On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

Layer-Dependent Quantum Anomalous Hall and Quantum Spin Hall Effects in Two-Dimensional LiFeTe

The emergence of an intrinsic quantum anomalous Hall (QAH) insulator with long-range magnetic order triggers unprecedented prosperity for combining topology and magnetism in low dimensions. Here, based on stacked two-dimensional LiFeTe, we confirm that magnetic coupling and topological electronic states can be simultaneously manipulated by just changing the layer numbers. Monolayer LiFeTe shows intralayer ferrimagnetic coupling, behaving as a QAH insulator with Chern number C = 2. Beyond the monolayer, the odd and even layers of LiFeTe correspond to uncompensated and compensated interlayer antiferromagnets, resulting in unexpected QAH and quantum spin Hall (QSH) states, respectively. Moreover, the spin Chern number is proportional to the stacking layer numbers in even-layer LiFeTe, proving that the spin Hall conductivity can be continuously enhanced by increasing layer numbers. Therefore, the odd-even-layer-dependent QAH and QSH effects found in LiFeTe topological insulators offer new insight into regulating quantum states in two-dimensional topological materials.

Large valley polarization and the valley-dependent Hall effect in a Janus TiTeBr monolayer

Ferrovalley materials hold great promise for implementation of logic and memory devices in valleytronics. However, there have so far been limited ferrovalley materials exhibiting significant valley polarization and high Curie temperature (TC). Using first-principles calculations, we predict that the TiTeBr monolayer is a promising ferrovalley candidate. It exhibits intrinsic ferromagnetism with TC as high as 220 K. It is indicated that an out-of-plane alignment of magnetization demonstrates a valley polarization up to 113 meV in the topmost valence band, as further verified by perturbation theory considering both the spin polarization and spin-orbit coupling. Under an in-plane electric field, the valley-dependent Berry curvature results in the anomalous valley Hall effect (AVHE). Moreover, under a suitable in-plane biaxial strain, the TiTeBr monolayer transforms into a Chern insulator with a nonzero Chern number, yet retains its ferrovalley characters and thus the emergent quantum anomalous valley Hall effect (QAVHE). Our study indicates that the TiTeBr monolayer is a promising ferrovalley material, and it provides a platform for investigating the valley-dependent Hall effect.

Genuine Dirac Half-Metals in Two-Dimensions

When spin-orbit coupling (SOC) is absent, all proposed half-metals with twofold degenerate nodal points at the K (or K') point in 2D materials are classified as "Dirac half-metals" owing to the way graphene is utilized in the earliest studies. Actually, each band crossing point at the K or K' point is described by a 2D Weyl Hamiltonian with definite chirality; hence, it should be a Weyl point. To the best of its knowledge, there have not yet been any reports of a genuine (i.e., fourfold degenerate) 2D Dirac point half-metal. In this work, using first-principles calculations, it proposes for the first time that the 2D d0 -type ferromagnet Mg4 N4 is a genuine 2D Dirac half-metal candidate with a fourfold degenerate Dirac point at the S high-symmetry point, intrinsic magnetism, a high Curie temperature, 100% spin polarization, topology robust under the SOC and uniaxial and biaxial strains, and spin-polarized edge states. This work can serve as a starting point for future predictions of intrinsically magnetic materials with genuine 2D Dirac points, which will aid the frontier of topo-spintronics research in 2D systems.

Prediction of a two-dimensional high Curie temperature Weyl nodal line kagome semimetal

Kagome lattices may have numerous exotic physical properties, such as stable ferromagnetism and topological states. Herein, combining the particle swarm structure search method with first-principles calculations, we identify a two-dimensional (2D) kagome Mo2Se3 crystal structure with space group P6/mmm. The results show that 2D kagome Mo2Se3 is a 100% spin-polarized topological nodal line semimetal and exhibits excellent ambient stability. The band crossing points form two nodal loops around the high-symmetry points Γ and K. On the other hand, Mo2Se3 shows intrinsic ferromagnetism with a large magnetic moment of 3.05 μB per Mo atom and magnetic anisotropy energy (MAE) of 4.78 meV. Monte Carlo simulations estimate that Mo2Se3 possesses a high Curie temperature of about 673 K. In addition, its ferromagnetic ground state can be well preserved under external strain, and the MAE can be improved by increasing the strain. More importantly, the position of each nodal line can be adjusted to the Fermi level through hole doping. This multifunctional 2D magnetic material that combines spin and topology has great potential in the field of nanoscale spintronic devices.

2D antiferromagnetic semiconducting FeCN with interesting properties

Two-dimensional magnetic materials have demonstrated favorable properties (e.g., large spin polarization and net magnetization) for the development of next-generation spintronic devices. The discovery of such materials and insight into their magnetic coupling mechanism has become a research focus. Here, on the basis of first-principles structural search calculations, we have identified a fresh FeCN monolayer consisting of edge-sharing Fe triangle sublattices and FeC3N2 rings, which integrates antiferromagnetism, semiconductivity, and planarity. Interestingly, it possesses a large magnetic anisotropy energy (MAE) of 614 μeV per Fe atom, a narrow band gap (Eg) of 0.47 eV, a large magnetic moment of 3.15 μB, and a proper Néel temperature (TN) of 97 K. The direct exchange between the nearest-neighbor Fe atoms in the triangle sublattice is mainly responsible for the AFM ordering. Its high structural stability, stemming from the collective contribution of covalent C-C and C-N bonds, ionic Fe-N bonds, and metallic Fe-Fe bonds, provides a strong feasibility for experimental synthesis.

Strong spin-orbital coupling induced tunable electronic structures and enhanced visible-light absorption in one-dimensional RhTe6I3 systems

Considering the demand for device miniaturization, low-dimensional materials have been widely employed in various fields due to their unique and fascinating physical and chemical properties. Here, based on first-principles calculations, we predict a novel one-dimensional (1D) RhTe6I3 chain system. Our calculations indicate that a 1D RhTe6I3 single chain can be prepared from its bulk counterpart by an exfoliation method and exists stably at room temperature. The 1D RhTe6I3 single chain is a direct semiconductor with a moderate bandgap of 1.75 eV under a strong spin-orbital coupling (SOC) effect dominated by Te. This bandgap can be modulated by the chain number and the application of external strain. Notably, the 1D RhTe6I3 single chain has a high electron mobility (1093 cm2 V-1 s-1), which is one to two orders of magnitude higher than those of most previously reported 1D materials. The strong SOC effect can also enhance the visible-light absorption capacity of the 1D RhTe6I3 single chain. The moderate direct bandgap, high electron mobility, excellent visible-light absorption, and strong spin-orbital coupling make 1D RhTe6I3 systems ideal candidates in electronic and optoelectronic devices.

Piezoelectricity and valley polarization in a semilithiated 2H-TiTe2 monolayer with near room-temperature ferromagnetism

Two-dimensional ferromagnetic semiconductors with coupled valley physics and piezoelectric responses offer unprecedented opportunities to miniaturize low-power multifunctional integrated devices. Prompted by epitaxial fabrication of nonmagnetic 2H-TiTe2 monolayer on the Au(111) substrate, we predict through both density functional theory and Monte Carlo simulations that the semilithiated 2H-TiTe2 monolayer (Li@2H-TiTe2) is a stable near room-temperature semiconducting ferromagnet. Under an out-of-plane magnetization, Li@2H-TiTe2 exhibits a clean valley polarization up to 160 meV in its conduction band and a valley-contrasting Berry curvature due to the broken inversion and time-reversal symmetries, in favor of achievable anomalous valley Hall effect. Alternatively, the simultaneous charge, spin, valley Hall currents can be realized as well in the ferromagnetic system with circularly polarized light. Furthermore, the missing mirror symmetry generates a scarce vertical piezoelectricity as large as 0.89 pm V-1. These findings indicate that asymmetric surface functionalization by Li deposition on the 2H-TiTe2 monolayer opens up a vital avenue to predesign superior and tailored multifunctional materials.

Three-Dimensional Carbon Foam Modified with Mg3N2 for Ultralong Cyclability of a Dendrite-Free Li Metal Anode

Uncontrolled growth of lithium dendrites and huge volume change during the lithium plating/stripping process as well as poor mechanical properties of the solid electrolyte interphase (SEI) are key obstacles to the development of a stable Li metal anode. Here, an ultralight Mg3N2-modified carbon foam (CF-Mg3N2) was fabricated as a collector to address these issues. The calculated results show that the CF-Mg3N2 composite is relatively stable in terms of energy. Based on the synergistic effect of the three-dimensional skeleton and the lithiophilic nature of Mg3N2, homogeneous lithium deposition/stripping was realized around the foam carbon skeleton with an extremely low nucleation overpotential (∼9.3 mV) and high retention of Coulombic efficiency (99.3%) as well as long cyclability (700 cycles and 3000 h in half and symmetrical cells, respectively). Meanwhile, Mg3N2-CF@Li//LiFePO4 full cells also showed better rate capability and more stable cycling capability than CF@Li//LiFePO4 and Li//LiFePO4 cells, exhibiting extreme practicality. Accordingly, the design concept mentioned in this work provides a far-reaching influence on the development of a stable Li metal anode.

DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space

We present Deep learning for Collective Variables (DeepCV), a computer code that provides an efficient and customizable implementation of the deep autoencoder neural network (DAENN) algorithm that has been developed in our group for computing collective variables (CVs) and can be used with enhanced sampling methods to reconstruct free energy surfaces of chemical reactions. DeepCV can be used to conveniently calculate molecular features, train models, generate CVs, validate rare events from sampling, and analyze a trajectory for chemical reactions of interest. We use DeepCV in an example study of the conformational transition of cyclohexene, where metadynamics simulations are performed using DAENN-generated CVs. The results show that the adopted CVs give free energies in line with those obtained by previously developed CVs and experimental results. DeepCV is open-source software written in Python/C++ object-oriented languages, based on the TensorFlow framework and distributed free of charge for noncommercial purposes, which can be incorporated into general molecular dynamics software. DeepCV also comes with several additional tools, i.e., an application program interface (API), documentation, and tutorials.

Intrinsic spin, valley and piezoelectric polarizations in room-temperature ferrovalley Janus TiXY (XY = SCl and SeBr) monolayers

Two-dimensional room-temperature Janus ferrovalley semiconductors with large spin, valley and piezoelectric polarizations provide fertile platforms for designing multifunctional nanodevices. Little research has been reported to date on such materials. Here, using first-principles calculations, we predict two dynamically stable Janus titanium chalcohalide (TiSCl and TiSeBr) monolayers, which are excellent piezoelectric ferrovalley semiconductors with in-plane magnetization and high magnetic transition temperatures (738 and 884 K). When an extrinsic magnetic field is used to force the magnetization along the out-of-plane direction, a large valley polarization (64 and 146 meV) can be generated in the highest valence band with a large spin-orbit coupling by the breaking of time-reversal and space-inversion symmetry, which can be further clarified by a two-band k·p model. This robust valley-contrasting physics characterized by the valley-dependent Berry curvature leads to the anomalous valley Hall effect. It can be observed by suitable hole doping or light irradiation under an in-plane electric field. Besides, we find that the missing mirror symmetry results in giant out-of-plane piezoelectric polarization (2.05 and 2.04 pm V^-1). These outstanding properties give the Janus TiSCl and TiSeBr monolayers potential for a wide variety of applications in nanoelectronics, spintronics, valleytronics, piezoelectrics and other demanding areas.

Computer-Aided Drug Design Boosts RAS Inhibitor Discovery

The Rat Sarcoma (RAS) family (NRAS, HRAS, and KRAS) is endowed with GTPase activity to regulate various signaling pathways in ubiquitous animal cells. As proto-oncogenes, RAS mutations can maintain activation, leading to the growth and proliferation of abnormal cells and the development of a variety of human cancers. For the fight against tumors, the discovery of RAS-targeted drugs is of high significance. On the one hand, the structural properties of the RAS protein make it difficult to find inhibitors specifically targeted to it. On the other hand, targeting other molecules in the RAS signaling pathway often leads to severe tissue toxicities due to the lack of disease specificity. However, computer-aided drug design (CADD) can help solve the above problems. As an interdisciplinary approach that combines computational biology with medicinal chemistry, CADD has brought a variety of advances and numerous benefits to drug design, such as the rapid identification of new targets and discovery of new drugs. Based on an overview of RAS features and the history of inhibitor discovery, this review provides insight into the application of mainstream CADD methods to RAS drug design.

Exploring CCRL2 chemerin binding using accelerated molecular dynamics

Chemokine (C–C motif) receptor‐like 2 (CCRL2), is a seven transmembrane receptor closely related to the chemokine receptors CCR1, CCR2, CCR3, and CCR5. Nevertheless, CCRL2 is unable to activate conventional G‐protein dependent signaling and to induce cell directional migration. The only commonly accepted CCRL2 ligand is the nonchemokine chemotactic protein chemerin (RARRES2). The chemerin binding to CCLR2 does induce leukocyte chemotaxis, yet, genetic targeting of CCRL2 was shown to modulate the inflammatory response in different experimental models. This mechanism was shown to be crucial for lung dendritic cell migration, neutrophil recruitment, and Natural Killer cell‐dependent immune surveillance in lung cancer. To gain more insight in the interactions involved in the CCRL2‐chemerin, the binding complexes were generated by protein–protein docking, then submitted to accelerated molecular dynamics. The obtained trajectories were inspected by principal component analyses followed by kernel density estimation to identify the ligand‐receptor regions most frequently involved in the binding. To conclude, the reported analyses led to the identification of the putative hot‐spot residues involved in CCRL2‐chemerin binding.

High electron mobility and wide-bandgap properties in a novel 1D PdGeS3 nanochain

As a versatile platform, one-dimensional (1D) electronic systems host plenty of excellent merits, such as high length-to-diameter ratios, flexible mechanical properties, and manageable electronic characteristics, which endow them with significant potential applications in catalysts, flexible wearable devices, and multifunctional integrated circuits. Herein, based on first-principles calculations, we propose a versatile 1D PdGeS₃ nanochain system. Our calculations show that the 1D PdGeS₃ nanochain can be synthesized simply from its bulk crystal by exfoliation methods and can stably exist at room temperature. The 1D PdGeS₃ nanochain is an indirect semiconductor with a wide bandgap of 2.86 eV, and such a bandgap can be effectively modulated by strain. Remarkably, the electron mobility of the 1D PdGeS₃ nanochain reaches as high as 1506 cm² V^-1 s^-1, which is one to two orders of magnitude larger than those of most reported 1D materials and even some 2D materials. Such high electron mobility accompanied with low hole mobility endow the 1D PdGeS₃ nanochain with the capacity of the separation of carriers. Our work shows that the 1D PdGeS₃ nanochain is a promising candidate for applications in novel multifunctional nanoelectronic devices.

Designing Multifunctional Donor-Acceptor-Type Molecules to Passivate Surface Defects Efficiently and Enhance Charge Transfer of CsPbI2Br Perovskite for High Power Conversion Efficiency

High-density and multitype surface defects of CsPbI₂Br perovskite induce charge recombination and accumulation, hindering its device efficiency and stability. However, the surface defect types of CsPbI₂Br perovskite are still unclear, and conventional organic molecules only passivate one specific defect and cannot achieve good overall passivation. Here, density functional theory is used to explore surface defect types and properties of CsPbI₂Br with calculating the defect formation energy and electronic structure. Results show that the dominant deep-level defects are cationic defects (Pb_Br) under Br-poor conditions and anionic defects (I_i and Br_i) under moderate and Br-rich conditions, originating from Pb-Pb bonding and I-I bonding. Multifunctional organic molecules containing donor and acceptor groups are used to passivate both cationic and anionic defects simultaneously. It turns out that the deep-level defects are effectively decreased by forming strong interaction of N-Pb, O-Pb, and halide-Pb bonds. Moreover, the electron and hole transfers from perovskite to molecules increase dramatically to -9.06 × 10¹² and 2.60 × 10¹² e/cm² and maybe improve the efficiency of power conversion. Our findings not only reveal the surface defect properties of CsPbI₂Br, but also offer an approach for designing new multifunctional passivators for perovskite solar cells with high conversion efficiency.

Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants

The severe acute respiratory syndrome (SARS) coronavirus 2 (CoV-2) variant Omicron spread more rapid than the other variants of SARS-CoV-2 virus. Mutations on the Spike (S) protein receptor-binding domain (RBD) are critical for the antibody resistance and infectivity of the SARS-CoV-2 variants. In this study, we have used accelerated molecular dynamics (aMD) simulations and free energy calculations to present a systematic analysis of the affinity and conformational dynamics along with the interactions that drive the binding between Spike protein RBD and human angiotensin-converting enzyme 2 (ACE2) receptor. We evaluate the impacts of the key mutation that occur in the RBDs Omicron and other variants in the binding with the human ACE2 receptor. The results show that S protein Omicron has stronger binding to the ACE2 than other variants. The evaluation of the decomposition energy per residue shows the mutations N440K, T478K, Q493R and Q498R observed in Spike protein of SARS-CoV-2 provided a stabilization effect for the interaction between the SARS-CoV-2 RBD and ACE2. Overall, the results demonstrate that faster spreading of SARS-CoV-2 Omicron may be correlated with binding affinity of S protein RBD to ACE2 and mutations of uncharged residues to positively charged residues such as Lys and Arg in key positions in the RBD.

Ultrahigh mechanical flexibility induced superior piezoelectricity of InSeBr-type 2D Janus materials

InSeBr-Type monolayers, ternary In(Se,S)(Br,Cl) compounds, are typical two-dimensional (2D) Janus materials and can be exfoliated from their bulk crystals. The structural stability, electronic properties, mechanical flexibility, and intrinsic piezoelectricity of these InSeBr-type 2D Janus monolayers are comprehensively investigated by first-principles calculations. Our calculations show that the stable InSeBr-type monolayers exhibit ultrahigh mechanical flexibility with low Young's moduli. Due to the amazing flexibility of the InSeBr monolayer with an ultra-low Young's modulus of 0.81 N m^-1, the piezoelectric strain coefficient d₁₁ can reach 10³ pm V^-1 orders of magnitude (around 2361-3224 pm V^-1), which is larger than those of reported 2D materials and even superior to those of conventional perovskite bulk materials. Such a superior piezoelectric response of InSeBr-type monolayers could facilitate their practical applications in sensors and energy harvesters.

A biphenylene nanoribbon-based 3D metallic and ductile carbon allotrope

Assembling two-dimensional (2D) sheets for three-dimensional (3D) functional materials is of current interest. Motivated by the recent experimental synthesis of 2D biphenylene [Science372 (2021) 852], we propose a new porous 3D metallic carbon structure, named T48-carbon, by using biphenylene nanoribbons as the building block. Based on state-of-the-art theoretical calculations, we find that T48-carbon is not only dynamically, thermally, and mechanically stable, but also energetically more favorable as compared with some other theoretically predicted carbon allotropes. Especially, T48-carbon exhibits mechanical anisotropy, ductility and intrinsic metallicity. A detailed analysis of electronic properties reveals that the metallicity mainly comes from the p_z-orbital of sp²-hybridized carbon atoms. This work shows the promise of design and synthesis of 3D biphenylene-based metallic carbon materials with novel properties.

Monolayer gadolinium halides, GdX2 (X = F, Cl, Br): intrinsic ferrovalley materials with spontaneous spin and valley polarizations

Two-dimensional (2D) intrinsic ferrovalley semiconductors provide unprecedented opportunities to investigate valley physics as well as providing promising device applications due to their exceptional combination of spontaneous spin and valley polarizations. Here, we have predicted from first-principles calculations and Monte Carlo simulations that monolayers (MLs) GdX₂ are such extremely rare excellent materials. Apart from their robust stabilities energetically, dynamically, thermally, and mechanically, these 2D materials are found to be semiconducting intrinsic ferromagnets where the magnetic coupling is ascribed to 5d-electron-mediated 4f-4f exchange interactions. Moreover, MLs GdX₂ (X = F, Cl, Br) not only exhibit significant magnetic anisotropy energy of 351, 268, and 30 μeV per Gd, but also have a high Curie temperature of 300, 245, and 225 K, respectively. In particular, spontaneous valley polarization in three systems occurs due to the cooperative interplay between the spin-orbit coupling and magnetic exchange interactions, whose magnitude is as sizable as 55, 38, and 82 meV for MLs GdF₂, GdCl₂, and GdBr₂, respectively. Under the action of an in-plane longitudinal electrical field, the valley-contrasting Berry curvatures arising from the broken space-inversion and time-reversal symmetries in MLs GdX₂ could yield opposite transverse velocities of the carriers, giving rise to the occurrence of a spin-polarized anomalous valley Hall effect. Overall, these findings render 2D GdX₂ a class of promising candidate materials for experimental studies and practical spintronics and valleytronics applications.

Targeting a cryptic allosteric site of SIRT6 with small-molecule inhibitors that inhibit the migration of pancreatic cancer cells

SIRT6 belongs to the conserved NAD⁺-dependent deacetylase superfamily and mediates multiple biological and pathological processes. Targeting SIRT6 by allosteric modulators represents a novel direction for therapeutics, which can overcome the selectivity problem caused by the structural similarity of orthosteric sites among deacetylases. Here, developing a reversed allosteric strategy AlloReverse, we identified a cryptic allosteric site, Pocket Z, which was only induced by the bi-directional allosteric signal triggered upon orthosteric binding of NAD⁺. Based on Pocket Z, we discovered an SIRT6 allosteric inhibitor named JYQ-42. JYQ-42 selectively targets SIRT6 among other histone deacetylases and effectively inhibits SIRT6 deacetylation, with an IC₅₀ of 2.33 μmol/L. JYQ-42 significantly suppresses SIRT6-mediated cancer cell migration and pro-inflammatory cytokine production. JYQ-42, to our knowledge, is the most potent and selective allosteric SIRT6 inhibitor. This study provides a novel strategy for allosteric drug design and will help in the challenging development of therapeutic agents that can selectively bind SIRT6.

Closer Look at Inverse Electron Demand Diels–Alder and Nucleophilic Addition Reactions on s-Tetrazines Using Enhanced Sampling Methods

Inverse electron demand [4+2] Diels–Alder (iEDDA) reactions as well as unprecedented nucleophilic (azaphilic) additions of R-substituted silyl-enol ethers (where R is Phenyl, Methyl, and Hydrogen) to 1,2,4,5-tetrazine (s-tetrazine) catalyzed by \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {BF}_{3}$$\end{document}BF3 have recently been discovered (Simon et al. in Org Lett 23(7):2426–2430, 2021), where static calculations were employed for calculation of activation energies. In order to have a more realistic dynamic description of these reactions in explicit solution at ambient conditions, in this work we use a semiempirical tight-binding method combined with enhanced sampling techniques to calculate free energy surfaces (FESs) of the iEDDA and azaphilic addition reactions. Relevant products of not only s-tetrazine but also its derivatives such as \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {BF}_{3}$$\end{document}BF3-mediated s-tetrazine adducts are investigated. We reconstruct the FESs of the iEDDA and azaphilic addition reactions using metadynamics and blue moon ensemble, and compare the ability of different collective variables (CVs) including bond distances, Social PeRmutation INvarianT (SPRINT) coordinates, and path-CV to describe the reaction pathway. We find that when a bulky Phenyl is used as a substituent at the dienophile the azaphilic addition is preferred over the iEDDA reaction. In addition, we also investigate the effect of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {BF}_{3}$$\end{document}BF3 in the diene and steric hindrance in the dienophile on the competition between the iEDDA and azaphilic addition reactions, providing chemical insight for reaction design.

Computational prediction of a novel 1D InSeI nanochain with high stability and promising wide-bandgap properties

Low-dimensional materials have aroused widespread interest for their novel and fascinating properties. Based on first-principles calculations, we predict the one-dimensional (1D) InSeI nanochains with van der Waals (vdW) interchain interactions, which could be exfoliated mechanically and kept at steady states at room temperature. Compared with bulk InSeI, the single nanochain InSeI has a larger direct bandgap of 3.15 eV. Its calculated carrier mobility is as high as 54.17 and 27.49 cm2 V-1 s-1 for holes and electrons, respectively, comparable with those of other 1D materials. In addition, a direct-to-indirect bandgap transition is implemented under a small applied strain (∼6%). More importantly, the nanochains are found to be promising candidates for optoelectronic devices since they possess a high absorption coefficient of ∼105 cm-1 in the ultraviolet region. The results thus pave a novel avenue for the applications of InSeI nanochains with excellent thermal stability in nanoelectronic and optoelectronic devices.

Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy

Allostery, which is one of the most direct and efficient methods to fine-tune protein functions, has gained increasing recognition in drug discovery. However, there are several challenges associated with the identification of allosteric sites, which is the fundamental cornerstone of drug design. Previous studies on allosteric site predictions have focused on communication signals propagating from the allosteric sites to the orthosteric sites. However, recent biochemical studies have revealed that allosteric coupling is bidirectional and that orthosteric perturbations can modulate allosteric sites through reversed allosteric communication. Here, we proposed a new framework for the prediction of allosteric sites based on reversed allosteric communication using a combination of computational and experimental strategies (molecular dynamics simulations, Markov state models, and site-directed mutagenesis). The desirable performance of our approach was demonstrated by predicting the known allosteric site of the small molecule MDL-801 in nicotinamide dinucleotide (NAD⁺)-dependent protein lysine deacetylase sirtuin 6 (Sirt6). A potential novel cryptic allosteric site located around the L116, R119, and S120 residues within the dynamic ensemble of Sirt6 was identified. The allosteric effect of the predicted site was further quantified and validated using both computational and experimental approaches. This study proposed a state-of-the-art computational pipeline for detecting allosteric sites based on reversed allosteric communication. This method enabled the identification of a previously uncharacterized potential cryptic allosteric site on Sirt6, which provides a starting point for allosteric drug design that can aid the identification of candidate pockets in other therapeutic targets.

Using reversed allosteric communication, we performed MD simulations, MSMs, and mutagenesis experiments, to discover allosteric sites. It reproduced the known allosteric site for MDL-801 on Sirt6 and uncovered a novel cryptic allosteric Pocket X.

Zinc-mediated conformational preselection mechanism in the allosteric control of DNA binding to the zinc transcriptional regulator (ZitR)

The zinc transcriptional regulator (ZitR) functions as a metalloregulator that fine tunes transcriptional regulation through zinc-dependent DNA binding. However, the molecular mechanism of zinc-driven allosteric control of the DNA binding to ZitR remains elusive. Here, we performed enhanced sampling accelerated molecular dynamics simulations to figure out the mechanism, revealing the role of protein dynamics in the zinc-induced allosteric control of DNA binding to ZitR. The results suggest that zinc-free ZitR samples distinct conformational states, only a handful of which are compatible with DNA binding. Remarkably, zinc binding reduces the conformational plasticity of the DNA-binding domain of ZitR, promoting the population shift in the ZitR conformational ensemble towards the DNA binding-competent conformation. Further co-binding of DNA to the zinc–ZitR complex stabilizes this competent conformation. These findings suggest that ZitR–DNA interactions are allosterically regulated in a zinc-mediated conformational preselection manner, highlighting the importance of conformational dynamics in the regulation of transcription factor family.

Penta-BCN: A New Ternary Pentagonal Monolayer with Intrinsic Piezoelectricity

Going beyond conventional hexagonal sheets, pentagonal 2D structures are of current interest due to their novel properties and broad applications. Herein, for the first time, we study a ternary pentagonal BCN monolayer, penta-BCN, which exhibits intrinsic piezoelectric properties. Based on state-of-the-art theoretical calculations, we find that penta-BCN is stable mechanically, thermally, and dynamically and has a direct band gap of 2.81 eV. Due to its unique atomic configuration with noncentrosymmetric and semiconducting features, penta-BCN displays high spontaneous polarization of 3.17 × 10^-10 C/m and a prominent piezoelectricity with d₂₁ = 0.878 pm/V, d₂₂ = -0.678 pm/V, and d₁₆ = 1.72 pm/V, which are larger than those of an h-BN sheet and functionalized pentagraphene. Since B, C, and N are rich in resources, light in mass, and benign to the environment, the intrinsic polarization and piezoelectricity make the penta-BCN monolayer promising for technological applications. This study expands the family of 2D pentagonal structures with new features.

p-Type conductivity mechanism and defect structure of nitrogen-doped LiNbO3 from first-principles calculations

The charge-state transition level and geometry structure of non-metallic N-doped LiNbO₃ are calculated by DFT, which reveal the p-type conductivity mechanism of LiNbO₃:N.

Insight into the mechanism of allosteric activation of PI3Kα by oncoprotein K-Ras4B

Ras is a key member in the superfamily of small GTPase. Transforming between GTP-bound active state and GDP-bound inactive state in response to exogenous signals, Ras serves as a binary switch in various signaling pathways. One of its downstream effectors is phosphatidylinositol-4,5-bisphosphate 3-kinase α (PI3Kα), which phosphorylates phosphatidylinositol 4,5-bisphosphate into phosphatidylinositol 3,4,5-trisphosphate in the PI3K/Akt/mTOR pathway and mediates an array of important cellular activities including cell growth, migration and survival. Hyperactivation of PI3Kα induced by the Ras isoform K-Ras4B has been unveiled as a key event during the oncogenesis of pancreatic ductal adenocarcinoma, but the underlying mechanism of how K-Ras4B allosterically activates PI3Kα still remains largely unsolved. Here, we employed accelerated molecular dynamic simulations and allosteric pathway analysis to explore into the activation process of PI3Kα by K-Ras4B and unraveled the underlying structural mechanisms. We found that K-Ras4B binding induced more conformational dynamics within PI3Kα and triggered its step-wise transition from a self-inhibited state towards an activated state. Moreover, K-Ras4B binding markedly disrupted the interactions along the p110/p85 interface, especially the ones between nSH2 in p85 and its nearby functional domains in p110 like C2, helical, and kinase domains. The altered inter-domain interactions exposed the kinase domain, which promoted the membrane association and substrate phosphorylation of PI3Kα, thereby facilitating its activation. In particular, the community networks and allosteric pathways analysis further revealed that in PI3Kα/K-Ras4B system, allosteric signaling regulating p110/p85 interaction was rewired from the helical domain to the kinase domain and several important residues and their related allosteric pathways mediating PI3Kα autoinhibition were bypassed. The obtained structural mechanisms provide an in-depth mechanistic insight into the allosteric activation of PI3Kα by K-Ras4B as well as shed light on its drug discovery.

Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water

In this study, we examined the folding processes of eight helical proteins (2I9M, TC5B, 1WN8, 1V4Z, 1HO2, 1HLL, 2KFE, and 1YYB) at room temperature using the explicit solvent model under the AMBER14SB force field with the accelerated molecular dynamics (AMD) and traditional molecular dynamics (MD), respectively. We analyzed and compared the simulation results obtained by these two methods based on several aspects, such as root mean square deviation (RMSD), native contacts, cluster analysis, folding snapshots, free energy landscape, and the evolution of the radius of gyration, which showed that these eight proteins were successfully and consistently folded into the corresponding native structures by AMD simulations carried out at room temperature. In addition, the folding occurred in the range of 40~180 ns after starting from the linear structures of the eight proteins at 300 K. By contrast, these stable folding structures were not found when the traditional molecular dynamics (MD) simulation was used. At the same time, the influence of high temperatures (350, 400, and 450 K) is also further investigated. Study found that the simulation efficiency of AMD is higher than that of MD simulations, regardless of the temperature. Of these temperatures, 300 K is the most suitable temperature for protein folding for all systems. To further investigate the efficiency of AMD, another trajectory was simulated for eight proteins with the same linear structure but different random seeds at 300 K. Both AMD trajectories reached the correct folded structures. Our result clearly shows that AMD simulation are a highly efficient and reliable method for the study of protein folding.

Combining the biased and unbiased sampling strategy into one convenient free energy calculation method

Constructing a free energy landscape for a large molecule is difficult. One has to use either a high temperature or a strong driving force to enhance the sampling on the free energy barriers. In this work, we propose a mixed method that combines these two kinds of acceleration strategies into one simulation. First, it applies an adaptive biasing potential to some replicas of the molecule. These replicas are particularly accelerated in a collective variable space. Second, it places some unbiased and exchangeable replicas at various temperature levels. These replicas generate unbiased sampling data in the canonical ensemble. To improve the sampling efficiency, biased replicas transfer their state variables to the unbiased replicas after equilibrium by Monte Carlo trial moves. In comparison to previous integrated methods, it is more convenient for users. It does not need an initial reference biasing potential to guide the sampling of the molecule. And it is also unnecessary to insert many replicas for the requirement of passing the free energy barriers. The free energy calculation is accomplished in a single stage. It samples the data as fast as a biased simulation and it processes the data as simple as an unbiased simulation. The method provides a minimalist approach to the construction of the free energy landscape. © 2019 Wiley Periodicals, Inc.

Highly Promoted Carrier Mobility and Intrinsic Stability by Rolling Up Monolayer Black Phosphorus into Nanoscrolls

Rolling up two-dimensional (2D) materials into nanoscrolls could not only retain the excellent properties of their 2D hosts but also display intriguing physical and chemical properties that arise from their 1D tubular structures. Here, we report a new class of black phosphorus nanoscrolls (bPNSs), which are stable at room-temperature and energetically more favorable than 2D bP. Most strikingly, these bPNSs hold tunable direct band gaps and extremely high mobilities (e.g., the mobility of the double-layer bPNS is about 20-fold higher than that of 2D bP monolayer). Their unique self-encapsulation structure and layer-dependent conduction band minimum can largely prevent the entrance of O₂ and the production of O₂^- and thereby suppress the possible environmental degradation as well. The enhanced intrinsic stability and promoted electronic properties render bPNSs great promise in many advanced electronics or optoelectronics applications.

Chromium sulfide halide monolayers: intrinsic ferromagnetic semiconductors with large spin polarization and high carrier mobility

Two-dimensional (2D) ferromagnetic semiconductors (FMSs) are desirable for their potential to enhance the functionality of semiconductor devices via the utilization of spin degrees of freedom. Herein, we predict a series of intrinsic FMS monolayers in the chromium sulfide halide CrSX (X = Cl, Br, I) family with large spin polarization, large magnetic moments and high Curie temperatures. Such CrSCl and CrSBr monolayers also have high hole mobilities up to 6.6 × 103 and 5.3 × 103 cm2 V-1 s-1, respectively. Furthermore, these 2D monolayers exhibit excellent dynamic and thermal stabilities and a small exfoliation energy from the bulk. These intrinsic FMSs with their high mobilities may provide competitive candidates for next-generation spintronics and electronics.

An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation

In this paper, we present a novel hybrid Molecular Dynamics/kinetic Monte Carlo (MD/kMC) algorithm and apply it to protein folding and aggregation in explicit solvent. The new algorithm uses a dynamical definition of biases throughout the MD component of the simulation, normalized in relation to the unbiased forces. The algorithm guarantees sampling of the underlying ensemble in dependency of one average linear coupling factor 〈α〉_τ. We test the validity of the kinetics in simulations of dialanine and compare dihedral transition kinetics with long-time MD-simulations. We find that for low 〈α〉_τ values, kinetics are in good quantitative agreement. In folding simulations of TrpCage and TrpZip4 in explicit solvent, we also find good quantitative agreement with experimental results and prior MD/kMC simulations. Finally, we apply our algorithm to study growth of the Alzheimer Amyloid Aβ 16-22 fibril by monomer addition. We observe two possible binding modes, one at the extremity of the fibril (elongation) and one on the surface of the fibril (lateral growth), on timescales ranging from ns to 8 μs.

Constructing a multidimensional free energy surface like a spider weaving a web

Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials. Fast-growing biasing potential accelerates the sampling speed but decreases the accuracy of the free energy result. Slow-growing biasing potential gives an optimized result but needs more simulation time. In this article, we propose an alternative method. It adds the biasing potential to a representative point of the molecule in the collective variable space to improve the conformational sampling. And the free energy surface is calculated from the free energy gradient in the constrained simulation, not given by the negative of the biasing potential as previous methods. So the presented method does not require the biasing potential to remove all the barriers and basins on the free energy surface exactly. Practical applications show that the method in this work is able to produce the accurate free energy surfaces for different molecules in a short time period. The free energy errors are small in the cases of various biasing potentials. © 2017 Wiley Periodicals, Inc.

Room-Temperature Ferromagnetism in Two-Dimensional Fe2Si Nanosheet with Enhanced Spin-Polarization Ratio

Searching experimental feasible two-dimensional (2D) ferromagnetic crystals with large spin-polarization ratio, high Curie temperature and large magnetic anisotropic energy is one key to develop next-generation spintronic nanodevices. Here, 2D Fe₂Si nanosheet, one counterpart of Hapkeite mineral discovered in meteorite with novel magnetism is proposed on the basis of first-principles calculations. The 2D Fe₂Si crystal has a slightly buckled triangular lattice with planar hexacoordinated Si and Fe atoms. The spin-polarized calculations with hybrid HSE06 function method indicate that 2D Fe₂Si is a ferromagnetic half metal at its ground state with 100% spin-polarization ratio at Fermi energy level. The phonon spectrum calculation and ab initio molecular dynamic simulation shows that 2D Fe₂Si crystal has a high thermodynamic stability and its 2D lattice can be retained at the temperature up to 1200 K. Monte Carlo simulations based on the Ising model predict a Curie temperature over 780 K in 2D Fe₂Si crystal, which can be further tuned by applying a biaxial strain. Moreover, 2D structure and strong in-plane Fe-Fe interaction endow Fe₂Si nanosheet sizable magnetocrystalline anisotropy energy with the magnitude of at least two orders larger than those of Fe, Co and Ni bulks. These novel magnetic properties render the 2D Fe₂Si crystal a very promising material for developing practical spintronic nanodevices.

(1)H NMR spectroscopic elucidation in solution of the kinetics and thermodynamics of spin crossover for an exceptionally robust Fe(2+) complex

A series of Fe(2+) spin crossover (SCO) complexes [Fe(5/6)](2+) employing hexadentate ligands (5/6) with cis/trans-1,2-diamino cyclohexanes (4) as central building blocks were synthesised. The ligands were obtained by reductive amination of 4 with 2,2'-bipyridyl-6-carbaldehyde or 1,10-phenanthroline-2-carbaldehyde 3. The chelating effect and the rigid structure of the ligands 5/6 lead to exceptionally robust Fe(2+) and Zn(2+) complexes conserving their structure even in coordinating solvents like dmso at high temperatures. Their solution behavior was investigated using variable temperature (VT) (1)H NMR spectroscopy and VT Vis spectroscopy. SCO behavior was found for all Fe(2+) complexes in this series centred around and far above room temperature. For the first time we have demonstrated that the thermodynamics as well as kinetics for SCO can be deduced by using VT (1)H NMR spectroscopy. An alternative scheme using a linear correction term C(1) to model chemical shifts for Fe(2+) SCO complexes is presented. The rate constant for the SCO of [Fe(rac-trans-5)](2+) obtained by VT (1)H NMR was validated by Laser Flash Photolysis (LFP), with excellent agreement (1/(kHL + kLH) = 33.7/35.8 ns for NMR/LFP). The solvent dependence of the transition temperature T1/2 and the solvatochromism of complex [Fe(rac-trans-5)](2+) were ascribed to hydrogen bond formation of the secondary amine to the solvent. Enantiomerically pure complexes can be prepared starting with R,R- or S,S-1,2-diaminocyclohexane (R,R-trans-4 or S,S-trans-4). The high robustness of the complexes reduces a possible ligand scrambling and allows preparation of quasiracemic crystals of [Zn(R,R-5)][Fe(S,S-5)](ClO4)4·(CH3CN) composed of a 1 : 1 mixture of the Zn and Fe complexes with inverse chirality.

Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations

Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass of the fictitious particles, are proposed. The present on-the-fly eABF implementation can be viewed as the second generation of the ABF algorithm, expected to be widely utilized in the theoretical investigation of recognition and association phenomena relevant to physics, chemistry, and biology.

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.

Calculation of the Local Free Energy Landscape in the Restricted Region by the Modified Tomographic Method

The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.

Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.

The true nature of rotary movements in rotaxanes

Reveal the intricate nature of movements within rotaxanes by means of multidimensional free-energy landscapes.

Disentangling the different movements observed in rotaxanes is critical to characterize their function as molecular and biological motors. How to achieve unidirectional rotation is an important question for successful construction of a highly efficient molecular motor. The motions within a rotaxane composed of a benzylic amide ring threaded on a fumaramide moiety were investigated employing atomistic molecular dynamics simulations. The free-energy profiles describing the rotational process of the ring about the thread were determined from multi-microsecond simulations. Comparing the theoretical free-energy barriers with their experimental counterpart, the syn–anti isomerization of the amide bond within the ring was ruled out. The free-energy barriers arise in fact from the disruption of hydrogen bonds between the ring and the thread. Transition path analysis reveals that complete description of the reaction coordinate requires another collective variable. The free-energy landscape spanned by the two variables characterizing the coupled rotational and shuttling processes of the ring in the rotaxane was mapped. The calculated free-energy barrier, amounting to 9.3 kcal mol^–1, agrees well with experiment. Further analysis shows that shuttling is coupled with the isomerization of the ring, which is not limited to a simplistic chair-to-chair transition. This work provides a cogent example that contrary to chemical intuition, molecular motion can result from complex, entangled movements requiring for their accurate description careful modeling of the underlying reaction coordinate. The methodology described here can be used to evaluate the different components of the multifaceted motion in rotaxanes, and constitutes a robust tool for the rational design of molecular machines.

Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space

Replica-exchange molecular dynamics (REMD) is a popular sampling method in the molecular simulation. By frequently exchanging the replicas at different temperatures, the molecule can jump out of the minima and sample efficiently in the conformational space. Although REMD has been shown to be practical in a lot of applications, it does have a critical limitation. All the replicas at all the temperatures must be simulated for a period between the replica-exchange steps. This may be problematic for the reaction with high free energy barriers. In that case, too many replicas are required in the simulation. To reduce the calculation quantity and improve its performance, in this paper we propose a modified REMD method. During the simulation, each replica at each temperature can stay in either the active or inactive state and only switch between the states at the exchange step. In the active state, the replica moves freely in the canonical ensemble by the normal molecular dynamics, and in the inactive state, the replica is frozen temporarily until the next exchange step. The number of the replicas in the active states (active replicas) depends on the number of CPUs in the computer. Using the additional inactive replicas, one can perform an REMD simulation in a wider temperature space. The practical applications show that the modified REMD method is reliable. With the same number of active replicas, this REMD method can produce a more reasonable free energy surface around the free energy minima than the standard REMD method.

What causes tumbling of altro-α-CD derivatives? Insight from computer simulations

Spontaneous tumbling of altro-α-CD derivatives stems from the solvent and the side chain. Simulation results provide a theoretical basis for design of novel rotaxane-based molecular reels.

Trypsinogen activation as observed in accelerated molecular dynamics simulations

Serine proteases are involved in many fundamental physiological processes, and control of their activity mainly results from the fact that they are synthetized in an inactive form that becomes active upon cleavage. Three decades ago Martin Karplus's group performed the first molecular dynamics simulations of trypsin, the most studied member of the serine protease family, to address the transition from the zymogen to its active form. Based on the computational power available at the time, only high frequency fluctuations, but not the transition steps, could be observed. By performing accelerated molecular dynamics (aMD) simulations, an interesting approach that increases the configurational sampling of atomistic simulations, we were able to observe the N-terminal tail insertion, a crucial step of the transition mechanism. Our results also support the hypothesis that the hydrophobic effect is the main force guiding the insertion step, although substantial enthalpic contributions are important in the activation mechanism. As the N-terminal tail insertion is a conserved step in the activation of serine proteases, these results afford new perspective on the underlying thermodynamics of the transition from the zymogen to the active enzyme.

Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics

BACKGROUND

Accelerated molecular dynamics (aMD) has been proven to be a powerful biasing method for enhanced sampling of biomolecular conformations on general-purpose computational platforms. Biologically important long timescale events that are beyond the reach of standard molecular dynamics can be accessed without losing the detailed atomistic description of the system in aMD. Over other biasing methods, aMD offers the advantages of tuning the level of acceleration to access the desired timescale without any advance knowledge of the reaction coordinate.

SCOPE OF REVIEW

Recent advances in the implementation of aMD and its applications to small peptides and biological macromolecules are reviewed here along with a brief account of all the aMD variants introduced in the last decade.

MAJOR CONCLUSIONS

In comparison to the original implementation of aMD, the recent variant in which all the rotatable dihedral angles are accelerated (RaMD) exhibits faster convergence rates and significant improvement in statistical accuracy of retrieved thermodynamic properties. RaMD in conjunction with accelerating diffusive degrees of freedom, i.e. dual boosting, has been rigorously tested for the most difficult conformational sampling problem, protein folding. It has been shown that RaMD with dual boosting is capable of efficiently sampling multiple folding and unfolding events in small fast folding proteins.

GENERAL SIGNIFICANCE

RaMD with the dual boost approach opens exciting possibilities for sampling multiple timescales in biomolecules. While equilibrium properties can be recovered satisfactorily from aMD-based methods, directly obtaining dynamics and kinetic rates for larger systems presents a future challenge. This article is part of a Special Issue entitled Recent developments of molecular dynamics.