Enthalpic Contributions Research Articles

Unraveling the Ag+ ion coordination and solvation thermodynamics in the 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid

The solvation of the Ag+ ion in the 1-butyl-3-methylimidazolium tetrafluoroborate ([C4mim][BF4]) ionic liquid (IL) has been studied by means of experimental and theoretical methods with the aim of elucidating the cation coordination structure and thermodynamic properties. Car-Parrinello molecular dynamics (CPMD) simulations showed that the Ag+ ion is coordinated by an average number of four [BF4]− anions in a pseudo-tetrahedral geometry. A high configurational disorder of the first solvation sphere is found, where the anions can be found both in mono- and bidentate coordination mode around the Ag+ ion. Also, a solvational equilibrium is observed as due to [BF4]− anion dissociation along the trajectory. The analysis of X-ray absorption spectroscopy data confirmed the picture provided by the CPMD simulation. Classical molecular dynamics simulations were carried out to obtain the single-ion solvation thermodynamic parameters. The negative water → IL free energy of transfer suggests that the Ag+ ion is more favorably solvated in the [C4mim][BF4] IL than in water. This behavior is due to a balance between the enthalpic and entropic contributions, which allows to find a rationale to the strong solvation capabilities of BF4-based ILs towards Ag+.

Cytochrome c - silver nanoparticle interactions: Spectroscopy, thermodynamic and enzymatic activity studies

Cytochrome c, an iron containing metalloprotein in the mitochondria of the cells with an oxide/redox property, plays key role in the cell apoptotic pathway. In this study, the interaction of silver nanoparticles (AgNPs) with cytochrome c (Cyt c) was investigated by using a combination of spectroscopic, imaging and thermodynamic techniques, including dynamic light scattering (DLS), ultraviolet–visible (UV–vis) spectroscopy, transmission electron microscopy (TEM), fluorescence spectroscopy, near and far circular dichroism (CD) spectroscopy, and isothermal titration calorimetry (ITC). DLS and UV–vis analysis evidenced the formation of surface complexes of Cyt c on AgNPs. The saturation of surface coverage of AgNPs was observed at 4.36 Cyt c molecules per nm2 of AgNPs. The surface complexation resulted in a promotion of the Ag dissolution overtime. The negative sign of enthalpic (ΔH) contribution suggested that electrostatic forces are indicative forces in the interaction between protein and AgNPs. Moreover, the fluorescence spectra revealed that the conformation of protein was altered around tryptophan (Trp) and tyrosine (Tyr) residues indicating the alteration of the tertiary structure of Cyt c. CD analysis evidenced that the secondary structure of Cyt c was modified under AgNPs-Cyt c interactions and the binding of Cyt c onto AgNPs resulted in remarkable structural perturbation around the active site heme, which in turn alter the protein enzymatic activity. The results of the present study contributed to a deeper insight on the mechanisms of interaction between NPs and biomacromolecules and could help establish the in vivo fate of AgNPs on cellular redox homeostasis.

Determinants for macromolecular crowding-induced thermodynamic stabilization of acid-denatured cytochrome c to molten globules

The macromolecular crowding effect transforms the acid-denatured ferricytochrome c (cyt cIII) (UA-state) to molten-globule (MGMC-state) at pH 1.85. Crowding-induced stabilization free energy (ΔΔG) and preferential hydration ΔΓW were estimated for the UA → MGMC transition. The magnitudes of ΔΔG and ΔΓW were found to be decreased as dextran 70 (D70) > dextran 40 (D40) > ficoll 70 (F70), which demonstrates that ΔΔG and ΔΓW track the molecular size and shape of the crowder towards refolding and stabilization of UA-state to MGMC-state. Analysis of effects of crowders (D40, D70, F70) on thermal and chemical-denaturations of acid-denatured cyt cIII provided several important information, (i) macromolecular crowding increased the thermodynamic stability of acid-denatured cyt cIII, (ii) concentration, size and shape of crowder control the crowding-induced thermodynamic stabilization of MGMC-state, (iii) crowding effect increased the thermal-denaturation midpoint (Tm) with a slight change in enthalpy (ΔHm), suggesting that the steric-excluded volume effect contributes to the crowding-induced increased thermal stability of the acid-denatured protein. Analysis of entropy − enthalpy plots for D40, D70, and F70 reveals that in addition to the steric-excluded volume effect, the enthalpic contribution is also added to the macromolecular crowding-induced stabilization of acid-denatured cyt cIII. The dilute-medium, compound-crowder, purely entropic-crowder and purely enthalpic-crowder curves were obtained for acid-denatured cyt cIII for D70, D40 and F70. The crossover temperature, Tx was calculated from the dilute and compound-crowder curves. The Tx values measured for D40, D70, and F70 were found to be ∼ 250.15 K, 272.15 K, and 275.15 K, respectively, which suggests that the Tx value depends on the size and shape of the crowder. Furthermore, the observation of a lower value of Tx and a minor enthalpic component for D40, D70, and F70 is likely due to the formation of weaker soft interactions of acid-denatured cyt cIII with D40, D70, and F70.

Cell-Effective Transition-State Analogue of Phenylethanolamine N-Methyltransferase.

Phenylethanolamine N-methyltransferase (PNMT) catalyzes the S-adenosyl-l-methionine (SAM)-dependent methylation of norepinephrine to form epinephrine. Epinephrine is implicated in the regulation of blood pressure, respiration, Alzheimer's disease, and post-traumatic stress disorder (PTSD). Transition-state (TS) analogues bind their target enzymes orders of magnitude more tightly than their substrates. A synthetic strategy for first-generation TS analogues of human PNMT (hPNMT) permitted structural analysis of hPNMT and revealed potential for second-generation inhibitors [Mahmoodi, N.; J. Am. Chem. Soc. 2020, 142, 14222-14233]. A second-generation TS analogue inhibitor of PNMT was designed, synthesized, and characterized to yield a Ki value of 1.2 nM. PNMT isothermal titration calorimetry (ITC) measurements of inhibitor 4 indicated a negative cooperative binding mechanism driven by large favorable entropic contributions and smaller enthalpic contributions. Cell-based assays with HEK293T cells expressing PNMT revealed a cell permeable, intracellular PNMT inhibitor with an IC50 value of 81 nM. Structural analysis demonstrated inhibitor 4 filling catalytic site regions to recapitulate both norepinephrine and SAM interactions. Conformation of the second-generation inhibitor in the catalytic site of PNMT improves contacts relative to those from the first-generation inhibitors. Inhibitor 4 demonstrates up to 51,000-fold specificity for PNMT relative to DNA and protein methyltransferases. Inhibitor 4 also exhibits a 12,000-fold specificity for PNMT over the α2-adrenoceptor.

Entropic barrier of water permeation through single-file channels

Facilitated water permeation through narrow biological channels is fundamental for all forms of life. Despite its significance in health and disease as well as for biotechnological applications, the energetics of water permeation are still elusive. Gibbs free energy of activation is composed of an enthalpic and an entropic component. Whereas the enthalpic contribution is readily accessible via temperature dependent water permeability measurements, estimation of the entropic contribution requires information on the temperature dependence of the rate of water permeation. Here, we estimate, by means of accurate activation energy measurements of water permeation through Aquaporin-1 and by determining the accurate single channel permeability, the entropic barrier of water permeation through a narrow biological channel. Thereby the calculated value for triangle {S}^{{{ddagger}} } = 2.01 ± 0.82 J/(mol·K) links the activation energy of 3.75 ± 0.16 kcal/mol with its efficient water conduction rate of ~1010 water molecules/second. This is a first step in understanding the energetic contributions in various biological and artificial channels exhibiting vastly different pore geometries.

A Free Energy Decomposition Analysis: Insight into Binding Thermodynamics from Absolutely Localized Molecular Orbitals.

Traditional energy decomposition analysis (EDA) methods can provide an interpretive decomposition of non-covalent electronic binding energies. However, by definition, they neglect entropic effects and nuclear contributions to the enthalpy. With the objective of revealing the chemical origins of trends in free energies of binding, we introduce the concept of a Gibbs decomposition analysis (GDA) by coupling the absolutely localized molecular orbital treatment of electrons in non-covalent interactions with the simplest possible quantum rigid rotor-harmonic oscillator treatment of nuclear motion at finite temperature. The resulting pilot GDA is employed to decompose enthalpic and entropic contributions to the free energy of association of the water dimer, fluoride-water dimer, and water binding to an open metal site in the metal-organic framework Cu(I)-MFU-4l. The results show enthalpic trends that generally track the electronic binding energy and entropic trends that reveal the increasing price of loss of translational and rotational degrees freedom with temperature.

Polymer complexation: Partially ionizable asymmetric polyelectrolytes.

Theories of bulk coacervation of oppositely charged polyelectrolytes (PE) obscure single molecule level thermodynamic details, considered significant for coacervate equilibrium, whereas simulations account for only pairwise Coulomb interaction. Also, studies of effects of asymmetry on PE complexation are rare compared to symmetric PEs. We develop a theoretical model, accounting for all entropic and enthalpic contributions at the molecular level, and the mutual segmental screened Coulomb and excluded volume interactions between two asymmetric PEs, by constructing a Hamiltonian following Edwards and Muthukumar. Assuming maximal ion-pairing in the complex, the system free energy comprising configurational entropy of the polyions and free-ion entropy of the small ions is minimized. The effective charge and size of the complex, larger than sub-Gaussian globules as for symmetric chains, increase with asymmetry in polyion length and charge density. The thermodynamic drive for complexation is found to increase with ionizability of symmetric polyions and with a decrease in asymmetry in length for equally ionizable polyions. The crossover Coulomb strength demarcating the ion-pair enthalpy-driven (low strength) and counterion release entropy-driven (high strength) is marginally dependent on the charge density, because so is the degree of counterion condensation, and strongly dependent on the dielectric environment and salt. The key results match the trends in simulations. The framework may provide a direct way to calculate thermodynamic dependencies of complexation on experimental parameters such as electrostatic strength and salt, thus to better analyze and predict observed phenomena for different sets of polymer pairs.

Investigation of Nonidealities through an Extended Flory–Huggins Model of Ionic Liquid Mixtures with Ammonia

The phase behavior of ionic liquids and ammonia is critical due to their application in various fields such as sorption-based heating/cooling cycles and direct ammonia capture. To date, various ionic liquids have been developed and investigated to enhance the solubility of ammonia without compromising the reversibility due to recycling concerns and various thermodynamic models have been used to correlate the experimental vapor–liquid equilibria data. Surely, high ammonia sorption capacities are required and understanding the interaction between ammonia and ionic liquids can lead to synthesizing targeted ionic liquids for ammonia. In this study, we developed an extended Flory–Huggins model on ammonia and imidazolium-based ionic liquid systems, where both combinatorial and residual terms are considered, to understand the interaction between ammonia and ionic liquids. The results showed that the nonidealities in ammonia and imidazolium-based IL mixtures are due to both entropic and enthalpic contributions. Therefore, increasing the size of the IL would not be enough to achieve higher solubilities. A deeper understanding of the molecular-level interaction between ionic liquids and ammonia can be investigated via molecular simulations.

Fine-Tuning and Enhancement of pH-Dependent Membrane Permeation of Cyclic Peptides by Utilizing Noncanonical Amino Acids with Extended Side Chains.

The development of cyclic peptides that exhibit pH-sensitive membrane permeation is a promising strategy for tissue-selective drug delivery. We investigated the pH-dependent interactions of designed cyclic peptides bearing noncanonical amino acids of long acidic side chains with lipid membranes, including surface binding, insertion, and translocation across the membrane. As the length of the side chain of acidic amino acid increased, the binding affinity of the peptides to phosphatidylcholine bilayer surfaces decreased, while the pH for the 50% insertion of the peptides into the bilayers increased. The pH for membrane permeation of the peptides increased with the side chain length, resulting in specific membrane permeation at pH ∼6.5. The longer side chain of acidic amino acids improved the maximum rate of membrane permeation at low pH, where both entropic and enthalpic contributions affected the permeation. Our peptide also showed intracellular delivery of cargo molecules into living cells in a pH-dependent manner.

Thermodynamic insight into the interaction mechanism of an ESIPT drug with a serum transport protein: Slower solvent-relaxation dynamics explored through wavelength-sensitive fluorescence behavior

Recently, 3,5-diiodosalicylic acid (3,5-DISA) has garnered enormous research attention owing to its wide-spread medicinal/biological applications, use as a model to study the role of halogen bonding in drug-protein interaction and so forth. However, the arena of the study of interaction of 3,5-DISA with relevant biological targets, particularly serum transport protein still starves for meticulous exploration of a number of fundamental aspects, such as, the thermodynamics and strength of binding, effect of drug binding on the native protein conformation and functionality, rotational and solvent-relaxation dynamics within the protein scaffolds etc. The present investigation endeavors to unveil these important aspects of 3,5-DISA:HSA interaction scenario. Our spectroscopic results demonstrate a remarkable modification of the excited-state intramolecular proton transfer (ESIPT) photophysics of 3,5-DISA upon interaction with HSA. A detailed isothermal titration calorimetry (ITC) study reveals that the interaction process is governed by favorable enthalpic (∆H0 < 0) and unfavorable entropic (T∆S0 < 0) contributions. The modulation of the hydration structure at the interfaces accompanying the binding phenomenon is also delineated in this context. Circular dichroism (CD) spectroscopy has been exploited to show the slight perturbation of the native protein conformation as a result of drug binding. In complementarity, the functionality of HSA (in terms of esterase-like activity) has also been shown to decrease with added 3,5-DISA. Our cumulative exploration of the wavelength-sensitive fluorescence parameters including red-edge excitation shift (REES) points out a remarkably slower rate of solvent-relaxation dynamics of the HSA-bound 3,5-DISA in the photoexcited state. The modification of the rotational-relaxation behavior of 3,5-DISA within the protein is also addressed and rationalized on the basis of the two-step and wobbling-in-cone model.

Multiple Modes of Zinc Binding to Histatin 5 Revealed by Buffer-Independent Thermodynamics.

Histatin 5 (Hist5) is an antimicrobial peptide found in human saliva as part of the innate immune system. Hist5 can bind several metal ions in vitro, and Zn2+ has been shown to function as an inhibitory switch to regulate the peptide's biological activity against the opportunistic fungal pathogen Candida albicans in cell culture. Here, we studied Zn2+ binding to Hist5 at four temperatures from 15 to 37 °C using isothermal titration calorimetry to obtain thermodynamic parameters that were corrected for competing buffer effects. Hist5 bound Zn2+ with a buffer-dependent association constant of ∼105 M-1 and a buffer-independent association constant of ∼6 × 106 M-1 at pH 7.4 and at all temperatures tested. Zn2+ binding was both enthalpically and entropically favorable, with larger entropic contributions at 15 °C and larger enthalpic contributions at 37 °C. Additionally, the Zn:Hist5 binding stoichiometry increased from 1:1 to 2:1 as temperature increased. The enthalpy-entropy compensation and the variable stoichiometry lead us to propose a model in which the Zn-Hist5 complex exists in an equilibrium between two distinct binding modes with different Zn:Hist5 stoichiometries. The in-depth thermodynamic analysis presented herein may help illuminate the biophysical basis for Zn-dependent changes in the antifungal activity of Hist5.

Influence of SiO2 addition on the sintering behavior and kinetics of fine-sized α-Al2O3 nanoparticles

Due to the low solubility of Si in Al2O3, SiO2 additives/impurities can segregate at grain boundaries, altering the grain boundary kinetic behaviors in Al2O3 and inducing the abnormal grain growth of Al2O3—which also makes preparing high-density SiO2-doped Al2O3 sintered samples with uniform microstructures difficult during free sintering. Almost all the work thus far has focused on analyzing the reason for the abnormal grain growth of Al2O3 induced by SiO2, while the effect of SiO2 on the sintering behaviors and/or grain boundary kinetics of Al2O3 is less studied. Here, using homemade 15 nm dispersed α-Al2O3 nanoparticles as a raw material, we systematically investigated the effect of SiO2 additives on the sintering behaviors (including densification and grain growth) and kinetics (including grain boundary diffusion and grain boundary migration) of high-purity α-Al2O3 nanoparticles. The kinetic results show that doping SiO2 does not change the enthalpic contribution (i.e., activation energy) of α-Al2O3 but significantly reduces its entropic contribution (i.e., preexponent term). Furthermore, based on the explored sintering behaviors combined with two-step free sintering, a dense SiO2-doped Al2O3 nanocrystalline ceramic with an average grain size of 43 nm and ultra-uniform microstructure (the standard deviation of the grain size distribution to the average grain size is only 0.33) was successfully obtained at the optimal sintering parameters.

Iron response elements (IREs)-mRNA of Alzheimer's amyloid precursor protein binding to iron regulatory protein (IRP1): a combined molecular docking and spectroscopic approach

The interaction between the stem-loop structure of the Alzheimer's amyloid precursor protein IRE mRNA and iron regulatory protein was examined by employing molecular docking and multi-spectroscopic techniques. A detailed molecular docking analysis of APP IRE mRNA∙IRP1 reveals that 11 residues are involved in hydrogen bonding as the main driving force for the interaction. Fluorescence binding results revealed a strong interaction between APP IRE mRNA and IRP1 with a binding affinity and an average binding sites of 31.3 × 106 M−1 and 1.0, respectively. Addition of Fe2+(anaerobic) showed a decreased (3.3-fold) binding affinity of APP mRNA∙IRP1. Further, thermodynamic parameters of APP mRNA∙IRP1 interactions were an enthalpy-driven and entropy-favored event, with a large negative ΔH (–25.7 ± 2.5 kJ/mol) and a positive ΔS (65.0 ± 3.7 J/mol·K). A negative ΔH value for the complex formation suggested the contribution of hydrogen bonds and van der Waals forces. The addition of iron increased the enthalpic contribution by 38% and decreased the entropic influence by 97%. Furthermore, the stopped-flow kinetics of APP IRE mRNA∙IRP1 also confirmed the complex formation, having the rate of association (kon) and the rate of dissociation (koff) as 341 μM−1 s−1, and 11 s−1, respectively. The addition of Fe2+ has decreased the rate of association (kon) by ~ three-fold, whereas the rate of dissociation (koff) has increased by ~ two-fold. The activation energy for APP mRNA∙IRP1 complex was 52.5 ± 2.1 kJ/mol. The addition of Fe2+ changed appreciably the activation energy for the binding of APP mRNA with IRP1. Moreover, circular dichroism spectroscopy has confirmed further the APP mRNA∙IRP1 complex formation and IRP1 secondary structure change with the addition of APP mRNA. In the interaction between APP mRNA and IRP1, iron promotes structural changes in the APP IRE mRNA∙IRP1 complexes by changing the number of hydrogen bonds and promoting a conformational change in the IRP1 structure when it is bound to the APP IRE mRNA. It further illustrates how IRE stem-loop structure influences selectively the thermodynamics and kinetics of these protein-RNA interactions.

Characterization of ligand-induced thermal stability of the human organic cation transporter 2 (OCT2).

Introduction: The human organic cation transporter 2 (OCT2) is involved in the transport of endogenous quaternary amines and positively charged drugs across the basolateral membrane of proximal tubular cells. In the absence of a structure, the progress in unraveling the molecular basis of OCT2 substrate specificity is hampered by the unique complexity of OCT2 binding pocket, which seemingly contains multiple allosteric binding sites for different substrates. Here, we used the thermal shift assay (TSA) to better understand the thermodynamics governing OCT2 binding to different ligands. Methods: Molecular modelling and in silico docking of different ligands revealed two distinct binding sites at OCT2 outer part of the cleft. The predicted interactions were assessed by cis-inhibition assay using [3H]1-methyl-4-phenylpyridinium ([3H]MPP+) as a model substrate, or by measuring the uptake of radiolabeled ligands in intact cells. Crude membranes from HEK293 cells harboring human OCT2 (OCT2-HEK293) were solubilized in n-Dodecyl-β-D-Maltopyranoside (DDM), incubated with the ligand, heated over a temperature gradient, and then pelleted to remove heat-induced aggregates. The OCT2 in the supernatant was detected by western blot. Results: Among the compounds tested, cis-inhibition and TSA assays showed partly overlapping results. Gentamicin and methotrexate (MTX) did not inhibit [3H]MPP+ uptake but significantly increased the thermal stabilization of OCT2. Conversely, amiloride completely inhibited [3H]MPP+ uptake but did not affect OCT2 thermal stabilization. [3H]MTX intracellular level was significantly higher in OCT2-HEK293 cells than in wild type cells. The magnitude of the thermal shift (ΔTm) did not provide information on the binding. Ligands with similar affinity showed markedly different ΔTm, indicating different enthalpic and entropic contributions for similar binding affinities. The ΔTm positively correlated with ligand molecular weight/chemical complexity, which typically has high entropic costs, suggesting that large ΔTm reflect a larger displacement of bound water molecules. Discussion: In conclusion, TSA might represent a viable approach to expand our knowledge on OCT2 binding descriptors.

Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations

BRD9 and TAF1(2) have been regarded as significant targets of drug design for clinically treating acute myeloid leukemia, malignancies, and inflammatory diseases. In this study, multiple short molecular dynamics simulations combined with the molecular mechanics generalized Born surface area method were employed to investigate the binding selectivity of three ligands, 67B, 67C, and 69G, to BRD9/TAF1(2) with IC50 values of 230/59 nM, 1400/46 nM, and 160/410 nM, respectively. The computed binding free energies from the MM-GBSA method displayed good correlations with that provided by the experimental data. The results indicate that the enthalpic contributions played a critical factor in the selectivity recognition of inhibitors toward BRD9 and TAF1(2), indicating that 67B and 67C could more favorably bind to TAF1(2) than BRD9, while 69G had better selectivity toward BRD9 over TAF1(2). In addition, the residue-based free energy decomposition approach was adopted to calculate the inhibitor-residue interaction spectrum, and the results determined the gatekeeper (Y106 in BRD9 and Y1589 in TAF1(2)) and lipophilic shelf (G43, F44, and F45 in BRD9 and W1526, P1527, and F1528 in TAF1(2)), which could be identified as hotspots for designing efficient selective inhibitors toward BRD9 and TAF1(2). This work is also expected to provide significant theoretical guidance and insightful molecular mechanisms for the rational designs of efficient selective inhibitors targeting BRD9 and TAF1(2).

Determining the mechanisms of the allosteric architecture of DHFR.

Our ability to rationally optimize allosteric regulation is limited by incomplete knowledge of the mechanisms by which mutations tune allostery. To examine this, we investigated the effects of allosteric residues in a synthetic allosteric switch in which Dihydrofolate reductase (DHFR) is regulated by a blue-light sensitive LOV2 domain. In prior work using saturation mutagenesis, we showed that less than 5% of mutations had a statistically significant influence on allostery. While allostery disrupting mutations were located near the LOV2 insertion site, we found that allostery enhancing mutations were widely dispersed and enriched on the protein surface. However, these experiments did not reveal the mechanism by which the allosteric signal is propagated or how those mutations tune it. To understand these effects, we are characterizing the light-dependent changes in conformational dynamics for the chimeric enzyme by solution nuclear magnetic resonance spectroscopy and analysis of correlations between residue pairs in long timescale molecular dynamics. We have also measured the entropic and enthalpic contribution of select mutations towards the allosteric effect through kinetics assays. From these data, we aim to understand the mechanisms by which the global map of allosteric contributions inside the enzyme operates and provide insight into how allostery can be evolutionarily optimized.

Coordinating Additives as Activity Modulators in Diiodo Latent Olefin Metathesis Catalysts

AbstractThe ruthenium alkylidene catalyzed ring‐closing metathesis (RCM) of 5‐membered rings is an intramolecular reaction that is highly favored due to entropic and enthalpic contributions. Counterintuitively, by using trifluoromethyl sulfur‐chelated ruthenium benzylidene (Ru−SCF3−I), RCM of a diene with a hindered dimethyl terminus, diethyl 2‐allyl‐2‐(3‐methylbut‐2‐en‐1‐yl) malonate (S1), could be achieved at high concentrations but not at low concentrations. This finding led to the discovery that several additives, including ethyl acetate, significantly enhance the latent catalyst's activity. DFT computations and NMR control experiments suggest that additive coordination influences the catalytic cycle. Moreover, the “ethyl acetate effect” was studied in ring‐opening metathesis polymerizations (ROMP), providing a more efficient initiation when the reactions are run in environmentally friendly ethyl acetate as the solvent. The strong influence of simple coordinating additives (sometimes present in the substrate itself) on the activation of latent catalysts provides important insights into the reaction mechanism and opens a doorway towards improving the efficiency of these types of catalysts.

Thermodynamics of the self-assembly of N-annulated perylene bisimides in water. Disentangling the enthalpic and entropic contributions

The hydrophilic/hydrophobic ratio and the number of water molecules released during the self-assembly of N-PBIs 1–4 condition the enthalpic and entropic contributions associated with the self-assembly of these dyes.

Into the dynamics of rotaxanes at atomistic resolution.

Mechanically-interlocked molecules (MIMs) are at the basis of artificial molecular machines and are attracting increasing interest for various applications, from catalysis to drug delivery and nanoelectronics. MIMs are composed of mechanically-interconnected molecular sub-parts that can move with respect to each other, imparting these systems innately dynamical behaviors and interesting stimuli-responsive properties. The rational design of MIMs with desired functionalities requires studying their dynamics at sub-molecular resolution and on relevant timescales, which is challenging experimentally and computationally. Here, we combine molecular dynamics and metadynamics simulations to reconstruct the thermodynamics and kinetics of different types of MIMs at atomistic resolution under different conditions. As representative case studies, we use rotaxanes and molecular shuttles substantially differing in structure, architecture, and dynamical behavior. Our computational approach provides results in agreement with the available experimental evidence and a direct demonstration of the critical effect of the solvent on the dynamics of the MIMs. At the same time, our simulations unveil key factors controlling the dynamics of these systems, providing submolecular-level insights into the mechanisms and kinetics of shuttling. Reconstruction of the free-energy profiles from the simulations reveals details of the conformations of macrocycles on the binding site that are difficult to access via routine experiments and precious for understanding the MIMs' behavior, while their decomposition in enthalpic and entropic contributions unveils the mechanisms and key transitions ruling the intermolecular movements between metastable states within them. The computational framework presented herein is flexible and can be used, in principle, to study a variety of mechanically-interlocked systems.

Energy landscapes and heat capacity signatures for peptides correlate with phase separation propensity.

Phase separation plays an important role in the formation of membraneless compartments within the cell and intrinsically disordered proteins with low-complexity sequences can drive this compartmentalisation. Various intermolecular forces, such as aromatic-aromatic and cation-aromatic interactions, promote phase separation. However, little is known about how the ability of proteins to phase separate under physiological conditions is encoded in their energy landscapes and this is the focus of the present investigation. Our results provide a first glimpse into how the energy landscapes of minimal peptides that contain - and cation- interactions differ from the peptides that lack amino acids with such interactions. The peaks in the heat capacity () as a function of temperature report on alternative low-lying conformations that differ significantly in terms of their enthalpic and entropic contributions. The analysis and subsequent quantification of frustration of the energy landscape suggest that the interactions that promote phase separation lead to features (peaks or inflection points) at low temperatures in . More features may occur for peptides containing residues with better phase separation propensity and the energy landscape is more frustrated for such peptides. Overall, this work links the features in the underlying single-molecule potential energy landscapes to their collective phase separation behaviour and identifies quantities ( and frustration metric) that can be utilised in soft material design.