Multi-scale molecular simulation of random peptide phase separation and its extended-to-compact structure transition driven by hydrophobic interactions.

Intrinsically disordered proteins (IDPs) often undergo liquid-liquid phase separation (LLPS) and form membraneless organelles or protein condensates. One of the core problems is how do electrostatic repulsion and hydrophobic interactions in peptides regulate the phase separation process? To answer this question, this study uses random peptides composed of positively charged arginine (Arg, R) and hydrophobic isoleucine (Ile, I) as the model systems, and conduct large-scale simulations using all atom and coarse-grained model multi-scale simulation methods. In this article, we investigate the phase separation of different sequences using a coarse-grained model. It is found that the stronger the electrostatic repulsion in the system, the more extended the single-chain structure, and the more likely the system forms a low-density homogeneous phase. In contrast, the stronger the hydrophobic effect of the system, the more compact the single-chain structure, the easier phase separation, and the higher the critical temperature of phase separation. Overall, by taking the random polypeptides composed of two types of amino acid residues as model systems, this study discusses the relationship between the protein sequence and phase behaviour, and provides theoretical insights into the interactions within or between proteins. It is expected to provide essential physical information for the sequence design of functional IDPs, as well as data to support the diagnosis and treatment of the LLPS-associated diseases.

Systematic research on gallium atom-doped neutral small- and medium-sized gas-phase magnesium clusters: A DFT study of GaMgn (n=2-12) clusters.

Structure, stability, charge transfer, chemical bonding, and spectroscopic properties of Ga atom-doped neutral Mgn (n = 2-12) clusters have been systematically investigated by CALYPSO and density functional theory. All cluster structures are based on "tetrahedral" and "yurt-like" growth except for GaMg2. The ground state isomer of GaMg8 with high symmetry structure is predicted to be the best-fit candidate for the "magic" cluster because of its excellent stability. Natural bond orbital calculations reveal that Ga and Mg atoms play the role of electron acceptor and donor in all ground state isomers, while the orbitals in both Ga and Mg are sp-hybridized. Most importantly, chemical bonding studies based on atom-in-molecular theory have shown that the lowest-energy state of GaMg4 is so special, in that it has not only the critical size for the appearance of Mg-Mg covalent bonds, but also the only cluster that has both Ga-Mg covalent and non-covalent bonds. Finally, theoretical calculations of IR and Raman spectra of all ground state isomers indicate that the spectra of these clusters are observable in the low-frequency band, and thus they can be identified by spectroscopic experiments. Furthermore, the bond heterogeneity of the Ga-Mg in the GaMg4 ground state isomer has also been specifically investigated, including the fixed GaMg4 structure with Mg atoms added in different directions, as well as ab initio molecular dynamics sampling at different temperatures.

Searching new structures of beryllium-doped in small-sized magnesium clusters: Be2 Mgn Q (Q = 0, -1; n = 1-11) clusters DFT study.

Using CALYPSO method to search new structures of neutral and anionic beryllium-doped magnesium clusters followed by density functional theory (DFT) calculations, an extensive study of the structures, electronic and spectral properties of Be2 Mgn Q (Q = 0, -1; n = 2-11) clusters is performed. Based on the structural optimization, it is found that the Be2 Mgn Q (Q = 0, -1) clusters are shown by tetrahedral-based geometries at n = 2-6 and tower-like-based geometries at n = 7-11. The calculations of stability indicate that Be2 Mg5 Q=0 , Be2 Mg5 Q=-1 , and Be2 Mg8 Q=-1 clusters are "magic" clusters with high stability. The NCP shows that the charges are transferred from Mg atoms to Be atoms. The s- and p-orbitals interactions of Mg and Be atoms are main responsible for their NEC. In particular, chemical bond analysis including molecular orbitals (MOs) and chemical bonding composition for magic clusters to further study their stability. The results confirmed that the high stability of these clusters is due to the interactions between the Be atom and the Mg5 or Mg8 host. Finally, theoretical calculations of infrared and Raman spectra of the ground state of Be2 Mgn Q (Q = 0, -1; n = 1-11) clusters were performed, which will be absolutely useful for future experiments to identify these clusters.

Density functional theory-based study on the structural, electronic and spectral properties of gas-phase PbMg n - (n = 2-12) clusters.

Gas-phase PbMg n- (n = 2-12) cluster structures were globally searched on their potential energy surfaces by means of the CALYPSO prediction software. Structural optimization and calculations of properties such as relative energy and electronic structure were then carried out by density functional theory for each size of low energy isomer. The structural, relative stability, natural charge population, natural electronic configuration and distribution of the strongest peaks of the infrared and Raman spectra of the low energy isomers of PbMg n- (n = 2-12) clusters were systematically investigated in the present work. It was shown that the PbMg7- cluster ground state isomer exhibits the highest stability, for which special electronic excitation and chemical bonding analyses were performed. It is reasonable to believe that this work enriches the structural, spectroscopic and other data of magnesium-based clusters and provides some theoretical basis for possible future experimental syntheses.

Structural and spectral properties of Gas-phase FMgn (n = 2-20) clusters based on DFT.

Structure, stability, electronic structure, spectroscopy and chemical bonding properties of a fluorine atom doped gas-phase small to medium-sized magnesium clusters, FMgn (n = 2-20), systematically investigated by CALYPSO software together with density functional theory (DFT). Structural calculations showed that FMgn has a structural diversity which is rarely reported in other magnesium-based clusters before. F atoms were always located in the outer layer of the Mgn host clusters and only two or three Mg atoms surround it. FMg18 was revealed to be supposed to have robust relative stability. Charge transfer and density of states were calculated for analyzing the electronic structure characteristics. Theoretical calculations of IR, Raman and UV-Vis spectra were computed to provide data guidelines for future experimental observations. Finally, the F-Mg and Mg-Mg chemical bonds of the FMgn clusters were analyzed, including the critical bonding points (BCPs) of Laplacian of electron density (Δρ), electron localization function (ELF) and interaction region indicator (IRI). The kind and strength of chemical bonds reveal the mechanism by which the F atom was rapidly stabilized by Mgn (n = 2-20) host clusters.

DFT-Based Study of the Structure, Stability, and Spectral and Optical Properties of Gas-Phase NbMgn (n = 2-12) Clusters.

Gas-phase NbMgn (n = 2-12) clusters were fully searched by CALYPSO software, and then the low-energy isomers were further optimized and calculated under DFT. It is shown that the three lowest energy isomers of NbMgn (n = 3-12) at each size are grown from two seed structures, i.e., tetrahedral and pentahedral structures, and the transition size occurs at the NbMg8 cluster. Interestingly, the relative stability calculations of the NbMg8 cluster ground-state isomer stand out under the examination of several parameters' calculations. The charge-transfer properties of the clusters of the ground-state isomers of various sizes had been comprehensively investigated. In order to be able to provide data guidance for future experimental probing of these ground-state clusters, this work also predicted infrared and Raman spectra at the same level of theoretical calculations. The results show that the multipeak nature of the IR and Raman spectra predicts that it is difficult to distinguish them directly. Finally, the optical properties of these clusters were investigated by calculating the static linear, second-order nonlinear, and third-order nonlinear coefficients. Importantly and interestingly, the NbMg8 cluster was shown to have superior nonlinear optical characteristics to all other clusters; thus, it is a powerful candidate for a potentially ultrasensitive nonlinear optical response device for some special purpose.

Computational Exploration on the Structural and Optical Properties of Gold-Doped Alkaline-Earth Magnesium AuMgn (n = 2-12) Nanoclusters: DFT Study.

Using CALYPSO crystal search software, the structural growth mechanism, relative stability, charge transfer, chemical bonding and optical properties of AuMgn (n = 2-12) nanoclusters were extensively investigated based on DFT. The shape development uncovers two interesting properties of AuMgn nanoclusters contrasted with other doped Mg-based clusters, in particular, the planar design of AuMg3 and the highly symmetrical cage-like of AuMg9. The relative stability study shows that AuMg10 has the robust local stability, followed by AuMg9. In all nanoclusters, the charge is transferred from the Mg atoms to the Au atoms. Chemical bonding properties were confirmed by ELF analysis that Mg-Mg formed covalent bonds in nanoclusters larger than AuMg3. Static polarizability and hyperpolarizability calculations strongly suggest that AuMg9 nanocluster possesses interesting nonlinear optical properties. Boltzmann distribution weighted average IR and Raman spectroscopy studies at room temperature verify that these nanoclusters are identifiable by spectroscopic experiments. Finally, the average bond distance and average nearest neighbor distance were fully investigated.

Rapid 3D roll-up of gas-phase planar gold clusters and affinity and alienation for Mg and Ge: A theoretical study of MgGeAun (n=1-12) clusters.

A cluster is a special matter level above a single atom and between macroscopic and microscopic matter, and it is an important bridge to understanding the relationship between the structure and function of matter. Here, we perform a comprehensive theoretical study of 2D planar Aun (n = 1-12) clusters doped with both magnesium and germanium. Two interesting results are found, namely the rapid 3D "roll-up" structural growth of the GeMgAun (n = 1-12) cluster ground state isomers, and the relative "alienation" of the different sizes of the Aun (n = 1-12) cluster framework towards the Ge atom, and the relative "affinity" towards the Mg atom. This study will not only enrich the data on gold-based clusters but will also provide a simple and clear theoretical guide for the 3D structuring of planar clusters, i.e. the doping of different classes of "affinition" and "alienatation" atoms.

New potential stable structures of XMg n (X = Ge, C, Sn; n = 2-12) clusters: XMg8 with high stability.

Several potential stable structures of X-doped magnesium (X = Ge, C, Sn) clusters have been fully investigated by using CALYPSO structure searching software together with density functional theory calculations. XMg n (X = Ge, C, Sn; n = 3-7) clusters have similar geometric structure grows in tetrahedron, while the structures of XMg n (X = Ge, C, Sn; n = 8-12) are based on a kind of tower-like geometry. Interestingly, the relative stability computations indicate that XMg8 (X = Ge, C, Sn) are more stable than other clusters, and thus can be identified as magic clusters. In addition, XMg8's (X = Ge, C, Sn) high stability and atomic interactions contained in structures are studied through their electronic localization function and molecular orbitals. It is shown that the covalent σ bond interaction of X-Mg and Mg-Mg are mainly responsible for their robust stability. Finally, the theoretical calculations of IR and Raman spectra of XMg8 (X = Ge, C, Sn) clusters were implemented for guiding further experimental observation.

Systematic Theoretical Study on Structural, Stability, Electronic, and Spectral Properties of Si2 Mg n Q (Q = 0, ±1; n = 1-11) Clusters of Silicon-Magnesium Sensor Material.

By using CALYPSO searching method and Density Functional Theory (DFT) method at the B3LYP/6-311G (d) level of cluster method, a systematic study of the structures, stabilities, electronic and spectral properties of Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon-magnesium sensor material, is performed. According to the calculations, it was found that when n > 4, most stable isomers in Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon-magnesium sensor material are three-dimensional structures. Interestingly, although large size Si2 Mg n Q clusters show cage-like structures, silicon atoms are not in the center of the cage, but tend to the edge. The Si2 Mg 1 , 5 , 6 , 8 - 1 and Si2 Mg 13 , 4 , 7 , 9 , 10 + 1 clusters obviously differ to their corresponding neutral structures, which are in good agreement with the calculated values of VIP, AIP, VEA, and AEA. |VIP-VEA| values reveal that the hardness of Si2Mgn clusters decreases with the increase of magnesium atoms. The relative stabilities of neutral and charged Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon-magnesium sensor material is analyzed by calculating the average binding energy, fragmentation energy, second-order energy difference and HOMO-LUMO gaps. The results reveal that the Si2 Mg 3 0 , Si2 Mg 3 - 1 , and Si2 Mg 3 + 1 clusters have stronger stabilities than others. NCP and NEC analysis results show that the charges in Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon-magnesium sensor material transfer from Mg atoms to Si atoms except for Si2 Mg 1 + 1 , and strong sp hybridizations are presented in Si atoms of Si2 Mg n Q clusters. Finally, the infrared (IR) and Raman spectra of all ground state of Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon magnesium sensor material are also discussed.