Molecular Simulations in Materials Science

Molecular Simulations in Materials Science

Guest Editor:
Professor Huai Sun
School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
Research Interests: Force field methods and parameterizations; Applications of enhanced sampling techniques; Prediction of physical properties of soft matters and interfaces using molecular simulations

Special Issue Information

Dear Colleagues,
Although the fundamental challenge of pursuing simulation accuracy and efficiency is the same in both life sciences and materials sciences, molecular simulations in materials have special concerns because of significant diversity in the substances of interest and the broad range of thermodynamic conditions applied. Materials include many types of substances, such as fluids, polymers, liquid crystals, colloids, gels, grains, metals, alloys, semiconductors, silicates, oxides, clays, and minerals. The thermodynamic, transport, and mechanical properties of materials are strongly dependent on conditions such as material composition, temperature, and pressure. Due to these special concerns, the underlying interaction models are diverse, and new simulation methods are often required to get statistically meaningful results.

As a relatively new technology, molecular simulation is still undergoing rapid development. Over the recent decade, there have been significant advances in sampling techniques and interaction models, as well as numerous applications. This special issue focuses on the advances of molecular simulations in materials science. We invite experts from around the world to present their latest work on theory, method, interaction model, and applications in subjects related to materials. We hope that this special issue presents an overview of the current status of molecular simulations in materials science and stimulates further advances in this exciting frontier.

Professor Huai Sun
Guest Editor

Submission
Manuscripts should be submitted online at http://www.whxb.pku.edu.cn/journalx_wlhx_en/authorLogOn.action. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles, communications and perspectives are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office (whxb@pku.edu.cn) for announcement on this website. Manuscripts written in English or Chinese can be accepted.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere. All manuscripts are refereed through a peer-review process. We do not charge any fees from authors.

 Influence of Photoisomerization on Binding Energy and Conformation of Azobenzene-Containing Host-Guest Complex   Collect Pingying LIU,Chunyan LIU,Qian LIU,Jing MA Acta Phys. -Chim. Sin.   2018,34(10 ):1171 -1178. DOI:10.3866/PKU.WHXB201803024 Abstract  （434） HTML （6） PDF（pc） （1634KB）（117） The construction of a photo-controllable artificial molecular machine capable of realizing the light-driven motion on a molecular scale and of performing a specific function is a fascinating topic in supramolecular chemistry. The bistable switchable molecule, azobenzene (AZO), has been introduced into the supramolecular architecture as a key building block, owing to its efficient and reversible trans (E)-cis (Z) photoisomerization. The binding strength of the dibenzo[24]crown-8 (DB24C8) host and dialkylammonium-based rod-like guest consisting of an AZO moiety and the Z$\to$E photoisomerization process in an interlocked host-guest complex have been investigated by the density functional theory (DFT) calculations and the reactive molecular dynamics (RMD) simulations by considering both torsion and inversion paths. The strong host-guest binding strength provides a necessary premise to stabilize the complex during the E-Z photoisomerization of the AZO unit, which is a terminal stopper to control the directional motion of the guest. A stronger binding strength for the Z isomer can be induced by the stronger hydrogen-bonding interaction. The steric effect is introduced into the Z isomer to force the ring slipping exclusively over the cyclopentyl terminal (pseudostopper). The host-guest complexation has a slight effect on the conformation of the AZO functional subunit for the two isomers. The faster Z$\to$E photoisomerization process within the picosecond timescale is kinetically more favored than the dethreading of the ring through the pseudostopper subunit of the rod. After isomerization, a structure relaxation is observed for the crown ether ring within 500 ps. The flexible backbone of the crown ether ring is helpful in realizing steady and stable host-guest recognition during photoisomerization. Moreover, the orthogonality of the site-specific binding interaction is revealed by the similar binding energies obtained at similar hydrogen bonding recognition sites for various interlocked host-guest supramolecular systems although the constituents of the guests are different from each other. The introduction of two stereoisomers of the AZO subunit has little influence on the other conformations of guest subunits. These results are useful for the rational design of more sophisticated stimuli-controlled artificial molecular machines. Table and Figures丨 Reference丨 Related Articles丨 Metrics
 Microscopic Investigation of Ethylene Carbonate Interface: A Molecular Dynamics and Vibrational Spectroscopic Study   Collect Lin WANG,Liang XIN,Tatsuya ISHIYAMA,Qiling PENG,Shen YE,Akihiro MORITA Acta Phys. -Chim. Sin.   2018,34(10 ):1124 -1135. DOI:10.3866/PKU.WHXB201801291 Abstract  （397） HTML （7） PDF（pc） （1352KB）（166） Ethylene carbonate (EC) liquid and its vapor-liquid interface were investigated using a combination of molecular dynamics (MD) simulation and vibrational IR, Raman and sum frequency generation (SFG) spectroscopies. The MD simulation was performed with a flexible and polarizable model of the EC molecule newly developed for the computation of vibrational spectra. The internal vibration of the model was described on the basis of the harmonic couplings of vibrational modes, including the anharmonicity and Fermi resonance coupling of C＝O stretching. The polarizable model was represented by the charge response kernel (CRK), which is based on ab initio molecular orbital calculations and can be readily applied to other systems. The flexible and polarizable model can also accurately reproduce the structural and thermodynamic properties of EC liquid. Meanwhile, a comprehensive set of vibrational spectra of EC liquid, including the IR and Raman spectra of the bulk liquid as well as the SFG spectra of the liquid interface, were experimentally measured and reported. The set of experimental vibrational spectra provided valuable information for validating the model, and the MD simulation using the model comprehensively elucidates the observed vibrational IR, Raman, and SFG spectra of EC liquid. Further MD analysis of the interface region revealed that EC molecules tend to orientate themselves with the C＝O bond parallel to the interface. The MD simulation explains the positive Im[$\chi ^{(2)}$](ssp) band of the C＝O stretching region in the SFG spectrum in terms of the preferential orientation of EC molecules at the interface. This work also elucidates the distinct lineshapes of the C＝O stretching band in the IR, Raman, and SFG spectra. The lineshapes of the C＝O band are split by the Fermi resonance of the C＝O fundamental and the overtone of skeletal stretching. The Fermi resonance of C＝O stretching was fully analyzed using the empirical potential parameter shift analysis (EPSA) method. The apparently different lineshapes of the C＝O stretching band in the IR, Raman, and SFG spectra were attributed to the frequency shift of the C＝O fundamental in different solvation environments in the bulk liquid and at the interface. This work proposes a systematic procedure for investigating the interface structure and SFG spectra, including general modeling procedure based on ab initio calculations, validation of the model using available experimental data, and simultaneous analysis of molecular orientation and SFG spectra through MD trajectories. The proposed procedure provides microscopic information on the EC interface in this study, and can be further applied to investigate other interface systems, such as liquid-liquid and solid-liquid interfaces. Table and Figures丨 Reference丨 Related Articles丨 Metrics
 Free Energy Change of Micelle Formation for Sodium Dodecyl Sulfate from a Dispersed State in Solution to Complete Micelles along Its Aggregation Pathways Evaluated by Chemical Species Model Combined with Molecular Dynamics Calculations   Collect Noriyuki YOSHII,Mika KOMORI,Shinji KAWADA,Hiroaki TAKABAYASHI,Kazushi FUJIMOTO,Susumu OKAZAKI Acta Phys. -Chim. Sin.   2018,34(10 ):1163 -1170. DOI:10.3866/PKU.WHXB201802271 Abstract  （304） HTML （2） PDF（pc） （1773KB）（119） Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics (MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run (Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ΔGi+j†, where two aggregates with sizes i and j associate to form the (i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, Gi†, which was obtained through MD calculations. The calculated ΔGi+j† was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy $\sum\limits_i {{n_i}\left( {l, k} \right)G_i^\dagger }$ and the free energy of mixing $\sum\limits_i {{n_i}(l, k){k_B}Tln({n_i}(l, k)/n(l, k))}$, where ni(l, k) is the number of i-mer in the system at the l-th aggregation path and k-th state, with $n\left( {l, k} \right) = \sum\limits_i {{n_i}\left( {l, k} \right)}$. All the aggregation pathways were obtained from the initial state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggregates, but rather the kinetics that inhibit the association of the fragments. The time required for a collision between aggregates, one of the kinetic factors, was evaluated using the fast passage time, tFPT. The calculated tFPT was about 20 ns for the aggregates with N = 31. Therefore, if aggregation is a diffusion-controlled process, it should be completed within the 100 ns-simulation. However, aggregation does not occur due to the free energy barrier between the aggregates, that is, the repulsive force acting on them. This may be caused by electrostatic repulsions produced by the overlap of the electric double layers, which are formed by the negative charge of the hydrophilic groups and counter sodium ions on the surface of the aggregates. Table and Figures丨 Reference丨 Related Articles丨 Metrics
 Simple Ligand Modifications to Modulate the Activity of Ruthenium Catalysts for CO2 Hydrogenation: Trans Influence of Boryl Ligands and Nature of Ru―H Bond   Collect Tian LIU,Jun LI,Weijia LIU,Yudan ZHU,Xiaohua LU Acta Phys. -Chim. Sin.   2018,34(10 ):1097 -1105. DOI:10.3866/PKU.WHXB201712131 Abstract  （416） HTML （1） PDF（pc） （1633KB）（133） The development of efficient catalysts for the hydrogenation of CO2 to formic acid (FA) or formate has attracted significant interest as it can address the increasingly severe energy crisis and environmental problems. One of the most efficient methods to transform CO2 to FA is catalytic homogeneous hydrogenation using noble metal catalysts based on Ir, Ru, and Rh. In our previous work, we demonstrated that the activity of CO2 hydrogenation via direct addition of hydride to CO2 on Ir(Ⅲ) and Ru(Ⅱ) complexes was determined by the nature of the metal-hydride bond. These complexes could react with the highly stable CO2 molecule because they contain the same distinct metal-hydride bond formed from the mixing of the sd2 hybrid orbital of metal with the 1s orbital of H, and evidently, this property can be influenced by the trans ligand. Since boryl ligands exhibit a strong trans influence, we proposed that introducing such ligands may enhance the activity of the Ru―H bond by weakening it as a result of the trans influence. In this work, we designed two potential catalysts, namely, Ru-PNP-HBcat and Ru-PNP-HBpin, which were based on the Ru(PNP)(CO)H2 (PNP = 2, 6-bis(dialkylphosphinomethyl)pyridine) complex, and computationally investigated their reactivity toward CO2 hydrogenation. Bcat and Bpin (cat = catecholate, pin = pinacolate) are among the most popular boryl ligands in transition metal boryl complexes and have been widely applied in catalytic reactions. Our optimization results revealed that the complexes modified by boryl ligands possessed a longer Ru―H bond. Similarly, natural bond orbital (NBO) charge analysis indicated s\vl VEs\vl Vr of the hydride in Ru-PNP-HBcat and Ru-PNP-HBpin was higher as compared to that in Ru-PNP-H2. NBO analysis of the nature of Ru―H bond indicated that these complexes also followed the law of the bonding of Ru―H bond proved in the previous works (Bull. Chem. Soc. Jpn. 2011, 84 (10), 1039; Bull. Chem. Soc. Jpn. 2016, 89 (8), 905), and the d orbital contribution of the Ru atom in Ru-PNP-HBcat and Ru-PNP-HBpin was smaller than that in Ru-PNP-H2. Consequently, the Ru-PNP-HBcat and Ru-PNP-HBpin complexes were more active than Ru-PNP-H2 for the direct hydride addition to CO2 because of the lower activation energy barrier, i.e., from 29.3 kJ∙mol-1 down to 24.7 and 23.4 kJ∙mol-1, respectively. In order to further verify our proposed catalyst-design strategy for CO2 hydrogenation, the free energy barriers of the complete pathway for the hydrogenation of CO2 to formate catalyzed by complexes Ru-PNP-H2, Ru-PNP-HBcat, and Ru-PNP-HBpin were calculated to be 76.2, 67.8, and 54.4 kJ∙mol-1, respectively, indicating the highest activity of Ru-PNP-HBpin. Thus, the reactivity of Ru catalysts for CO2 hydrogenation could be tailored by the strong trans influence of the boryl ligands and the nature of the Ru―H bond. Table and Figures丨 Reference丨 Related Articles丨 Metrics