Predicting Solvation Free Energies Using Parameter-Free Solvent Models

Single-crystal growth, crystal structure, and molecular dynamics of organic-inorganic [NH3(CH2)2NH3]CuBr4

As part of obtaining excellent properties that can be used as lead-free hybrid solar cells, the crystal growth, crystal structure, phase transition temperature, and thermal properties for [NH3(CH2)2NH3]CuBr4 were discussed. The crystal structure at 300 K was determined to be monoclinic by single-crystal X-ray diffraction (XRD) analysis. The phase transition temperatures were determined to be 447 and 473 K, and the results were consistent with the powder XRD patterns. Thermogravimetric analysis revealed thermal stability up to ~ 460 K. The continuous changes in the 1H and 13C chemical shifts and 14N static resonance frequency with increasing temperature are related to variations in the local environment and coordination geometry. The significant differences in activation energies obtained from the 1H and 13C spin-lattice relaxation times (t1ρ) at low and high temperatures were discussed. The activation energy results suggested that the energy barrier at low temperatures was related to the reorientation of the NH3 and CH2 groups around the three-fold symmetry axis, and the energy barrier at high temperatures was related to the reorientation of the [NH3(CH2)2NH3] cation. These physical properties will be provide important insights or potential applications of this crystal.Please check and confirm that the corresponding author and their respective corresponding affiliation have been correctly identified and amend if necessary.OK !

Exploring the potential applications of lead-free organic-inorganic perovskite type [NH3(CH2)nNH3]MCl4 (n = 2, 3, 4, 5, and 6; M = Mn, Co, Cu, Zn, and Cd) crystals

The organic-inorganic hybrid perovskite compounds have been extensively studied since the dawn of a new era in the field of photovoltaic applications. Up to now, perovskites have proven to be the most promising in terms of power conversion efficiency; however, their main disadvantages for use in solar cells are toxicity and chemical instability. Therefore, it is essential to develop a hybrid perovskite that can be replaced with lead-free materials. This review focuses on the possibility of applying lead-free organic-inorganic perovskite types [NH3(CH2)nNH3]MCl4 (n = 2, 3, 4, 5, and 6; M = Mn, Co, Cu, Zn, and Cd) crystals. We are seeking organic-inorganic hybrid perovskite materials with very high temperature stability or without phase transition temperature, and thermal stability. Thus, by considering the characteristics according to the methylene lengths and the various transition metals, we aim to identify improved materials meeting the criteria mentioned above. Consequently, the physicochemical properties of organic-inorganic hybrid perovskite [NH3(CH2)nNH3]MCl4 regarding the effects of various transition metal ions of the anion and the methylene lengths of the cation are expected to promote the development and application of lead-free hybrid perovskite solar cells.

Crystal growth, phase transition, and nuclear magnetic resonance of organic-inorganic hybrid perovskite NH2(CH3)2CdCl3

Understanding the physicochemical properties of organic-inorganic hybrid materials is essential to promote their applications. In this study, a single crystal of NH2(CH3)2CdCl3 was grown, and it exhibited a monoclinic structure. Its phase transition temperatures were 460 and 470 K, and it showed sufficient thermal stability. The changes in the NMR chemical shifts of each atom in the crystal with increasing temperature were determined; the chemical shift of 1H of NH2 in the NH2(CH3)2 cation changed with temperature, which was correlated to the changes in the chemical shift of 14N in NH2. The change in 113Cd chemical shifts indicate the change of six Cl atoms around Cd in CdCl6. Therefore, the change in the coordination geometry of CdCl6 is attributed to the change in the N-H⋯Cl hydrogen bond between the NH2(CH3)2 cation and CdCl6 anion. In addition, the 13C activation energies Ea obtained from the spin-lattice relaxation time T1ρ values are smaller than those of the 1H Ea values, suggesting that is free compared to 1H in the cation. We believe that this study furthers our fundamental understanding of organic-inorganic hybrid materials to promote their practical solar cell applications.

Investigation of the structure, phase transitions, molecular dynamics, and ferroelasticity of organic-inorganic hybrid NH(CH3)3CdCl3 crystals

Understanding the physical and chemical properties of the organic-inorganic hybrid NH(CH3)3CdCl3 is essential for its application. Considering its importance, a single crystal of NH(CH3)3CdCl3 was grown with an orthorhombic structure at 300 K. The phase transition temperatures were determined to be 345 (TC3), 376 (TC2), and 452 K (TC1) (phases IV, III, II, and I, respectively, starting from a low temperature). The partial decomposition temperature was 522 K (Td). Furthermore, the NMR chemical shifts of the 1H, 13C, and 113Cd atoms of the cation and anion varied with increasing temperature. Consequently, a significant change in the coordination geometry of Cl around Cd in CdCl6 and a change in the coordination geometry of H in NH was associated with changes in the N-H⋯Cl hydrogen bond near the phase transition temperature. The 13C activation energy Ea obtained from the spin-lattice relaxation time was smaller than that of 1H Ea, suggesting that energy transfer around 13C is easier. Additionally, a comparison of the twin domain walls measured via optical polarizing microscopy and Sapriel's theory indicated that the crystal structure in phase III was more likely to be orthorhombic than hexagonal.

Crystal structures, phase transitions, and nuclear magnetic resonance of organic-inorganic hybrid [NH2(CH3)2]2ZnBr4 crystals

Organic-inorganic hybrid [NH₂(CH₃)₂]₂ZnBr₄ crystals were grown via slow evaporation, and their monoclinic structure was determined using single-crystal X-ray diffraction (XRD). The two phase transition temperatures at 401 K (T _C1) and 436 K (T _C2) were defined using differential scanning calorimetry and powder XRD. In the nuclear magnetic resonance spectra, a small change was observed in the ¹H chemical shifts for NH₂, ¹³C chemical shifts for CH₃, and ¹⁴N resonance frequency for NH₂ near T _C1. ¹H spin-lattice relaxation times T _1ρ and ¹³C T _1ρ for NH₂ and CH₃, respectively, rapidly decreased near T _C1, suggesting that energy was easily transferred. NH₂ in the [NH₂(CH₃)₂]⁺ cation was significantly influenced by the surrounding environments of ¹H and ¹⁴N, indicating a change in the N-H⋯Br hydrogen bond with the coordination geometry of the ZnBr₄ anion. These fundamental properties open efficient avenues for the development of organic-inorganic hybrids, thus qualifying them for practical applications.

Organic-inorganic hybrid [NH3(CH2)6NH3]ZnBr4 crystal: structural characterization, phase transitions, thermal properties, and structural dynamics

Organic–inorganic hybrid [NH₃(CH₂)₆NH₃]ZnBr₄ crystals were prepared by slow evaporation; the crystals had a monoclinic structure with space group P2₁/c and lattice constants a = 7.7833 Å, b = 14.5312 Å, c = 13.2396 Å, β = 90.8650°, and Z = 4. They underwent two phase transitions, at 370 K (T_C1) and 430 K (T_C2), as confirmed by powder X-ray diffraction patterns at various temperatures; the crystals were stable up to 600 K. The nuclear magnetic resonance spectra, obtained using the magic-angle spinning method, demonstrated changes in the ¹H and ¹³C chemical shifts were observed near T_C1, indicating changing structural environments around ¹H and ¹³C. The spin–lattice relaxation time, T_1ρ, increased rapidly near T_C1 suggesting very large energy transfer, as indicated by a large thermal displacement around the ¹³C atoms of the cation. However, the environments of ¹H, ¹⁴N, and C1 located close to NH₃ in the [NH₃(CH₂)₆NH₃] cation did not influence it significantly, indicating a minor change in the N–H⋯Br hydrogen bond with the coordination geometry of the ZnBr₄ anion. We believe that the information on the physiochemical properties and thermal stability of [NH₃(CH₂)₆NH₃]ZnBr₄, as discussed in this study, would be key to exploring its application in stable, environment friendly solar cells.

Organic–inorganic hybrid [NH₃(CH₂)₆NH₃]ZnBr₄ crystals were prepared by slow evaporation; the crystals had a monoclinic structure with space group P2₁/c and lattice constants a = 7.7833 Å, b = 14.5312 Å, c = 13.2396 Å, β = 90.8650°, and Z = 4.

Bridging Gaussian Density Fluctuations from Microscopic to Macroscopic Volumes: Applications to Non-Polar Solute Hydration Thermodynamics

The hydration of hydrophobic solutes is intimately related to the spontaneous formation of cavities in water through ambient density fluctuations. Information theory-based modeling and simulations have shown that water density fluctuations in small volumes are approximately Gaussian. For limiting cases of microscopic and macroscopic volumes, water density fluctuations are known exactly and are rigorously related to the density and isothermal compressibility of water. Here, we develop a theory—interpolated gaussian fluctuation theory (IGFT)—that builds an analytical bridge to describe water density fluctuations from microscopic to molecular scales. This theory requires no detailed information about the water structure beyond the effective size of a water molecule and quantities that are readily obtained from water’s equation-of-state—namely, the density and compressibility. Using simulations, we show that IGFT provides a good description of density fluctuations near the mean, that is, it characterizes the variance of occupancy fluctuations over all solute sizes. Moreover, when combined with the information theory, IGFT reproduces the well-known signatures of hydrophobic hydration, such as entropy convergence and solubility minima, for atomic-scale solutes smaller than the crossover length scale beyond which the Gaussian assumption breaks down. We further show that near hydrophobic and hydrophilic self-assembled monolayer surfaces in contact with water, the normalized solvent density fluctuations within observation volumes depend similarly on size as observed in the bulk, suggesting the feasibility of a modified version of IGFT for interfacial systems. Our work highlights the utility of a density fluctuation-based approach toward understanding and quantifying the solvation of non-polar solutes in water and the forces that drive them toward surfaces with different hydrophobicities.

Accurate prediction of hydration free energies and solvation structures using molecular density functional theory with a simple bridge functional

This paper assesses the ability of molecular density functional theory to predict efficiently and accurately the hydration free energies of molecular solutes and the surrounding microscopic water structure. A wide range of solutes were investigated, including hydrophobes, water as a solute, and the FreeSolv database containing 642 drug-like molecules having a variety of shapes and sizes. The usual second-order approximation of the theory is corrected by a third-order, angular-independent bridge functional. The overall functional is parameter-free in the sense that the only inputs are bulk water properties, independent of the solutes considered. These inputs are the direct correlation function, compressibility, liquid-gas surface tension, and excess chemical potential of the solvent. Compared to molecular simulations with the same force field and the same fixed solute geometries, the present theory is shown to describe accurately the solvation free energy and structure of both hydrophobic and hydrophilic solutes. Overall, the method yields a precision of order 0.5 k_BT for the hydration free energies of the FreeSolv database, with a computer speedup of 3 orders of magnitude. The theory remains to be improved for a better description of the H-bonding structure and the hydration free energy of charged solutes.

Toward Physics-Based Solubility Computation for Pharmaceuticals to Rival Informatics

We demonstrate that physics-based calculations of intrinsic aqueous solubility can rival cheminformatics-based machine learning predictions. A proof-of-concept was developed for a physics-based approach via a sublimation thermodynamic cycle, building upon previous work that relied upon several thermodynamic approximations, notably the 2RT approximation, and limited conformational sampling. Here, we apply improvements to our sublimation free-energy model with the use of crystal phonon mode calculations to capture the contributions of the vibrational modes of the crystal. Including these improvements with lattice energies computed using the model-potential-based Ψ_mol method leads to accurate estimates of sublimation free energy. Combining these with hydration free energies obtained from either molecular dynamics free-energy perturbation simulations or density functional theory calculations, solubilities comparable to both experiment and informatics predictions are obtained. The application to coronene, succinic acid, and the pharmaceutical desloratadine shows how the methods must be adapted for the adoption of different conformations in different phases. The approach has the flexibility to extend to applications that cannot be covered by informatics methods.

Assessing the correctness of pressure correction to solvation theories in the study of electron transfer reactions

Liquid state theories have emerged as a numerically efficient alternative to costly molecular dynamics simulations of electron transfer reactions in solution. In a recent paper [Jeanmairet et al., Chem. Sci. 10, 2130-2143 (2019)], we introduced the framework to compute the energy gap, free energy profile, and reorganization free energy using molecular density functional theory. However, this technique, as other molecular liquid state theories, overestimates the bulk pressure of the fluid. Because of the very high pressure, the predicted free energy is dramatically exaggerated. Several attempts were made to fix this issue, either based on simple a posteriori correction or by introducing bridge terms. By studying two model half reactions in water, Cl → Cl⁺ and Cl → Cl^-, we assess the correctness of these two types of corrections to study electron transfer reactions. We found that a posteriori correction, because it violates the Variational principle, leads to an inconsistency in the definition of the reorganization free energy and should not be used to study electron transfer reactions. The bridge approach, because it is theoretically well grounded, is perfectly suitable for this type of systems.

Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet?

The parallel artificial membrane permeability assay (PAMPA), a non-cellular lab-based assay, is extensively used to measure the permeability of pharmaceutical compounds. PAMPA experiments provide a working mimic of a molecule passing through cells and PAMPA values are widely used to estimate drug absorption parameters. There is an increased interest in developing computational methods to predict PAMPA permeability values. We developed an in silico model to predict the permeability of compounds based on the PAMPA assay. We used the three-dimensional reference interaction site model (3D-RISM) theory with the Kovalenko-Hirata (KH) closure to calculate the excess chemical potentials of a large set of compounds and predicted their apparent permeability with good accuracy (mean absolute error or MAE = 0.69 units) when compared to a published experimental data set. Furthermore, our in silico PAMPA protocol performed very well in the binary prediction of 288 compounds as being permeable or impermeable (precision = 94%, accuracy = 93%). This suggests that our in silico protocol can mimic the PAMPA assay and could aid in the rapid discovery or screening of potentially therapeutic drug leads that can be delivered to a desired tissue.

Structural characterization, thermal properties, and molecular motions near the phase transition in hybrid perovskite [(CH2)3(NH3)2]CuCl4 crystals: 1H, 13C, and 14N nuclear magnetic resonance

The structural characterization of the [(CH2]3(NH3)2]+ cation in the perovskite [(CH2)3(NH3)2]CuCl4 crystal was performed by solid-state 1H nuclear magnetic resonance (NMR) spectroscopy. The 1H NMR chemical shifts for NH3 changed more significantly with temperature than those for CH2. This change in cationic motion is enhanced at the N-end of the organic cation, which is fixed to the inorganic layer by N-H···Cl hydrogen bonds. The 13C chemical shifts for CH2-1 increase slowly without any anomalous change, while those for CH2-2 move abruptly compared to CH2-1 with increasing temperature. The four peaks of two groups in the 14N NMR spectra, indicating the presence of a ferroelastic multidomain, were reduced to two peaks of one group near TC2 (= 333 K); the 14N NMR data clearly indicated changes in atomic configuration at this temperature. In addition, 1H and 13C spin-lattice have shorter relaxation times (T1ρ), in the order of milliseconds because T1ρ is inversely proportional to the square of the magnetic moment of paramagnetic ions. The T1ρ values for CH2 and NH3 protons were almost independent of temperature, but the CH2 moiety located in the middle of the N-C-C-C-N bond undergoes tumbling motion according to the Bloembergen-Purcell-Pound theory. Ferroelasticity is the main cause for the phase transition near TC2.

Application of the Approximate 3D-Reference Interaction Site Model (RISM) Molecular Solvation Theory to Acetonitrile as Solvent

The integral equation formalism based reference interaction site model (RISM) molecular solvation theory is applied to pure liquid acetonitrile and water-acetonitrile binary mixtures of different compositions. Solvate formation of d- and f-block ions by ACN is also calculated to check applicability of the RISM theory. The generalized Amber force field (GAFF) and the universal force field (UFF) parameters were found to be suitable for applications with the RISM theory for acetonitrile solvent. The presence of local microsolvated clusters for water-acetonitrile mixtures is validated in the RISM calculations.

Multisolvent Models for Solvation Free Energy Predictions Using 3D-RISM Hydration Thermodynamic Descriptors

The potential to predict solvation free energies (SFEs) in any solvent using a machine learning (ML) model based on thermodynamic output, extracted exclusively from 3D-RISM simulations in water is investigated. The models on multiple solvents take into account both the solute and solvent description and offer the possibility to predict SFEs of any solute in any solvent with root mean squared errors less than 1 kcal/mol. Validations that involve exclusion of fractions or clusters of the solutes or solvents exemplify the model's capability to predict SFEs of novel solutes and solvents with diverse chemical profiles. In addition to being predictive, our models can identify the solute and solvent features that influence SFE predictions. Furthermore, using 3D-RISM hydration thermodynamic output to predict SFEs in any organic solvent reduces the need to run 3D-RISM simulations in all these solvents. Altogether, our multisolvent models for SFE predictions that take advantage of the solvation effects are expected to have an impact in the property prediction space.

Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory

Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using special purpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.

Li-Binding Thermodynamics and Redox Properties of BNOPS-Based Organic Compounds for Cathodes in Lithium-Ion Batteries

Cyclic organic compounds with pentagon rings have been paid less attention for cathodes in lithium-ion batteries as compared with aromatic compounds. In this study, we investigate the Li-binding thermodynamics, redox properties, and theoretical performance for a selected set of heteroatom-containing, pentagon-shaped, organic compounds, namely borole, pyrrole, furan, phosphole, thiophene, and their derivatives to assess their potential for organic cathode materials. This investigation provides us with three important findings. First, the Li-binding thermodynamics and redox properties for the organic compounds would be systematically tailored by the type of the incorporated heteroatom and backbone length, exhibiting both the strongest Li-binding and the highest redox potential for borole. Second, it is highlighted that borole can store up to two Li atoms per molecule exhibiting the exceptionally high charge capacity (839 mA h/g) despite the absence of any well-known redox-active moieties (e.g., carbonyl). Third, dibenzothiophene exhibits weak and comparable Li-binding strengths at multiple feasible binding configurations with an indication of its low Li-storage capability, while the others dominantly bind with Li at their most stable binding configurations. All these findings will provide an insight into the guidelines for the systematic design of promising heterocyclic organic compounds (i.e., borole-based insoluble polymeric forms) for cathodes in secondary batteries.

A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular dynamics simulations, recent developments in the 3D reference interaction site model (3D-RISM) theory allow many of the same quantities to be calculated in a fraction of the time. However, 3D-RISM produces atomic-site, rather than molecular, density distributions, which are difficult to extract physical meaning from. To overcome this difficulty, we introduce a method to reconstruct molecular density distributions from atomic-site density distributions. Furthermore, we assess the quality of the resulting solvation thermodynamics density distributions by analyzing the binding site of coagulation Factor Xa with both GIST and 3D-RISM. We find good qualitative agreement between the methods for oxygen and hydrogen densities as well as direct solute-solvent energetic interactions. However, 3D-RISM predicts lower energetic and entropic penalties for moving water from the bulk to the binding site.

Closure for the Ornstein-Zernike equation with pressure and free energy consistency

The Ornstein-Zernike (OZ) integral equation theory is a powerful approach to simple liquids due to its low computational cost and the fact that, when combined with an appropriate closure equation, the theory is thermodynamically complete. However, approximate closures proposed to date exhibit pressure or free energy inconsistencies that produce inaccurate or ambiguous results, limiting the usefulness of the Ornstein-Zernike approach. To address this problem, we combine methods to enforce both pressure and free energy consistency to create a new closure approximation and test it for a single-component Lennard-Jones fluid. The closure is a simple power series in the direct and total correlation functions for which we have derived analytical formulas for the excess Helmholtz free energy and chemical potential. These expressions contain a partial molar volumelike term, similar to excess chemical potential correction terms recently developed. Using our bridge approximation, we have calculated the pressure, Helmholtz free energy, and chemical potential for the Lennard-Jones fluid using the Kirkwood charging, thermodynamic integration techniques, and analytic expressions. These results are compared with those from the hypernetted chain equation and the Verlet-modified closure against Monte Carlo and equations-of-state data for reduced densities of ρ^{*}<1 and temperatures of T^{*}=1.5, 2.74, and 5. Our closure shows consistency among all thermodynamic paths, except for one expression of the Gibbs-Duhem relation, whereas the hypernetted chain equation and the Verlet-modified closure exhibit consistency between only a few relations. Accuracy of the closure is comparable to the Verlet-modified closure and a significant improvement to results obtained from the hypernetted chain equation.

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2

HtrA2 (high-temperature requirement 2) is a human mitochondrial protease that has a role in apoptosis and Parkinson's disease. The structure of HtrA2 with an intact catalytic triad was determined, revealing a conformational change in the active site loops, involving mainly the regulatory LD loop, which resulted in burial of the catalytic serine relative to the previously reported structure of the proteolytically inactive mutant. Mutations in the loops surrounding the active site that significantly restricted their mobility, reduced proteolytic activity both in vitro and in cells, suggesting that regulation of HtrA2 activity cannot be explained by a simple transition to an activated conformational state with enhanced active site accessibility. Manipulation of solvent viscosity highlighted an unusual bi-phasic behavior of the enzymatic activity, which together with MD calculations supports the importance of motion in the regulation of the activity of HtrA2. HtrA2 is an unusually thermostable enzyme (T_M=97.3 °C), a trait often associated with structural rigidity, not dynamic motion. We suggest that this thermostability functions to provide a stable scaffold for the observed loop motions, allowing them a relatively free conformational search within a rather restricted volume.

SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling

Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing ([Formula: see text] for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining [Formula: see text] compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to [Formula: see text]. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple [Formula: see text] correction improved agreement with experiment from [Formula: see text] to [Formula: see text], despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.