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The viscosity is one of the most important properties of ionic liquids (ILs). To uncover the relationship between structure and viscosity from the molecular level is beneficial to designing the ILs with desired viscosity by choice of different cation and anion. The influence of hydrogen bonds on the viscosity for five pyridine-based ILs, [EPy][OTf], [EPy][NTf], [BPy][OTf], [BPy][NTf], and [BPy][BF], is theoretically studied by combination of molecular dynamics and quantum chemistry. Effect of different alkyl chain lengths, cations, and anions on the viscosity is compared to find the critical item. Besides the molecular structure, the roles of hydrogen bond played in the viscosity are analyzed by various factors. [ABSTRACT FROM AUTHOR]

Binding properties of wild type (WT) and six single amino acid substituted variants (E3A, E9A, D12A, D20A, F23A, and E58A) of insulin-like growth factor I (IGF-I) were analyzed with respect to their binding details to IGF binding proteins (IGFBPs) by molecular dynamics (MD) simulations. The binding sites and binding interactions on IGF-I and IGFBPs are screened and compared with the static X-ray structure. Electrostatic interaction is the primary driving force of the interaction between IGF-I and IGFBPs. Mutation may cause the rearrangement of binding sites, however, the unfolding of protein induced by mutation is not obvious in this work. We also provide the detailed picture of binding factors. And the results show that, whether the unfolding of helix occurs or not, the Ala mutation will change the molecular atmosphere of the binding interface by the rearrangement of conformation, and further affects the binding residues and binding interactions. [ABSTRACT FROM AUTHOR]

Prion diseases are invariably fatal and highly infectious neurodegenerative diseases related to the structure transition of α-helix into β-sheet. In order to gain more direct insight into the molecular basis of the disease, the stability of the wild-type human prion protein (hPrPc) and the R220K mutant (m-hPrPc) was studied by molecular dynamics (MD) and flow MD simulation. Both the thermodynamic stability and the mechanical properties of hPrPc were investigated in this work. It was found that β-sheet was more readily to be unfolded in m-hPrPc. In the case of hPrPc, less content of helix was preserved after water turbulence. The H-bond network formed by the mutation-related residue 220 was found to play a key role in the stability of hPrPc. [ABSTRACT FROM PUBLISHER]

To elucidate the structural stability and the unfolding dynamics of the animal prion protein, the temperature induced structural evolution of turtle prion protein (tPrPc) and bank vole prion protein (bvPrPc) have been performed with molecular dynamics (MD) simulation. The unfolding behaviors of secondary structures showed that the α-helix was more stable than β-sheet. Extension and disruption of β-sheet commonly appeared in the temperature induced unfolding process. The conversion of α-helix to π-helix occurred more readily at the elevating temperature. Furthermore, it was suggested in this work that the unfolding of prion protein could be regulated by the temperature. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Abstract: The rate constants of the hydrogen abstraction reactions of CF3CHFCF3 +H (R1) and CF3CF2CHF2 +H (R2) have been calculated by means of the dual-level direct dynamics method. Optimized geometries and frequencies of stationary points and extra points along the minimum-energy path (MEP) are obtained at the MPW1K/6-311+G(d,p) level, and the classical energetic information is further corrected with the interpolated single-point energy (ISPE) approach by the G3(MP2) level of theory. Using the canonical variational transition state theory (CVT) with small-curvature tunneling corrections (SCT), the rate constants are evaluated over a wide temperature range of 200–2000K. The calculated CVT/SCT rate constants are in good agreement with available experimental values. It is found that the variational effect is very small and almost negligible over the whole temperature region. However, the small-curvature tunneling correction plays an important role in the lower temperature range. Furthermore, the heats of formation of species CF3CF2CHF2 (SC1 or SC2) and CF3CF2CF2 are studied using isodesmic reactions to further elucidate the thermodynamic properties. [Copyright &y& Elsevier]

The mechanism for the cycloaddition of carbon dioxide and epoxides catalyzed by ionic liquids has been elucidated in lots of theoretical literature. It is well known that the calculated barrier height could not be compared with the activation energy. However, it is expected that the sequence of activity estimated by barrier height could be consistent with the experimental result. Actually, the calculated results are not accurate enough to be reliable. One of possible reasons is attributed to the improper treatment for the solvent effect. The solvent effect induced by ionic liquids is not carefully considered or neglected at all in most of previous theoretical studies. In this work, ionic liquids are really included in the catalytic system to consider the solvent effect by the ONIOM method along with the molecular dynamics simulations. When the solvent effect is considered, the theoretical reliability is greatly improved. More important, this model is suitable not only for non-protic ionic liquids but also for protic ones and not only for imidazolium ionic liquids but also for pyrazolium ionic liquids. The solvent effect aroused by epoxides is also considered by the same model. Unlabelled Image • The solvent effect is considered by ONIOM model. • ONIOM model is reliable for both imidazolium and pyrazolium ionic liquids. • OINOM model is suitable for both non-protic and protic ionic liquids. [ABSTRACT FROM AUTHOR]

Abstract The properties of three D1-π-D2-A dyes with dithiafulvenyl as donor (D1), phenothiazine as ancillary donor (D2), cyanoacrylic acid as acceptor along with different π groups, diphenyl for 1 , dithienyl for 2 , and thiopheneyl-benzothiadiazole for 3 , are studied. Besides the isolated dyes, the monomeric and dimeric adsorptions are also studied by combination of first principle and molecular dynamic simulations. There is no distinct difference among three dyes on the basis of only isolated dyes. When the dye-TiO 2 adsorption is considered, 3 is excluded because of its inferior items. However, it is still a difficult task to differentiate 1 and 2 even if the aggregation effect is included. The fluctuation of 1 is larger than that of 2 during the dynamic simulation resulting in the larger electronic coupling. The aggregation, especially for the aggregation during the dynamic simulation, is necessary to evaluate the performance of organic dye. Additionally, a new D-π-A dye 4 with the identical donor, π-bridge and acceptor is designed to compare with 2. 2 is totally superior to 4 indicating that suitable groups and appropriate configuration are both important to enhance the performance of organic dye. Graphical abstract fx1 [ABSTRACT FROM AUTHOR]

Abstract The knowledge of viscosity about ionic liquids is important for their large scale-up application. Although some theoretical models and experimental methods are developed to evaluate the viscosity, there are some common disadvantages for them including complexity, time consuming, and unreliable. It is necessary to develop a simple method to evaluate the viscosity. Even if the accurate value of viscosity could not be obtained, the relative sequence for a series of ionic liquids with similar structures is still beneficial for their applications. The relationship between hydrogen bond and viscosity for TBA pyruvate, TBA L‐lactate, and TBA L‐malate are studied by combination of molecular dynamics simulation and quantum chemistry methods. The strength of hydrogen bond in TBA L‐malate is the larger resulting in the larger viscosity. In contrast, the number of hydrogen bond has a minor influence on the viscosity. It is expected that this study would provide some useful information to build the relationship between hydrogen bond and viscosity for task functionalized ionic liquids. Graphical abstract Unlabelled Image Highlights • Relationship between hydrogen bond and viscosity • The inclusion of hydroxyl group is helpful to improve the strength of hydrogen bonds. • Strength of hydrogen bonds is determined items for viscosity rather than the number. [ABSTRACT FROM AUTHOR]

Aggregation is inevitable for the organic dyes, and it is difficult to evaluate its effects due to its complexity. Herein, we combine first principles and molecular dynamics (MD) simulations to explore the influence of aggregation on the optical and electronic properties for THI-BTZ-2T-C . If only the static properties are considered, the configuration of dye is not varied greatly when the adsorbed dyes are increased from monomer to hexamer. However, the absorption spectrum varies regularly with the increased aggregation order. In addition, the contribution of different orbitals of various atoms to density of states (DOS) gradually increases with the aggregation order increasing. When dynamics simulation is performed, the torsion between different components of dye is enlarged. Meanwhile, the perpendicular model is altered during the dynamics simulations, the dye would like to bend towards the TiO 2 surface. Moreover, the electronic coupling is greatly improved during the molecular dynamics simulations especially for the H-aggregation. The dye aggregation mainly affects the electrons injection process resulting in the reduction of the photoelectric conversion efficiency for dye sensitized solar cells (DSSCs). Reduction of perfect face to face stacking would be an efficient pathway to weaken the aggregation. [ABSTRACT FROM AUTHOR]

The relationship between molecular structure and viscosity for four pyridinium ionic liquids is explored by combination of molecular dynamics and quantum chemistry. Our central aim is to study the relationship between hydrogen bond and viscosity. It is expected that a simple method would be built to judge the relative sequence of viscosity for a series of ionic liquids with similar structures. Although some items related with the viscosity are omitted, it is no doubt a direct method to estimate the range of viscosity. The methyl group substituted in ortho position would greatly increase the viscosity since more hydrogen bonds would be formed with stronger strength. While the pyridinium ionic liquids with the substitution in meta and para position has the similar viscosity, which is consistent with the similar features of hydrogen bonds in them. [ABSTRACT FROM AUTHOR]

Based upon two thermally activated delayed fluorescence (TADF) emitters 1 and 2 , compounds 3 – 6 have been designed by replacing the carbazol group with the bis(4-biphenyl)amine one ( 3 and 4 ) and introducing the electron-withdrawing CF 3 group into the acceptor unit of 3 and 4 ( 5 and 6 ). It is found that the present calculations predict comparable but relatively large energy differences (approximate 0.5 eV) between the lowest singlet S 1 and triplet T 1 states (∆ E ST ) for the six targeted compounds. In order to explain the highly-efficient TADF behavior observed in compounds 1 and 2 , the“triplet reservoir” mechanism has been proposed. In addition, the fluorescence rates of all six compounds are very large, in 10 7 –10 8 orders of magnitude. According to the present calculations, it is a reasonable assumption that the newly designed compounds 3 – 6 could be considered as the potential TADF emitters, which needs to be further verified by experimental techniques. [ABSTRACT FROM AUTHOR]

[Display omitted] • Solvent effect of ionic liquids on the fixation of CO 2 is studied by ONIOM and MD. • Critical hydrogen bond and C-Br interaction are analyzed by NCI and AIM. • ONIOM model displays the more reasonable result than PCM model. • Which one is more important, nucleophilic or electrophilic activation? The solvent effect of ionic liquids on CO 2 fixation catalyzed by hydroxyl-functionalized quaternary ammonium-based ionic liquids is thoroughly investigated by ONIOM method associated with the molecular dynamics simulation. As compared with the catalytic activity determined in experiment, the catalytic activity estimated by ONIOM model is more credible than previous result calculated by the polarized continuum model. The critical hydrogen bond and C-Br interaction are analyzed by non-covalent interaction and the atoms in molecules methods. The analysis indicates that the electrophilic activation aroused by hydrogen bond provides more contribution than nucleophilic activation aroused by C-Br interaction in reaction catalyzed by trihydroxyethylethyl ammonium bromide. In contrast, the nucleophilic activation is more important in reactions catalyzed by other three ionic liquids. Choice of the suitable model is possible to obtain the reliable catalytic activity, which would be comparable with the experimental result. [ABSTRACT FROM AUTHOR]

The electronic, optical, and hole transporting mobility of three organic hole transporting materials (HTMs), X59, X59-P, and X59-T, are investigated by combination of first principle and molecular dynamics associated with Marcus theory and Einstein equation. As compared with the experimental reported X59, the new designed X59-P has more stable HOMO energy level. Moreover, the latter has smaller reorganization energy and larger hole transfer integral resulting in the larger hole transporting mobility. Besides the hole transporting mobility, the solubility and stability of two designed molecules are also evaluated by comparison with X59, which are two important items to determine the cost and performance in real application of solar cell. More importantly, they would be synthesized in a benign condition without expensive materials. Our studies introduce a possible pathway to explore the efficient HTMs by suitable combination mode rather than development of new groups. [ABSTRACT FROM AUTHOR]

The luck of low cost and highly efficient HTMs is one challenge for perovskite solar cells toward future commercialization. Inspired by two important HTMs ( CBP and 2TPA-2-DP See Scheme 1), three new organic molecules, CBP-OD , CBP-2OD , and CBP-3OD (See Scheme 1) are theoretically designed and their structure-property relationship is studied by the first principle and molecular dynamics associated with the Marcus theory and Einstein-Smoluchowski relation (See Eq. (1)). The HOMO energy level of designed three molecules is lower than that of 2TPA-2-DP but higher than that of CBP . Moreover, their reorganization energies are all larger than that of CBP and 2TPA-2-DP , which is not favorable to be HTMs. However, they have the smaller exciton binding energies, which is beneficial for the separation of hole and electron. Although reorganization energies of three designed molecules are similar, CBP-OD has the largest hole mobility because of the larger transfer integral, which is even larger than that of CBP indicating a superior potential to be HTM candidate. On the contrary, hole mobilities of CBP-2OD and CBP-3OD are similar or less than that of CBP . Additionally, all of designed molecules have the much larger hole mobility than 2TPA-2-DP . The influence of the packing model and the elongation of π-conjugation on the hole mobility is importantly discussed. [ABSTRACT FROM AUTHOR]

Highlights: [•] A stepwise molecular design of peptide to functionalize the large-diameter SWCNT. [•] Two kinds of functional peptides were designed for the armchair (24, 24) SWCNT. [•] The residues with aromatic rings and long alkylene chains were found to be most effective in the adsorption of peptide on the SWCNT surface. [•] The predominant driving force of protein/peptide onto the SWCNT surface was VDW interaction. [•] The adsorption manner of the protein/peptide was affected by the flexibility of size chains. [Copyright &y& Elsevier]

• Both [BPP][NTf2] and [OTP][NTf2] are efficient inhibitors for Mg Alloy in NaCl solution. • The inhibition efficiency is improved with the longer soaking time. • Corrosion resistance would be kept after 240 h immersion. • The inhibition mechanism is proposed by theoretical and XPS result. The corrosion resistance of two ionic liquids, [BPP][NTf 2 ] and [OTP][NTf 2 ], for Mg alloys is explored in NaCl solution by electrochemical approach, SEM, XRD, and XPS measurements along with theoretical calculations. The inhibition efficiency of [BPP][NTf 2 ] is better than that of [OTP][NTf 2 ] in three tested NaCl solution. Their inhibition performance is improved after long time immersion. Moreover, the [OTP][NTf 2 ] would exceed [BPP][NTf 2 ] after 96 h immersion. The essential item to affect the long-term inhibition performance is elucidated by the molecular dynamics simulations. The possible inhibition mechanism is proposed according to the XPS results along with the quantum chemical calculations. [ABSTRACT FROM AUTHOR]

Theoretical calculation is a powerful tool to uncover the reaction mechanism. Besides it, the theoretical calculation is expected to provide more helpful clues and play more important role for catalysis. Although the calculated barrier height could not be directly compared with the experimental measured activation energy, the range of barrier heights would be the same with that of experimental yields. It would be beneficial to estimating the experimental result and designing the efficient catalysts. For the coupling reaction of carbon dioxide with epoxides catalyzed by ionic liquids, both the interactions among ionic liquids and microenvironment of ionic liquids would affect the calculated barrier heights. They are considered by combination of density functional theory and molecular dynamics in this work. The reliability of calculated barrier heights is improved. More important, this method not only is suitable for the ionic liquids with the similar structures but also be applied to ionic liquids with different structures. Unlabelled Image • The method is suitable for three different kinds of ionic liquids. • Interaction among ionic liquids are included. • Influence of microenvironment of ionic liquids are considered. [ABSTRACT FROM AUTHOR]

Three new organic hole transport materials (HTMs), 2 , 3 and 4 , are designed with NP-core along with bis(4-methoxyphenyl)amine, p -methoxytriphenylamine, and 9- p -tolyl-9 H -carbazole as side group on the basis of reported HTM NP2 (1), respectively. For isolated molecules, frontier molecular orbitals, absorption and emission spectra, and hole mobility are evaluated by density functional theory (DFT) and molecular dynamics simulations. In addition, the following properties, hydrophobility, solubility, and glass transition temperatures (T g), related with the overall performance of devices are also calculated. The HTM@CH 3 NH 3 PbI 3 adsorbed system is investigated to consider the effect of interfacial properties between HTM and CH 3 NH 3 PbI 3 on HTM properties. Our theoretical results indicate that the new designed molecule 4 has better properties than 1. More importantly, 1 has been fabricated in perovskite solar cells (PSCs) as a HTM with the power conversion efficiency of 16.4%. It is reasonable to infer that the new designed molecules would be potential candidates. Unlabelled Image • Three new NP-based HTMs are designed. • The hydrophoby, solubility and glass transition temperatures of HTMs are estimated. • Interfacial properties between HTM and CH 3 NH 3 PbI 3 are theoretically investigated. • 9- p -tolyl-9 H -carbazole is more suitable side group with NP core to form HTM. [ABSTRACT FROM AUTHOR]

The reaction mechanism for the coupling reaction of carbon dioxide with epoxides catalyzed by single-component protic pyrazolium ionic liquids has been extensively elucidated. However, the calculated barrier heights are not accurate enough to predict the catalytic results for a series of ionic liquids with similar structures. The cluster of protic pyrazolium ionic liquids is regarded as catalyst to consider the effect of interactions among ionic liquids on the barrier heights. Moreover, the ionic liquids or epoxides would also affect the barrier heights as the environmental factors, which is also considered by ONIOM method. When the environmental influence is involved, the accuracy is greatly improved. The analysis of interactions between ionic liquid and reactant indicates that the electrophilic attacking plays the more critical role than nucleophilic attacking. Unlabelled Image • Number of ionic liquids is not the sole factor to determine the accuracy of results. • PO as solvent is more suitable than ionic liquids as solvent. • The electrophilic activation is more important than nucleophilic activation. [ABSTRACT FROM AUTHOR]

It is an easy task to simulate the spectrum properties for the organic dyes applied in dye-sensitized solar cells (DSSCs) if the suitable method is chosen. However, it is still difficult to quantitatively determine the overall performance for them. In this work, the short-circuit photocurrent density (J SC) and open circuit photovoltage (V OC) are quantitatively calculated by combination of the density functional theory and first principle for DSSCs based on four different organic dyes, 2-((4′-((4-(bis(4-methoxyphenyl)amino)phenyl)diazenyl)biphenyl-4-yl)methylene)but-3-ynoic acid (1), 2-((5-(4-((4-(bis(4-methoxyphenyl)amino)phenyl)diazenyl)phenyl)thiophen-2-yl)methylene)but-3-ynoic acid (2), 3-(7-(4-((4-(bis(4-methoxyphenyl)amino)phenyl)diazenyl)-4 H -cyclopenta[2,1- b :3,4- b ′]-dithiophene)-2-cyanoacrylic acid (3), and 3-(7-(4-((4-(bis(4-methoxyphenyl)amino)phenyl)diazenyl)phenyl)-2,3-dihydrothieno[3,4- b ][1,4]dioxin-5-yl)-2-cyanoacrylic acid (4), in which the triarylamine is donor and the cyanoacrylic acid is acceptor along with variable π group. The 3 and 4 are new theoretically designed organic dyes on the basis of 1 and 2 with different electron-rich group as π group. Both J SC and V OC of 3 and 4 are improved as compared with those of 1 and 2 , which breaks the normal "trade-off" rule. As a result, the power conversion efficiency (PCE) of 3 and 4 is improved, especially for 3. The aggregation effect is also considered to evaluate the overall performance, which is favorable to further enhance the reliability of theoretical design. Unlabelled Image • "Trade-off" effect is disappeared. • Influence of different π groups is explored. • J SC , V OC , and PCE values are calculated. • Aggregation effect on the PCE is considered. [ABSTRACT FROM AUTHOR]