On the relative stabilities of H‐ and D‐bonded water dimers

Effects of Hydrogen/Deuterium Exchange on Protein Stability in Solution and in the Gas Phase

Mass spectrometry (MS)-based techniques are widely used for probing protein structure and dynamics in solution. H/D exchange (HDX)-MS is one of the most common approaches in this context. HDX is often considered to be a "benign" labeling method, in that it does not perturb protein behavior in solution. However, several studies have reported that D₂O pushes unfolding equilibria toward the native state. The origin, and even the existence of this protein stabilization remain controversial. Here we conducted thermal unfolding assays in solution to confirm that deuterated proteins in D₂O are more stable, with 2-4 K higher melting temperatures than unlabeled proteins in H₂O. Previous studies tentatively attributed this phenomenon to strengthened H-bonds after deuteration, an effect that may arise from the lower zero-point vibrational energy of the deuterated species. Specifically, it was proposed that strengthened water-water bonds (W···W) in D₂O lower the solubility of nonpolar side chains. The current work takes a broader view by noting that protein stability in solution also depends on water-protein (W···P) and protein-protein (P···P) H-bonds. To help unravel these contributions, we performed collision-induced unfolding (CIU) experiments on gaseous proteins generated by native electrospray ionization. CIU profiles of deuterated and unlabeled proteins were indistinguishable, implying that P···P contacts are insensitive to deuteration. Thus, protein stabilization in D₂O is attributable to solvent effects, rather than alterations of intraprotein H-bonds. Strengthening of W···W contacts represents one possible explanation, but the stabilizing effect of D₂O can also originate from weakened W···P bonds. Future work will be required to elucidate which of these two scenarios is correct, or if both contribute to protein stabilization in D₂O. In any case, the often-repeated adage that "D-bonds are more stable than H-bonds" does not apply to intramolecular contacts in native proteins.

Water: new aspect of hydrogen bonding in the solid state

All water-water contacts in the crystal structures from the Cambridge Structural Database with d _OO ≤ 4.0 Å have been found. These contacts were analysed on the basis of their geometries and interaction energies from CCSD(T)/CBS calculations. The results show 6729 attractive water-water contacts, of which 4717 are classical hydrogen bonds (d _OH ≤ 3.0 Å and α ≥ 120°) with most being stronger than -3.3 kcal mol^-1. Beyond the region of these hydrogen bonds, there is a large number of attractive interactions (2062). The majority are antiparallel dipolar interactions, where the O-H bonds of two water molecules lying in parallel planes are oriented antiparallel to each other. Developing geometric criteria for these antiparallel dipoles (β₁, β₂ ≥ 160°, 80 ≤ α ≤ 140° and T _HOHO > 40°) yielded 1282 attractive contacts. The interaction energies of these antiparallel oriented water molecules are up to -4.7 kcal mol^-1, while most of the contacts have interaction energies in the range -0.9 to -2.1 kcal mol^-1. This study suggests that the geometric criteria for defining attractive water-water interactions should be broader than the classical hydrogen-bonding criteria, a change that may reveal undiscovered and unappreciated interactions controlling molecular structure and chemistry.

Calcium Ion-Induced Structural Changes in Carboxymethylcellulose Solutions and Their Effects on Adsorption on Cellulose Surfaces

The adsorption of carboxymethylcellulose (CMC) on cellulose surfaces is one of the most studied examples of the adsorption of an anionic polyelectrolyte on a like-charged surface. It has been suggested that divalent ions can act as a bridge between CMC chains and the surface of cellulose and enhance the CMC adsorption: they can, however, also alter the structure of CMCs in the solution. In previous investigations, the influence of cations on solution properties has been largely overlooked. This study investigates the effect of Ca²⁺ ions on the properties of CMC solutions as well as the influence on cellulose nanofibers (CNFs), which was studied by dynamic light scattering and correlated with the adsorption of CMC on a cellulose surface probed using QCM-D. The presence of Ca²⁺ facilitated the multichain association of CMC chains and increased the hydrodynamic diameter. This suggests that the adsorption of CMCs at high concentrations of CaCl₂ is governed mainly by changes in solution properties rather than by changes in the cellulose surface. Furthermore, an entropy-driven mechanism has been suggested for the adsorption of CMC on cellulose. By comparing the adsorption of CMC from H₂O and D₂O, it was found that the release of water from the cellulose surface is driving the adsorption of CMC.

Evaluation of Ar tagging toward the vibrational spectra and zero point energy of X-HOH, X-DOH, and X-HOD, for X = F, Cl, Br

In this study, we theoretically evaluated the effect of argon tagging toward the binding energy and vibrational spectra of water halide anion complexes Ar.X-HOH, Ar.X-HOD, and Ar.X-DOH (X = F, Cl, Br). The ionic hydrogen bond (IHB) OH stretching mode was calculated to have a strong peak in the vibrational spectra, and coupling to intermolecular modes as well as bending modes was observed as combination bands and Fermi resonances. We found that the argon tagging affected the IHB OH stretching peak position in Ar.F-H2O, but not in Ar.Cl-H2O and Ar.Br-H2O. Furthermore, D-binding is favored for Cl and Br based on zero point energies, but for F our calculated zero point energies did not show a preference between H- and D-binding. We show that the competition of the energy lowering in the zero point energy of the anharmonic IHB OH (OD) stretching mode versus the intermolecular out-of-plane IHB OH (OD) wagging mode is important for determining the preference between H- and D-binding for these monohydrated halide clusters. We also found that for X-HOD the HOD bending fundamental peak is blue shifted compared to bare HOD, but is redshifted for F-DOH.

Hydrated Metal Ion Salts of the Weakly Coordinating Fluoroanions PF6-, TiF62-, B12F122-, Ga(C2F5)4-, B(3,5-C6H3(CF3)2)4-, and Al(OC(CF3)3)4-. In Search of the Weakest HOH···F Hydrogen Bonds

FTIR spectra of microcrystalline samples of 11 metal ion salt hydrates of a variety of weakly coordinating fluoroanions are reported. The compounds studied were Li(H₂O)₄(Al(OC(CF₃)₃)₄), Li(H₂O)(B(3,5-C₆H₃(CF₃)₂)₄), Li(H₂O)_n(Ga(C₂F₅)₄), Li(H₂O)(PF₆), Li₂(H₂O)₂(TiF₆), Li₂(H₂O)₄(B₁₂F₁₂), Na(H₂O)(PF₆), Na₂(H₂O)₂(B₁₂F₁₂), K₂(H₂O)₂(B₁₂F₁₂), Rb₂(H₂O)₂(B₁₂F₁₂), Cs₂(H₂O)(B₁₂F₁₂), and their partially or completely deuterated isotopologs and isotopomers. The O-D···F hydrogen bonds in Li(HOD)(H₂O)₃(Al(OC(CF₃)₃)₄) (ν(OD) = 2706 cm^-1), Li(HOD)(B(3,5-C₆H₃(CF₃)₂)₄) (ν(OD) = 2705 cm^-1), and Li(HOD)(H₂O)_n(Ga(C₂F₅)₄) (ν(OD) = 2697 cm^-1) rival HOD absorbed in polyvinylidene difluoride (ν(OD) = 2696 cm^-1) and HOD···FCH₃ in a frozen Ar matrix (ν(OD) = 2685 cm^-1) for the weakest hydrogen bonds between a water molecule and an F atom in any compound. As weak as they are, minor differences in O-H···F hydrogen bonds in the same fluoroanion salt can be distinguished spectroscopically. Uncoupled HOD molecules in asymmetric F···HOD···F' hydrogen bonding environments in Rb⁺, Cs⁺, Mg²⁺, and Co²⁺ hydrates of B₁₂F₁₂^2- gave rise to two observable ν(OD) bands even though the two R(O···F) distances differ by only 0.010(4) Å (Mg²⁺), 0.033(2) Å (Co²⁺), 0.074(4) Å (Rb⁺), and 0.106(6) Å (Cs⁺). A plot of ν(OD) for hydrates with a single uncoupled HOD molecule per metal ion (e.g., Li(HOD)(H₂O)₃(Al(OC(CF₃)₃)₄)) vs R(O···F) distance from single-crystal X-ray or neutron diffraction structures was prepared. The ν(OD) values range from 2305 to 2706 cm^-1 and the R(O···F) distances range from 2.58 to 3.17 Å. The plot consists of 53 {ν(OD), R(O···F)} data points, 23 of which are new and have ν(OD) > 2600 cm^-1, in contrast to a 1994 ν(OD) vs R(O···F) plot with 28 data points, none of which had ν(OD) > 2600 cm^-1. There is a clear and significant difference between the new ν(OD) vs R(O···F) plot and a literature ν(OD) vs R(O···O) plot for hydrates containing O-D···O hydrogen bonds. For a given ν(OD) stretching frequency, the exponential regression curves show that R(O···F) is typically 0.1-0.2 Å shorter than R(O···O), in harmony with the lower basicity and smaller size of F atoms vs O atoms.

The influence of large-amplitude librational motion on the hydrogen bond energy for alcohol–water complexes

The intermolecular large-amplitude OH librational modes for mixed hydrogen-bonded complexes of water with methanol and t-butanol are unambiguously assigned for the first time.

Self-assembly of the triblock copolymer 17R4 poly(propylene oxide)₁₄-poly(ethylene oxide)₂₄-poly(propylene oxide)₁₄ in D₂O

Our recent investigation of the three regions of the phase diagram of 17R4 in D2O (Huff et al., 2011) has led us to study the copolymer structure in this system by small-angle neutron scattering, rheometry, and dynamic light scattering. In region I at low temperatures and copolymer concentrations (0-30°C, 0.1-0.2 mass fraction ω), the cloudy solution contains the copolymer in large clusters made of hydrophobic PPO-rich "knots" bridged by dissolved hydrophilic PEO chains. These clusters vanish in region I at the lower temperatures and concentrations (below 39°C and ω=0.01). In region I over long times (weeks) at 25°C, a white liquid/gel film forms at the air-D2O interface. In region II at temperatures above the micellization line (above about 35°C, at ω=0.22) the large clusters dissipate and unimers coexist with "flower micelles," where the PPO blocks are the centers of the micelles and the PEO blocks loop into the solvent. In region III at still higher temperatures (above about 40°C at ω=0.2), the solution separates into coexisting liquid phases, where the upper phase of higher copolymer concentration is in region II, and the lower phase is in region I. The concentrated upper phase may contain micelles so crowded as to form a network.

Micelles of polybutadiene-b-poly(ethylene oxide) in deuterated methanol and deuterated cyclohexane

Micellization of the diblock copolymer poly(ethylene oxide)-b-polybutadiene, PEO(132)-PB(89), where the subscripts denote the number of monomers in each block, has been studied in solution in deuterated methanol and in deuterated cyclohexane, in order to compare the micellar assembly in deuterated solvents to that in protonated solvents. The methods used were dynamic light scattering and small angle neutron scattering. In CD(3)OD, PEO(132)-PB(89) forms only spherical micelles that change little in size or shape over the temperature range 21-68°C. In CH(3)OH, PEO(132)-PB(89) forms coexisting cylindrical and spherical structures over the entire temperature range. Thus cylindrical micelles form in CH(3)OH, but do not form in CD(3)OD. In C(6)D(12), the copolymer forms flexible, cylindrical micelles at lower temperatures; above about 40°C, spherical micelles and free copolymers appear and coexist with the cylindrical micelles. The behavior in C(6)H(12) is the same as in C(6)D(12), except that no free copolymers are observed in C(6)H(12). The stronger hydrogen bonding in deuterated methanol as compared to protonated methanol is assumed to be the source of the difference in assembly.

Micellization and phase separation for triblock copolymer 17R4 in H2O and in D2O

The reverse Pluronic triblock copolymer 17R4 is formed from poly(propylene oxide) (PPO) and poly(ethylene oxide) (PEO): PPO(14)-PEO(24)-PPO(14), where the subscripts denote the number of monomers in each block. In water, 17R4 shows both a transition to aggregated micellar species at lower temperatures and a separation into copolymer-rich and copolymer-poor liquid phases at higher temperatures. For 17R4 in H(2)O and in D(2)O, we have determined (1) the phase boundaries corresponding to the micellization line, (2) the cloud point curves marking the onset of phase separation at various compositions, and (3) the coexistence curves for the phase separation (the compositions of coexisting phases). In both H(2)O and in D(2)O, 17R4 exhibits coexistence curves with lower consolute temperatures and compositions that differ from the minima in the cloud point curves; we take this as an indication of the polydispersity of the micellar species. The coexistence curves for compositions near the critical composition are described well by an Ising model. For 17R4 in both H(2)O and D(2)O, the critical composition is 0.22 ± 0.01 in volume fraction. The critical temperatures differ: 44.8 °C in H(2)O and 43.6 °C in D(2)O. The cloud point curve for the 17R4/D(2)O is as much as 9 °C lower than in H(2)O.

The polymerization of actin: structural changes from small-angle neutron scattering

We present a new analysis of small-angle neutron-scattering data from rabbit muscle actin in the course of the polymerization from G-actin to F-actin as a function of temperature. The data, from Ivkov et al. [J. Chem. Phys. 108, 5599 (1998)], were taken in D2O buffer with Ca2+ as the divalent cation on the G-actin in the presence of ATP and with KCl as the initiating salt. The new analysis of the data using modeling and the method of generalized indirect fourier transform (O. Glatter, GIFT, University of Graz, Austria, http://physchem.kfunigraz.ac.at/sm/) provide shapes and dimensions of the G-actin monomer and of the growing actin oligomer in solution as a function of temperature and salt concentration. This analysis indicates that the G-actin monomer, under the conditions given above, is a sphere 50-54 A in diameter as opposed to the oblate ellipsoid seen by x-ray crystallography. The F-actin dimensions are consistent with x-ray crystal structure determinations.

Proton and deuteron position preferences in water clusters: an ab initio study

In order to explore the effect of H-to-D substitution on the zero-point energy (ZPE) of water clusters, Hessians were computed for a database of 53 optimized (H2O)n clusters, 5 < or = n < or = 21, at the B3LYP6-311 + + G** level. The 53 clusters contained 1524 protons, which were sorted into 18 categories according to the type of their donor O and (if not free) acceptor O. Letting deltaZPE[H]* denote the change in ZPE when the proton H* is replaced by D, mean values for deltaZPE[H*] for the H-bonded categories ranged from -2172 cal mol(-1) for H* in a DDAA-DDAA bond to -2118 for H* in a DAA-DDA bond. Mean value for H* free on DAA (respectively, DA) was -2018 (respectively, -1969). For DAA-DDA bonds, and for short H bonds in general, there was a strong inverse correlation between /deltaZPE[H*]/ and the O-H* distance. deltaZPE for multiple H-to-D substitutions was additive, except for a cooperativity effect of -13.7 to -19.7 cal mol(-1) when two substituted protons were in the same H2O unit and a much smaller cooperativity when one proton's donor was the other's acceptor. Implications of these data include a relative preference for D to occupy H bonded rather than free positions in finite water clusters, a value of 3.82 for the disproportionation equilibrium constant of mixed ice at 150 K, increased occupation by H at surface positions of mixed ice, and a larger average coordination number for liquid D2O than for liquid H2O.

FTIR and ab Initio Study of the 1/1 Complex between Water and Carbon Dioxide in Solid Nitrogen

Infrared spectra of the 1/1 complex between water and carbon dioxide isolated in a nitrogen matrix are reported. Isotopic substitution of water (HOD, D2O) suggests the existence of two very weak complexes with a nearly T-shaped structure where the C atom is bonded to the water oxygen: one of C2v symmetry and another one of Cs symmetry, in which a slight distortion results in a very weak interaction between one hydrogen atom of water and one oxygen atom of carbon dioxide. This result is supported by force constant calculations, consistent with a double, symmetrical, and unsymmetrical force field, and ab initio calculations. At the MP2/aug-cc-PVTZ level corrected from basis set superposition error the C2v structure is a saddle point with an imaginary frequency for H2O rocking, in contrast to a Cs structure, which would have nonequivalent hydrogen atoms. Nevertheless, the energies of both structures, with a stabilization energy of 1.97 kcal mol-1, differ by less than 0.01 kcal mol-1 from each other. A comparison of calculated and observed frequency shifts allows us to suggest the presence in the matrix of both C2v and Cs complexes.

Dynamics of the Concerted Triple Proton Transfer in Cyclic Water Trimer Using the Multiconfiguration Molecular Mechanics Algorithm

Cyclic water clusters are important molecular species to understand the nature of hydrogen bonded networks. Theoretical studies for the dynamics of triple proton transfer in the cyclic water trimer were performed. The potential energy surface (PES) of triple proton transfer is generated by the multiconfiguration molecular mechanics (MCMM) algorithm. We have used the MP2/6-31G(d,p) level for high-level ab initio data (energies, gradients, and Hessians), which are used in the Shepard interpolation. Eight high-level reference points were added step by step, including two points for the critical configurations of the large curvature tunneling paths. The more high-level points are used, the better the potential energy surfaces become. The rate constant and kinetic isotope effect (KIE) for the triple proton transfer at 300 K, which have been calculated by the canonical variational transition-state theory with microcanonical optimized multidimensional semiclassical tunneling approximation, are 1.6 x 10(-3) s(-1) and 230, respectively. Tunneling is very important not only for the triple proton transfer but also for the triple deuterium transfer. The MCMM results show good agreement with those from the direct ab initio dynamics calculations.

Phase behavior of block co-poly(ethylene oxide–butylene oxide), E18B9 in water, by small angle neutron scattering

We present a small angle neutron scattering (SANS) study into the micellar structures of diblock copolymer E18B9 (where E denotes a ethylene oxide unit and B denotes a butylene oxide unit, 18 and 9 being the number of repeat units respectively) in aqueous solution over a range of five different concentrations (0.2, 1.0, 10.0, 20.0, and 40.0% (by mass fraction)) and eight temperatures (10 to 90 degrees C). The NG7 30 m SANS instrument provides a q range of 0.0009 to 0.5548 A(-1), thus probing the structure over a very broad length scale. At low temperature and low concentration, spherical micelles exist, elongating into worm-like structures at higher temperatures. This transition is observed by the scaling of the scattered intensity at low q and confirmed upon fitting to an appropriate model. Upon increasing concentration, the micelles pack into ordered arrays of either hexagonally packed rod-like micelles or lamellar sheets, again dependent on temperature. Both concentration and temperature effects of this block copolymer have been discussed.

The effect of cooperative hydrogen bonding on the OH stretching-band shift for water clusters studied by matrix-isolation infrared spectroscopy and density functional theory

Infrared spectra of the water clusters have been measured in the N2 + O2 matrix. The aggregation process of water in the matrix has been monitored by annealing the deposited samples up to 40 K and UV irradiation. The monomer, dimer, cyclic trimer and cyclic pentamer are found as water clusters in the matrix. For the hexamer, several structures such as chair, cage, prism, bag 1 and/or book 1 are likely to exist. By UV irradiation, the cyclic pentamer is predominantly formed from the monomer and dimer. On the other hand, by annealing the deposited sample, several hexamers are formed. The theoretical calculation for water clusters has revealed that the formation of one hydrogen bonding in a hydrogen-bonded chain cooperatively enhances or diminishes the strength of another hydrogen bond. Both proton donor (D) and acceptor (A) participating in a hydrogen-bonding pair DA are capable of forming hydrogen bonding with the other water molecules; D can additionally accept two protons and donate one proton, and A can additionally donate two protons and accept one proton. We have proposed the classification of hydrogen-bonding patterns considering the cooperativity, denoting as d'a'DAd''a'', where d and a are integers indicating the number of proton donors and acceptors to D (the single prime) and A (the double prime), respectively. Then, a magnitude given by MOH = -d' + a' + d'' - a'' has been introduced, which is very useful for connecting the hydrogen-bonding patterns to their OH wavenumbers. As a result, it is revealed that the OH stretching bands of water clusters are characterized by eight indicators (free and MOH = -2, -1, 0, 1, 2, 3 and 4). The classification proposed here is applicable to the OH band analysis for the hydrogen-bonded water and alcohols in a condensed phase.

Calculation of isotope effects from first principles

Various means of calculating the effect of changing the mass of a given atom upon a chemical process are reviewed. Of particular interest is the deuterium isotope effect comparing the normal protium nucleus with its heavier deuterium congener. The replacement of the bridging protium in a neutral hydrogen bond such as the water dimer by a deuterium strengthens the interaction by a small amount via effects upon the vibrational energy. In an ionic H-bond such as the protonated water dimer, on the other hand, the reverse trend is observed in that replacement of the bridging protium by dimer weakens the interaction. In addition to the stability of a given complex, the rate at which a proton transfers from one group to another is likewise affected by deuterium substitution, viz. kinetic isotope effects (KIEs). The KIE is enlarged as the temperature drops, particularly so if the calculation of KIE includes proton tunneling. The KIE is also sensitive to any angular distortions or stretches present in the H-bond of interest. KIEs can be computed either by the standard transition state theory which is derived via only two points on the potential energy surface, or by more complete formalisms which take account of larger swaths of the surface. While more time intensive, the latter can also be applied to provide insights important in interpretation of experimental data.