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Poly(N,N-diethylacrylamide) (PdEA), one of the thermoresponsive polymers, in aqueous solutions has attracted much attention because of its characteristic properties, such as coil-to-globule (CG) transition. We performed two-dimensional infrared spectroscopy and molecular dynamics (MD) simulations to understand the hydration dynamics in the vicinity of the CG transition at the molecular level via vibrational frequency fluctuations of the carbonyl stretching modes in the side chains of PdEA. Furthermore, N,N-diethylpropionamide, a repeating monomer unit of PdEA, is also investigated for comparison. From decays of the frequency–frequency time correlation functions (FFTCFs) of the carbonyl stretching modes, we consider that inhomogeneity of the hydration environments originates from various backbone configurations of PdEA. The degree of the inhomogeneity depends on temperature. Hydration water molecules near the carbonyl groups are influenced by the confinements of the polymers. The restricted reorientation of the embedded water, the local torsions of the backbone, and the rearrangement of the whole structure contribute to the slow spectral diffusion. By performing MD simulations, we calculated the FFTCFs and dynamical quantities, such as fluctuations of the dihedral angles of the backbone and the orientation of the hydration water molecules. The simulated FFTCFs match well with the experimental results, indicating that the retarded water reorientations via the excluded volume effect play an important role in the vibrational frequency fluctuations of the carbonyl stretching mode. It is also found the embedded water molecules are influenced by the local torsions of the backbone structure within the time scales of the spectral diffusion. [ABSTRACT FROM AUTHOR]

The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable states of alanine dipeptide in vacuum, i.e., C7eq (β-sheet structure) and C7ax (left handed α-helix structure), have been primarily characterized using the main chain dihedral angles, φ (C–N–Cα–C) and ψ (N–Cα–C–N). However, our recent deep learning combined with the "Explainable AI" (XAI) framework has shown that the transition state can be adequately captured by a free energy landscape using φ and θ (O–C–N–Cα) [Kikutsuji et al., J. Chem. Phys. 156, 154108 (2022)]. In the perspective of extending these insights to other collective variables, a more detailed characterization of the transition state is required. In this work, we employ interatomic distances and bond angles as input variables for deep learning rather than the conventional and more elaborate dihedral angles. Our approach utilizes deep learning to investigate whether changes in the main chain dihedral angle can be expressed in terms of interatomic distances and bond angles. Furthermore, by incorporating XAI into our predictive analysis, we quantified the importance of each input variable and succeeded in clarifying the specific interatomic distance that affects the transition state. The results indicate that constructing a free energy landscape based on the identified interatomic distance can clearly distinguish between the two stable states and provide a comprehensive explanation for the energy barrier crossing. [ABSTRACT FROM AUTHOR]

Stretching or compression can induce significant energetic, geometric, and spectroscopic changes in materials. To fully exploit these effects in the design of mechano- or piezo-chromic materials, self-healing polymers, and other mechanoresponsive devices, a detailed knowledge about the distribution of mechanical strain in the material is essential. Within the past decade, Judgement of Energy DIstribution (JEDI) analysis has emerged as a useful tool for this purpose. Based on the harmonic approximation, the strain energy in each bond length, bond angle, and dihedral angle of the deformed system is calculated using quantum chemical methods. This allows the identification of the force-bearing scaffold of the system, leading to an understanding of mechanochemical processes at the most fundamental level. Here, we present a publicly available code that generalizes the JEDI analysis, which has previously only been available for isolated molecules. Now, the code has been extended to two- and three-dimensional periodic systems, supramolecular clusters, and substructures of chemical systems under various types of deformation. Due to the implementation of JEDI into the Atomic Simulation Environment, the JEDI analysis can be interfaced with a plethora of program packages that allow the calculation of electronic energies for molecular systems and systems with periodic boundary conditions. The automated generation of a color-coded three-dimensional structure via the Visual Molecular Dynamics program allows insightful visual analyses of the force-bearing scaffold of the strained system. [ABSTRACT FROM AUTHOR]

Methyl nitrite has two stable conformational isomers resulting from rotation about the primary C–O–N–O dihedral angle: cis-CH3ONO and trans-CH3ONO, with cis being more stable by ∼5 kJ/mol. The barrier to rotational interconversion (∼45 kJ/mol) is too large for isomerization to occur under ambient conditions. This paper presents evidence of a change in conformer abundance when dilute CH3ONO is deposited onto a cold substrate; the relative population of the freshly deposited cis conformer is seen to increase compared to its gas-phase abundance, measured by in situ infrared spectroscopy. We observe abundance changes depending on the identity of the bath gas (N2, Ar, and Xe) and deposition angle. The observations indicate that the surface properties of the growing matrix influence conformer abundance—contrary to the widely held assumption that conformer abundance in matrices reflects gas-phase abundance. We posit that differences in the angle-dependent host-gas deposition dynamics affect the growing surfaces, causing changes in conformer abundances. Quantum chemistry calculations of the binding energies between CH3ONO and a single bath-gas component reveal that significant energetic stabilization is not observed in 1:1 complexes of N2:CH3ONO, Ar:CH3ONO, or Xe:CH3ONO. From our results, we conclude that the growing surface plays a significant role in trapping cis-CH3ONO more effectively than trans-CH3ONO, likely because cis-CH3ONO is more compact. Taken together, the observations highlight the necessity for careful characterization of conformers in matrix-isolated systems, emphasizing a need for further study into the deposition dynamics and surface structure of chemically inert matrices. [ABSTRACT FROM AUTHOR]

We rely on a total of 23 (cluster size, 8 structural, and 14 connectivity) descriptors to investigate structural patterns and connectivity motifs associated with water cluster aggregation. In addition to the cluster size n (number of molecules), the 8 structural descriptors can be further categorized into (i) one-body (intramolecular): covalent OH bond length (rOH) and HOH bond angle (θHOH), (ii) two-body: OO distance (rOO), OHO angle (θOHO), and HOOX dihedral angle (ϕHOOX), where X lies on the bisector of the HOH angle, (iii) three-body: OOO angle (θOOO), and (iv) many-body: modified tetrahedral order parameter (q) to account for two-, three-, four-, five-coordinated molecules (qm, m = 2, 3, 4, 5) and radius of gyration (Rg). The 14 connectivity descriptors are all many-body in nature and consist of the AD, AAD, ADD, AADD, AAAD, AAADD adjacencies [number of hydrogen bonds accepted (A) and donated (D) by each water molecule], Wiener index, Average Shortest Path Length, hydrogen bond saturation (% HB), and number of non-short-circuited three-membered cycles, four-membered cycles, five-membered cycles, six-membered cycles, and seven-membered cycles. We mined a previously reported database of 4 948 959 water cluster minima for (H2O)n, n = 3–25 to analyze the evolution and correlation of these descriptors for the clusters within 5 kcal/mol of the putative minima. It was found that rOH and % HB correlated strongly with cluster size n, which was identified as the strongest predictor of energetic stability. Marked changes in the adjacencies and cycle count were observed, lending insight into changes in the hydrogen bond network upon aggregation. A Principal Component Analysis (PCA) was employed to identify descriptor dependencies and group clusters into specific structural patterns across different cluster sizes. The results of this study inform our understanding of how water clusters evolve in size and what appropriate descriptors of their structural and connectivity patterns are with respect to system size, stability, and similarity. The approach described in this study is general and can be easily extended to other hydrogen-bonded systems. [ABSTRACT FROM AUTHOR]

The cis-trans isomerization of amide bonds leads to wide range of structural and functional changes in proteins and can easily be the rate-limiting step in folding. The trans isomer is thermodynamically more stable than the cis, nevertheless the cis form can play a role in biopolymers' function. The molecular system of N-methylacetamide · 2H2O is complex enough to reveal energetics of the cis-trans isomerization at coupled cluster single-double and coupled cluster single–double and perturbative triple [CCSD(T)] levels of theory. The cis-trans isomerization cannot be oversimplified by a rotation along ω, since this rotation is coupled with the N-atom pyramidal inversion, requesting the introduction of a second dihedral angle "α." Full f(ω,α) potential energy surfaces of the different amide protonation states, critical points and isomerization reaction paths were determined, and the barriers of the neutral, O-protonated and N-deprotonated amides were found too high to allow cis-trans interconversion at room temperature: ∼85, ∼140, and ∼110 kJ mol−1, respectively. For the N-protonated amide bond, the cis form (ω = 0°) is a maximum rather than a minimum, and each ω state is accessible for less than ∼10 kJ mol−1. Here we outline a cis-trans isomerization pathway with a previously undescribed low energy transition state, which suggests that the proton is transferred from the more favorable O- to the N-protonation site with the aid of nearby water molecules, allowing the trans → cis transition to occur at an energy cost of ≤11.6 kJ mol−1. Our results help to explain why isomerase enzymes operate via protonated amide bonds and how N-protonation of the peptide bond occurs via O-protonation. [ABSTRACT FROM AUTHOR]

Single molecule junctions based on selected 4,4′-biphenyldithiol and 4,4′-dicyanobiphenyl derivatives bonded to gold electrodes are analyzed from a dynamical point of view. A fully quantum mechanical description of the internal rotation of the biphenyl moiety is carried out in terms of the nuclear wavepacket dynamics obtained by the solution of the time-dependent Schrödinger equation expressed in terms of the torsion angle between the phenyl rings. The required potential energy surfaces are computed using ab initio electronic structure methods. The nature and positions of the substituents on the phenyl rings determine the features of the potential energy surfaces. The effect of the initial conditions on the time propagation of the nuclear wavepackets and, as a consequence, on the evolution of the conformational distribution is also analyzed. In addition, the conductances at zero bias for the nanojunctions were computed for different conformations of the biphenyl fragments. Weighted by the wavepacket amplitudes, non-stationary conductance expectation values, and time-averaged torsion angles and conductances for the entire simulation are obtained. The consequences of using the time-averaged values to perform a linear regression between the conductance and the square of the cosine of the dihedral angle between the phenyl rings are analyzed and compared to the usual static approach based only on the information for equilibrium geometries. The study of the time dependent conformational variations of the biphenyl moieties in the nanojunctions allows for a better understanding of the quantum chemical phenomena that affect their transport properties. [ABSTRACT FROM AUTHOR]

To examine the conventional idea that the gauche conformation of the OCCO dihedral angle promotes the dissolution of polyethylene glycol (PEG) in water through strong hydration, the thermodynamic properties of liquid mixtures of PEG and water were studied by means of polymer reference interaction site model (PRISM) theory. The intramolecular correlation functions required as input for PRISM theory were calculated by the generator matrix method, accompanied by changes in the distribution of dihedral angles. In the infinite dilution limit, the increased probability of gauche conformation of the OCCO dihedral angles stabilizes the hydration of PEG through enhanced hydrogen bonding between the ether oxygen of PEG and water. The mixing Gibbs energies of the liquid mixtures were also calculated in the whole concentration range based on the Gibbs–Duhem equation, as per our recent proposal. A liquid–liquid phase separation was observed when all the dihedral angles of PEG were in the trans conformation; for the liquid mixture to be miscible in the whole concentration range, the introduction of the OCCO gauche conformation was found to be indispensable. The above theoretical results support the conventional idea that the OCCO gauche conformation is important for the high miscibility of PEG and water. [ABSTRACT FROM AUTHOR]

The influence of the composition of the functional used for density functional theory computations on one structural parameter (a dihedral angle) and a spectroscopic parameter (absorption wavelength) is assessed in this study on the basis of two molecules (flavonols). In this kind of molecules, these two parameters should be correlated according to the nature of the electronic transition involved. However, it is shown herein that by varying the proportion of true exchange and correlation while building a functional, it is possible to obtain independently a large range of values for these parameters without any relation with the underlying real values. Therefore, it is concluded that the choice of a functional after a benchmark, especially using user‐defined functionals, should be carried out with great care to avoid such effects. [ABSTRACT FROM AUTHOR]

In the title molecule, C25H29N5O, the diydroquinoxaline unit is not quite planar (r.m.s. deviation = 0.030 Å) as there is a dihedral angle of 2.69 (3)° between the mean planes of the constituent rings and the molecule adopts a hairpin conformation. In the crystal, the polar portions of the molecules are associated through C—H⋯O and C—H⋯N hydrogen bonds and C—H⋯π(ring) and C=O⋯π(ring) interactions, forming thick layers parallel to the bc plane and with the n-octyl groups on the outside surfaces. [ABSTRACT FROM AUTHOR]

Thiolate containing mercury(II) complexes of the general formula [Hg(SR) n] 2−n have been of great interest since the toxicity of mercury was recognized. 199Hg nuclear magnetic resonance spectroscopy (NMR) is a powerful tool for characterization of mercury complexes. In this work, the Hg shielding constants in a series of [Hg(SR) n] 2−n complexes are therefore investigated computationally with particular emphasis on their geometry dependence. Geometry optimizations and NMR chemical shift calculations are performed at the density functional theory (DFT) level with both the zeroth‐order regular approximation (ZORA) and four‐component relativistic methods. The four exchange‐correlation (XC) functionals PBE0, PBE, B3LYP, and BLYP are used in combination with either Dyall's Gaussian‐type (GTO) or Slater‐type orbitals (STOs) basis sets. Comparing ZORA and four‐component calculations, one observes that the calculated shielding constants for a given molecular geometry have a constant difference of ∼1070 ppm. This confirms that ZORA is an acceptable relativistic method to compute NMR chemical shifts. The combinations of four‐component/PBE0/v3z and ZORA/PBE0/QZ4P are applied to explore the geometry dependence of the isotropic shielding. For a given coordination number, the distance between mercury and sulfur is the key factor affecting the shielding constant, while changes in bond and dihedral angles and even different side groups have relatively little impact. [ABSTRACT FROM AUTHOR]

Recent studies of the Cretaceous lower arc crust exposed in Fiordland, New Zealand, conclude that shear zones are sites of melt migration and mass transfer through the deep crust. Here, we investigate the 4–10 km‐wide George Sound Shear Zone, which cuts the Western Fiordland Orthogneiss, comprising two main rock types: two‐pyroxene gneiss and hornblende gneiss. Previous studies infer a predominantly igneous origin for the two types of gneiss. However, this study finds that melt‐rock interaction within the George Sound Shear Zone formed the hornblende gneiss from the precursor two‐pyroxene gneiss. Petrographic analyses of samples collected in transects across the shear zone show hydration reaction textures ranging from rims of hornblende + quartz around pyroxene grains to complete replacement of pyroxene grains. Plagioclase is recrystallized and partially replaced by clinozoisite. Additionally, biotite mode increases towards the higher strain rocks in the shear zone. Backscatter images and polarized light microscopy show microstructures indicative of former melt‐present deformation, including (a) interconnected mineral films of quartz and K‐feldspar along grain boundaries, (b) grains that terminate with low apparent dihedral angles, (c) interstitial grains, with some (d) undulose extinction in plagioclase and (e) serrated grain boundaries. In addition, zircon microstructures are consistent with Zr mobility, further supporting the former presence of melt; geochemical data show enrichment of Zr in the hornblende gneiss as compared to the two‐pyroxene gneiss. From the above observations, it is inferred that a felsic to intermediate hydrous melt migrated through the George Sound Shear Zone reacting with the host two‐pyroxene gneiss of the Western Fiordland Orthogneiss. Melt migration along grain boundaries was deformation assisted, (i) causing hydration of pyroxene to hornblende + quartz, and plagioclase to clinozoisite, (ii) increasing proportions of biotite within the shear zone and (iii) causing depletion of Cr + Ni and Zr enrichment in the hydrated rock. Our interpretation is supported by published observations of pegmatite dyke swarms that intruded into the George Sound Shear Zone, the P‐T conditions of deformation and characterization of microstructures that contrast sharply with those typically found in mylonitic rocks formed under solid‐state metamorphic conditions. Our results confirm that hydrous shear zones within otherwise anhydrous country rock are retrogressive and may represent evidence of melt migration through zones of deformation. [ABSTRACT FROM AUTHOR]

We found that during the chiral co-assembly process, the structural symmetry of achiral Py-based emitters could cause different chiral co-assembly modes, leading to the tunable CPL emission behaviors of the resulting co-assemblies. Most importantly, this kind of chiral co-assembly (R / S -B) 1 -(Py-2) 7 can form highly ordered helical nanofiber through intermolecular layered packing mode, leading to the promoted chiral induction and amplification effects. [Display omitted] The regulation of circularly polarized luminescence (CPL) behavior is of great significance for practical applications. Herein, we deliberately designed three achiral pyrene derivatives (Py-1 , Py-2 , and Py-3) with different butoxy-phenyl substituents and the chiral binaphthyl-based inducer ( R/S -B) with anchored dihedral angle to construct chiral co-assemblies, and explored their induced CPL behaviors. Interestingly, the resulting co-assemblies demonstrate tunable CPL emission behaviors caused by the structural symmetry effect of achiral pyrene-based emitters during the chiral co-assembly process. And in spin-coated films, the dissymmetry factor (g em) values were 9.1 × 10-3 for (R/S- B) 1 -(Py-1) 10 , 5.6 × 10-2 for (R/S- B) 1 -(Py-2) 7 , and 8.6 × 10-4 for (R/S- B) 1 -(Py-3) 1 , respectively. The strongest CPL emission (| g em | = 5.6 × 10-2, λ em = 423 nm, QY = 34.8 %) was detected on (R/S- B) 1 -(Py-2) 7 due to the formation of regular and ordered helical nanofibers through the strong π-π stacking interaction between the R/S- B and the achiral Py-2 emitter. The strategy presented here provides a creative approach for progressively regulating CPL emission behaviors in the chiral co-assembly process. [ABSTRACT FROM AUTHOR]

The interplay between conformation and hydrogen bond pattern was studied in 211 (C(O)NH)(N)2P(O)-based phosphoric triamides retrieved from the Cambridge Structural Database (CSD) and one new molecular structure, (CHCl2C(O)NH)(CH3CH2CH2NH)2P(O). The O═C–N–P and C–N–P═O torsion angles were extracted for the conformational study of the C(O)NP(O) segment, and the conformations of ±sp±ap, ±sp±sc and ±ap±sp were found (sp = synperiplanar, ap = antiperiplanar, sc = synclinal). The conformations of hydrogen bond donor group(s) with respect to the acceptor group(s) were also considered. The investigated structures belong to three classes of (RC(O)NH)(R1R2N)2P(O) (R1 and R2 ≠ H), (RC(O)NH)(R1NH)2P(O) (R1 ≠ H) and heterocyclic (RC(O)NH)P(O)[NR1]2R2 phosphoric triamides (R1 = H or ≠ H, R2 = a hydrocarbon fragment), and the hydrogen bond patterns include dimer, tetramer, chain, tape, ladder, two-dimensional assembly and three-dimensional architecture. In the new structure, the conformation of the C(O)NP(O) fragment is –sp+ap, and molecules are assembled in a tape arrangement (parallel to the [110] axis) through NCP–H···O═P and NP–H···O═C hydrogen bonds (NCP is the nitrogen atom of the C(O)NHP(O) fragment and NP is the other N atom bonded to phosphorus). The interplay between conformation and hydrogen bond pattern was studied in 211 (C(O)NH)(N)2P(O)-based phosphoric triamides retrieved from the Cambridge Structural Database (CSD) and one new structure, (CHCl2C(O)NH)(CH3CH2CH2NH)2P(O). [ABSTRACT FROM AUTHOR]

Intramolecular charge transfer (ICT) effects of para‐nitroaniline (pNA) in eight solvents (cyclohexane, toluene, acetic acid, dichloroethane, acetone, acetonitrile, dimethylsulfoxide, and water) are investigated extensively. The second‐order algebraic diagrammatic construction, ADC(2), ab initio wave function is employed with the COSMO implicit and discrete multiscale solvation methods. We found a decreasing amine group torsion angle with increased solvent polarity and a linear correlation between the polarity and ADC(2) transition energies. The first absorption band involves π → π* transitions with ICT from the amine and the benzene ring to the nitro group, increased by 4%–11% for different solvation models of water compared to the vacuum. A second band of pNA is characterized for the first time. This band is primarily a local excitation on the nitro group, including some ICT from the amine group to the benzene ring that decreases with the solvent polarity. For cyclohexane, the COSMO implicit solvent model shows the best agreement with the experiment, while the explicit model has the best agreement for water. [ABSTRACT FROM AUTHOR]

Birefringent crystals as an important optical anisotropic material play a crucial role in modulating the polarization state of light. To date, most birefringent crystals are purely inorganic compounds with small birefringence. Developing large birefringent crystals remains a great challenge primarily because of the absence of tunable anisotropic structural units for inorganic materials. Herein, a hydrogen‐bonding self‐assembly strategy is reported to construct a robust hydrogen‐bonded organic framework (HOF, namely m‐H3L) birefringent crystal, which consists of π‐conjugated benzene rings and tetrahedral phosphonate groups interconnected via multiple H‐bonding interactions. Interestingly, the birefringence is as large as ∆n = 0.17@550 nm and catches up with those of commercial birefringent crystals. A combination of theoretical calculation and single‐crystal structural analyses reveals that the H‐bonding interactions control the dihedral angle of π‐conjugated benzene rings and the smaller the dihedral angle, the greater the birefringence. This discovery opens the door for the tunable HOFs to be used as a promising new class of birefringence materials. [ABSTRACT FROM AUTHOR]

AbstractIn the present work, five pyrazole-hydrazone biomolecule ligands (L1–L5) were synthesized by condensation between 1H-pyrazole-3-carbohydrazide (2) and aromatic benzaldehydes. Their corresponding structures were elucidated employing NMR and FT-IR spectra and ESI-MS data. Li-Cu(II) complexes (i = 1–5) were evaluated for catecholase activity in situ at standard conditions. The findings disclose that the catecholase oxidation rate varies with the substituted functional groups in ligand and the anion type in the copper (II) salt. Catecholase activity results showed that the L(i = 1–5) -Cu(II)SO4 complexes exhibited efficient catalytic activity, and a maximum activity of 105 ± 42 µM.min−1 is obtained with L5-Cu(II)SO4. DFT and NBO calculations have been carried out to identify the global reactivity and the strength of interaction bonds between the donors and acceptors in L1–L5. The optimized structure of L1–L3 and L5 were found planar, while that of L4 is out of the molecular plan and forms a torsion angle of 18 degrees due to the presence of methoxy and hydroxyl group at meta and para. In L4, the 5-methyl-1H-pyrazole moiety. NBO findings show that the strongest interactions in L1–L5 are those involved in the electronic transition from π-bonding → π*-antibonding and LP → π*- antibonding molecular orbitals. Further, the anti-SARS-CoV-2 of L1–L5 are investigated by estimating their binding affinities into its binding. The docking results reveal that L1–L5 may act as SARS-CoV-2 main protease inhibitors with estimated binding energies in the −6.00 to −8.0 kcal.mol−1 range. [ABSTRACT FROM AUTHOR]

Molecular-based magnetic materials are expected to serve as building blocks for quantum bits. To realize high-dimensional Hilbert space and addressability, we constructed anisotropic multi-level systems based on CuII and VIV with orthogonal magnetic orbitals. The crystal structures and intramolecular magnetic couplings of four CuIIVOII complexes [{CuVO(appen)2}2], [{CuVO(fhma)2EDA}2], [{CuVO(hfca)2EDA}2] and [CuVO(hfca)2DPEDA]n are characterized. Due to the orthogonal magnetic orbitals of CuII and VIV, the Cu–V pairs in the four complexes have strong ferromagnetic couplings, and the coupling strength is linearly related to the dihedral angle between the two equatorial planes of the two coordination polyhedra. Because of the triplet ground state, the system can be described by an effective Hamiltonian model consisting of two S = 1 spins coupled together. The anisotropy parameters of [{CuVO(hfca)2EDA}2] and [CuVO(hfca)2DPEDA]n were obtained by the simulation of X-band continuous wave electron paramagnetic resonance (cw-EPR) spectra, confirming that both complexes have zero-field splitting addressable on the relative energy scale. The results indicate that constructing multi-centre complexes based on orthogonal magnetic orbitals is a promising strategy for designing multidimensional quantum bits. [ABSTRACT FROM AUTHOR]

AbstractChiral structure can be used for compression-twist coupling (CTC) metamaterials, exhibiting twist deformation under axial compression. In this study, a series of chiral CTC metamaterials were designed based on the 3D tetra-chiral structure, including cube-type and cylinder-type structures. The CTC properties of these metamaterials were investigated in detail by finite element simulations and experiments. The results show that the proposed chiral configurations have better CTC effects than the original 3D tetra-chiral structure. Furthermore, a wide range of adjustable torsion angles can be achieved by changing the geometrical parameters. Finally, the energy absorption properties of these structures were also discussed. [ABSTRACT FROM AUTHOR]

A homologous series of 1,2-dimethylimidazolium-based ionic liquids with halide anions are examined by Hirshfeld surface analysis to draw out key structural details of the cation, allowing for a deep understanding of the structure and interactions present within this class of ionic liquids. With respect to cation structures, three distinct alkyl torsion angles are noted when examining the compounds currently reported within the structural database. These alkyl chains account for the largest percentage of cation⋯cation close contacts through a combination of H⋯H and H⋯π interactions. Further, the halide-containing crystals are contrasted with a hydrated form of the compounds, allowing for detailed examination of the changes in non-covalent interactions within the asymmetric unit. It is noted that for the hydrated compound, hydrogen bonding interactions between the water molecule and cation replace the anion⋯cation interactions, accounting, in part, for the lower melting points of these hydrated species. [ABSTRACT FROM AUTHOR]

The study presents a thorough and detailed analysis of bicalutamide's structural and conformational properties. Quantum chemical calculations were employed to explore the conformational properties of the molecule, identifying significant energy differences between conformers. Analysis revealed that hydrogen bonds stabilise the conformers, with notable variations in torsion angles. Conformers were classified into 'closed' and 'open' types based on the relative orientation of the cyclic fragments. NOE spectroscopy in different solvents (CDCl3 and DMSO-d6) was used to study the conformational preferences of the molecule. NOESY experiments provided the predominance of 'closed' conformers in non-polar solvents and a significant presence of 'open' conformers in polar solvents. The proportions of open conformers were 22.7 ± 3.7% in CDCl3 and 59.8 ± 6.2% in DMSO-d6, while closed conformers accounted for 77.3 ± 3.7% and 40.2 ± 6.2%, respectively. This comprehensive study underscores the solvent environment's impact on its structural behaviour. The findings significantly contribute to a deeper understanding of conformational dynamics, stimulating further exploration in drug development. [ABSTRACT FROM AUTHOR]

The compound N,N'-Diphenylthiourea acetone monosolvate was synthesized using slow evapouration technique and characterized by FT-IR, FT-Raman, UV-visible spectra. The optimized molecular geometry (bondlength, bondangle and dihedral angle), the complete vibrational frequency were calculated by using density functional theory (DFT) B3LYP method with the help of 6-31 G(d,p) basis set. The protonated N–H...O intermolecular interaction liable for the NLO activity was deliberated using DFT method along with experimental spectroscopic techniques. The inter and intramolecular interactions accountable for the stabilization of the material was done via NBO and AIM analysis. In addition, the molecular electrostatic potential, frontier molecular orbital, global reactivity descriptors, Hirshfeld surface and 2D-fingerprint was analyzed to acquire a greater understanding of the molecular effect. UV-Vis spectrum of DPTA crystal exhibits good optical transmittance in the spectral analysis. By using spectroflurometer technique the green band region was observed in fluorescence emission spectrum. The dipole moment, polarizability, first-order hyperpolarizability (α0), related properties (β, α0 and Δα) and second-order hyperpolarizabilties were calculated for the identification of non-linear optical activity of the molecule. The molecular docking studies were performed to investigate the binding affinity of legend with target receptor. [ABSTRACT FROM AUTHOR]

The reaction of Mn(II) salts in the air with different R-salicylaldehyde oximes and the sodium or cesium salts of 9-anthracenecarboxylato (9-AC) allows for the isolation of new six polynuclear compounds: [Mn3NaO(salox)3(9-AC)2(EtOH)3H2O]n·2EtOH (1), [Mn3NaO(3-Me-salox)3(9-AC)2(EtOH)3H2O]n·EtOH (2), [Mn6O2(salox)6(9-AC)2(EtOH)2(H2O)2]·3EtOH (3), [Mn3O(3-Me-salox)3(9-AC)(EtOH)3(H2O)]·1.8EtOH·3H2O (4), [Mn6O2(Me-salox)6(9-AC)2(EtOH)4(H2O)2]·0.5H2O (5), and [Mn6O2(Et-salox)6(9-AC)2(EtOH)4(H2O)2]·3EtOH (6). H2salox is a salicylaldehyde oxime, H2(3-Me-salox) is a 3-methyl-salicylaldehyde oxime, H2Me-salox is a 1-(2-hydroxyphenyl)ethan-1-one oxime and a H2-Et-salox is 1-(2-hydroxyphenyl)propan-1-one oxime. Structurally, compounds 1 and 2 consist of chains of trinuclear {MnIII3(μ3-O)(salox)3}+ units connected by Na+ ions. Compounds 3, 5, and 6 are hexanuclear units formed by two parallel trinuclear units {MnIII3(μ3-O)(salox)3}+ or {MnIII3(μ3-O)(Me-salox)3}+ planes related through an inversion center. Compound 4 consists of two isolated [Mn3O(3-Me-salox)3(9-AC)(EtOH)3(H2O)] trinuclear molecules in the unit cell showing crystallographic differences. Magnetic studies reveal a set of antiferromagnetic interactions in compounds 1 and 2 and a combination of antiferromagnetic and ferromagnetic interactions in compounds 3, 5, and 6. In all cases, the magneto-structural correlation between the intramolecular MnIII-N-O-MnIII torsion angle and the magnetic exchange within these units have been confirmed. For compounds 5 and 6, ac magnetic measurements reveal the slow relaxation of magnetization with moderate energy barriers of 19.9 cm−1 and 31.1 cm−1, respectively. Absorbance and fluorescence measurements in solution show the transitions of the 9-anthracenecarboxylate chromophore for all the compounds. [ABSTRACT FROM AUTHOR]

The performance of triboelectric polymers relies on their molecular structure. Therefore, investigating how to construct high‐performance molecular structures of triboelectric polymers becomes imperative, yet the relationship between microscopic structural parameters and triboelectric performance remains unclear. In this study, the relationship is studied between dihedral angles of adjacent conjugated planes and triboelectric performance. Various polyimide monomers are synthesized to manipulate the conjugated dihedral angles within the molecular chains. Introducing larger dihedral angles in polyimides (PIs) reduces the conjugation between molecular chains, suppressing the formation of charge transfer complexes (CTCs), and widening the energy gap between molecular orbitals. With the increase in dihedral angles, the output performance improved by 100%. The surface charge density of 335 µC·m−2 is achieved through the synergistic effect of the high charge retention capability of the PI film and the high triboelectric properties of the corona‐polarized fluorinated ethylene propylene (FEP). A large dihedral angle can form numerous deep traps and effectively prevent charge escaping while ensuring stable output. This study provides a feasible strategy for investigating the construction of high triboelectric performance molecular structures, enriching the understanding of how molecular structures influence the triboelectric properties of polymer materials and promote high‐performance fluorine‐free and environmentally friendly polymers. [ABSTRACT FROM AUTHOR]

AbstractDrawing on the driving mechanism of biological muscles and combining the nonlinear hyperelastic characteristics of silicone rubber, a multi-degree-of-freedom pneumatic soft bionic actuator is designed, which can be used as the executing mechanism for soft robots and robotic arms. Using response surface analysis and numerical simulation algorithms, the optimal combination of structural dimensions parameters is determined with the maximum bending and torsion angles output by the actuator as the optimization objectives. Based on the idea of flexible mechanism Piecewise Constant Curvature (PCC) modeling, the kinematics equation of the actuator is derived. Analyze the equivalent motion structure of the actuator and establish a dynamic model of the actuator based on the Lagrange method. The physical model of the actuator is manufactured using rapid prototyping technology. Finally, experimental testing and analysis are conducted on the physical model to obtain the motion and dynamic characteristics curves and empirical formulas of the actuator, which are compared with theoretical and simulation results to verify that the pneumatic soft bionic actuator is feasible and effective. The above research methods, processes, and results can provide reference and inspiration for the research and implementation of pneumatic and hydraulic soft robots and gripping actuators for soft robotic arms. [ABSTRACT FROM AUTHOR]

The hydrogen bonding interaction between an amide N−H and the amide N of the preceding residue is prevalent in proline‐containing proteins and peptides. However, the N−H⋅⋅⋅N hydrogen bonding interaction is rare in non‐prolyl natural peptides due to restricted dihedral angles. Herein, we stabilize this type of interaction in 8‐aminoquinoline appended non‐prolyl peptides through bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bond. The 8‐aminoquinoline‐incorporated model peptides 2 a–i were designed, synthesized, and the crystal structures of 2 a–c and 2 i were solved. Analysis of crystal data reveals that the amide N−H of aminoquinoline is involved in bifurcated hydrogen bonding interaction with the nitrogen of the preceding amino acid residue and the nitrogen in quinoline. Analysis of crystal packing, Hirshfeld surface and fingerprint plots confirms that the intermolecular O⋅⋅⋅H contacts significantly contribute to stabilizing bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bonding interaction. Furthermore, NMR experiments and CD spectroscopy were conducted to examine the preferred conformation in solution, and the data corroborate with the crystal structure conformation. [ABSTRACT FROM AUTHOR]

A small molecule disulfide unit technology platform based on dynamic thiol exchange chemistry at the cell membrane has the potential for drug delivery. However, the alteration of the CSSC dihedral angle of the disulfide unit caused by diverse substituents directly affects the effectiveness of this technology platform as well as its own chemical stability. The highly stable open-loop relaxed type disulfide unit plays a limited role in drug delivery due to its low dihedral angle. Here, we have built a novel disulfide unit starship based on the 3,4,5-trihydroxyphenyl skeleton through trigonometric bundling. The intracellular delivery results showed that the trigonometric bundling of the disulfide unit starship effectively promoted cellular uptake without any toxicity, which is far more than 100 times more active than that of equipment with a single disulfide unit in particular. Then, the significant reduction in cell uptake capacity (73–93%) using thiol erasers proves that the trigonometric bundling of the disulfide starship is an endocytosis-independent internalization mechanism via a dynamic covalent disulfide exchange mediated by thiols on the cell surface. Furthermore, analysis of the molecular dynamics simulations demonstrated that trigonometric bundling of the disulfide starship can significantly change the membrane curvature while pushing lipid molecules in multiple directions, resulting in a significant distortion in the membrane structure and excellent membrane permeation performance. In conclusion, the starship system we built fully compensates for the inefficiency deficiencies induced by poor dihedral angles. [ABSTRACT FROM AUTHOR]

The microstructure of realistic fluid–rock systems evolves to minimize the overall interfacial energy, enabling local variations in fluid geometry beyond ideal models. Consequently, the permeability–porosity relationship and fluid distribution in these systems may deviate from theoretical expectations. Here, we aimed to better understand the permeability development and fluid retention in deep-seated rocks at low fluid fractions by using a combined approach of high-resolution synchrotron radiation X-ray computed microtomography imaging of synthesized rocks and numerical permeability computation. We first synthesized quartzite using a piston-cylinder apparatus at different fluid fractions and wetting properties (wetting and non-wetting systems with dihedral angles of 52° and 61°–71°, respectively) under conditions of efficient grain growth. Although all fluids should be connected along grain edges and tubules in the homogeneous isotropic wetting fluid–rock system enabling segregation by gravitational compaction in natural settings, the fluid connectivity rapidly decreased to ~ 0 when the total fluid fraction decreased to 0.030–0.037, as the non-ideality of quartzite, including the interfacial energy anisotropy (i.e., grain faceting), became critical. In non-wetting systems, where the minimum energy fluid fraction based solely on the dihedral angle is ~ 0.015–0.035, the isolated (disconnected) fractions was 0.048–0.062. A streamline computation in the non-wetting system revealed that with decreasing total porosity, flow focusing into fewer channels maintained permeability, allowing the effective segregation of the connected fluids. These results provide insight into how non-wetting fluids segregate from rocks and exemplify the fraction of retained fluids in non-wetting systems. Thus, the findings suggest a potential way for wetting system fluids to be transported into the deep Earth's interior, and the amount of fluids dragged down to the Earth's interior could be higher than what was previously estimated. [ABSTRACT FROM AUTHOR]

MA'AT analysis has been applied to two biologically‐important O‐glycosidic linkages in two disaccharides, α‐D‐Galp‐(1→3)‐β‐D‐GalpOMe (3) and β‐D‐Galp‐(1→3)‐β‐D‐GalpOMe (4). Using density functional theory (DFT) to obtain parameterized equations relating a group of trans‐O‐glycosidic NMR spin‐couplings to either phi (ϕ') or psi (ψ'), and experimental 3JCOCH, 2JCOC, and 3JCOCC spin‐couplings measured in aqueous solution in 13C‐labeled isotopomers, probability distributions of ϕ' and ψ' in each linkage were determined and compared to those determined by aqueous 1‐μs molecular dynamics (MD) simulation. Good agreement was found between the MA'AT and single‐state MD conformational models of these linkages for the most part, with modest (approximately <15°) differences in the mean values of ϕ' and ψ', although the envelope of allowed angles (encoded in circular standard deviations or CSDs) is consistently larger for ϕ' determined from MA'AT analysis than from MD for both linkages. The MA'AT model of the α‐Galp‐(1→3)‐β‐Galp linkage agrees well with those determined previously using conventional NMR methods (3JCOCH values and/or 1H‐1H NOEs), but some discrepancy was observed for the β‐Galp‐(1→3)‐β‐Galp linkage, which may arise from errors in the conventions used to describe the linkage torsion angles. Statistical analyses of X‐ray crystal structures show ranges of ϕ' and ψ' for both linkages that include the mean angles determined from MA'AT analyses, although both angles adopt a wide range of values in the crystalline state, with ϕ' in β‐Galp‐(1→3)‐β‐Galp linkages showing greater‐than‐expected conformational variability. [ABSTRACT FROM AUTHOR]

Motivation Sidechain rotamer libraries of the common amino acids of a protein are useful for folded protein structure determination and for generating ensembles of intrinsically disordered proteins (IDPs). However, much of protein function is modulated beyond the translated sequence through the introduction of post-translational modifications (PTMs). Results In this work, we have provided a curated set of side chain rotamers for the most common PTMs derived from the RCSB PDB database, including phosphorylated, methylated, and acetylated sidechains. Our rotamer libraries improve upon existing methods such as SIDEpro, Rosetta, and AlphaFold3 in predicting the experimental structures for PTMs in folded proteins. In addition, we showcase our PTM libraries in full use by generating ensembles with the Monte Carlo Side Chain Entropy (MCSCE) for folded proteins, and combining MCSCE with the Local Disordered Region Sampling algorithms within IDPConformerGenerator for proteins with intrinsically disordered regions. Availability and implementation The codes for dihedral angle computations and library creation are available at https://github.com/THGLab/ptm_sc.git. [ABSTRACT FROM AUTHOR]

Factory made steel fiber and steel fiber derived from worn tires was used to develop cement concrete, which was subjected to torsional forces. A dedicated stand for torsion tests, allowing for the measurement of force, deflection, and torsion angle, was used. The test results showed that both the factory-made fiber and the waste steel fiber significantly improved torsional properties of the concrete matrix. The test results of specimens made with waste fiber were characterized by slightly worse results compared to factory-made fibers, but there was a significant improvement in torsional properties compared to samples without fibers. Taking into account the financial and environmental benefits, the application of waste steel fiber recovered from car tires could be an interesting alternative to using commercially sold steel fiber applied for the production of construction elements subjected to torsional forces. [ABSTRACT FROM AUTHOR]

The main objective of this article is to develop a way for calculating the volume like element of an -dimensional simplex in non-Euclidean spaces. The volume of a Euclidean tetrahedron can be calculated by this method, which encourages us to apply it in the case of non-Euclidean spaces. Although it can be useful to have an analytical solution to the problem but the solution will be more complicated as the number of dimensions increases. Compared to analytical methods, our methodology is some computational technique that is not only more practical but also very effective. First, we calculate the volume like element for a non-Euclidean tetrahedron (3-simplex) and proceed to dimensions, while specifying the volume like element in terms of the tetrahedron's face angles, circumradii, and inradii. Also, we derive the formulas for the inradii and circumradii of a spherical and hyperbolic triangle of use in calculating the volume like element. Moreover, we suggest a recursive approach to determining the volume like element in an -dimensional non-Euclidean space, avoiding intricate computations in a higher-dimensional space. [ABSTRACT FROM AUTHOR]

We report a three-stage scheme (1) Pbt–NH2 + CS2 → (Pbt–NH)2C=S (1) (Pbt = 4-(1′,3′-benzothiazole-2′-yl)phenyl), (2) 1 + PPh3 + I2 → Pbt–N=C=N–Pbt (2), (3) 2 + Ph2PH → (Pbt–N)(Pbt–NH)CPPh2 (3) for the synthesis of a novel luminescent phosphoguanidine 3 with an unprecedentedly high yield (90%) at the last catalyst-free stage. It is demonstrated by the density functional theory (DFT) method that high reactivity of 2, leading to such an yield, is explained by a high electrostatic potential at the central carbon atom. For 3, two polymorphs 3α, 3β and a solvatomorph 3γ·THF are prepared. The structures of 2, 3α, 3β, and 3γ·THF are determined by single-crystal XRD. The tendency of crystals of different phenylbenzothiazole derivatives to form different conformations is explained by the computational (DFT) data indicating that the energy change of the molecule of 3 considered as a function of the torsion angle between phenyl and benzothiazole fragments does not exceed 2 kJ/mol in the –15...30° range. Photophysical properties of 3β and 3γ·THF phases are studied. It is shown that these compounds exhibit photoluminescence with an emission maximum at 510 nm. [ABSTRACT FROM AUTHOR]

Previous studies on bimetallic paddlewheel compounds have established a direct correlation between metal–metal distance and ligand torsion angles, leading to the rule that higher torsion results in longer metal‐metal bond distances. Here, the new discovery based on diarylformamidinate Ru₂⁵⁺ paddlewheel compounds [Ru2Cl(DArF)4] that show an opposite behavior is reported: higher torsions lead to shorter metal–metal distances. This discovery challenges the assumption that internal rotation solely impacts the δ bond. By combining experimental and theoretical techniques, it is demostrated that this trend is associated with previously overlooked π metal‐ligand interactions. These π metal‐ligand interactions are a direct consequence of the paddlewheel structure and the conjugated nature of the bidentate ligands. This findings offer far‐reaching insights into the influence of equatorial ligands and their π‐conjugation characteristics on the electronic properties of paddlewheel complexes. That this effect is not exclusive of diruthenium compounds but also occurs in other bimetallic cores such as ditungsten or dirhodium is demonstrated, and with other ligands showing allyl type conjugation. These results provide a novel approach for fine‐tuning the properties of these compounds with significant implications for materials design. [ABSTRACT FROM AUTHOR]

Methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐2‐acetamido‐2‐deoxy‐β‐d‐glucopyranoside (methyl β‐chitobioside), (IV), crystallizes from aqueous methanol at room temperature to give a structure (C17H30N2O22·CH3OH) containing conformational disorder in the exocyclic hydroxymethyl group of one of its βGlcNAc residues. As observed in other X‐ray structures of disaccharides containing β‐(1→4) O‐glycosidic linkages, inter‐residue hydrogen bonding between O3H of the βGlcNAc bearing the OCH3 aglycone and O5 of the adjacent βGlcNAc is observed based on the 2.79 Å internuclear distance between the O atoms. The structure of (IV) was compared to that determined previously for 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐2‐acetamido‐2‐deoxy‐β‐d‐glucopyranose (β‐chitobiose), (III). The O‐glycosidic linkage torsion angles, phi (ϕ) and psi (ψ), in (III) and (IV) differ by 6–8°. The N‐acetyl side chain conformation in (III) and (IV) shows some context dependence, with the C1—C2—N—Ccar torsion angle 10–15° smaller for the βGlcNAc residue involved in the internal O‐glycosidic linkage. In (IV), conformational disorder is observed in the exocyclic hydroxymethyl (–CH2OH) group in the βGlcNAc residue bearing the OCH3 aglycone, and a fitting of the electron density indicates an approximate 50:50 distribution of the gauche–gauche (gg) and gauche–trans (gt) conformers in the lattice. Similar behavior is not observed in (III), presumably due to the different packing structure in the vicinity of the –CH2OH substituent that affects its ability to hydrogen bond to proximal donors/acceptors. Unlike (IV), a re‐examination of the previously reported electron density of (III) revealed conformational disorder in the N‐acetyl side chain attached to the reducing‐end βGlcNAc residue caused by rotation about the C2—N bond. [ABSTRACT FROM AUTHOR]

The compounds 2′,3′,4′,6′-tetra-O-acetyl-β-D-gluco­pyranosyl N′-cyano-N-phenyl­carbamimido­thio­ate (C22H25N3O9S, 5a), 2′,3′,4′,6′-tetra-O-acetyl-β-D-galacto­pyranosyl N′-cyano-N-phenyl­carbamimido­thio­ate, (C22H25N3O9S, 5b), 2′,3′,4′,6′-tetra-O-acetyl-β-D-galacto­pyranosyl N′-cyano-N-methyl­carbamimido­thio­ate (C17H23N3O9S, 5c), and 2′,3′,4′,6′-tetra-O-acetyl-β-D-galacto­pyranosyl N′-cyano-N-p-tolyl­carbamimido­thio­ate (C23H27N3O9S, 5d) all crystallize in P212121 with Z = 4. For all four structures, the configuration across the central (formal) C=N(CN) double bond of the carbamimido­thio­ate group is Z. The torsion angles C5--O1--C1--S (standard sugar numbering) are all close to 180°, confirming the β position of the substituent. Compound 5b involves an intra­molecular hydrogen bond N--H O1; in 5c this contact is the weaker branch of a three-centre inter­action, whereas in 5a and 5d the H O distances are much longer and do not represent significant inter­actions. The C--N bond lengths at the central carbon atom of the carbamimido­thio­ate group are almost equal. All C--O--C=O torsion angles of the acetyl groups correspond to a synperiplanar geometry, but otherwise all four mol­ecules display a high degree of conformational flexibility, with many widely differing torsion angles for equivalent groups. In the crystal packing, 5a, 5c and 5d form layer structures involving the classical hydrogen bond N--H...Ncyano and a variety of 'weak' hydrogen bonds C--H...O or C--H...S. The packing of 5b is almost featureless and involves a large number of borderline 'weak' hydrogen bonds. In an appendix, a potted history of wavelength preferences for structure determination is presented and it is recommended that, even for small organic crystals in non-centrosymmetric space groups, the use of Mo radiation should be considered. [ABSTRACT FROM AUTHOR]

In order to prevent damage to the support equipment caused by rock burst, a torsion plate energy absorption member is designed to be used with hydraulic columns. Explicit dynamic simulation is used and compared with the tests. The equations of structural parameters to the mean value of the reaction force (F mean), specific energy absorption (SEA), and mean squared deviation (σ) are constructed based on the response surface method. The structural parameters are optimized using MOPSO. The results indicate that the torsion plate exhibits excellent energy absorption characteristics. The error rate of the simulation compared to the test is less than 5%, indicating a high level of simulation accuracy. All three sets of response fitted equations have R 2 above 0.97, indicating a good fit. The three evaluation indexes demonstrate a trend of increasing then decreasing as the torsion angle increases. The wall thickness is positively correlated with the influence of each parameter index, while the effect of fillet radius is reversed. The maximum relative error of the predicted value is 9.50%. After optimization, the F mean is effectively increased by more than 78%, the SEA is increased by more than 24.72%. The σ is increased by 8.31%, the optimization effect is remarkable. [Display omitted] [ABSTRACT FROM AUTHOR]

In this work, an attention is paid to the prediction of torsional vibration frequencies of functionally graded porous nanotubes based on the Lam strain gradient elasticity theory. The nanotubes are formed of functionally graded porous nanomaterials that vary in the radial direction. This study also aims to obtain the analytical solution of the strain gradient model presented by Lam for torsional vibration response, in a simple manner, for different rigid or restrained boundary conditions. The torsion angle of a functionally graded nanotube is defined by an infinite Fourier series. Then, the Stokes' transformation is applied to force the boundary conditions to the desired state. An eigenvalue problem is established with the help of the two systems of equations obtained. This eigenvalue problem, which includes deformable springs at both ends of the nanotube, appears as a general analytical solution that can find torsional vibration frequencies. It is shown that the vibrational responses can be significantly influenced by the through‐radius gradings of material, material length scale parameters and deformable springs of the functionally graded nanotubes and consequently can be predicted by giving proper values to torsional spring parameters. [ABSTRACT FROM AUTHOR]

This work follows a companion article, which will be referred to as Paper I [Campeggio et al., J. Chem. Phys. 158, 244104 (2023)] in which a quantum-stochastic Liouville equation for the description of the quantum–classical dynamics of a molecule in a dissipative bath has been formulated in curvilinear internal coordinates. In such an approach, the coordinates of the system are separated into three subsets: the quantum coordinates, the classical relevant nuclear degrees of freedom, and the classical irrelevant (bath) coordinates. The equation has been derived in natural internal coordinates, which are bond lengths, bond angles, and dihedral angles. The resulting equation needs to be parameterized. In particular, one needs to compute the potential energy surfaces, the friction tensor, and the rate constants for the nonradiative jumps among the quantum states. While standard methods exist for the calculation of energy and dissipative properties, an efficient evaluation of the transition rates needs to be developed. In this paper, an approximated treatment is introduced, which leads to a simple explicit formula with a single adjustable parameter. Such an approximated expression is compared with the exact calculation of transition rates obtained via molecular dynamics simulations. To make such a comparison possible, a simple sandbox system has been used, with two quantum states and a single internal coordinate (together with its conjugate momentum). Results show that the adjustable parameter, which is an effective decoherence time, can be parameterized from the effective relaxation times of the autocorrelation functions of the conjugated momenta of the relevant nuclear coordinates. [ABSTRACT FROM AUTHOR]

Multiscale methods are powerful tools to describe large and complex systems. They are based on a hierarchical partitioning of the degrees of freedom (d.o.f.) of the system, allowing one to treat each set of d.o.f. in the most computationally efficient way. In the context of coupled nuclear and electronic dynamics, a multiscale approach would offer the opportunity to overcome the computational limits that, at present, do not allow one to treat a complex system (such as a biological macromolecule in explicit solvent) fully at the quantum mechanical level. Based on the pioneering work of Kapral and Ciccotti [R. Kapral and G. Ciccotti, J. Chem. Phys.110, 8919 (1999)], this work is intended to present a nonadiabatic theory that describes the evolution of electronic populations coupled with the dynamics of the nuclei of a molecule in a dissipative environment (condensed phases). The two elements of novelty that are here introduced are (i) the casting of the theory in the natural, internal coordinates, that are bond lengths, bond angles, and dihedral angles; (ii) the projection of those nuclear d.o.f. that can be considered at the level of a thermal bath, therefore leading to a quantum-stochastic Liouville equation. Using natural coordinates allows the description of structure and dynamics in the way chemists are used to describe molecular geometry and its changes. The projection of bath coordinates provides an important reduction of complexity and allows us to formulate the approach that can be used directly in the statistical thermodynamics description of chemical systems. [ABSTRACT FROM AUTHOR]

A novel method combining the maximum entropy principle, the Bayesian-inference of ensembles approach, and the optimization of empirical forward models is presented. Here, we focus on the Karplus parameters for RNA systems, which relate the dihedral angles of γ, β, and the dihedrals in the sugar ring to the corresponding 3J-coupling signal between coupling protons. Extensive molecular simulations are performed on a set of RNA tetramers and hexamers and combined with available nucleic-magnetic-resonance data. Within the new framework, the sampled structural dynamics can be reweighted to match experimental data while the error arising from inaccuracies in the forward models can be corrected simultaneously and consequently does not leak into the reweighted ensemble. Carefully crafted cross-validation procedure and regularization terms enable obtaining transferable Karplus parameters. Our approach identifies the optimal regularization strength and new sets of Karplus parameters balancing good agreement between simulations and experiments with minimal changes to the original ensemble. [ABSTRACT FROM AUTHOR]

Allostery in proteins involves, broadly speaking, ligand-induced conformational transitions that modulate function at active sites distal to where the ligand binds. In contrast, the concept of cooperativity (in the sense used in phase transition theory) is often invoked to understand protein folding and, therefore, function. The modern view on allostery is one based on dynamics and hinges on the time-dependent interactions between key residues in a complex network, interactions that determine the free-energy profile for the reaction at the distal site. Here, we merge allostery and cooperativity, and we discuss a joint model with features of both. In our model, the active-site reaction is replaced by the reaction pathway that leads to protein folding, and the presence or absence of the effector is replaced by mutant-vs-wild type changes in key residues. To this end, we employ our recently introduced time-lagged independent component analysis (tICA) correlation approach [Ray et al. Proc. Natl. Acad. Sci. 118(43) (2021), e2100943118] to identify the allosteric role of distant residues in the folded-state dynamics of a large protein. In this work, we apply the technique to identify key residues that have a significant role in the folding of a small, fast folding-protein, chignolin. Using extensive enhanced sampling simulations, we critically evaluate the accuracy of the predictions by mutating each residue one at a time and studying how the mutations change the underlying free energy landscape of the folding process. We observe that mutations in those residues whose associated backbone torsion angles have a high correlation score can indeed lead to loss of stability of the folded configuration. We also provide a rationale based on interaction energies between individual residues with the rest of the protein to explain this effect. From these observations, we conclude that the tICA correlation score metric is a useful tool for predicting the role of individual residues in the correlated dynamics of proteins and can find application to the problem of identifying regions of protein that are either most vulnerable to mutations or—mutatis mutandis—to binding events that affect their functionality. [ABSTRACT FROM AUTHOR]

Tryptophan synthase (TRPS) is a bifunctional enzyme consisting of α- and β-subunits that catalyzes the last two steps of L-tryptophan (L-Trp) biosynthesis. The first stage of the reaction at the β-subunit is called β-reaction stage I, which converts the β-ligand from an internal aldimine [E(Ain)] to an α-aminoacrylate [E(A-A)] intermediate. The activity is known to increase 3–10-fold upon the binding of 3-indole-D-glycerol-3′-phosphate (IGP) at the α-subunit. The effect of α-ligand binding on β-reaction stage I at the distal β-active site is not well understood despite the abundant structural information available for TRPS. Here, we investigate the β-reaction stage I by carrying out minimum-energy pathway searches based on a hybrid quantum mechanics/molecular mechanics (QM/MM) model. The free-energy differences along the pathway are also examined using QM/MM umbrella sampling simulations with QM calculations at the B3LYP-D3/aug-cc-pVDZ level of theory. Our simulations suggest that the sidechain orientation of βD305 near the β-ligand likely plays an essential role in the allosteric regulation: a hydrogen bond is formed between βD305 and the β-ligand in the absence of the α-ligand, prohibiting a smooth rotation of the hydroxyl group in the quinonoid intermediate, whereas the dihedral angle rotates smoothly after the hydrogen bond is switched from βD305-β-ligand to βD305-βR141. This switch could occur upon the IGP-binding at the α-subunit, as evidenced by the existing TRPS crystal structures. [ABSTRACT FROM AUTHOR]

The aggregation morphologies of conjugated polymers in solutions and solid films are important for their optoelectronic applications. Due to the amorphous state of the polymers, it remains a great challenge to determine their conformations in either liquids or solids. Herein, a ps/fs synchronized 2D IR technique is applied to investigate the molecular conformations of a high-mobility n-type low-bandgap copolymer, N2200, dissolved in CHCl3 and CCl4, and in solid films cast from both solutions by the vibrational cross-angle method. In CCl4, the polymer forms more aggregates and folds more and the backbone dihedral angle of C–C(NDI)/C–S(Thiophene) of its average conformation is about 10° more distorted than that in CHCl3 and the most stable conformation for a free molecule. Anti-intuitively, the solid films cast from both solutions have the same molecular conformation, and the conformation is similar to that of the polar CHCl3 rather than the conformation of the less polar CCl4. The results imply that the interaction between the polymer backbones is probably stronger than its interaction with CCl4, which can naturally guide the rearrangement of polymer chains during the evaporation of solvent molecules. This work also implies that the balance and competition between the polymer/polymer interaction and the polymer/solvent interaction seem to be the dominant factors responsible for what morphology can form in a solid film cast from solution. It is not always true that different molecular conformations must exist in solid films grown from different solutions with different polarity or different extents of aggregates with different conformations. [ABSTRACT FROM AUTHOR]

Hydrogen-enriched compressed natural gas (HCNG) technology is one of the most critical developments in the natural gas industry. To ensure the safe utilization of HCNG, the mixing effect of the two gases must be characterized and evaluated. In this paper, five types of static mixers were developed and numerically simulated. The results showed that the velocity, hydrogen blending ratio (HBR), mixer types, element aspect ratio, torsion angle, and number of elements affected the mixing effect to different degrees. Specifically, the increase in velocity and HBR improved the mixing uniformity of hydrogen and methane, but with a limited impact. Additionally, the mixing uniformity increased with the increase in the torsion angle and the number of elements, as well as the decrease in the element aspect ratio. Overall, the torsion angle had the most significant effect on mixing uniformity. Comparing the five types of static mixers, it was found that the new LPD static mixers yielded the best mixing effect, while the Y-type static mixers had the worst mixing effect. It is noted here that all the static mixers could satisfy the mixing uniformity requirements of industrial production. [Display omitted] • The influence of five models on the gas mixing effect is comprehensively analyzed. • The gas mixing effect is analyzed by three evaluation indexes. • The effects of operating conditions and spoilers on the mixing effect are studied. • The new LPD static mixer has the best effect on gas mixing. [ABSTRACT FROM AUTHOR]

Photoacoustic (PA) tomography is an emerging biomedical imaging technology for precision cancer medicine. Conventional small‐molecule PA probes usually exhibit a single PA signal and poor tumor targeting that lack the imaging reliability. Here, we introduce a series of cyanine/hemicyanine interconversion dyes (denoted Cy‐HCy) for PA/fluorescent dual‐mode probe development that features optimized ratiometric PA imaging and tunable tumor‐targeting ability for precise diagnosis and resection of colorectal cancer (CRC). Importantly, Cy‐HCy can be presented in cyanine (inherent tumor targeting and long NIR PA wavelength) and hemicyanine (poor tumor targeting and short NIR PA wavelength) by fine‐tuning torsion angle and the ingenious transformation between cyanine and hemicyanine through regulation optically tunable group endows the NIR ratiometric PA and tunable tumor‐targeting properties. To demonstrate the applicability of Cy‐HCy dyes, we designed the first small‐molecule tumor‐targeting and NIR ratiometric PA probe Cy‐HCy‐H2S for precise CRC liver metastasis diagnosis, activated by H2S (a CRC biomarker). Using this probe, we not only visualized the subcutaneous tumor and liver metastatic cancers in CRC mouse models but also realized PA and fluorescence image‐guided tumor excision. We expect that Cy‐HCy will be generalized for creating a wide variety of inherently tumor‐targeting NIR ratiometric PA probes in oncological research and practice. [ABSTRACT FROM AUTHOR]

Electron delocalization and aromaticity was comparatively evaluated in recently synthesized figure‐eight molecules made of two condensed U‐shaped polycyclic aromatic hydrocarbon moieties connected either by two single bonds or by two para‐phenylene groups. The selected examples include molecules that incorporate eight‐membered and sixteen‐membered rings, as well as a doubly [5]helicene‐bridged (1,4)cyclophane. We probe whether some electron delocalization could occur through the stereogenic single bonds in these molecules: Is aromaticity purely (semi‐)local, or possibly also global in these molecules? It was concluded that the situation can go from a purely (semi‐)local character when the dihedral angle at the connecting single bonds is large, such as in biphenyl, to a predominantly (semi‐)local character with a minor global contribution when the dihedral angle is small, such as in the para‐phenylene connectors of the [5] helicene‐bridged cyclophane. [ABSTRACT FROM AUTHOR]

Honeycomb structures have attracted wide attention due to outstanding mechanical properties as promising light material structures. Inspired by nature and artistic design, various honeycombs with different microstructural configurations have been designed for the sake of better mechanical performances and functions. Here, the Miura-origami reentrant honeycomb (MRH) structure integrating reentrant honeycombs (RH) and Miura-origami structures is investigated systematically. Dynamic impact behaviors of the present MRH structure are investigated numerically. The deformation modes and energy absorption capacity of RH and MRH are compared under different impact velocities, including low-velocity, medium-velocity and high-velocity. The results show that the plateau stress and the specific energy absorption(SEA) of MRH is much higher than RH. Moreover, the parametric study indicates that raising the inclined angle will decrease the plateau stress and the absolute value of Poisson'ratio for MRH structures. The specific energy absorption curves increase as the inclined angle of MRH grows up. In addition, the MRH with smaller dihedral angle can absorb much more impact energy and the variation of absorbed energy is proportional to the cell wall thickness of the MRH structure. This work is expected to provide a new thought for designing advanced energy absorption metastructures and achieving superior mechanical performances. [ABSTRACT FROM AUTHOR]

Buckling may cause drill string damage or even drilling failure. For the 3 000-m-long horizontal section drill string, a simplified analysis model of drill string in horizontal well is established, and the dynamic response results of axial displacement, angular displacement and contact force are obtained. When buckling, the closer the position of drill string is to the bottom, the later the buckling time, the smaller the buckling deformation degree, the slower the growth rate of axial displacement, and the smaller the attenuation degree of angular displacement and contact force amplitude. After buckling, drill string undergoes tensile deformation and eventually remains stable in the tensile state. After stabilization, from the top of drill string to the bottom of drill string, axial displacement increment increases first, then remains unchanged and then decreases, and the relative torsion angle between different positions gradually decreases. The drill string is always in horizontal contact with the wellbore, resulting in the same contact force values at different locations. The change of well inclination angle does not affect the change law of displacement and contact force. The absolute value of angular displacement is negatively correlated with the change of well inclination angle, and the value of axial displacement increment and contact force is positively correlated with the change of well deviation angle, but the value of contact force is quite close. The research results can provide reference for alleviating the buckling of drill string in horizontal wells. [ABSTRACT FROM AUTHOR]

How defects between layers of porous membranes affect their gas separation performance is still a problem. Here, we design three bilayer porous graphene membranes with different and representative defect torsion angles to regulate gas separation. We find from first-principles density functional theory calculations that the selectivity of the H 2 /CH 4 mixture can be varied by several orders of magnitude, of about 107:1 (E barrier/CH4 : 0.24, 0.18, 0.24 eV), 1019:1 (E barrier/CH4 : 0.49, 0.37, 0.47 eV) and 1012:1 (E barrier/CH4 : 0.42, 0.15, 0.45 eV), when going through the models of bi-H pore10 -20 x , bi-H pore10 -20 y and bi-H pore10 -47 y. Every barrier curve of gas penetration features three peaks. Additionally, molecular dynamics simulations show that the bilayer porous graphene membrane with a defect torsion angle of 20° along the x / y -axis possesses high H 2 /CH 4 separation ratio (up to 56–58:1) at room temperature after 5000 ps. The defect torsion angle of bilayer porous graphene improves the selectivity exponentially by regulating the three high penetration energy barriers of CH 4 , while the three energy barriers of H 2 are all very low. This work provides a new strategy to achieve highly selective separation of mixture by porous 2D-materials via regulating defect torsion angle between layers. [Display omitted] • The defect torsion angle is a powerful knob for regulating gas separation. • The potential energy curve for defect torsion angle model features three peaks. • Bi-H pore10 -20 y shows a high separation selectivity of 1019:1 for H 2 over CH 4. [ABSTRACT FROM AUTHOR]