Cal Mol Research Articles

Exploring conformational changes in β-lactoglobulin (β-LG) induced by silibinin: A comprehensive analysis of polyphenol-protein interaction

This study investigates the comprehensive characterization of the interaction between β-lactoglobulin (β-LG) and Silibinin using various spectroscopic techniques. Fluorescence quenching experiments at different temperatures (298, 303, 308, and 313 K) revealed substantive interactions between β-LG and Silibinin, as indicated by a reduction in fluorescence intensity and a red shift in emission maxima. Further analysis, including Stern-Volmer quenching constants (KSV), bimolecular quenching rate constants (kq), and thermodynamic parameters demonstrated static quenching mechanism and strong binding affinities (Ka range: 0.138–1.483 × 105 M−1) between BLG-Silibinin complex. Thermodynamic study suggested positive enthalpy and entropy changes (ΔHo=43.31 kcal mol−1; ΔSo=164.33 cal mol−1 K−1), suggesting a spontaneous reaction with negative ΔGo values (-5.66 to -7.30 kcal mol−1). Forster resonance energy transfer (FRET) measurements confirmed optimal distances (r and Ro) for FRET occurrence, endorsing the static quenching mechanism. Molecular docking supported these findings, showcasing a 1:1 stoichiometric binding ratio for β-LG: Silibinin. The β-LG and Silibinin complex is primarily stabilized by hydrogen bonds and hydrophobic interactions. Molecular dynamics simulations over 200 ns highlighted stability in the β-LG-Silibinin complex, indicated by RMSD convergence, consistent RMSF values, and compactness illustrated by Rg. Conformational changes in β-LG upon Silibinin binding were further confirmed through UV-Vis absorption spectroscopy, FTIR, far-UV CD, synchronous fluorescence, and 3D fluorescence analyses. Functionally, the antioxidant capacity of β-LG increased after complexation with silibinin as quantified by DPPH assay. These results collectively depict the intricate network of interactions between Silibinin and β-LG, shedding light on the molecular details of their binding and offering insights into potential functional implications in biological contexts.

Experiment and kinetics study on OH∗ chemiluminescence up to 3150 K in hydrogen combustion behind reflected shock waves

Chemiluminescence of OH∗ is commonly employed as an optical indicator for the combustion process. It is widely recognized that the generation of OH∗ in hydrogen flames is primarily governed by the reaction H + O + M=>OH∗+M. In this study, the time histories of OH∗ chemiluminescence from the A→X band around 308 nm were recorded behind reflected shock waves for stoichiometric and lean H2/O2 mixtures highly diluted in argon over the temperature range of 1130–3150 K and at the pressure of approximately 0.9 atm. Based on the time histories of OH∗ chemiluminescence, the best-fit reaction rate coefficient for the reaction H + O + M=>OH∗+M was determined as k = 3.17 × 1027exp(-121968 cal mol−1/RT) + 2.25 × 1017exp(-4246 cal mol−1/RT) cm6 mol−2 s−1 over the temperature range studied. Furthermore, by using the current rate coefficient in mechanism predictions, the predicted time histories and relative peak intensities of OH∗ chemiluminescence are in good agreement with experimental results reported in literature.

Demystifying group-4 polyolefin hydrogenolysis catalysis: Gaseous propane hydrogenolysis mechanism over the same catalysts

A kinetic/mechanistic investigation of gaseous propane hydrogenolysis over the single-site heterogeneous polyolefin depolymerization catalysts AlS/ZrNp2 and AlS/HfNp2 (AlS = sulfated alumina, Np = neopentyl), is use to probe intrinsic catalyst properties without the complexities introduced by time- and viscosity-dependent polymer medium effects. In a polymer-free automated plug-flow catalytic reactor, propane hydrogenolysis turnover frequencies approach 3,000 h-1 at 150 °C. Both catalysts exhibit approximately linear relationships between rate and [H2] at substoichiometric [H2] with rate law orders of 0.66 ± 0.09 and 0.48 ± 0.07 for Hf and Zr, respectively; at higher [H2], the rates approach zero-order in [H2]. Reaction orders in [C3H8] and [catalyst] are essentially zero-order under all conditions, with the former implying rapid, irreversible alkane binding/activation. This rate law, activation parameter, and DFT energy span analysis support a scenario in which [H2] is pivotal in one of two plausible and competing rate-determining transition states-bimolecular metal-alkyl bond hydrogenolysis vs. unimolecular β-alkyl elimination. The Zr and Hf catalyst activation parameters, ΔH‡ = 16.8 ± 0.2 kcal mol-1 and 18.2 ± 0.6 kcal mol-1, respectively, track the relative turnover frequencies, while ΔS‡ = -19.1 ± 0.8 and -16.7 ± 1.4 cal mol-1 K-1, respectively, imply highly organized transition states. These catalysts maintain activity up to 200 °C, while time-on-stream data indicate multiday activities with an extrapolated turnover number ~92,000 at 150 °C for the Zr catalyst. This methodology is attractive for depolymerization catalyst discovery and process optimization.

Sequential Oxygenation of Bis(β-diketiminate) on a Selective Diruthenium Platform.

This article demonstrated the redox-noninnocent phenylene-linked bis(β-diketiminate) (L2-)-bridged first example of isomeric diruthenium(III)-acac species (acac = acetylacetonate) and its ability to activate dioxygen. The coordination of deprotonated L2- to the {Ru(acac)2} in bis(bidentate) mode led to isomeric {(acac)2RuIII}2(μ-L2-) (S = 1, 1-trans/1-cis, green). 1 displayed Ru(III)-based anisotropic EPR in CH3CN but without the resolution of the forbidden (ΔMs = 2) g1/2 signal at 77 K. 1-cis, however, slowly transformed to the energetically favored 1-trans form. 1 underwent two-step oxygenation at the Cβ sites of L2- to form the β-diketiminate/α-ketodiimine (L'-)-bridged mixed valent (acac)2RuIII(μ-L'-)RuII(acac)2 (2, S = 1/2, pink) followed by bis(α-ketodiimine) (L″)-bridged isovalent (acac)2RuII(μ-L″)RuII(acac)2 (3, S = 0, red). The role of O2 toward 1 → 2/3 was corroborated by 18O2 labeling experiment. Redox steps of 1-3 varied as a function of isomeric identity, bridge, and metal oxidation state. The calculated MOs and Mulliken spin densities attributed to the noninnocence of L2-, L'-, and L″ in the respective complexes. Spectrophotometric monitoring of 1 → 2 revealed pseudo-first-order rate constants (105k s-1) of 1.8 (303 K), 3.5 (313 K), 7.7 (323 K), and 17.0 (333 K) and ΔH⧧/ΔS⧧/ΔG⧧ of 14.3 kcal mol-1/-33.1 cal mol-1 K-1/24.2 kcal mol-1 (298 K), respectively. Moreover, characterization of the short-lived blue intermediate obtained during the conversion of 1 → 2/3 upon exposure to O2 supported its valence tautomeric form (VT1, RuIII-L2--RuIII ↔ RuIII-L•--RuII, S = 1), which in effect facilitated oxygen activation at the ligand backbone.

CYP116B5-SOX: An artificial peroxygenase for drug metabolites production and bioremediation.

CYP116B5 is a class VII P450 in which the heme domain is linked to a FMN and 2Fe2S-binding reductase. Our laboratory has proved that the CYP116B5 heme domain (CYP116B5-hd) is capable of catalyzing the oxidation of substrates using H2O2. Recently, the Molecular Lego approach was applied to join the heme domain of CYP116B5 to sarcosine oxidase (SOX), which provides H2O2 in-situ by the sarcosine oxidation. In this work, the chimeric self-sufficient fusion enzyme CYP116B5-SOX was heterologously expressed, purified, and characterized for its functionality by absorbance and fluorescence spectroscopy. Differential scanning calorimetry (DSC) experiments revealed a TM of 48.4 ± 0.04 and 58.3 ± 0.02°C and a enthalpy value of 175,500 ± 1850 and 120,500 ± 1350 cal mol-1 for the CYP116B5 and SOX domains respectively. The fusion enzyme showed an outstanding chemical stability in presence of up to 200 mM sarcosine or 5 mM H2O2 (4.4 ± 0.8 and 11.0 ± 2.6% heme leakage respectively). Thanks to the in-situ H2O2 generation, an improved kcat/KM for the p-nitrophenol conversion was observed (kcat of 20.1 ± 0.6 min-1 and KM of 0.23 ± 0.03 mM), corresponding to 4 times the kcat/KM of the CYP116B5-hd. The aim of this work is the development of an engineered biocatalyst to be exploited in bioremediation. In order to tackle this challenge, an E. coli strain expressing CYP116B5-SOX was employed to exploit this biocatalyst for the oxidation of the wastewater contaminating-drug tamoxifen. Data show a 12-fold increase in tamoxifen N-oxide production-herein detected for the first time as CYP116B5 metabolite-compared to the direct H2O2 supply, equal to the 25% of the total drug conversion.

Investigating the Performance of Newly Designed Benzothiophene‐4,8‐Dione‐Based Dyes for Dye‐Sensitized Solar Cells

This research analyzes newly designed benzo1,2‐b:4,5‐b'dithiophene‐4,8‐dione‐based electron–hole transport dyes (BDD1‐BDD5), focusing mainly on their electronic and photovoltaic parameters. The calculations are performed using density functional theory with the M‐06X/6‐31G+(d,p) level of theory. Their highest occupied molecular orbital energies (EHOMO) range from −5.46 to −2.58 eV, while their lowest occupied molecular orbital energies (ELUMO) to range from −0.32 to −1.31 eV, with energy gaps (Egaps) of 2.67 to −5.88 eV. Their photovoltaic parameters show light harvesting efficiency (LHE) ranging from 0.84 to 0.93 eV, open‐circuit voltage (Voc) ranging from 0.88 to 1.45 eV, fill factor (FF) ranging from 0.883 to 0.9117, short‐circuit current (Jsc) ranging from 29.22 to 37.71 mA cm−2, and maximum incident power (Pmax) ranging from 24.01 to 39.92 W with maximum absorbance (λmax) ranging from 390 to 557 nm. Their range of global chemical reactivity parameters, such as ionization potential (IP, 2.58–5.46 eV), electron affinity (EA, −0.25–0.32 eV), electronegativity (x, 1.25–2.61 eV), global hardness (η, 1.33–2.94 eV), electrophilicity index (0.17–0.38 eV), and softness (σ, 0.18–0.45 eV), provides insights into the stability, reactivity, electron transfer capabilities, and planarity of molecules. Their natural bond orbital analysis reveals transitions with perturbation energies ranging from 0.34 to 30.85 K cal mol−1. These findings provide valuable insights into their properties and potential applications, particularly in photovoltaics as organic dyes.

A Steric-Repulsion-Driven Clutch Stack of Triaryltriazines: Correlated Molecular Rotations and a Thermoresponsive Gearshift in the Crystalline Solid.

We report that a newly developed type of triaryltriazine rotor, which bears bulky silyl moieties on the para position of its peripheral phenylene groups, forms a columnar stacked clutch structure in the crystalline phase. The phenylene units of the crystalline rotors display two different and interconvertible correlated molecular motions. It is possible to switch between these intermolecular geared rotational motions via a thermally induced crystal-to-crystal phase transition. Variable-temperature solid-state 2H NMR measurements and X-ray diffraction studies revealed that the crystalline rotor is characterized by a vertically stacked columnar structure upon introducing a bulky Si moiety with bent geometry as the stator. The structure exhibits correlated flapping motions via a combination of 85° and ca. 95° rotations between 295 and 348 K, concurrent with a negative entropy change (ΔS‡ = -23 ± 0.3 cal mol-1 K-1). Interestingly, heating the crystal beyond 348 K induces an anisotropic expansion of the column and lowers the steric congestion between the adjacent rotators, thus altering the correlated motions from a flapping motion to a correlated 2-fold 180° rotation with a lower entropic penalty (ΔS‡ = -14 ± 0.5 cal mol-1 K-1). The obtained results of our study suggest that the intermolecular stacking of the C3-symmetric rotator driven by the steric repulsion of the bulky stator represents a promising strategy for producing various correlated molecular motions in the crystalline phase. Moreover, direct and reversible modulation of the intermolecularly correlated rotation is achieved via a thermally induced crystal-to-crystal phase transition, which operates as a gearshift function at the molecular level.

Enhancing catalytic activity of gold nanoparticles in a standard redox reaction by investigating the impact of AuNPs size, temperature and reductant concentrations

In this work, the catalytic activity of three different sizes of gold nano particles (AuNPs) (12, 30, and 45 nm) synthesized by the citrate reduction process studied in the conventional redox reaction of K3Fe (CN6)−3 to K4Fe (CN6)−4 using NaBH4(reductant) at four different temperatures (5 °C, 10 °C, 15 °C, and 20 °C) and measured by UV–visible spectrophotometry. Comparative kinetic analysis of different sizes of AuNPs including rate constant, activation energy, Entropy values and Frequency of collisions are reported for the first time. Transmission electron microscopy analysis is employed to investigate morphology and particle size. Spherical nanoparticles of size 12, 30, and 45 nm were observed. The UV–visible spectra were recorded at regular intervals, and it was seen that the peak of K3Fe (CN6)−3 decreased gradually with time, at the same time surface plasmon resonance of AuNPs remained constant. As reaction catalysts, AuNPs maintain their optical density which shows their stability during the course of reaction. The kinetic parameters i.e., rate constant, and activation energy (k, t1/2, Ea) were determined for three distinct sizes of gold nanoparticles (AuNPs) using the reductant at various concentrations. The value of k increases by increasing reductant concentration. This rise was significant for the small AuNPs. Increasing gold nanoparticle size (12, 30, 45 nm) decreased rate constant. As the size of AuNPs decreased the Ea reduced as well, i.e. 17.325 k cal mol−1 for 12 nm, 19 k cal mol−1 for 30 nm and 21 k cal mol−1 for 45 nm AuNPs. For 50 mM of NaBH4, k for 45 nm AuNPs is 0.10728 s−1, but for 12 nm AuNPs, the value of k is 0.145 s−1, indicating that the 12 nm AuNPs have the greatest rate constant values. The rate of reaction rises with an increase in reductant concentration and temperature, but this increase is significant in the case of small-sized nanoparticles, i.e., 12 nm, which have a high surface area and low Ea. Besides being a model redox reaction, the reduction of K3Fe (CN6)−3 to K4Fe (CN6)−4 has industrial use in making fertilizers and paint industry, anti-coating agent in colour photography, in dot etching and in amperometric biosensors.

Gas-phase thermochemistry of noncovalent ligand-alkali metal ion clusters: An impact of low frequencies.

The experimental gas-phase thermochemistry of reactions: M+ (S)n-1 + S → M+ (S)n and M+ + nS→ M+ (S)n , where M is an alkali metal and S is acetonitrile/ammonia, is reproduced. Three approximations are tested: (1) scaled rigid-rotor-harmonic-oscillator (sRRHO); (2) the sRRHO(100) identical to (1), but with all vibrational frequencies smaller than 100 cm-1 replaced with 100 cm-1 ; (3) Grimme's modified scaled RRHO (msRRHO) (Grimme, Chem. Eur. J., 2012, 18, 9955-9964). The msRRHO approach provides the most accurate reaction entropies with the mean unsigned error (MUE) below 5.5 cal mol-1 K-1 followed by sRRHO(100) and sRRHO with MUEs of 7.2 and 16.9 cal mol-1 K-1 . For the first time, we propose using the msRRHO scheme to calculate the enthalpy contribution that is further utilized to arrive at reaction Gibbs free energies (∆Gr ) ensuring the internal consistency. The final ∆Gr MUEs for msRRHO, sRRHO(100) and sRRHO schemes are 1.2, 3.6 and 3.1 kcal mol-1 .

Intracluster O–O Coupling Pathway Evidenced for an Anderson-Type Single-Cobalt Polymolybdate Water Oxidation Catalyst

Toward the establishment of a carbon-neutral society, artificial photosynthesis, replacing fossil fuels with renewable energies (H2, HCOOH, CH3OH, etc.), has attracted great attention in recent years. One of the most important issues in this area has been to advance our knowledge and technical skills in handling water oxidation (WO) catalysis often considered as the bottleneck in the overall photosynthetic processes. The polyoxometalate water oxidation catalysts (WOCs) studied herein belong to one of the most highly active as well as the most highly robust family of WOCs. Nevertheless, due to their structural complexity and the high molecular weight associated with the high content of heavy elements, their mechanism of action remains largely unexplored from both theoretical and experimental viewpoints. To solve these problems, here we focus on one of the smallest and lightest polyoxometalate WOCs, single-cobalt polyoxometalate (NH4)3[CoMo6O24H6]·5H2O (Co-POM-Mo), which was previously demonstrated to be highly active for WO [Tanaka, S. , Chem. Commun. 2012, 48, 1653−1655]. The temperature dependence of the WO rate observed by mixing Co-POM-Mo and [RuIII(bpy)3]3+ using a stopped-flow technique revealed a positive entropy of activation (ΔS‡ = ca. 20–40 cal mol–1 K–1), revealing the promotion of intramolecular O–O coupling via the dissociative activation of the oxygens preinstalled in the cluster. The 17O NMR and 18O-labeling experiments, conducted to understand the source of oxygens in the O2 evolved, clarified the major contribution of the preinstalled 16O oxygens in the O–O coupling by Co-POM-Mo. The O2 evolved from the three catalysis cycles by Co-POM-Mo (100% in 16O) from an 18O-enriched aqueous solution (49% in 18O) resulted in the 16O2, 16O18O, and 18O2 abundances of 46, 40, and 14%, respectively. The Monte Carlo simulation reproduced the observed abundances under the assumption that the three consecutive O–O coupling proceed by only adopting a single μ3-OH site among the six available sites. Our simulation also supposed the O–O coupling process competes with the exchange of the catalytically active μ3-OH oxygen with the bulk water oxygen with the former twice higher in rate than the latter. Our DFT results also agree well with the promotion of O–O coupling between the inner μ3-OH oxygen bound to the central cobalt ion and the adjacent μ2-O oxygen constructing the Mo6(μ2-O)6 ring. This study strongly suggests that the O–O coupling among the preinstalled oxygens is the only available pathway to promote the WO by one of the highly active polyoxometalate WOCs, providing a new perspective on the catalysis by oxo clusters.

Phosphine substitution and linkage isomerization in cyclopentadienylruthenium bis(triphenylphosphine)thiocyanide and selenocyanide, CpRu(PPh3)2NCS and CpRu(PPh3)2SeCN.

The reaction between CpRu(PPh3)2NCS (1a) and PMePh2 yields CpRu(PPh3)(PMePh2)NCS (2a) while CpRu(PPh3)(PMePh2)Cl reacts with SCN- to form the S-bonded isomer, CpRu(PPh3)(PMePh2)SCN (2b). Compound 1a and the linkage isomers of 2 were characterized by X-ray crystallography. The kinetics of the reaction between 1a and PMePh2 under pseudo-first order conditions in THF and in fluorobenzene to form 2a are consistent with a dissociative interchange mechanism. Activation parameters for the reaction are: ΔH† = 15.7 ± 0.6 kcal mol-1 and ΔS† = -35 ± 2 cal mol-1 K-1 in THF vs. ΔH† = 24.8 ± 1.2 kcal mol-1 and ΔS† = -6 ± 4 cal mol-1 K-1 in C6H5F. In the presence of added SCN-, the rate of phosphine substitution is unchanged but a mixture of 2a and 2b is observed. The selenocyanate derivative, CpRu(PPh3)2SeCN (3b), crystallizes as the Se-bonded linkage isomer. Compound 3b reacts with PMePh2 under pseudo-first order conditions in fluorobenzene to form CpRu(PPh3)(PMePh2)SeCN (4b) at a much faster rate than 1a with activation parameters: ΔH† = 30.9 ± 4.8 kcal mol-1 and ΔS† = 22.4 ± 15.9 cal mol-1 K-1 with no evidence for linkage isomerization to the N-bonded products.

Acetate exchange mechanism on a Zr12 oxo hydroxo cluster: relevance for reshaping Zr-carboxylate coordination adaptable networks.

The kinetics and mechanism of the acetate ligand exchange with free acetic acid in [Zr6O4(OH)4(O2CCH3)12]2, used as a molecular model of crosslink migration in [Zr6O4(OH)4(carboxylate)12-n(OH)n]-based coordination adaptable networks with vitrimer-like properties, has been thoroughly investigated by dynamic 1H NMR and DFT calculations. The compound maintains its C2h-symmetric Zr12 structure in CD2Cl2 and C6D6, while it splits into its Zr6 subunits in CD3OD and D2O. In the Zr12 structure, the topologically different acetates (3 chelating, 6 belt-bridging, 2 intercluster-bridging and 1 inner-face-bridging) of the Zr6 subunits behave differently in the presence of free CH3COOH: very fast exchange for the chelating (coalesced resonance at room temperature), slower exchange for the belt-bridging (line broadening upon warming), no observable exchange up to 65 °C (by EXSY NMR) for the intercluster- and inner-face-bridging. The rates of the first two exchange processes have zero-order dependence on [CH3COOH]. Variable-temperature line broadening studies yielded ΔH‡ = 15.0 ± 0.4 kcal mol-1, ΔS‡ = 8 ± 1 cal mol-1 K-1 (-30 to +25 °C range in CD2Cl2) for the chelating acetates and ΔH‡ = 22.7 ± 1.6, 22.9 ± 2.1 and 20.6 ± 1.0 kcal mol-1 and ΔS‡ = 13 ± 5, 14 ± 6 and 9 ± 3 cal mol-1 K-1, respectively (+25 to +70 °C range in C6D6), for three distinct resonances of magnetically inequivalent belt-bridging acetates. With support of DFT calculations, these results point to an operationally associative mechanism involving a rate-determining partial dissociation to monodentate acetate, followed by rapid acid coordination and proton transfer. The cluster μ3-OH ligands accelerate the exchange processes through H-bonding stabilization of the coordinatively unsaturated intermediate. The lower exchange barrier for the chelated vs. bridging acetates is associated to the release of ring strain. The results presented in this investigation may help the interpretation of carboxylate exchange phenomena in other systems and the design of new carboxylate-based materials.

Nitrene transfer from a sterically confined copper nitrenoid dipyrrin complex.

Despite the myriad Cu-catalyzed nitrene transfer methodologies to form new C-N bonds (e.g., amination, aziridination), the critical reaction intermediates have largely eluded direct characterization due to their inherent reactivity. Herein, we report the synthesis of dipyrrin-supported Cu nitrenoid adducts, investigate their spectroscopic features, and probe their nitrene transfer chemistry through detailed mechanistic analyses. Treatment of the dipyrrin CuI complexes with substituted organoazides affords terminally ligated organoazide adducts with minimal activation of the azide unit as evidenced by vibrational spectroscopy and single crystal X-ray diffraction. The Cu nitrenoid, with an electronic structure most consistent with a triplet nitrene adduct of CuI, is accessed following geometric rearrangement of the azide adduct from κ1-N terminal ligation to κ1-N internal ligation with subsequent expulsion of N2. For perfluorinated arylazides, stoichiometric and catalytic C-H amination and aziridination was observed. Mechanistic analysis employing substrate competition reveals an enthalpically-controlled, electrophilic nitrene transfer for primary and secondary C-H bonds. Kinetic analyses for catalytic amination using tetrahydrofuran as a model substrate reveal pseudo-first order kinetics under relevant amination conditions with a first-order dependence on both Cu and organoazide. Activation parameters determined from Eyring analysis (ΔH‡ = 9.2(2) kcal mol-1, ΔS‡ = -42(2) cal mol-1 K-1, ΔG‡298K = 21.7(2) kcal mol-1) and parallel kinetic isotope effect measurements (1.10(2)) are consistent with rate-limiting Cu nitrenoid formation, followed by a proposed stepwise hydrogen-atom abstraction and rapid radical recombination to furnish the resulting C-N bond. The proposed mechanism and experimental analysis are further corroborated by density functional theory calculations. Multiconfigurational calculations provide insight into the electronic structure of the catalytically relevant Cu nitrene intermediates. The findings presented herein will assist in the development of future methodology for Cu-mediated C-N bond forming catalysis.

Benchmark Dynamics of Dipolar Molecular Rotors in Fluorinated Metal-Organic Frameworks.

Fluorinated Metal-Organic Frameworks (MOFs), comprising a wheel-shaped ligand with geminal rotating fluorine atoms, produced benchmark mobility of correlated dipolar rotors at 2 K, with practically null activation energy (Ea =17 cal mol-1 ). 1 H T1 NMR revealed multiple relaxation phenomena due to the exchange among correlated dipole-rotor configurations. Synchrotron radiation X-ray diffraction at 4 K, Density Functional Theory, Molecular Dynamics and phonon calculations showed the fluid landscape and pointed out a cascade mechanism converting dipole configurations into each other. Gas accessibility, shown by hyperpolarized-Xe NMR, allowed for chemical stimuli intervention: CO2 triggered dipole reorientation, reducing their collective dynamics and stimulating a dipole configuration change in the crystal. Dynamic materials under limited thermal noise and high responsiveness enable the fabrication of molecular machines with low energy dissipation and controllable dynamics.

Benchmark Dynamics of Dipolar Molecular Rotors in Fluorinated Metal‐Organic Frameworks

AbstractFluorinated Metal‐Organic Frameworks (MOFs), comprising a wheel‐shaped ligand with geminal rotating fluorine atoms, produced benchmark mobility of correlated dipolar rotors at 2 K, with practically null activation energy (Ea=17 cal mol−1). 1H T1 NMR revealed multiple relaxation phenomena due to the exchange among correlated dipole‐rotor configurations. Synchrotron radiation X‐ray diffraction at 4 K, Density Functional Theory, Molecular Dynamics and phonon calculations showed the fluid landscape and pointed out a cascade mechanism converting dipole configurations into each other. Gas accessibility, shown by hyperpolarized‐Xe NMR, allowed for chemical stimuli intervention: CO2 triggered dipole reorientation, reducing their collective dynamics and stimulating a dipole configuration change in the crystal. Dynamic materials under limited thermal noise and high responsiveness enable the fabrication of molecular machines with low energy dissipation and controllable dynamics.

Formation of Protamine and Zn-Insulin Assembly: Exploring Biophysical Consequences.

The insulin-protamine interaction is at the core of the mode of action in many insulin formulations (Zn + insulin + protamine) and to treat diabetes, in which protamine is added to the stable form of hexameric insulin (Zn-insulin). However, due to the unavailability of quantitative data and a high-resolution structure, the binding mechanism of the insulin-protamine complex remains unknown. In this study, it was observed that Zn-insulin experiences destabilization as observed by the loss of secondary structure in circular dichroism (CD), and reduction in thermal stability in melting study, upon protamine binding. In isothermal titration calorimetry (ITC), it was found that the interactions were mostly enthalpically driven. This is in line with the positive ΔC m value (+880 cal mol-1), indicating the role of hydrophilic interactions in the complex formation, with the exposure of hydrophobic residues to the solvent, which was firmly supported by the 8-anilino-1-naphthalene sulfonate (ANS) binding study. The stoichiometry (N) value in ITC suggests the multiple insulin molecules binding to the protamine chain, which is consistent with the picture of the condensation of insulin in the presence of protamine. Atomic force microscopy (AFM) suggested the formation of a heterogeneous Zn-insulin-protamine complex. In fluorescence, Zn-insulin experiences strong Tyr quenching, suggesting that the location of the protamine-binding site is near Tyr, which is also supported by the molecular docking study. Since Tyr is critical in the stabilization of insulin self-assembly, its interaction with protamine may impair insulin's self-association ability and thermodynamic stability while at the same time promoting its flexible conformation desired for better biological activity.

Gain of function studies on predicted host receptors for white spot virus

Three decades after its first outbreak, the shrimp white spot virus (WSV) is still a global cause of concern due to considerable losses and lack of effective control measures. Several candidate host receptor proteins have been identified, but the pathogenesis is not clearly understood, although the key role of the WSV envelope protein VP28 in virus internalization is established. Here, protein-protein docking is applied to evaluate the interaction of VP28 trimeric extracellular region with four host (Penaeus monodon) receptors reported earlier, Rab7 GTPase (PmRab7), glucose transporter 1 (PmGLUT1), C-type lectin (PmCTL) and calreticulin (PmCRT). The stability of predicted complexes evaluated in terms of binding energy per unit buried surface area ranged from −8.46 to −11.82 cal mol−1/Å2, which is not sufficient for functional interaction. Nevertheless, each of these host proteins was tested by a gain-of-function approach by observing their ability to make a fish cell line permissive to the shrimp WSV. Full-length expression constructs of the four receptors were transfected into SSN1 snakehead fish cells that are non-permissive to WSV. Transfected SSN1 cells and WSV permissive insect Sf9 cells were challenged with purified WSV. After 24 h, the presence of receptor transcripts was confirmed in the treated SSN1 cells, and not in the non-transfected SSN1 cells. Further, vp28 transcript was detected in Sf9 cells, but not in any of the treated SSN1 cells, indicating that none of the receptors were singly sufficient to make SSN1 cells permissive to WSV, even though PmRab7 was a strong candidate that alone showed >85% protection in virus neutralization experiments. For the other 3 candidates, previous reports predicted the involvement of co-receptors, which is confirmed here by their inability to act singly.

Molecular Characterization of a DNA Polymerase from Thermus thermophilus MAT72 Phage vB_Tt72: A Novel Type-A Family Enzyme with Strong Proofreading Activity.

We present a structural and functional analysis of the DNA polymerase of thermophilic Thermus thermophilus MAT72 phage vB_Tt72. The enzyme shows low sequence identity (<30%) to the members of the type-A family of DNA polymerases, except for two yet uncharacterized DNA polymerases of T. thermophilus phages: φYS40 (91%) and φTMA (90%). The Tt72 polA gene does not complement the Escherichia coli polA− mutant in replicating polA-dependent plasmid replicons. It encodes a 703-aa protein with a predicted molecular weight of 80,490 and an isoelectric point of 5.49. The enzyme contains a nucleotidyltransferase domain and a 3′-5′ exonuclease domain that is engaged in proofreading. Recombinant enzyme with His-tag at the N-terminus was overproduced in E. coli, subsequently purified by immobilized metal affinity chromatography, and biochemically characterized. The enzyme exists in solution in monomeric form and shows optimum activity at pH 8.5, 25 mM KCl, and 0.5 mM Mg2+. Site-directed analysis proved that highly-conserved residues D15, E17, D78, D180, and D184 in 3′-5′ exonuclease and D384 and D615 in the nucleotidyltransferase domain are critical for the enzyme’s activity. Despite the source of origin, the Tt72 DNA polymerase has not proven to be highly thermoresistant, with a temperature optimum at 55 °C. Above 60 °C, the rapid loss of function follows with no activity > 75 °C. However, during heat treatment (10 min at 75 °C), trehalose, trimethylamine N-oxide, and betaine protected the enzyme against thermal inactivation. A midpoint of thermal denaturation at Tm = 74.6 °C (ΔHcal = 2.05 × 104 cal mol−1) and circular dichroism spectra > 60 °C indicate the enzyme’s moderate thermal stability.

Understanding the Structure-Polymerization Thermodynamics Relationships of Fused-Ring Cyclooctenes for Developing Chemically Recyclable Polymers.

Polymers that can be chemically recycled to their constituent monomers offer a promising solution to address the challenges in plastics sustainability through a circular use of materials. The design and development of monomers for next-generation chemically recyclable polymers require an understanding of the relationships between the structure of the monomers/polymers and the thermodynamics of polymerization/depolymerization. Here we investigate the structure-polymerization thermodynamics relationships of a series of cyclooctene monomers that contain an additional ring fused at the 5,6-positions, including trans-cyclobutane, trans-cyclopentane, and trans-five-membered cyclic acetals. The four- and five-membered rings trans-fused to cyclooctene reduce the ring strain energies of the monomer, and the enthalpy changes of polymerizations are found to be in the range of -2.1 to -3.3 kcal mol-1. Despite the narrow range of enthalpy changes, the ceiling temperatures at 1.0 M span from 330 to 680 °C, due to the low entropy changes, ranging from -2.7 to -5.0 cal mol-1 K-1. Importantly, geminal substituents on the trans-five-membered cyclic acetal fused cyclooctenes are found to reduce the ceiling temperature by ∼300 °C, although they are not directly attached to the cyclooctene. The remote gem-disubstituent effect demonstrated here can be leveraged to promote depolymerization of the corresponding polymers and to tune their thermomechanical properties.

Frustrated Lewis Pair Stabilized Phosphoryl Nitride (NPO), a Monophosphorus Analogue of Nitrous Oxide (N2O).

Phosphoryl nitride (NPO) is a highly reactive intermediate, and its chemistry has only been explored under matrix isolation conditions so far. Here we report the synthesis of an anthracene (A) and phosphoryl azide based molecule (N3P(O)A) that acts as a molecular synthon of NPO. Experimentally, N3P(O)A dissociates thermally with a first-order kinetic half-life that is associated with an activation enthalpy of ΔH⧧ = 27.5 ± 0.3 kcal mol-1 and an activation entropy of ΔS⧧ = 10.6 ± 0.3 cal mol-1 K-1 that are in good agreement with calculated DLPNO-CCSD(T)/cc-pVTZ//PBE0-D3(BJ)/cc-pVTZ energies. In solution N3P(O)A undergoes Staudinger reactivity with tricyclohexylphosphine (PCy3) and subsequent complexation with tris(pentafluorophenyl)borane (B(C6F5)3, BCF) to form Cy3P-NP(A)O-B(C6F5)3. Anthracene is cleaved off photochemically to form the frustrated Lewis pair (FLP) stabilized NPO complex Cy3P⊕-N═P-O-B⊖(C6F5)3. An intrinsic bond orbital (IBO) analysis suggests that the adduct is zwitterionic, with a positive and negative charge localized on the complexing Cy3P and BCF, respectively.