solution. In this work, the solute-solvent interaction of pro-drug Sulfasalazine (SSZ) in neat and binary media was investigated experimentally and computationally. The solute-solvent interactions of interest were spectrophotometrically probed and computationally investigated for providing insights concerning the molecular aspects of SSZ:media interaction. Experimentally, the obtained results in 1,4-dioxane:water binary mixture demonstrated a dramatic non-linear changes in the spectral behavior of SSZ indicative of the dependency of its molecular behaviors on the compositions of the molecular microenvironment in the essence of solute-solvent interaction. Computationally, geometry optimization and simulation of the absorption spectra of SSZ in media of interest were performed employing DFT and TD-DFT methods, respectively, where the solvent effects on the absorption were examined implicitly using IEFPCM method. Obtained results revealed a nonpolar nature of the molecular orbitals that are directly involved in the SSZ:medium interaction. As in good correspondence with the experimental results, these simulations demonstrated that these orbitals are of non-polar nature and hence minimally affected by polarity of the media and in turn favoring the non-polar molecular environments. On the other hand, the molecular origin of SSZ:media interaction was demonstrated explicitly through complexation of SSZ with water molecules revealing a cooperative hydrogen bonding stabilization with an average length of 1.90 Å. The findings of this work demonstrate the significance of the preferential solvation and composition of the molecular microenvironment on the physicochemical properties of molecules of pharmaceutical importance.

Microhydration of protonated 5-hydroxyindole revealed by infrared spectroscopy

Controlled microsolvation of protonated aromatic biomolecules with water is fundamental to understand proton transfer reactions in aqueous environments. We measured infrared photodissociation (IRPD) spectra of mass-selected microhydrates of protonated 5-hydroxyindole (5HIH+-Wn, W = H2O, n = 1-3) in the OH and NH stretch ranges (2700-3800 cm-1), which are sensitive to the spectroscopic characteristics of interior solvation, water network formation, and proton transfer to solvent. Analysis of the IRPD spectra by dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ) reveals the coexistence of C3- and C4-protonated carbenium ions, 5HIH+(C3) and 5HIH+(C4), as well as the O-protonated oxonium ion, 5HIH+(O). Monohydrated 5HIH+-W clusters are formed by hydrogen-bonding (H-bonding) of the first water to the most acidic functional group, namely, the NH group in the case of 5HIH+(C3), the OH group for 5HIH+(C4), and the OH2 group for 5HIH+(O). The latter benefits from its twofold degeneracy and the outstandingly high binding energy of D0 ∼ 100 kJ mol-1. Larger 5HIH+-W2/3 clusters preferably grow (i) by H-bonding of the second water to the remaining vacant functional group and and/or (ii) by formation of W2 water chains at the respective most acidic functional group. Our IRPD spectra of 5HIH+-Wn do not indicate any proton transfer to the solvent up to n = 3, in line with the proton affinities of 5HI and Wn. Comparison of 5HIH+-Wn to neutral 5HI-W and cationic 5HI+-Wn clusters elucidates the impact of different charge states on the topology of the initial solvation shell. Furthermore, to access the influence of the size of the arene ion and a second functional group, we draw a comparison to microhydration of protonated phenol.

Ion-peptide interactions between alkali metal ions and a termini-protected dipeptide: modeling a portion of the selectivity filter in K+ channels

Potassium channels have the unique ability to allow the selective passage of potassium ions at near diffusion-free rates while inhibiting the passage of more abundant sodium ions. Local interactions between chemical functional groups and the ions are responsible for both selectivity and transport. As an initial step in characterizing these interactions, the structures of Na+ and K+ complexed to the Ac-Tyr-NHMe peptide have been determined from infrared laser spectroscopy and supporting ab initio calculations. Ac-Tyr-NHMe, a termini-protected peptide sequence, replicates the GYG portion of one of the four peptide chains comprising the selectivity filter of a K+ channel. This peptide contains two carbonyl groups, among the eight C[double bond, length as m-dash]O groups forming the S1 binding site of the selectivity filter. Three conformations have been identified for both ions by laser IR-IR double resonance methods. Two conformations have the ion bound to the two C[double bond, length as m-dash]O groups. The third conformation has, in addition, a cation-π interaction with the aromatic ring of tyrosine, i.e. tridentate binding. The relative contributions of the three conformers are approximately the same for K+Ac-Tyr-NHMe, while the tridentate conformer is preferred for Na+Ac-Tyr-NHMe. These differences will be discussed in the context of ion mobility and selectivity.

The complete conformational panorama of formanilide–water complexes: the role of water as a conformational switch

Different interactions of water and formanilide were observed. Water reverts the stability of the cis–trans formanilide conformational equilibrium.

Probing solvation and reactivity in ionized polycyclic aromatic hydrocarbon–water clusters with photoionization mass spectrometry and electronic structure calculations

Synchrotron based mass spectrometry coupled with theoretical calculations provides insight into polycyclic aromatic hydrocarbon water interactions.

Infrared photodissociation spectroscopy of ion-radical networks in cationic dimethylamine complexes

Infrared photodissociation spectroscopy was employed to establish the general trends in the stepwise growth motif of cationic dimethylamine (DMA)n+ (n = 4-13) complexes. Electronic structure calculations were performed to identify the structure of the low-lying isomers and to assign the observed spectral features. The results showed the preference of the formation of the proton-transferred (CH3)2NH2+ ion core. The (CH3)2NH2+-[(CH3)2N] ion-radical pair contact and the ion-radical separated pair could coexist at n = 4. The [(CH3)2N] radical is separated from the (CH3)2NH2+ ion core by one DMA molecule at n = 4-6 and by two or more DMA molecules in the larger clusters. This suggests that the (CH3)2NH2+-[(CH3)2N] ion-radical contact pair is not stable in the subsequent radiation-induced processes of DMA, and the [(CH3)2N] radical is released from the charged site in the cationic DMA networks.

Photophysics of Protonated and Microhydrated 2-Aminobenzaldehyde: Theoretical Insights into Photoswitchability of Protonated Systems

The photoswitchability of a protonated aromatic compound (2-aminobenzaldehyde, 2ABZH⁺) in its individual and microhydrated states has been addressed based on the RI-MP2/RI-CC2 theoretical methods. Our calculated results give insight into the ultrafast nonradiative deactivation mechanism of the 2ABZH⁺, driven by a conical intersection between the S₁/ S₀ potential energy surfaces. Also, it has been predicted that protonation accompanies a significant blue shift effect on the first ¹ππ* excited state of 2ABZ by 0.87 eV (at least 50 nm).

Unmasking Rare, Large-Amplitude Motions in D2-Tagged I-·(H2O)2 Isotopomers with Two-Color, Infrared-Infrared Vibrational Predissociation Spectroscopy

We describe a two-color, isotopomer-selective infrared-infrared population-labeling method that can monitor very slow spectral diffusion of OH oscillators in H-bonded networks and apply it to the I^-·(HDO)·(D₂O) and I^-·(H₂O)·(D₂O) systems, which are cryogenically cooled and D₂-tagged at an ion trap temperature of 15 K. These measurements reveal very large (>400 cm^-1), spontaneous spectral shifts despite the fact that the predissociation spectra in the OH stretching region of both isotopologues are sharp and readily assigned to four fundamentals of largely decoupled OH oscillators held in a cyclic H-bonded network. This spectral diffusion is not observed in the untagged isotopologues of the dihydrate clusters that are generated under the same source conditions but does become apparent at about 75 K. These results are discussed in the context of the large-amplitude "jump" mechanism for H-bond relaxation dynamics advanced by Laage and Hynes in an experimental scenario where rare events can be captured by following the migration of OH groups among the four available positions in the quasi-rigid equilibrium structure.

Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents

Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o-cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o-cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o-cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260-280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o-cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o-cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively.

Microhydration of PAH+ cations: evolution of hydration network in naphthalene+-(H2O) n clusters (n ≤ 5)

The interaction of polycyclic aromatic hydrocarbon molecules with water (H2O = W) is of fundamental importance in chemistry and biology. Herein, size-selected microhydrated naphthalene cation nanoclusters, Np+-W n (n ≤ 5), are characterized by infrared photodissociation (IRPD) spectroscopy in the C-H and O-H stretch range to follow the stepwise evolution of the hydration network around this prototypical PAH+ cation. The IRPD spectra are highly sensitive to the hydration structure and are analyzed by dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ) to determine the predominant structural isomers. For n = 1, W forms a bifurcated CH···O ionic hydrogen bond (H-bond) to two acidic CH protons of the bicyclic ring. For n ≥ 2, the formation of H-bonded solvent networks dominates over interior ion solvation, because of strong cooperativity in the former case. For n ≥ 3, cyclic W n solvent structures are attached to the CH protons of Np+. However, while for n = 3 the W3 ring binds in the CH···O plane to Np+, for n ≥ 4 the cyclic W n clusters are additionally stabilized by stacking interactions, leading to sandwich-type configurations. No intracluster proton transfer from Np+ to the W n solvent is observed in the studied size range (n ≤ 5), because of the high proton affinity of the naphthyl radical compared to W n . This is different from microhydrated benzene+ clusters, (Bz-W n )+, for which proton transfer is energetically favorable for n ≥ 4 due to the much lower proton affinity of the phenyl radical. Hence, because of the presence of polycyclic rings, the interaction of PAH+ cations with W is qualitatively different from that of monocyclic Bz+ with respect to interaction strength, structure of the hydration shell, and chemical reactivity. These differences are rationalized and quantified by quantum chemical analysis using the natural bond orbital (NBO) and noncovalent interaction (NCI) approaches.

Real-time observation of the photoionization-induced water rearrangement dynamics in the 5-hydroxyindole-water cluster by time-resolved IR spectroscopy

Solvation plays an essential role in controlling the mechanism and dynamics of chemical reactions in solution. The present study reveals that changes in the local solute-solvent interaction have a great impact on the timescale of solvent rearrangement dynamics. Time-resolved IR spectroscopy has been applied to a hydration rearrangement reaction in the monohydrated 5-hydroxyindole-water cluster induced by photoionization of the solute molecule. The water molecule changes the stable hydration site from the indolic NH site to the substituent OH site, both of which provide a strongly attractive potential for hydration. The rearrangement time constant amounts to 8 ± 2 ns, and is further slowed down by a factor of more than five at lower excess energy. These rearrangement times are slower by about three orders of magnitude than those reported for related systems where the water molecule is repelled from a repulsive part of the interaction potential toward an attractive well. The excess energy dependence of the time constant is well reproduced by RRKM theory. Differences in the reaction mechanism are discussed on the basis of energy relaxation dynamics.

Stepwise microhydration of aromatic amide cations: water solvation networks revealed by the infrared spectra of acetanilide+-(H2O)n clusters (n ≤ 3)

The structure and activity of peptides and proteins strongly rely on their charge state and the interaction with their hydration environment. Here, infrared photodissociation (IRPD) spectra of size-selected microhydrated clusters of cationic acetanilide (AA⁺, N-phenylacetamide), AA⁺-(H₂O)_n with n ≤ 3, are analysed by dispersion-corrected density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the stepwise microhydration process of this aromatic peptide model. The IRPD spectra are recorded in the informative X-H stretch (ν_OH, ν_NH, ν_CH, amide A, 2800-3800 cm^-1) and fingerprint (amide I-II, 1000-1900 cm^-1) ranges to probe the preferred hydration motifs and the cluster growth. In the most stable AA⁺-(H₂O)_n structures, the H₂O ligands solvate the acidic NH proton of the amide by forming a hydrogen-bonded solvent network, which strongly benefits from cooperative effects arising from the excess positive charge. Comparison with neutral AA-H₂O reveals the strong impact of ionization on the acidity of the NH proton and the topology of the interaction potential. Comparison with related hydrated formanilide clusters demonstrates the influence of methylation of the amide group (H → CH₃) on the shape of the intermolecular potential and the structure of the hydration shell.