Simulating Vibronic Spectra by Direct Application of Doktorov Formulas on a Superconducting Quantum Simulator.

In this work, a direct quantum implementation of the Doktorov formulas for calculating the vibronic spectrum of molecules under the harmonic approximation is presented. It is applied to the three-atom molecules H2O, SO2, ClO2, HS2, and ZnOH. The method solves the classically hard problem of estimating the Franck-Condon (FC) factors by using the Duschinsky matrices as the only input via the Doktorov quantum circuit. This has the advantage of avoiding basis changes, artificial squeezing parameters, and symmetry dependencies. In other words, it is a general method for three-atom molecules that can easily be generalized to bigger molecules. The results are compared with other quantum algorithms and classical anharmonic algorithms. Furthermore, the circuit requirements are studied in order to estimate its applicability on real superconducting quantum hardware.

A comparative study of polyethylene oxide (PEO) using different coarse-graining methods.

Polyethylene oxide (PEO) holds significant importance in the field of batteries due to its high processability, intrinsic properties, and potential for high ionic conductivity. Achieving simulation at different scales is crucial for gaining a comprehensive understanding of its properties and thus improving them. In this context, we conducted a comparative study on the molecular physical structure, thermodynamic, and dynamic properties of PEO using three distinct coarse-grained (CG) procedures and all-atom (AA) simulations. The three CG simulation procedures involved modeling with MARTINI forcefield, SPICA forcefield, and an IBI derived potential from AA simulations. The AA simulation has been performed using the class 2 pcff+ forcefield. The ensuing simulated densities align significantly with the literature data, indicating the reliability of our approach. The solubility parameter from the AA simulation closely corresponds to literature reported values. MARTINI and SPICA yield almost similar solubility parameters, consistent with the similar density predicted by both the forcefields. Notably, SPICA forcefield closely reproduces the intermolecular structure of atomistic systems, as evidenced by radial distribution function (RDF). It also comprehensively replicates the distribution of radius of gyration (Rg) and the end-to-end distance (Re) of the atomistic samples. IBI ranks second to SPICA in emulating the structural properties of the atomistic systems, such as Rg, Re, and RDF. However, IBI falls short in accurately representing the solubility parameter of the amorphous PEO samples, while MARTINI does not provide an accurate representation of the structural properties of the systems. The use of SPICA forcefield results in enhanced dynamics of the systems in comparison with IBI and MARTINI.

Supercritical Water: A Simulation Study to Unravel the Heterogeneity of Its Molecular Structures.

(1) Background: In the quest to accurately model the radiolysis of water in its supercritical state, a detailed understanding of water's molecular structure, particularly how water molecules are arranged in this unique state, is essential. (2) Methods: We conducted molecular dynamics simulations using the SPC/E water model to investigate the molecular structures of supercritical water (SCW) over a wide temperature range, extending up to 800 °C. (3) Results: Our results show that at a constant pressure of 25 MPa, the average intermolecular distance around a reference water molecule remains remarkably stable at ~2.9 Å. This uniformity persists across a substantial temperature range, demonstrating the unique heterogeneous nature of SCW under these extreme conditions. Notably, the simulations also reveal intricate patterns within SCW, indicating the simultaneous presence of regions with high and low density. As temperatures increase, we observe a rise in the formation of molecular clusters, which are accompanied by a reduction in their average size. (4) Conclusions: These findings highlight the necessity of incorporating the molecular complexity of SCW into traditional track-structure chemistry models to improve predictions of SCW behavior under ionizing radiation. The study establishes a foundational reference for further exploration of the properties of supercritical water, particularly for its application in advanced nuclear technologies, including the next generation of water-cooled reactors and their small modular reactor variants that utilize SCW as a coolant.

Ro-translational dynamics of confined water. I. The confined asymmetric rotor model.

Confinement effects on the ro-translational (RT) dynamics of water, trapped in rare gas matrices or within endofullerenes (i.e., H2O@C60), can be experimentally assessed using rotationally resolved far-infrared, or mid-infrared, spectroscopy [Putaud et al., J. Chem. Phys. 156, 074305 (2022) (Paper II)]. The confined rotor model is used here to reveal how the quantized rotational and frustrated translational energy levels of confined water interact and mix by way of the confinement-induced rotation-translation coupling (RTC). An eccentric but otherwise isotropic 3D harmonic effective potential is used to account for confinement effects, thereby allowing the dependence of the magnitude of the RTC on the topology of the model confinement potential, the resulting intricate mixing schemes, and their impact on the RT energy levels to be examined in detail. The confined rotor model thus provides a convenient framework to investigate the matrix and isotope effects on the RT dynamics of water under extreme confinement probed spectroscopically, thereby potentially providing insight into the mechanisms and rates for ortho-H2O ↔ para-H2O nuclear spin isomer interconversion in confined water.

Antimicrobial Activity and DFT Studies of a Novel Set of Spiropyrrolidines Tethered with Thiochroman-4-one/Chroman-4-one Scaffolds.

A novel series of 14 spiropyrrolidines bearing thiochroman-4-one/chroman-4-one, and oxindole/acenaphthylene-1,2-dione moieties were synthesized and characterized by spectroscopic techniques, as well as by three X-ray diffraction studies, corroborating the stereochemistry. Quantum chemical calculations studies, using the DFT approach, were performed to rationalize the stereochemical outcome. These N-heterocycles were evaluated for their antibacterial and antifungal activities against some pathogenic organisms. Several compounds displayed moderate to excellent activity towards the screened microbe strains in the study compared to Amoxicillin (AMX), Ampicillin (AMP), and Amphotericin B. Furthermore, a structural activity relationship (SAR) was established considering the synthesized compounds. Pharmacokinetic studies reveal that these derivatives exhibit an acceptable predictive ADMET profile (Absorption, Distribution, Metabolism, Excretion and Toxicity) and good drug-likeness.

Diversity-Oriented Synthesis of Spiropyrrolo[1,2-a]isoquinoline Derivatives via Diastereoselective and Regiodivergent Three-Component 1,3-Dipolar Cycloaddition Reactions: In Vitro and in Vivo Evaluation of the Antidiabetic Activity of Rhodanine Analogues.

An efficient diastereoselective route is developed to get access to novel spiropyrrolo[1,2-a]isoquinoline-oxindole skeletons by a one-pot three-component [3 + 2] cycloaddition reaction of (Z)-5-arylidene-1,3-thiazolidine-2,4-diones, isatin derivatives, and 1,2,3,4-tetrahydroisoquinoline (THIQ). Interestingly, the regioselectivity of the reaction is both temperature- and solvent-dependent, allowing the synthesis of two regioisomeric endo-dispiropyrrolo[2,1-a]isoquinolineoxindoles in excellent yield. Unprecedentedly, each isomeric dispiropyrrolo[2,1-a]isoquinolineoxindole endured retro-1,3-dipolar cycloaddition/recycloaddition reactions under thermal or catalytic conditions to regenerate the corresponding regioisomeric counterpart. In addition, DFT calculations were performed at the M062X/6-31++g(d,p) level of theory to unravel the origin of the reversal of regioselectivity and endo-stereoselectivity of the title 1,3-dipolar cycloaddition reactions. Upon treatment of Isatin, THIQ with (Z)-4-arylidene-5-thioxo-thiazolidin-2-ones as dipolarophiles, unusual rhodanine analogues were formed, along with smaller amounts of a dispirooxindole-piperazine. The structure and the relative configuration of these N-heterocycles were unambiguously assigned by spectroscopic techniques and confirmed by four single-crystal structures. In vitro and in vivo studies reveal that the novel rhodanine derivatives exert antidiabetic activity. The binding affinity with the active site of the enzyme α-amylase was studied by molecular docking. Furthermore, the bioavailability assessed through virtual ADME parameters (Absorption, Distribution, Metabolism, Elimination pharmacokinetics) and the excellent fit with the Lipinski and Veber rules predict good drug-likeness properties for a bromo-substituted 2-sulfanylidene-1,3-thiazolidin-4-one.

The TDDFT Excitation Energies of the BODIPYs; The DFT and TDDFT Challenge Continues.

The derivatives of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) are pivotal ingredients for a large number of functional, stimuli-responsive materials and therapeutic molecules based on their photophysical properties, and there is a urgent need to understand and predict their optical traits prior to investing a large amount of resources in preparing them. Density functional theory (DFT) and time-dependent DFT (TDDFT) computations were performed to calculate the excitation energies of the lowest-energy singlet excited state of a large series of common BODIPY derivatives employing various functional aiming at the best possible combination providing the least deviations from the experimental values. Using the common "fudge" correction, a series of combinations was investigated, and a methodology is proposed offering equal or better performances than what is reported in the literature.

The Unusual Conductivity of Na+ in PEO-Based Statistical Copolymer Solid Electrolytes: When Less Means More.

The low conductivity of Na+ electrolytes in solid polymer electrolytes (SPEs) curtails the development of Na polymer batteries. In this study, NaClO4 (3-24 wt %, 90-9:1 O:Na) is dissolved in statistical copolymers of ethylene oxide (EO) and propylene oxide (PO) (0-20 mol %). Remarkably, the conductivity of these SPEs increases as the concentration of Na+ decreases, thus departing from the usual Nernstian behavior. Using a combination of calorimetric measurements and molecular dynamic simulations, this unusual phenomenon is attributed to the presence of physical cross-links generated by Na+ . As a result, polymers containing a low salt concentration (3 wt %) display a drastically enhanced ionic conductivity (up to 0.2 10-4  S cm-1 at 25 °C), thus paving the way for the design of all-solid-state PEO-based sodium batteries operational at room temperature.

A Novel Side-Chain Liquid Crystal Elastomer Exhibiting Anomalous Reversible Shape Change.

Liquid crystalline elastomers (LCEs) have been actively investigated as stimuli-controlled actuators and soft robots. The basis of these applications is the ability of LCEs to undergo a reversible shape change upon a liquid crystalline (LC)-isotropic phase transition. Herein, we report the synthesis of a novel LCE based on a side-chain liquid crystalline polymer (SCLCP). In contrast to known LCEs, this LCE exhibits a striking anomalous shape change. Subjecting a mechanically stretched monodomain strip to LC-disorder phase transition, both the length and width of the strip contract in isotropic phase, and both elongate in LC phase. This thermally induced behaviour is the result of a subtle interplay between the relaxation of polymer main chain oriented along the stretching direction and the disordering of side-group mesogens oriented perpendicularly to the stretching direction. This finding points out potential design of LCEs of this peculiar type and possible applications to exploit.

Synthesis, liquid crystalline behaviour and structure-property relationships of 1,3-bis(5-substituted-1,3,4-oxadiazol-2-yl)benzenes.

Two series containing 1,3-bis(1,3,4-oxadiazol-2-yl)benzene as a rigid core (RC) and alkyl or perfluoroalkyl as terminal chains were synthesized and characterized. Liquid crystal properties of the synthesized compounds have been investigated by polarizing optical microscopy, differential scanning calorimetry and X-ray diffraction techniques. Conformation effects of the synthesized products on the dipole moments were also investigated.

The Proprotein Convertase Subtilisin/Kexin Type 9-resistant R410S Low Density Lipoprotein Receptor Mutation: A NOVEL MECHANISM CAUSING FAMILIAL HYPERCHOLESTEROLEMIA.

Familial hypercholesterolemia (FH) is characterized by severely elevated low density lipoprotein (LDL) cholesterol. Herein, we identified an FH patient presenting novel compound heterozygote mutations R410S and G592E of the LDL receptor (LDLR). The patient responded modestly to maximum rosuvastatin plus ezetimibe therapy, even in combination with a PCSK9 monoclonal antibody injection. Using cell biology and molecular dynamics simulations, we aimed to define the underlying mechanism(s) by which these LDLR mutations affect LDL metabolism and lead to hypercholesterolemia. Our data showed that the LDLR-G592E is a class 2b mutant, because it mostly failed to exit the endoplasmic reticulum and was degraded. Even though LDLR-R410S and LDLR-WT were similar in levels of cell surface and total receptor and bound equally well to LDL or extracellular PCSK9, the LDLR-R410S was resistant to exogenous PCSK9-mediated degradation in endosomes/lysosomes and showed reduced LDL internalization and degradation relative to LDLR-WT. Evidence is provided for a tighter association of LDL with LDLR-R410S at acidic pH, a reduced LDL delivery to late endosomes/lysosomes, and an increased release in the medium of the bound/internalized LDL, as compared with LDLR-WT. These data suggested that LDLR-R410S recycles loaded with its LDL-cargo. Our findings demonstrate that LDLR-R410S represents an LDLR loss-of-function through a novel class 8 FH-causing mechanism, thereby rationalizing the observed phenotype.

The extent of the glass transition from molecular simulation revealing an overcrank effect.

A deep understanding of the transition between rubber and amorphous state characterized by a glass transition temperature, Tg , is still a source of discussions. In this work, we highlight the role of molecular simulation in revealing explicitly this temperature dependent behavior. By reporting the specific volume, the thermal expansion coefficient and the heat capacity versus the temperature, we actually show that the glass transition domain extends to a greater range of temperature, compared with experiments. This significant enlargement width is due to the fast cooling rate, and actually explains the difficulty to locate Tg . This result is the manifestation of an overcranking effect used by high-speed cameras to reveal slow-motion. Accordingly, atomistic simulation offers the significant opportunity to show that the transition from the rubber state to the glass phase should be detailed in terms of the degrees of freedom freeze. © 2017 Wiley Periodicals, Inc.

Unraveling the interplay between hydrogen bonding and rotational energy barrier to fine-tune the properties of triazine molecular glasses.

Mexylaminotriazine derivatives form molecular glasses with outstanding glass-forming ability (GFA), high resistance to crystallization (glass kinetic stability, GS), and a glass transition temperature (Tg) above room temperature that can be conveniently modulated by selection of the headgroup and ancillary groups. A common feature of all these compounds is their secondary amino linkers, suggesting that they play a critical role in their GFA and GS for reasons that remain unclear because they can simultaneously form hydrogen (H) bonds and lead to a high interconversion energy barrier between different rotamers. To investigate independently and better control the influence of H bonding capability and rotational energy barrier on Tg, GFA and GS, a library of twelve analogous molecules was synthesized with different combinations of NH, NMe and O linkers. Differential scanning calorimetry (DSC) revealed that these compounds form, with a single exception, kinetically stable glasses with Tg values spanning a very broad range from -25 to 94 °C. While variable temperature infrared spectroscopy combined to chemometrics reveals that, on average, around 60% of the NH groups are still H-bonded as high as 40 °C above Tg, critical cooling rates obtained by DSC clearly show that molecules without H-bond donating linkers also present an outstanding GFA, meaning that H bonding plays a dominant role in controlling Tg but is not required to prevent crystallization. It is a high interconversion energy barrier, provoking a distribution of rotamers, that most efficiently promotes both GFA and resistance to crystallization. These new insights pave the way to more efficient glass engineering by extending the possible range of accessible Tg, allowing in particular the preparation of homologous glass-formers with high GS at ambient temperature in either the viscous or vitreous state.

Regio- and Stereoselective Synthesis of Spiropyrrolizidines and Piperazines through Azomethine Ylide Cycloaddition Reaction.

A series of original spiropyrrolizidine derivatives has been prepared by a one-pot three-component [3 + 2] cycloaddition reaction of (E)-3-arylidene-1-phenyl-pyrrolidine-2,5-diones, l-proline, and the cyclic ketones 1H-indole-2,3-dione (isatin), indenoquinoxaline-11-one and acenaphthenequinone. We disclose an unprecedented isomerization of some spiroadducts leading to a new family of spirooxindolepyrrolizidines. Furthermore, these cycloadducts underwent retro-1,3-dipolar cycloaddition yielding unexpected regioisomers. Upon treatment of the dipolarophiles with in situ generated azomethine ylides from l-proline or acenaphthenequinone, formation of spiroadducts and unusual polycyclic fused piperazines through a stepwise [3 + 3] cycloaddition pathway is observed. The stereochemistry of these N-heterocycles has been confirmed by several X-ray diffraction studies. Some of these compounds exhibit extensive hydrogen bonding in the crystalline state. To enlighten the observed regio- and stereoselectivity of the [3 + 2] cycloaddition, calculations using the DFT approach at the B3LYP/6-31G(d,p) level were carried out. It was found that this reaction is under kinetic control.

Luminescent P-chirogenic copper clusters.

P-chirogenic clusters of the cubanes [Cu4I4L4] (L = chiral phosphine) were prepared from (+)- and (-)-ephedrine with L = (S)- or (R)-(R)(Ph)(i-Pr)P (with R = CH3 (seven steps) or C17H35 (10 steps)) with e.e. up to 96%. The X-ray structure of [Cu4I4((R)-(CH3)(Ph)(i-Pr)P)4] confirmed the cubane structure with average Cu···Cu and Cu···I distances of 2.954 and 2.696 Å, respectively. The cubane structure of the corresponding [Cu4I4((S)-(CH3)(Ph)(i-Pr)P)4] was established by the comparison of the X-ray powder diffraction patterns, and the opposite optical activity of the (S)- and (R)-ligand-containing clusters was confirmed by circular dichroism spectroscopy. Small-angle X-ray scattering patterns of one cluster bearing a C17H35 chain exhibit a weak signal at 2θ ~ 2.8° (d ~ 31.6 Å), indicating some molecular ordering in the liquid state. The emission spectra exhibit two emission bands, both associated with triplet excited states. These two bands are assigned as follows: the high energy emission is due to a halide-to-ligand charge transfer, XLCT, state mixed with LXCT (ligand-to-halide-charge-transfer). The low energy band is assigned to a cluster-centered excited state. Both emissions are found to be thermochromic with the relative intensity changing between 77 and 298 K for the clusters in methylcyclohexane solution. Several differences are observed in the photophysical parameters, emission quantum yields and lifetimes for R = CH3 and C17H35. The measurements of the polarization along the emission indicate that the emission is depolarized, consistent with an approximate tetrahedral geometry of the chromophores.

Simulated infrared spectra of triflic acid during proton dissociation.

Vibrational analysis of triflic acid (TfOH) at different water uptakes was conducted. This molecule mimics the sulfonate end of the Nafion side-chain. As the proton leaves the sulfonic acid group, structural changes within the Nafion side-chain take place. They are revealed by signal shifts in the infrared spectrum. Molecular modeling is used to follow structural modifications that occur during proton dissociation. To confirm the accuracy of the proposed structures, infrared spectra were computed via quantum chemical modeling based on density functional theory. The requirement to use additional diffuse functions in the basis set is discussed. Comparison between simulated infrared spectra of 1 and 2 acid molecules with different water contents and experimental data was performed. An accurate description of infrared spectra for systems containing 2 TfOH was obtained.

Phase transition and morphology of polydispersed ABA(') triblock copolymers determined by continuous and discrete simulations.

The purpose of this study is to consider the effect of polydispersity in triblock copolymer on its order-to-disorder phase transition and morphology, by supplementing continuous description of polymer indices carried out using random phase approximation by a discrete sampling of the polydispersity performed at the mesoscale level. Both methods confirm that the increase in polydispersity involves a greater stability of the ordered state, in agreement with published data on the effect of polydispersity on diblock copolymers. The morphology simulations reveal that longer blocks are phase segregated and shorter blocks are more or less uniformly distributed throughout the polymer. It is proposed that avoiding very short polymer chains will increase the degree of phase segregation, thus improve the mechanical and conductive properties of proton exchange membrane more efficiently.

Local dynamics within the glass transition domain.

The glass transition of an amorphous material is a fundamental property characterized by an abrupt change in viscosity. Its very knowledge was a conundrum as no satisfying theory existed at the molecular level. We herein relate this complex phenomenon to events occurring at the molecular scale. By studying conformational transitions in the carbon-chain polymer of polyethylene, we clearly establish a relation between local dynamics and the classical dihedral potential energy diagram of a carbon-carbon bond. This methodology is applied to a carbon-chain polymer with a side-group, polystyrene. A direct link is proved between activation energy and glass transition temperature. This work thus provides the cornerstone for linking molecular structure to macroscopic polymer properties, and in particular, the glass transition temperature.

Highly diastereoselective construction of novel dispiropyrrolo[2,1-a]isoquinoline derivatives via multicomponent 1,3-dipolar cycloaddition of cyclic diketones-based tetrahydroisoquinolinium N-ylides.

In the quest for new heterocyclic scaffolds exhibiting potentially biological activities for medicinal chemistry, a multicomponent 1,3-dipolar cycloaddition reaction of tetrahydroisoquinolinium N-ylides, generated in situ from cyclic diketones and isoquinoline, and (E)-3-arylidene-1-phenyl-pyrrolidine-2,5-diones has been developed. This route provides workable access to dispiropyrrolo[2,1-a]isoquinoline-fused pyrrolidine-2,5-diones bearing two adjacent spiro-carbons. An unprecedented regioselectivity was observed in this 1,3-dipolar cycloaddition, leading to the construction of a novel dispirooxindole skeleton. The structure and relative stereochemistry of the spiranic adducts have been confirmed by three X-ray diffraction studies. To reinforce the observed regio- and stereoselectivity of the [3+2] cycloaddition, calculations using the DFT approach at the B3LYP/6-31G(d,p) level were carried out. It was found that this reaction affords the kinetic products.

Study of the influence of ester orientation on the thermal stability of the smectic C phase: Simulation investigation.

Two series of mesogenic molecules have been simulated using molecular dynamics with a full atomistic representation. The two series differ from each other only with the orientation of an ester linker inside the rigid core. Experimentally, this small difference leads to drastically different polymorphisms: one displays the smectic A phase while the other exhibits the smectic C and the smectic A phase. From molecular dynamics trajectories, intermolecular potentials are extracted and analyzed. It is then found that the minor difference inside the rigid core can be related to these various interactions. Finally, experimental and simulation results are integrated in a coherent analysis. The correlation between both types of data offers interesting insights in the role of the Coulomb and van der Waals interactions in the molecular origin of the smectic C phase.