Solvent Contribution Research Articles

FoldX Force Field revisited, an improved version.

The FoldX force field was originally validated with a database of 1000 mutants at a time when there were few high-resolution structures. Here we have manually curated a database of 5556 mutants affecting protein stability, resulting in 2484 highly confident mutations denominated FoldX Stability Dataset (FSD), represented in non-redundant X-ray structures with less than 2.5 Å resolution, not involving duplicates, metals or prosthetic groups. Using this database, we have created a new version of the FoldX force field by introducing Pi stacking, pH dependency for all charged residues, improving aromatic-aromatic interactions, modifying the Ncap contribution and α-helix dipole, recalibrating the side chain entropy of Methionine, adjusting the H-bond parameters, and modifying the solvation contribution of Tryptophan and others. These changes have led to significant improvements for the prediction of specific mutants involving the above residues/interactions and a statistically significant increase of FoldX predictions, as well as for the majority of the 20 aa. Removing all training sets data from FSD (VFSD dataset), resulted in improved predictions from R = 0.693 (RMSE = 1.277 kcal/mol) to R = 0.706 (RMSE = 1.252 kcal/mol) when compared with the previously released version. FoldX achieves 95% accuracy considering an error of ± 0.85 kcal/mol in prediction, and an AUC = 0.78, for the VFSD, predicting the sign of the energy change upon mutation. FoldX versions 4.1 & 5.1 are freely available for academics at https://foldxsuite.crg.eu/. Supplementary data are available at Bioinformatics online.

Effects of Co/Fe doping on the optical limiting behaviors of copper-based sulfides under low energy densities

Abstract Copper-based sulfides have demonstrated excellent potential in optical fields due to their unique optical properties. In this work, heteroatom doping is conducted in copper-based sulfides to regulate their photo-physical properties. The average grain size of CuCo2S4/CuFeS2 is about 15 nm, whereas the average grain sizes of CuCo2S4 and CuFeS2 are 69 and 73 nm, respectively. The as-obtained derivations of CuCo2S4, CuFeS2, and the coprecipitated CuCo2S4/CuFeS2 are systematically characterized, and the nonlinear optical properties (NLO) of the copper-based sulfides are investigated via the Z-scan technique in the low-laser intensity range of 1–4 µJ to avoid the contribution of solvent scattering in nonlinear optical results. All copper-based sulfides exhibit optical limiting effects, and the open aperture Z-scan results suggested the coexistence of both nonlinear absorption and nonlinear refraction in the sulfides. Co or Fe doping can enhance the optical limiting effects of copper sulfides to some extent, and the normalized transmittances in CuCo2S4 and CuFeS2 are reduced to about 72% from the pristine Cu1.8S (85%) at the input energy of 4 µJ. Interestingly, the optical limiting performances of the coprecipitated CuCo2S4/CuFeS2 are enhanced significantly, and the normalized transmittance in CuCo2S4/CuFeS2 is reduced to about 59% at an input energy of 4 µJ, much lower than the counterpart of the physical mixture of CuCo2S4 and CuFeS2. The highest nonlinear absorption coefficient (β) value is achieved in CuCo2S4/CuFeS2, consistent with the Z-scan results. The NLO enhancement in CuCo2S4/CuFeS2 may derive from the more efficient interfacial charge transfer between coprecipitated CuCo2S4 and CuFeS2, which give a higher efficiency in the carrier mobility.

Improving the Computational Efficiency of the Adaptive Biasing Force Sampling by Leveraging the Telescopic-Solvation Scheme.

The number of solvent molecules present in the system during molecular dynamics is the balancing act between the need to remove the boundary effects present in the system and the computational cost. Application of the telescopic-solvation box scheme during the estimation of the potential of mean force (PMF) can be advantageous in situations where the contribution of solvent far from the site of interest toward the whole PMF is negligible, as previously demonstrated in the case of adaptive steered molecular dynamics and umbrella sampling. This work explores the application of the telescopic-solvation box scheme during enhanced sampling by the stratified adaptive biasing force (ABF) family of methods, including ABF, extended ABF, well-tempered-metadynamics extended ABF, and multiwalker extended ABF. During this scheme, the number of water molecules differed in each stratified window, whose number depended on the value of the collective variable being sampled in that window. Two systems were used to verify the viability of the telescopic scheme: unfolding (Ala)10 peptide in water and insertion of α-tocopherol in a bilayer membrane. In the first system, the 1D and 2D PMFs obtained by the telescopic-solvation scheme matched well with the benchmark PMFs estimated with a standard solvation box. The minimal energy path connecting the α-helical and extended conformational states revealed that the unfolding process of (Ala)10 in water involved multiple closely spaced metastable states. As for the second system, the PMF, equilibrium location of α-tocopherol, and the free energy associated with the desorption and flipping of α-tocopherol obtained within the scope of the telescopic-solvation box scheme agreed with their standard solvation box values. Enhanced sampling with ABF and its variants in conjunction with the telescopic-solvation scheme results in a similar quality of the estimated PMF compared to sampling with a standard solvation box, albeit with reduced computational cost.

Nonradiative Deactivation of the Fluorescent Ag16-DNA and Ag10-DNA Emitters: The Role of Water.

The luminescent quantum yield of silver-cluster emitters stabilized by short oligonucleotides (AgN-DNA) may be efficiently tuned by replacing nucleobases in their stabilization DNA matrices with analogues. In the present study, we proposed a valuable and straightforward theoretical methodology for assessing the photophysical behaviors emerging in AgN-DNA emitters after excitation. Using green Ag10-DNA and near-IR Ag16-DNA emitters we demonstrate how point guanine/inosine replacement could affect the photophysical rate constants of radiative/nonradiative processes. The main deactivation channel of the fluorescence of Ag16-DNA is intersystem crossing, which is in line with experimental data, whereas for Ag10-DNA the calculations overestimate the intersystem crossing rate possibly due to pure solvent contributions.

Probing Bioinorganic Electron Spin Decoherence Mechanisms with an Fe2S2 Metalloprotein.

Recent efforts have sought to develop paramagnetic molecular quantum bits (qubits) as a means to store and manipulate quantum information. Emerging structure-property relationships have shed light on electron spin decoherence mechanisms. While insights within molecular quantum information science have derived from synthetic systems, biomolecular platforms would allow for the study of decoherence phenomena in more complex chemical environments and further leverage molecular biology and protein engineering approaches. Here we have employed the exchange-coupled ST = 1/2 Fe2S2 active site of putidaredoxin, an electron transfer metalloprotein, as a platform for fundamental mechanistic studies of electron spin decoherence toward spin-based biological quantum sensing. At low temperatures, decoherence rates were anisotropic, reflecting a hyperfine-dominated decoherence mechanism, standing in contrast to the anisotropy of molecular systems observed previously. This mechanism provided a pathway for probing spatial effects on decoherence, such as protein vs solvent contributions. Furthermore, we demonstrated spatial sensitivity to single point mutations via site-directed mutagenesis and temporal sensitivity for monitoring solvent isotope exchange. Thus, this study demonstrates a step toward the design and construction of biomolecular quantum sensors.

Exploring the molecular solvatochromism, stability, reactivity, and non-linear optical response of resveratrol.

This work analyzes the isomerization effects and solvent contributions to the stability, electronic excitations, reactivity, and non-linear optical properties (NLO) of resveratrol molecules within the formalism of the Density Functional Theory. The findings suggest that resveratrol solvatochromism is significantly influenced by solvent polarization. The electronic and free energies (E and G) indicate that trans is the most stable conformer. The system is classified as a strong nucleophile. However, the analysis of the Fukui functions and the Mulliken charges indicate that cis-trans isomerization jointly affects the reactive indices of the carbon and hydrogen atoms. The results also suggest that solvent is relevant to solvatochromism and the NLO response. Both cis and trans conformers present strong excitations that undergo a visible hypsochromic change when the polarity of the solvent increases. Once the absorption spectra are connected to the first hyperpolarization ( ) by the Oudar and Chemla relation, the hypsochromism of resveratrol is the reason for the drop in the generation of the second harmonic when the ambient polarity decreases. The CAM-B3LYP DFT results suggest that resveratrol is interesting for NLO applications. Depending on the choice of solvent, values 50 times those observed for urea ( esu), which is a standard NLO material. The optimized geometries of cis and trans isomers of resveratrol in vacuum were obtained using Density Functional Theory (DFT) with the hybrid exchange-correlation function (CAM-B3LYP) and Pople basis set functions, specifically 6-311++G(d,p). The solvent effect on the geometries of both isomers was included using the polarizable continuum model (PCM) with the same level of QM calculation. Vibrational analysis was conducted to confirm that all optimized geometries correspond to the minimum energy. Various electronic properties, including dipole moments, molecular orbitals, transition energy, dipole polarizabilities, and global reactivity parameters, were calculated using both continuum and discrete solvation models based on the sequential QM/MM methodology. All QM calculations were performed with the Gaussian 09 program and the MC simulations with the DICE program. All NLO analysis was carried out using the Multiwfn code.

On more insightful dimensionless numbers for computational viscoelastic rheology

Abrupt contraction flows involving viscoelastic fluids represent a longstanding computational challenge within the field of non-Newtonian fluid mechanics. Despite the apparent simplicity of the geometry, these flows have given rise to intricate discussions in the study of viscoelastic phenomena. This study aims to re-examine the numerical solutions for flows through abrupt contractions, offering a fresh interpretation through the lens of reformulated dimensionless numbers. These numbers are designed to consider the characteristic shear rate of the problem, providing a more comprehensive understanding of the underlying dynamics.When investigating models with intermediate levels of complexity, such as the Giesekus and Phan-Thien-Tanner constitutive equations, the usual comparison with the corresponding Oldroyd-B model becomes inadequate because it tends to rely on the nominal relaxation time (λ) and the nominal total viscosity (η) instead of their effective counterparts when defining the Reynolds number (Re), the Weissenberg number (Wi) and the ratio of solvent to total viscosities (β) (β plays a role only in rheological models involving a solvent contribution). If these dimensionless numbers are tailored to account for the characteristic shear rate specific to the problem under investigation, the choice of the corresponding Oldroyd-B flow, at the adequate values of Re, Wi, and β allows for significantly better quantification of the correct effects of nonlinear viscoelasticity of the original model.We show the conventional approach tends to overemphasize the role of the nonlinear parameter in nonlinear constitutive equations, like the Giesekus and PTT models, when examining standard abrupt contraction flow outputs such as the Couette correction and vortex size. This overestimation occurs because the conventional method does not allow the Reynolds and Weissenberg numbers (and possibly β) to carry the portion of the nonlinear effect that can potentially be captured by the linear Oldroyd-B model through the use of characteristic shear rate-based values. We believe the present approach provides a better perspective of the role played by the nonlinear parameter and its extension to more general flows is also discussed.

The positive contribution of natural deep eutectic solvent constructed by trehalose and fructooligosaccharides on rheological and 3D printing properties of mirror carp surimi

To increase the diversity and stability of surimi products, this study developed polysaccharide-based water-tailored natural deep eutectic solvent (NADES) for the development of surimi 3D printed products. As the mass ratio of trehalose to fructooligosaccharides increased (1:1, 5:4, 4:3, 3:2, 2:1, 3:1), the liquid state of NADES first became clear and then turned turbid. At a mass ratio of 3:2, NADES appeared pure and free of impurities under polarized light microscopy. It was confirmed by FTIR and NMR spectroscopy that trehalose and fructooligosaccharides interact through hydrogen bonding to form NADES. Adding water to NADES significantly reduced its viscosity (P < 0.05), although this also gradually weakened the hydrogen bonds. At a 14.52% water addition, NADES exhibited relatively low viscosity and high hydrogen bond strength. Increasing the amount of NADES (0, 2, 4, 6, 8%) led to a rise in the viscosity, storage modulus, loss modulus, and tanδ of the surimi, and a denser three-dimensional network structure was observed via SEM. Under optimized 3D printing parameters (nozzle diameter of 1.2 mm, layer height of 1.0 mm, fill percentage of 75%, and print speed of 30 mm/s), surimi containing 4% NADES demonstrated the finest textures, achieving the highest print accuracy (99.33%) and stability (99.31%) among all samples tested. This study provides a theoretical basis for developing polysaccharide-based NADES and enhancing surimi product quality.

Synthesis and crystal structure of the cluster (Et4N)[(Tp*)MoFe3S3(μ3-NSiMe3)(N3)3

The title compound, tetraethylammonium triazidotri-μ3-sulfido-[μ3-(trimethylsilyl)azanediido][tris(3,5-dimethylpyrazol-1-yl)hydroborato]triiron(+2.33)molybdenum(IV), (C8H20N)[Fe3MoS3(C15H22BN6)(C3H9NSi)(N3)3] or (Et4N)[(Tp*)MoFe3S3(μ3-NSiMe3)(N3)3] [Tp* = tris(3,5-dimethylpyrazol-1-yl)hydroborate(1−)], crystallizes as needle-like black crystals in space group P\overline{1}. In this cluster, the Mo site is in a distorted octahedral coordination model, coordinating three N atoms on the Tp* ligand and three μ3-bridging S atoms in the core. The Fe sites are in a distorted tetrahedral coordination model, coordinating two μ3-bridging S atoms, one μ3-bridging N atom from Me3SiN2−, and another N atom on the terminal azide ligand. This type of heterometallic and heteroleptic single cubane cluster represents a typical example within the Mo–Fe–S cluster family, which may be a good reference for understanding the structure and function of the nitrogenase FeMo cofactor. The residual electron density of disordered solvent molecules in the void space could not be reasonably modeled, thus the SQUEEZE [Spek (2015). Acta Cryst. C71, 9–18] function was applied. The solvent contribution is not included in the reported molecular weight and density.

Crystal structure and Hirshfeld surface analysis of 3,3′-[ethane-1,2-diylbis(oxy)]bis(5,5-dimethylcyclohex-2-en-1-one) including an unknown solvate

The title molecule, C18H26O4, consists of two symmetrical halves related by the inversion centre at the mid-point of the central –C—C– bond. The hexene ring adopts an envelope conformation. In the crystal, the molecules are connected into dimers by C—H...O hydrogen bonds with R 2 2(8) ring motifs, forming zigzag ribbons along the b-axis direction. According to a Hirshfeld surface analysis, H...H (68.2%) and O...H/H...O (25.9%) interactions are the most significant contributors to the crystal packing. The contribution of some disordered solvent to the scattering was removed using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18] in PLATON. The solvent contribution was not included in the reported molecular weight and density.

Impedance of nanocapacitors from molecular simulations to understand the dynamics of confined electrolytes

Nanoelectrochemical devices have become a promising candidate technology across various applications, including sensing and energy storage, and provide new platforms for studying fundamental properties of electrode/electrolyte interfaces. In this work, we employ constant-potential molecular dynamics simulations to investigate the impedance of gold-aqueous electrolyte nanocapacitors, exploiting a recently introduced fluctuation-dissipation relation. In particular, we relate the frequency-dependent impedance of these nanocapacitors to the complex conductivity of the bulk electrolyte in different regimes, and use this connection to design simple but accurate equivalent circuit models. We show that the electrode/electrolyte interfacial contribution is essentially capacitive and that the electrolyte response is bulk-like even when the interelectrode distance is only a few nanometers, provided that the latter is sufficiently large compared to the Debye screening length. We extensively compare our simulation results with spectroscopy experiments and predictions from analytical theories. In contrast to experiments, direct access in simulations to the ionic and solvent contributions to the polarization allows us to highlight their significant and persistent anticorrelation and to investigate the microscopic origin of the timescales observed in the impedance spectrum. This work opens avenues for the molecular interpretation of impedance measurements, and offers valuable contributions for future developments of accurate coarse-grained representations of confined electrolytes.

Dynamic and relativistic effects on Pt-Pt indirect spin-spin coupling in aqueous solution studied by abinitio molecular dynamics and two- vs four-component density functional NMR calculations.

Treating 195Pt nuclear magnetic resonance parameters in solution remains a considerable challenge from a quantum chemistry point of view, requiring a high level of theory that simultaneously takes into account the relativistic effects, the dynamic treatment of the solvent-solute system, and the dynamic electron correlation. A combination of Car-Parrinello molecular dynamics (CPMD) and relativistic calculations based on two-component zeroth order regular approximation spin-orbit Kohn-Sham (2c-ZKS) and four-component Dirac-Kohn-Sham (4c-DKS) Hamiltonians is performed to address the solvent effect (water) on the conformational changes and JPtPt1 coupling. A series of bridged PtIII dinuclear complexes [L1-Pt2(NH3)4(Am)2-L2]n+ (Am = α-pyrrolidonate and pivalamidate; L = H2O, Cl-, and Br-) are studied. The computed Pt-Pt coupling is strongly dependent on the conformational dynamics of the complexes, which, in turn, is correlated with the trans influence among axial ligands and with the angle N-C-O from the bridging ligands. The J-coupling is decomposed in terms of dynamic contributions. The decomposition reveals that the vibrational and explicit solvation contributions reduce JPtPt1 of diaquo complexes (L1 = L2 = H2O) in comparison to the static gas-phase magnitude, whereas the implicit solvation and bulk contributions correspond to an increase in JPtPt1 in dihalo (L1 = L2 = X-) and aquahalo (L1 = H2O; L2 = X-) complexes. Relativistic treatment combined with CPMD shows that the 2c-ZKS Hamiltonian performs as well as 4c-DKS for the JPtPt1 coupling.

S.O.S: Shape, orientation, and size tune solvation in electrocatalysis.

Current models to understand the reactivity of metal/aqueous interfaces in electrochemistry, e.g., volcano plots, are based on the adsorption free energies of reactants and products, which are often small hydrophobic molecules (such as in CO2 and N2 reduction). Calculations played a major role in the quantification and comprehension of these free energies in terms of the interactions that the reactive species form with the surface. However, solvation free energies also come into play in two ways: (i) by modulating the adsorption free energy together with solute-surface interactions, as the solute has to penetrate the water adlayer in contact with the surface and get partially desolvated (which costs free energy); (ii) by regulating transport across the interface, i.e., the free energy profile from the bulk to the interface, which is strongly non-monotonic due to the unique nature of metal/aqueous interfaces. Here, we use constant potential molecular dynamics to study the solvation contributions, and we uncover huge effects of the shape and orientation (on top of the already known size effect) of small hydrophobic and amphiphilic solutes on their adsorption free energy. We propose a minimal theoretical model, the S.O.S. model, that accounts for size, orientation, and shape effects. These novel aspects are rationalized by recasting the concepts at the base of the Lum-Chandler-Weeks theory of hydrophobic solvation (for small solutes in the so-called volume-dominated regime) into a layer-by-layer form, where the properties of each interfacial region close to the metal are explicitly taken into account.

Unveiling the binding mechanism between starch granule-surface proteins and glutenins during dough mixing process

Starch granule-surface proteins (SGSPs) and gluten proteins can interact to influence dough quality. Despite their pronounced effects, the interaction mechanism remains insufficiently understood. Herein, the binding mechanism between SGSPs and different molecular weight glutenin was explored by experimental methods and single-molecule techniques. Our findings revealed that SGSPs promoted strong binding with both high and low molecular weight glutenin (HMW-GS and LMW-GS). When the ratio of SGSPs and LMW-GS increased to 2:1, the content of disulfide bond increased from 0.03 μmol/L to 0.21 μmol/L while the free sulfhydryl showed the opposite pattern, indicating a tightly packed composite protein structure. A combination of unbiased and steered molecular dynamics simulations further revealed that SGSPs exhibited a higher binding affinity towards LMW-GS in comparison to HMW-GS due to the contributions of solvation and specific interaction energies. This endows the SGSPs-LMW-GS complex with significantly enhanced stability at free state and much higher unbinding force upon stretching, substantially improving the mechanical quality of dough. These findings indicate that SGSPs predominantly affects the interactions between starch and gluten, which will shed light on the dough formation and its properties.

Role of the Solvent and Intramolecular Hydrogen Bonds in the Antioxidative Mechanism of Prenylisoflavone from Leaves of Vatairea guianensis.

This work discusses the electron structure, antioxidative properties, and solvent contribution of two new antioxidant molecules discovered, named S10 and S11, extracted from a medicinal plant called Vatairea guianensis, found in the Amazon rain-forest. To gain a better understanding, a study using density functional theory coupled with the polarizable-continuum model and the standard 6-311++G(d,p) basis set was conducted. The results indicate that S10 has a higher antioxidant potential than S11, confirming the experimental expectations. In the gas phase, the hydrogen atom transfer route dominates the hydrogen scavenging procedure. However, in the water solvents, the antioxidant mechanism prefers the sequential proton loss electron transfer mechanism. Furthermore, the solvent plays a fundamental role in the antioxidant mechanism. The formation of an intramolecular OH···OCH3 hydrogen bond is crucial for accurately describing the hydrogen scavenging phenomenon, better aligning with the experimental data. The results suggest that the two isoflavones investigated are promising for the pharmacologic and food industries.

Mapping electronic decoherence pathways in molecules.

Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in [Formula: see text]30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the early-time decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it.

Thermodynamics of reactions of stepwise complex formation of silver(I) ion with pyridine in binary solvents

In this study, the enthalpies of stepwise complexation reactions between silver(I) ions and pyridine in methanol–acetonitrile mixed solvents (MeOH-AN, with molar fractions of AN varying from 0 to 1) were determined by the calorimetric method at 298.15 K. The analysis of the solvation contributions of the reactants to the alterations in the thermodynamic characteristics associated with the formation of [AgPy]+ and [AgPy2]+ complexes as the solvent composition transitions, i.e. from methanol to its mixtures with acetonitrile (MeOH → χAN), from methanol to its mixtures with N,N-dimethylformamide (MeOH → χDMF) and from acetonitrile to its mixtures with dimethyl sulfoxide (AN → χDMSO) was carried out. The research methodology was based on the provisions of the solvation-thermodynamic approach, based on the relationship between changes in the thermodynamic characteristics of the reactions of complex formation and solvation of reagents with a change in the composition of the solvent.

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-Guest Binding: IV. The QM Treatment, GB Models and the Multi-Trajectory Extension

Due to the similarity of host–guest complexes and protein–ligand and protein–protein assemblies, computational tools for protein–drug complexes are commonly applied in host–guest binding. One of the methods with the highest popularity is the end-point free energy technique, which estimates the binding affinity with gas-phase and solvation contributions extracted from simplified end-point sampling. Our series papers on a set of carboxylated-pillararene host–guest complexes have proven with solid numerical evidence that standard end-point techniques are practically useless in host–guest binding, but alterations, such as slightly increasing interior dielectric constant in post-processing calculation and shifting to the multi-trajectory realization in conformational sampling, could better the situation and pull the end-point method back to the pool of usable tools. Also, the force-field selection plays a critical role, as it determines the sampled region in the conformational space. In the current work, we continue the efforts to explore potentially promising end-point modifications in host–guest binding and further extend the sampling time to an unprecedent length. Specifically, we comprehensively benchmarked the shift from the original MM description to QM Hamiltonians in post-processing the popular single-trajectory sampling. Two critical settings in the multi-scale QM/GBSA regime are the selections of the QM Hamiltonian and the implicit-solvent model, and a scan of combinations of popular semi-empirical QM Hamiltonians and GB models is performed. The multi-scale QM/GBSA treatment is further combined with the three-trajectory sampling protocol, introducing a further advanced modification. The sampling lengths in the host–guest complex, solvated guest and solvated host ensembles are extended to 500 ns, 500 ns and 12,000 ns. As a result, the sampling quality in end-point calculations is unprecedently high, enabling us to draw conclusive pictures of investigated forms of modified end-point free energy methods. Numerical results suggest that the shift to the QM Hamiltonian does not better the situation in the popular single-trajectory regime, but noticeable improvements are observed in the three-trajectory sampling regime, especially for the DFTB/GBSA parameter combination (either DFTB2 or its third-order extension), the quality metrics of which reach an unprecedently high level and surpass existing predictions (including costly alchemical transformations) on this dataset, hinting on the applicability of the advanced three-trajectory QM/GBSA end-point modification for host–guest complexes.

Vertical distribution of VOCs in the boundary layer of the Lhasa valley and its impact on ozone pollution

To investigate the vertical distribution of volatile organic compounds (VOCs) concentrations in the Lhasa valley region, an intensive measurement campaign was first conducted in summer using a tethered balloon. The results showed that the average concentration of surface VOCs was 49.1 ± 30.1 ppbv, alkanes and aromatics were the main components. Notably, a very large discrepancy in VOCs was obtained between the wet (71.6 ± 25.9 ppbv) and dry (25.6 ± 8.0 ppbv) episodes, which was attributed to the atmospheric stability and diffusion capacity. Moreover, the total VOC (TVOCs) concentration declined under fluctuations, but it rapidly increased with height in the afternoon during the wet episode (2.50 ppbv/100 m, R2 = 0.47). According to the PMF results, combustion was the dominant emission source, additionally, the contribution of solvent coating in the wet episode and the background in the dry episode increased with height. Moreover, the O3 concentration increased with height, and the decrease in LNOx-OH could effectively prevent the occurrence of high O3 values. This study indicated that low wind speeds and high humidity levels highly likely cause the accumulation of atmospheric VOCs under static and stable conditions, while the control of high O3 concentrations must still greatly consider summertime NOx emissions in Lhasa.

From Local Hydration Motifs in Aqueous Acetic Acid Solutions to Macroscopic Mixing Thermodynamics: A Quantitative Connection from THz-Calorimetry.

We report the results of THz measurements (30-440 cm-1) of aqueous acetic acid solutions over the full mixing range (XAcAc = 0-1). We recorded spectroscopic observables as a function of the acetic acid concentration in the frequency range of the intermolecular stretch at 150 cm-1 and of the librational modes at 350-440 cm-1. This allowed us to unravel changes in hydrophobic and hydrophilic hydration motifs, respectively. By means of a novel THz-calorimetry approach, we quantitatively correlated these changes in local hydration motifs to excess mixing entropy and enthalpy. We find that ΔHmix is determined by both hydrophobic and hydrophilic solvation contributions. In contrast, ΔSmix is governed by hydrophobic cavity formation. Our results further suggest that acetic acid-water mixtures are systems at the edge of phase separation due to endothermic contributions from both hydrophilic and hydrophobic solvation in a large portion of the miscibility range. Our work establishes a quantitative relationship between the balance of local hydrophobic and hydrophilic solvation motifs and the macroscopic mixing thermodynamic properties.