Hydration water drives the self-assembly of guanosine monophosphate.

Guanosine monophosphate (GMP) is a nucleotide that can self-assemble in aqueous solution under certain conditions. An understanding of the process at the molecular level is an essential step to comprehend the involvement of DNA substructures in transcription and replication, as well as their relationship to genetic diseases such as cancer. We present the temperature-dependent terahertz (1.5-12 THz, 50-400 cm-1) absorptivity spectra of aqueous Na2 GMP solution in comparison with the aqueous solutions of other RNA nucleotides. Distinct absorption features were observed in the spectrum of GMP, which we attribute to the intramolecular modes of the self-assemblies (i.e., G-complexes) that, at 1 M, start to form at 313 K and below. Changes in broad-band features of the terahertz spectrum were also observed, which we associate with the release of hydration water in the temperature-dependent formation of guanine quadruplexes. Using a state-of-the-art THz calorimetry approach correlating spectroscopic to thermodynamic changes, we propose a molecular mechanism of hydrophilic hydration driving GMP self-assembly as a function of temperature. The free energy contribution of hydrophilic hydration is shown as a decisive factor in guanine-quadruplex formation. Our findings spotlight the role of hydration in the formation of macromolecular structures and suggest the potential of hydration tuning for regulating DNA transcription and replication.

Studying Local Electrostatics by Terahertz Spectroscopy Using Amines as a Probe.

In a previous study[1] we could show that a large amplitude mode of the zwitterion glycine can serve as a sensitive probe for protonation and allows to deduce local pKa values. Here we show that the underlying concept is more general: We present the results of a pH dependent measurement of Terahertz-FTIR (THz-FTIR) spectra of solvated amines, i. e. Diethylamine (DEA), Triethylamine (TEA), and Diisopropylamine (DiPA). We show that amines serve as a sensitive, label free probe for local protonation. Protonation of the amines yield intensity changes which can be quantified by precise THz spectroscopy (30 cm-1 -450 cm-1 ). A detailed analysis allows us to correlate the titration spectra of solvated amines in the THz range with pKa values. This demonstrates the potential of THz spectroscopy to probe the charge state of biomolecules in water in a label free manner.

Structural Characterization of Pyruvic Acid Dimers Formed inside Helium Nanodroplets by Infrared Spectroscopy and Ab Initio Study.

The structural arrangements of α-keto acid complexes hold significant interest across various fields of chemistry such as enzyme modeling, drug design, or polymer blending. Herein, we report mass-selective infrared (IR) spectra of pyruvic acid monomers and dimers in the range 1720-1820 cm-1 recorded in helium nanodroplets at 0.37 K. The monomer features IR bands at 1807.1 and 1734.5 cm-1, which are assigned to the carboxylic and ketonic C═O stretching vibrations, respectively. Furthermore, the pyruvic acid dimers generated inside the helium nanodroplets are characterized by carboxylic and ketonic C═O stretch vibrations appearing at 1799.2 and 1737.0 cm-1, respectively. This frequency shift of ±7 cm-1 for both C═O stretching bands from the monomer to the dimer demonstrates that the structural motif of the monomer is maintained upon dimer aggregation in helium nanodroplets. The structural assignments were supported by a comparison of the MP2/aug-cc-pVDZ-predicted harmonic vibrational spectra at the C═O stretching region with the experiments. The global minimum monomer structure with an intramolecular hydrogen bond and its dimer stabilized by both inter- and intramolecular hydrogen bonding interactions reproduce the experimental spectra from the monomer and dimer. This assigned dimer structure lies ca.11 kJ/mol above the corresponding global minimum and is favored in helium nanodroplets due to the long-range realignment of molecules via dipole-dipole interaction, followed by short-range stabilization upon intermolecular hydrogen bond formation. The barrier for reconfiguration of the precooled monomer conformer leading to the formation of the most stable dimer structure is around 58 kJ/mol, which is infeasible at 0.37 K.

Stripping away ion hydration shells in electrical double-layer formation: Water networks matter.

The double layer at the solid/electrolyte interface is a key concept in electrochemistry. Here, we present an experimental study combined with simulations, which provides a molecular picture of the double-layer formation under applied voltage. By THz spectroscopy we are able to follow the stripping away of the cation/anion hydration shells for an NaCl electrolyte at the Au surface when decreasing/increasing the bias potential. While Na+ is attracted toward the electrode at the smallest applied negative potentials, stripping of the Cl- hydration shell is observed only at higher potential values. These phenomena are directly measured by THz spectroscopy with ultrabright synchrotron light as a source and rationalized by accompanying molecular dynamics simulations and electronic-structure calculations.

Real-time measure of solvation free energy changes upon liquid-liquid phase separation of α-elastin.

Biological condensates are known to retain a large fraction of water to remain in a liquid and reversible state. Local solvation contributions from water hydrating hydrophilic and hydrophobic protein surfaces were proposed to play a prominent role for the formation of condensates through liquid-liquid phase separation (LLPS). However, although the total free energy is accessible by calorimetry, the partial solvent contributions to the free energy changes upon LLPS remained experimentally inaccessible so far. Here, we show that the recently developed THz calorimetry approach allows to quantify local hydration enthalpy and entropy changes upon LLPS of α-elastin in real time, directly from experimental THz spectroscopy data. We find that hydrophobic solvation dominates the entropic solvation term, whereas hydrophilic solvation mainly contributes to the enthalpy. Both terms are in the order of hundreds of kJ/mol, which is more than one order of magnitude larger than the total free energy changes at play during LLPS. However, since we show that entropy/enthalpy mostly compensates, a small entropy/enthalpy imbalance is sufficient to tune LLPS. Theoretically, a balance was proposed before. Here we present experimental evidence based on our spectroscopic approach. We finally show that LLPS can be steered by inducing small changes of solvation entropy/enthalpy compensation via concentration or temperature in α-elastin.

Highly Altered State of Proton Transport in Acid Pools in Charged Reverse Micelles.

Transport mechanisms of solvated protons of 1 M HCl acid pools, confined within reverse micelles (RMs) containing the negatively charged surfactant sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) or the positively charged cetyltrimethylammonium bromide (CTABr), are analyzed with reactive force field simulations to interpret dynamical signatures from TeraHertz absorption and dielectric relaxation spectroscopy. We find that the forward proton hopping events for NaAOT are further suppressed compared to a nonionic RM, while the Grotthuss mechanism ceases altogether for CTABr. We attribute the sluggish proton dynamics for both charged RMs as due to headgroup and counterion charges that expel hydronium and chloride ions from the interface and into the bulk interior, thereby increasing the pH of the acid pools relative to the nonionic RM. For charged NaAOT and CTABr RMs, the localization of hydronium near a counterion or conjugate base reduces the Eigen and Zundel configurations that enable forward hopping. Thus, localized oscillatory hopping dominates, an effect that is most extreme for CTABr in which the proton residence time increases dramatically such that even oscillatory hopping is slow.

An isolated water droplet in the aqueous solution of a supramolecular tetrahedral cage.

Water under nanoconfinement at ambient conditions has exhibited low-dimensional ice formation and liquid-solid phase transitions, but with structural and dynamical signatures that map onto known regions of water's phase diagram. Using terahertz (THz) absorption spectroscopy and ab initio molecular dynamics, we have investigated the ambient water confined in a supramolecular tetrahedral assembly, and determined that a dynamically distinct network of 9 ± 1 water molecules is present within the nanocavity of the host. The low-frequency absorption spectrum and theoretical analysis of the water in the Ga4L612- host demonstrate that the structure and dynamics of the encapsulated droplet is distinct from any known phase of water. A further inference is that the release of the highly unusual encapsulated water droplet creates a strong thermodynamic driver for the high-affinity binding of guests in aqueous solution for the Ga4L612- supramolecular construct.

Zwitter Ionization of Glycine at Outer Space Conditions due to Microhydration by Six Water Molecules.

We investigate glycine microsolvation with water molecules, mimicking astrophysical conditions, in our laboratory by embedding these clusters in helium nanodroplets at 0.37 K. We recorded mass selective infrared spectra in the frequency range 1500-1800 cm^{-1} where two bands centered at 1630 and 1724 cm^{-1} were observed. By comparison with the extensive accompanying calculations, the band at 1630 cm^{-1} was assigned to the COO^{-} asymmetric stretching mode of the zwitter ion and the band at 1724 cm^{-1} was assigned to redshifted C=O stretch within neutral clusters. We show that zwitter ion formation of amino acids readily occurs with only few water molecules available even under extreme conditions.

Reaction of lithium hexamethyldisilazide (LiHMDS) with water at ultracold conditions.

Alkali metal amides are highly reactive reagents that are broadly applied as strong bases in organic synthesis. Here, we use a combined helium nanodroplet IR spectroscopic and theoretical (DFT calculation) study to show that the reaction of the model compound lithium hexamethyldisilazide (LiHMDS) with water is close to barrierless even at ultra-cold conditions. Upon complex formation of dimeric (LiHMDS)2 with water in helium nanodroplets as ultra-cold nano-reactors (0.37 K) we observed the reaction product (LiOH)2(HMDS)2. This can be rationalized as aggregation induced reation upon stepwise addition of water. With increasing water partial pressure, only the product (LiOH)2(HMDS)2 is observed experimentally. This implies that the large interaction energy (69 kJ mol-1) of (LiHMDS)2 with water is sufficient to overcome the follow-up reaction barriers, in spite of the rapid cooling rates in He nanodroplets.

Observation of dissipating solvated protons upon hydrogel formation.

Aqueous hyaluronan solutions form an elastic hydrogel within a narrow pH range, around pH 2.4, making this a model system to study the conformational changes of the hydrogen bond network upon gelation. This pH-dependent behavior allows us to probe water surrounding a biologically relevant molecule in different environments (liquid versus elastic state) which change due to an environmental stimulus. Here, we use Terahertz (THz) reflection absorption spectroscopy in attenuated total reflection (ATR) geometry as a tool to study gelation. THz spectroscopy is sensitive to changes in the hydrogen-bonded water network, and here we show that we can correlate changes in macroscopic properties to changes in the solvation of hyaluronan. Above and below the gelation pH, solvated protons are present in the solutions, however, this spectral signature is completely absent between pH 2.4-2.8, which is the pH at which hyaluronan forms a hydrogel. We propose that solvated protons are forming ion pairs with hyaluronan in this pH range. Adding urea or glucose to hyaluronan solutions changes their elasticity, in which an increase or decrease in elasticity can be linked to the formation and destruction of these ion pairs, respectively.

Nanoconfinement effects on water in narrow graphene-based slit pores as revealed by THz spectroscopy.

The properties of water at interfaces have long been known to differ from those of bulk water in many distinctive ways. More recently, specific confinement effects different from mere interfacial effects have been discovered upon enclosing water in very narrow cylindrical pores and planar surfaces as offered by nanotubes and slit pores, respectively. Using experimental and theoretical THz spectroscopy, we elucidate nanoconfinement effects on the H-bond network of stratified water lamellae that are hosted within graphene-based two-dimensional pores. Characteristic confinement-induced changes of the THz response are traced back to the level of structural dynamics, notably distinct resonances due to intralayer and interlayer H-bonds at correspondingly low and high intermolecular stretching frequencies and impact of dangling (free) OH bonds at the water-graphene interface that enormously broaden the librational band in sufficiently narrow pores. The interplay of these molecular effects causes characteristic changes of the THz lineshape upon nanoconfining water.

Spectroscopic Fingerprints of Cavity Formation and Solute Insertion as a Measure of Hydration Entropic Loss and Enthalpic Gain.

Hydration free energies are dictated by a subtle balance of hydrophobic and hydrophilic interactions. We present here a spectroscopic approach, which gives direct access to the two main contributions: Using THz-spectroscopy to probe the frequency range of the intermolecular stretch (150-200 cm-1 ) and the hindered rotations (450-600 cm-1 ), the local contributions due to cavity formation and hydrophilic interactions can be traced back. We show that via THz calorimetry these fingerprints can be correlated 1 : 1 with the group specific solvation entropy and enthalpy. This allows to deduce separately the hydrophobic (i.e. cavity formation) and hydrophilic contributions to thermodynamics, as shown for hydrated alcohols as a case study. Accompanying molecular dynamics simulations quantitatively support our experimental results. In the future our approach will allow to dissect hydration contributions in inhomogeneous mixtures and under non-equilibrium conditions.

An infrared spectroscopic study of trifluoromethoxybenzene⋯methanol complexes formed in superfluid helium nanodroplets.

We have studied the intermolecular complex formation between trifluoromethoxybenzene and methanol (CD3OD) in superfluid helium droplets by infrared spectroscopy in the spectral range of 2630-2730 cm-1, covering the O-D stretches of methanol-d4 (CD3OD). The cluster size associated with the observed bands is deduced from the variation of infrared intensity of a particular band with the partial pressures of trifluoromethoxybenzene and methanol. Quantum chemical calculations are performed at the MP2/6-311++G(d,p) level of theory to complement the experimental results. As a result, we have identified six different conformers of the trifluoromethoxybenzene⋯methanol intermolecular complex: three bound via O-H⋯O hydrogen bonds and the other three via O-H⋯π hydrogen bonds. Furthermore, to access the effect of fluorination on the methyl unit of anisole molecules, we compare the IR spectrum of trifluoromethoxybenzene (C6H5OCF3)⋯methanol with our earlier reported spectrum of anisole (C6H5OCH3)⋯methanol.

Unravelling the microhydration frameworks of prototype PAH by infrared spectroscopy: naphthalene-(water)1-3.

Hydration of aromatic molecules is a fundamental chemical process. Herein, microhydration framework of the prototypical neutral polycyclic aromatic hydrocarbon (PAH), naphthalene (naphthalene-(water)n≤3), is investigated by infrared spectroscopy inside helium nanodroplets. The measured data are analyzed by quantum chemical calculations at the MP2/6-311++G(d,p) level. This combined experimental and theoretical approach demonstrates that water binds to the naphthalene ring via π hydrogen bond (H-bond) for n = 1 case. Further addition of the solvent molecules occurs via the formation of a H-bonded water network facilitated by the nonadditive cooperative force. No isomers are observed in which the solvent molecules separately bind to the aromatic ring. For n = 3 case, we observe the formation of a cyclic H-bonded water moiety. Comparison with corresponding cationic and anionic naphthalene±-(water)n clusters demonstrates the charge-induced modification of the hydration motif. Our results are further compared with the prototypical benzene-(water)n complexes to comprehend the effect of an additional phenyl ring on the solvation network.

Cation enrichment in the ion atmosphere is promoted by local hydration of DNA.

Electrostatic interactions are central to the structure and function of nucleic acids, including their folding, condensation, and interaction with proteins and other charged molecules. These interactions are profoundly affected by ions surrounding nucleic acids, the constituents of the so-called ion atmosphere. Here, we report precise Fourier Transform-Terahertz/Far-Infrared (FT-THz/FIR) measurements in the frequency range 30-500 cm-1 for a 24-bp DNA solvated in a series of alkali halide (NaCl, NaF, KCl, CsCl, and CsF) electrolyte solutions which are sensitive to changes in the ion atmosphere. Cation excess in the ion atmosphere is detected experimentally by observation of cation modes of Na+, K+, and Cs+ in the frequency range between 70-90 cm-1. Based on MD simulations, we propose that the magnitude of cation excess (which is salt specific) depends on the ability of the electrolyte to perturb the water network at the DNA interface: In the NaF atmosphere, the ions reduce the strength of interactions between water and the DNA more than in case of a NaCl electrolyte. Here, we explicitly take into account the solvent contribution to the chemical potential in the ion atmosphere: A decrease in the number of bound water molecules in the hydration layer of DNA is correlated with enhanced density fluctuations, which decrease the free energy cost of ion-hydration, thus promoting further ion accumulation within the DNA atmosphere. We propose that taking into account the local solvation is crucial for understanding the ion atmosphere.

Aqueous TMAO solution under high hydrostatic pressure.

Trimethylamine N-oxide (TMAO) is a well known osmolyte in nature, which is used by deep sea fish to stabilize proteins against High Hydrostatic Pressure (HHP). We present a combined ab initio molecular dynamics, force field molecular dynamics, and THz absorption study of TMAO in water up to 12 kbar to decipher its solvation properties upon extreme compression. On the hydrophilic oxygen side of TMAO, AIMD simulations at 1 bar and 10 kbar predict a change of the coordination number from a dominating TMAO·(H2O)3 complex at ambient conditions towards an increased population of a TMAO·(H2O)4 complex at HHP conditions. This increase of the TMAO-oxygen coordination number goes in line with a weakening of the local hydrogen bond network, spectroscopic shifts and intensity changes of the corresponding intermolecular THz bands. Using a pressure-dependent HHP force field, FFMD simulations predict a significant increase of hydrophobic hydration from 1 bar up to 4-5 kbar, which levels off at higher pressures up to 10 kbar. THz spectroscopic data reveal two important pressure regimes with spectroscopic inflection points of the dominant intermolecular modes: The first regime (1.5-2 kbar) is barely recognizable in the simulation data. However, it relates well with the observation that the apparent molar volume of solvated TMAO is nearly constant in the biologically relevant pressure range up to 1 kbar as found in the deepest habitats on Earth in the ocean. The second inflection point around 4-5 kbar is related to the amount of hydrophobic hydration as predicted by the FFMD simulations. In particular, the blueshift of the intramolecular CNC bending mode of TMAO at about 390 cm-1 is the spectroscopic signature of increasingly pronounced pressure-induced changes in the solvation shell of TMAO. Thus, the CNC bend can serve as local pressure sensor in the multi-kbar pressure regime.

Vibrational Spectroscopy of Benzonitrile-(Water)1-2 Clusters in Helium Droplets.

Polycyclic aromatic hydrocarbons are considered as primary carriers of the unidentified interstellar bands. The recent discovery of the first interstellar aromatic molecule, benzonitrile (C6H5CN), suggests a repository of aromatic hydrocarbons in the outer earth environment. Herein, we report an infrared (IR) study of benzonitrile-(D2O)n clusters using mass-selective detection in helium nanodroplets. In this work, we use isotopically substituted water, D2O, instead of H2O because of our restricted IR frequency range (2565-3100 cm-1). A comparison of the experimental and predicted spectra computed at the MP2/6-311++G(d,p) level of benzonitrile-(water)1-2 clusters reveals the formation of a unique local minimum structure, which was not detected in previous gas-phase molecular beam experiments. Here, the solvent water forms a nearly linear hydrogen bond (H-bond) with the nitrile nitrogen of benzonitrile, while the previously reported most stable cyclic H-bonded isomer is not observed. This can be rationalized by the stepwise aggregation process of precooled monomers. The addition of a second water molecule results in the formation of two different isomers. In one of the observed isomers, a H-bonded water chain binds linearly to the nitrile nitrogen similar to the monohydrated benzonitrile-water complex. In the other observed isomer, the water dimer forms a ring-type structure, where a H-bonded water dimer simultaneously interacts with the nitrile nitrogen and the adjacent ortho CH group. Finally, we compare the water-binding motif in the neutral benzonitrile-water complex with the corresponding positively and negatively charged benzonitrile-water monohydrates to comprehend the charge-induced alteration of the solvent binding motif.

Stepwise Microhydration of Isoxazole: Infrared Spectroscopy of Isoxazole-(Water)n≤2 Clusters in Helium Nanodroplets.

Hydration of heterocyclic molecules plays a crucial role in biological and chemical recognition. Here, we present an infrared (IR) spectroscopic investigation of microhydrated, heterocyclic isoxazole molecule. The IR spectra of isoxazole-(water)n≤2 clusters are recorded using helium nanodroplet spectroscopy and are analyzed by quantum chemical calculations at the MP2/6-311++g(d,p) level. In the most abundant isoxazole-water dimer, the solvent water participates in a N···HO hydrogen bonding (H-bond) interaction, while in another observed structure, water simultaneously interacts with ring nitrogen and the neighboring CH group via N···HO and CH···O H-bonds. The addition of another water molecule to the monohydrated cluster results in the formation of a single isomer that features a seven-membered ring, in which the water dimer simultaneously interacts with skeletal nitrogen and the adjacent CH group through N···HO and CH···O bonds.

Probing Local Electrostatics of Glycine in Aqueous Solution by THz Spectroscopy.

Based upon precise terahertz (THz) measurements of the solvated amino acid glycine and accompanying ab-initio molecular-dynamics simulations, we show that the N-C-C-O open/close mode at 315 cm-1 serves as a sensitive, label-free probe for the local protonation of the amide group. Experimentally, we can show that this holds not only for glycine but also for diglycine and valine. The approach is more general, since the changes due to protonation result in intensity changes which can be probed by THz time domain (0-50 cm-1 ) as well as by precise THz-FT spectroscopy (50-400 cm-1 ). A detailed analysis allows us to directly correlate the titration spectra with pKa values. This demonstrates the potential of THz spectroscopy to probe the charge state of a natural amino acid in water in a label-free manner.

A close competition between O-HO and O-Hπ hydrogen bonding: IR spectroscopy of anisole-methanol complex in helium nanodroplets.

Anisole is a multifunctional molecule that can form intermolecular complexes via its aromatic π-electron system as well as its methoxy group. We have studied the complexation of anisole with methanol. This serves as a prototype system to explore the competition between O-HO, O-Hπ, C-HO and C-Hπ hydrogen bonding. The anisolemethanol molecular complexes were formed in superfluid helium droplets and were detected using high-resolution laser-infrared spectroscopy, in the frequency range between 2630 and 2730 cm-1 covering the O-D stretches of methanol-d4 (CD3OD). Several bands assigned to (anisole)m(methanol)n complexes (where m = 1, and 2 and n = 1) were observed. The experimental results are complemented by the ab initio electronic structure calculations at the MP2/6-311++G(d,p) and B3LYP-D3/aug-cc-pVTZ levels of theory. Based on a comparison of the observed spectra with the ab initio theoretical spectra, we suggest that for the anisolemethanol complex, structures bound via O-HO and O-Hπ hydrogen bonding are almost equally preferred.