Dihedral Angle Distribution Research Articles

Unraveling the Mechanical Response of Short-Chain Branched Amorphous Polyethylene: Insights from Molecular Dynamics Simulations

The deformation behavior of short-chain branched, amorphous polyethylene (PE) was investigated using united atom molecular dynamics (MD) simulations under uniaxial stretching. Our research reported in this paper examined the internal mechanisms underlying the mechanical response of the PE by analyzing potential energies, dihedral angle distributions, chain orientation and entanglements. The findings indicated that the short-chain branching generally enhanced Young’s modulus, except for sample B60 with a critical ethyl branch content of 60/1000 (60 ethyl branches per 1000 backbone carbons). The Young’s modulus of B60 was the local minimum value in the various samples. Analysis of the evolution of dihedral angles shows that the short-chain branching hinders the transition from gauche to trans configurations, leading to a decrease in the trans population as the branch content increases. Regarding the sample B60 with critical branch content 60/1000, the orientation parameter and entanglement parameter of the molecular chains along the backbone were lowest in the initial structure, and the efficiency of chain disentanglement was at its lowest during deformation. The simulation results elucidated the deformation mechanism related to the conformational evolution of the molecular chains, which can provide atomic-scale insights into the mechanical properties and processability of branched polyethylene, thereby allowing for optimization in its design and application.

The influence of anions in the ionic liquid-water mixtures on the conformational structures of emeraldine base and emeraldine salt form of polyaniline

The development of antifouling membranes for water filtration applications is challenging. Conducting polymers can show enhanced antifouling characteristics by blending with various polymers, nanomaterials, and Ionic liquids (ILs). In this paper, we perform an all-atom molecular dynamics simulation on a conducting polymer polyaniline (PANI) immersed in IL-water mixtures. Two forms of PANI were considered, namely Emeraldine base (EB) and Emeraldine salt (ES) as well as two different water-mixed ILs are considered namely (a) 1-ethyl-3-methyl imidazolium [EMIM]+ hexafluorophosphate [PF6]- and (b) 1-ethyl-3-methyl imidazolium [EMIM]+ tetra-fluoroborate [BF4]-. We present various intra- and inter-molecular structural properties, solvation thermodynamics, and dynamic properties. We observe that with an increase in IL concentration, the radius of gyration (Rg) value shows a decrease for ES in pure state in both ILs; on the other hand, we see a minimal increase in the Rg values of EB in both ILs. The dihedral angle distribution analysis shows a combination of gauche and trans state for ES, whereas trans state is more pronounced for the case of EB in both water-IL mixtures. The radial distribution function (RDF) analysis between the ortho, meta carbons of the benzene rings, and the amine groups on ES with [BF4]- and [PF6]- show significant structural peaks. On the other hand, EB and ES show lower interaction with the water molecules. The number of hydrogen bonds (h-bonds) between polymer and water is higher for EB than ES in both IL-water mixtures. The hydrogen bond lifetime (τ) values show one-fold higher values for EB than ES. The self-diffusion coefficient (D) values of water show a decrease with an increase in IL concentration. The thermodynamic properties solvation enthalpy (ΔH) and excess molar volume (VmE) for both ES and EB show a more favorable solvation in [EMIM]+[BF4]- when compared to [EMIM]+[PF6]- with an increase in IL concentration. These observations are crucial for selecting ILs and designing sustainable polymers for antifouling membranes.

The Coiling Effect in Ether Ionic Liquids: Exploiting Acetate as a Probe for Transport Properties and Microenvironment Analysis.

The inherently high viscosity of ionic liquids (ILs) can limit their potential applications. One approach to address this drawback is to modify the cation side chain with ether groups. Herein, we assessed the structure-property relationship by focusing on acetate (OAc), a strongly coordinating anion, with 1,3-dialkylimidazolium cations with different side chains, including alkyl, ether, and hydroxyl functionalized, as well as their combinations. We evaluated their viscosity, thermal stabilities, and microstructure using Raman and infrared (IR) spectroscopies, allied to density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. The viscosity data showed that the ether insertion significantly enhances the fluidity of the ILs, consistent with the coiling effect of the cation chain. Through a combined experimental and theoretical approach, we analyzed how the OAc anion interacts with ether ILs, revealing a characteristic bidentate coordination, particularly in hydroxyl functionalized ILs due to specific hydrogen bonding with the OH group. IR spectroscopy showed subtle shifts in the acidic hydrogens of imidazolium ring C(2)-H and C(4,5)-H, suggesting weaker interactions between OAc and the imidazolium ring in ether-functionalized ILs. Additionally, spatial distribution functions (SDF) and dihedral angle distribution obtained via AIMD confirmed the intramolecular hydrogen bonding due to the coiling effect of the ether side chain.

COMPUTATIONAL MODELLING OF THE ACTIVATION PARAMETERS OF DIELS ALDER REACTION OF QUINOFLAVONOID AND 2, 3 DIMETHYLBUTA-1, 3-DIENE

Kinetics and thermodynamics of Diels alder reaction of quinoflavoniod and 2, 3 dimethylbuta-1,3-diene was studied using ab-initio method with Hartree Fock at 6-311G* basis set in spartan, Conformational search was carried out on the molecules to obtain the structures that has the lowest energy, an indication of the stability of the structure. Reaction path calculation was done on the most stable structure using C26 – C15 and C27 – C14 as reaction coordinate in 20 iterations, this was done to ascertain the reaction mechanism. Geometric calculation was carried out on the structures of the reactant, transition state and products to obtain the bond length, bond angle, dihedral angle and atomic charge distributions. Kinetics and thermodynamic parameters was calculated at 3480C. The reaction proceeded through a concerted asynchronous six-membered cyclic transition state. True saddle point was characterized and verified by the presence of only one imaginary vibrational frequency which smoothly connect the reactant, the transition state and the product. Negative values obtained for ?H* (-66.65kJ/mol shows that the reaction is exothermic and according to literature this may be as a result of conversion of two of the ?-bonds to two new ?-bonds). Values obtained for energy of formation (-1329.974 hatrees, -1329.911 hatrees, and 1330.023 hatrees for GS, TS and PRD respectively) according to Hammond’s postulate, confirms the exothermicity of the reaction. ?Greaction (-60.16kJ/mol, shows that the reaction is favourable, Negative ?S* (-11.29J/mol.K) suggests the spontaneity of the reaction and Ea (-63.76kJ/mol) suggests that the reaction involves transfer of electrons. It was also observed that rate constants decrease with increase in temperature, although very uncommon but suggested a complex reaction mechanism.

Effect of stereo-chemistry and hydrophilic nature of synthetic carboxylic acid polymers on conformation, intermolecular structure and hydration at air-water interface

Conformation, intermolecular structure and hydration of different stereo-isomers of poly(methacrylic acid) and poly(acrylic acid), specifically isotactic-poly(methacrylic acid) (i-PMA), syndiotactic-poly(methacrylic acid) (s-PMA) and syndiotactic-poly(acrylic acid) (s-PAA) at vacuum-water interface were studied using molecular dynamics simulations. The adsorbed chain conformation was analyzed by radius-of-gyration components parallel and perpendicular to the interface, relative shape anisotropy parameter, distribution and autocorrelation function of dihedral angles, and orientation distribution of different groups relative to interface plane. i-PMA and s-PAA adsorb in planar conformation (i-PMA is curved compared to s-PAA) whereas s-PMA adsorbs in random coil conformation. Different chemical groups of s-PAA and i-PMA show preferential orientation whereas it is absent in the case of s-PMA. The random coil conformation of s-PMA exhibits greater intra-chain hydrogen bonding whereas extended chain of s-PAA exhibits greater polymer-water hydrogen bonding. The overall contribution to polymer-water hydrogen bonds by carbonyl oxygen atoms is greater than that by hydroxyl hydrogen atom. Water molecules hydrogen bonded to s-PAA show faster dynamics compared to those bonded to i-PMA and s-PMA. The slower dynamics of polymer-water hydrogen bonds is correlated to the slower dynamics of polymer conformations. Knowledge of orientation of chemical groups is useful for understanding binding of adsorbed polymer with other polymers and ligands.

Effects of intramolecular chain conformation on the hydration and miscibility of polyethylene glycol in water studied by means of polymer reference interaction site model theory.

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.

Thermal Transport in Poly(p-phenylene): Anomalous Dimensionality Dependence and Role of π-π Stacking.

For heat conduction along polymer chains, a decrease in the axial thermal conductivity often occurs when the polymer structure changes from one-dimensional (1D) to three-dimensional (3D). For example, a single extended aliphatic chain (e.g., polyethylene or poly(dimethylsiloxane)) usually has a higher axial thermal conductivity than its double-chain or crystal counterparts because coupling between chains induces strong interchain anharmonic scatterings. Intuitively, for chains with an aromatic backbone, the even stronger π-π stacking, once formed between chains, should enhance thermal transport across chains and suppress the thermal conductivity along the chains. However, we show that this trend is the opposite in poly(p-phenylene) (PPP), a typical chain with an aromatic backbone. Using molecular dynamics simulations, we found that the axial thermal conductivity of PPP chains shows an anomalous dimensionality dependence where the thermal conductivity of double-chain and 3D crystal structures is higher than that of a 1D single chain. We analyzed the probability distribution of dihedral angles and found that π-π stacking between phenyl rings restricts the free rotation of phenyl rings and forms a long-range order along the chain, thus enhancing thermal transport along the chain direction. Though possessing a stronger bonding strength and stabilizing the multiple-chain structure, π-π stacking does not lead to a higher interchain thermal conductance between phenyl rings compared with that between aliphatic chains. Our simulation results on the effects of π-π stacking provide insights to engineer thermal transport in polymers at the molecular level.

Getting 'ϕψχal' with proteins: minimum message length inference of joint distributions of backbone and sidechain dihedral angles.

PhiSiCal mixture models and programs to sample from them are available for download at http://lcb.infotech.monash.edu.au/phisical.

Resolving the sintering conundrum of high-rhenium tungsten alloys

Tungsten-rhenium (W-Re) alloys with high-Re contents are the preferred refractory metal materials in many applications because of the improved ductility and processability over pure W and low-Re tungsten alloys. However, the sintering concurrently becomes increasingly more difficult with increasing Re contents. Here we proposed that the sintering conundrum is caused by the lowered crystal symmetry and the wider dihedral angle distribution when body-center-cubic (BCC) W is alloyed with more hexagonal-close-packed (HCP) Re, which results in inefficient pore removal in the final stage sintering. We showed that the conundrum can be resolved by pressureless two-step sintering (TSS) which suppresses accelerating final-stage grain growth, and our proposal is supported by the data of the critical density ρc that is required to start the second step for successful TSS at different W-Re compositions. Dense ultrafine-grained W-Re alloys with ∼300 nm average grain size and up to 25 wt% Re were successfully produced. Our work demonstrates the unique opportunities offered by two-step sintering to advance the scientific understanding and technological practices in powder metallurgy and related fields.

Confining donor conformation distributions for efficient thermally activated delayed fluorescence with fast spin-flipping

Fast spin-flipping is the key to exploit the triplet excitons in thermally activated delayed fluorescence based organic light-emitting diodes toward high efficiency, low efficiency roll-off and long operating lifetime. In common donor-acceptor type thermally activated delayed fluorescence molecules, the distribution of dihedral angles in the film state would have significant influence on the photo-physical properties, which are usually neglected by researches. Herein, we find that the excited state lifetimes of thermally activated delayed fluorescence emitters are subjected to conformation distributions in the host-guest system. Acridine-type flexible donors have a broad conformation distribution or bimodal distribution, in which some conformers feature large singlet-triplet energy gap, leading to long excited state lifetime. Utilization of rigid donors with steric hindrance can restrict the conformation distributions in the film to achieve degenerate singlet and triplet states, which is beneficial to efficient reverse intersystem crossing. Based on this principle, three prototype thermally activated delayed fluorescence emitters with confined conformation distributions are developed, achieving high reverse intersystem crossing rate constants greater than 106 s−1, which enable highly efficient solution-processed organic light-emitting diodes with suppressed efficiency roll-off.

Strategy for Modulating Dihedral Angle Distribution for Enhanced Anti-Kasha TADF Behavior

D–A type thermally activated delayed fluorescence (TADF) materials with aggregation-induced emission (AIE) have attracted extensive research interest for their intense emission and high quantum yield in aggregated state. Herein, TADF molecules with vertical twisted structures are achieved by the methylation strategy which effectively separated the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). With the increase of the dihedral angle, 18 times enhancement of the photoluminescence quantum yield (PLQY) is realized in the aggregated state. The density functional theory (DFT) calculations demonstrate that these TADF molecules exhibit excellent photophysical properties in violation of Kasha’s rule: fluorescence originates from the higher energy electronic excited state (S2) rather than the S1 state.

Unveiling polyamorphism and polyamorphic interconversions in pharmaceuticals: the peculiar case of hydrochlorothiazide.

Polyamorphism has been a controversial and highly debated solid-state phenomenon in both material and pharmaceutical communities. Although some evidence of this fascinating phenomenon has been reported for several inorganic systems, and more recently also for a few organic compounds, the occurrence of polyamorphism is poorly understood and the molecular-level organization of polyamorphic forms is still unknown. Here we have investigated the occurrence of polyamorphism and polyamorphic interconversions in hydrochlorothiazide (HCT), using both experimental and computational methods. Three distinct HCT polyamorphs, presenting distinct physical and thermal stabilities as well as distinct relaxation properties, were systematically prepared using spray-drying (SD), quench-cooling (QC) and ball milling (BM) methods. HCT polyamorph II (obtained by QC) was found to be more physically stable than polyamorphs I and III (obtained by SD and BM, respectively). Furthermore, polyamorphs I and III could be converted into polyamorph II after QC, while polyamorph II did not convert to any other polyamorph after SD or BM. Molecular dynamics simulations show that HCT dihedral angle distributions are significantly different for polyamorphs I and II, which is postulated as a possible explanation for their different physicochemical properties.

A trick of the tail: computing the entropic contribution to the energetics of quinone-protein unbindung.

We estimate the entropic contributions to the free energy of quinone unbinding in bacterial and mitochondrial respiratory chains using molecular dynamics (MD) and Monte Carlo (MC) computer simulations. For a varying length of the isoprenoid side chain, MD simulations in lipid bilayers and in unpolar solvents are used to assess the dihedral angle distributions along the chain. These form the basis of a MC estimate of the number of molecular structures that do not exhibit steric self-overlap and that are confined to the bilayer. We obtain an entropy drive of TΔS = 1.4 kcal mol-1 for each isoprene unit, which in sum is comparable to the redox potential differences involved in respiratory chain electron transfer. We postulate an entropy-driven zipper for quinone unbinding and discuss it in the context of the bioenergetics and the structure of complex I, and we indicate possible consequences of our findings for MD-based free energy computations.

Bimodal distribution of amphibole-melt apparent dihedral angles in the product of the early crystallization of hydrous basaltic melts

• Amp-Melt-Amp apparent dihedral angle distribution shows bimodality. • Bimodality becomes obvious after annealing for more than 1 h at 0.6 GPa and 970 °C. • Median-standard deviation evolution obeys no longer a unidirectional change. • The high anisotropy of amphibole is the main cause of the bimodality. The dihedral angle of mineral-melt is a very important parameter for further understanding the textural evolution of magma crystallization. In this study, we have investigated the amphibole-melt dihedral angle distribution of four previous experimental samples at 0.6 GPa and 970 °C with annealing time of 1 h, 10 h, 60 h, and 100 h, as well as two additional experiments with annealing time of 5 h and 30 h. In this experiment, we have achieved the assemblage of amphibole + granodioritic melt ± traces of other minerals in the process of melt crystallization under the above experimental conditions. The apparent dihedral angles of amphibole-melt of the experimental products were obtained by randomly measuring the dihedral angles in the backscattered images. The results indicate that the apparent dihedral angle presents a gradually obvious bimodal distribution with the increasing annealing time. The high anisotropy of amphibole is believed to be the main cause of the bimodal characteristics of the apparent dihedral angle distribution. Consequently, two Gauss functions are used to fit one distribution. As the annealing time increases, the median-standard deviation relationships of the apparent dihedral angle for these two Gauss functions show great differences. Therefore, our experiments proved that in the amphibole-melt system, the median-standard deviation with the growth of textural equilibrium in the early crystallization is no longer a unidirectional change. Furthermore, combining the results of this study and the previous work, whether the dihedral angle distribution in the early crystallization is unimodal or bimodal may have great relationship with the anisotropy of minerals.

Flight testing verification of lateral-directional dynamic stability of gliding birds due to wing dihedral

PurposeUnlike conventional aircraft, birds can glide without a vertical tail. The purpose of this paper is to analyse the influence of dihedral angle spanwise distribution on lateral-directional dynamic stability by the simulation, calculation in the development of the bird-inspired aircraft and the flight testing.Design/methodology/approachThe gliding magnificent frigatebird (Fregata magnificens) was selected as the study object. The geometric and mass model of the study object were developed. Stability derivatives and moments of inertia were obtained. The lateral-directional stability was assessed under different spanwise distributions of dihedral angle. A bird-inspired aircraft was developed, and a flight test was carried out to verify the analysed results.FindingsThe results show that spanwise distribution changing of dihedral angle has influence on the lateral-directional mode stability. All of the analysed configurations have convergent Dutch roll mode and rolling mode. The key role of dihedral angle changing is to achieve a convergent spiral mode. Flight test results show that the bird-inspired aircraft has a well-convergent Dutch roll mode.Practical implicationsThe theory that birds can achieve its lateral-directional stability by changing its dihedral angle spanwise distribution may explain the stability mechanism of gliding birds.Originality/valueThis paper helps to improve the understanding of bird gliding stability mechanism and provides bio-inspired solutions in aircraft designing.

Molecular dynamics simulation of thermophysical properties of binary RP-3 surrogate fuel mixtures containing trimethylbenzene, n-decane, and n-dodecane

• Binary RP-3 surrogate fuel mixtures containing trimethylbenzene (TMB), n-decane, and n-dodecane are investigated via EMD simulations. • TraPPE-UA force field can appropriately describe the densities and thermal conductivities of TMB and the mixtures. • Variation ranges of the bond angles become broader and n-decanes shrink with the increasing of the temperature. • Analysis of RDFs and the ADFs are carried out. Trimethylbenzene (TMB), n-decane, n-dodecane and their mixtures are commonly used in surrogate fuel of aviation kerosene. To date, molecular dynamic studies on the thermophysical properties of TMB and their mixtures are very few. In this study, equilibrium molecular dynamics (EMD) simulations with the TraPPE-UA force field are carried out to simulate the densities and thermal conductivities of Rocket Propellant-3 (RP-3) aviation kerosene surrogate mixtures, C 10 + 1,2,4-TMB and C 10 + C 12 , under sub/supercritical pressure. Results show that the simulated densities and thermal conductivities of TMB and the mixtures are in good agreement with the NIST data, and the two surrogate models can provide reasonable surrogate accuracy in predicting the thermophysical properties of aviation kerosene RP-3. The analysis of radial distribution functions, angular distribution functions, end-end length and dihedral angle distributions is carried out to better understand the temperature effect on the structure and thermophysical properties of the surrogates. It is found that the n-decane chains become shrinking and more twisted with the increasing of the temperature which reduce the thermal conductivity of the surrogates. This research offers a good reference for the analysis thermophysical properties of n-alkanes and TMB-based fuels.

Molecular signatures of the glass transition in polymers.

The glass transition temperature (T_{g}) is one of the most fundamental properties of polymers. T_{g} is predicted by some theories as a sudden change in a "macroscopic" quantity (e.g., compressibility). However, for systems with "soft" glass transitions where the change is gradual it becomes hard to pinpoint precisely the transition temperature as well as the set of molecular changes occurring during this transition. Here, we introduce two new molecular signatures for the glass transition of polymers that exhibit clear changes as one approaches T_{g}: (i) differential change of the probability distribution of dihedral angles as a function of temperature and (ii) the distribution of fractional of the time spent in the different torsional states. These new signatures provide insights into the glass transition in polymers by directly exhibiting the concept of spatial heterogeneity and dynamical ergodicity breaking in such systems, as well as provide a key step to quantitatively obtain the transition temperature from molecular characteristics of the polymeric systems.

Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon

Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is evidence to suggest that codon usage affects co-translational protein folding and the final structure of the expressed protein. Here we develop a method for computing and comparing codon-specific Ramachandran plots and demonstrate that the backbone dihedral angle distributions of some synonymous codons are distinguishable with statistical significance for some secondary structures. This shows that there exists a dependence between codon identity and backbone torsion of the translated amino acid. Although these findings cannot pinpoint the causal direction of this dependence, we discuss the vast biological implications should coding be shown to directly shape protein conformation and demonstrate the usefulness of this method as a tool for probing associations between codon usage and protein structure. Finally, we urge for the inclusion of exact genetic information into structural databases.

Microscopic Interface and Multiscale Failure Analysis of Proposed Molecular Chain Polymers Based on Aifantis Strain Gradient Theory.

A study on the microscopic morphology of real-world polymer blends and its mechanism of change showed that the microscopic morphology of equiproportional mixtures gradually changed from a dense body structure to a network structure with the addition of the total polymer concentration up to 20%; the microscopic morphology of mixtures with different proportions was characterized by the most uniform network structure of equiproportional mixtures when the total polymer concentration was 20%. The polymer acts as a defoamer in the mixed system. In this paper, the relationship between the microscopic morphology of each mixture and the physicochemical behavior of the two polymer chains in the mixed system was investigated on the basis of the Aifantis strain gradient theory. Molecular polymer microscopic interface and multiscale failure analysis are proposed. It is shown that for the dihedral angle distribution of four consecutive coarse-grained particles, the peaks obtained from all atomic-scale simulation data are reproduced in the coarse-grained model simulations. The deviation is within 2.5% in most places, except for the local area where the deviation exceeds 5%. Therefore, we have achieved good results for large-scale failures.

Molecular Dynamics Simulation of an ι-Carrageenan Hexamer as Single and Double Helices

Carrageenan gelation is characterized by a coil-to-helix transition. The conformation the polymer adopts in solution, however, is not yet fully understood at the molecular level. Here, molecular dynamics (MD) simulations were carried out on two possible conformations of ι-carrageenan hexamers – a single helix and a double helix. All-atom simulations were carried out using the Carbohydrate Solution Force Field (CSFF) in explicit water (SPC). Dihedral angle distributions from simulations of the single helix and the individual chains of the double helix were compared revealing similarity between these conformations. In the case of the double helix, an overall attractive interaction has been calculated between the two chains, possibly due to contribution from sulfate groups and hydroxyl groups, preventing it from unravelling. Simulation calculations revealed no significant difference in the total energy of the single helical and double helical carrageenan in equivalent systems indicating no strong preference by the polymer to adopt one configuration over the other. It is suggested that the double helix can form in solution due to the dihedral angle conformation within the single helices and is stabilized by attractive interactions identified. An increased understanding of gelation process, including the coil-to-helix transition, in carrageenans can allow for the development of processing methods to control their properties for specific applications.