Global Energy Minimum Research Articles

Formation of the quasi-planar B56 boron cluster: topological path from B12 and disk aromaticity.

Formation and stability of the B56 boron cluster were investigated using a topological approach and the disk aromaticity model. An extensive global energy minimum search for the B56 system which was carried out by means of the Mexican Enhanced Genetic Algorithm (MEGA) in conjunction with density functional theory computations, confirms a quasi-planar structure as its energetically most stable isomer. Such a structural motif is derived by applying a topological leapfrog operation to a B12 form. Its high thermodynamic stability can be explained by the disk aromaticity model in which the delocalization of its π orbitals can be assigned to the levels of a particle in a circular box with the [(1σ)2 (1π)4 (1δ)4 (1φ)4 (2σ)2 (1γ)4 (2π)4 (2δ)4 (1η)4 (2φ)4 (1θ)2] electronic configuration. This π delocalization is confirmed by other delocalization indices. While the B56 has a similar electron delocalization to that of the quasi-planar B50, they have opposite magnetic ring current properties because of the symmetry selection rules of their HOMO-LUMO electronic transitions. The π delocalization in the boron clusters is larger at long distances as compared to carbon clusters at similar sizes, but such a trend is reversed at shorter distances.

CSinGe4-n2+ (n = 1-3): prospective systems containing planar tetracoordinate carbon (ptC).

Density functional theory (DFT) based calculations have been carried out to explore the potential energy surface (PES) of CSinGe4-n2+/+/0 (n = 1-3) systems. The global minimum structures in the di-cationic states (1a, 1b, and 1c) contain a planar tetracoordinate carbon (ptC). For the CSi2Ge22+ system, the second stable isomer (2b) also contains a ptC with 0.67 kcal mol-1 higher energy than that of the 1b ptC isomer. The global minima of the neutral and mono-cationic states of the designed systems are not planar. The 1a, 1b, and 1c structures follow the 18 valence electron rule. The relative energies of the low-lying isomers of CSiGe32+, CSi2Ge22+, and CSi3Ge2+ systems with respect to the global minima were calculated using the CCSD(T)/aug-cc-pVTZ method. Ab initio molecular dynamics simulations for 50 ps time indicate that all the global minimum structures (1a, 1b, and 1c) are kinetically stable at 300 K and 500 K temperatures. The natural bond orbital (NBO) analysis suggests strong σ-acceptance of the ptC from the four surrounding atoms and simultaneously π-donation occurs from the ptC center. The nucleus independent chemical shift (NICS) showed σ/π-dual aromaticity. We hope that the designed di-cationic systems may be viable in the gas phase.

N-Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A*2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Simulations.

We have applied our advanced multicanonical molecular dynamics (McMD)-based dynamic docking methodology to investigate the binding mechanism of an HIV-1 Nef protein epitope to the Asian-dominant allele human leukocyte antigen (HLA)-A*2402. Even though pMHC complex formation [between a Major histocompatibility complex (MHC) class I molecule, which is encoded by an HLA allele, and an antigen peptide] is one of the fundamental processes of the adaptive human immune response, its binding mechanism has not yet been well studied, partially due to the high allelic variation of HLAs in the population. We have used our developed McMD-based dynamic docking method and have successfully reproduced the native complex structure, which is located near the free energy global minimum. Subsequent path sampling MD simulations elucidated the atomic details of the binding process and indicated that the peptide binding is initially driven by the highly positively charged N-terminus of the peptide that is attracted to the various negatively charged residues on the MHC molecule's surface. Upon nearing the pocket, the second tyrosine residue of the peptide anchors the peptide by strongly binding to the B-site of the MHC molecule via hydrophobic driven interactions, resulting in a very strong bound complex structure. Our methodology can be effectively used to predict the bound complex structures between MHC molecules and their antigens to study their binding mechanism in close detail, which would help with the development of new vaccines against cancers, as well as viral infections such as HIV and COVID-19.

Parameter dependent finite element analysis for ferronematics solutions

This paper focuses on the analysis of a free energy functional, that models a dilute suspension of magnetic nanoparticles in a two-dimensional nematic well. The first part of the article is devoted to the asymptotic analysis of global energy minimizers in the limit of vanishing elastic constant, ℓ→0 where the re-scaled elastic constant ℓ is inversely proportional to the domain area. The first results concern the strong H1-convergence and a ℓ-independent H2-bound for the global minimizers on smooth bounded 2D domains, with smooth boundary and topologically trivial Dirichlet conditions. The second part focuses on the discrete approximation of regular solutions of the corresponding non-linear system of partial differential equations with cubic non-linearity and non-homogeneous Dirichlet boundary conditions. We establish (i) the existence and local uniqueness of the discrete solutions using fixed point argument, (ii) a best approximation result in energy norm, (iii) error estimates in the energy and L2 norms with ℓ-discretization parameter dependency for the conforming finite element method. Finally, the theoretical results are complemented by numerical experiments on the discrete solution profiles, the numerical convergence rates that corroborates the theoretical estimates, followed by plots that illustrate the dependence of the discretization parameter on ℓ.

Gas-phase formation of cationic fullerene/9-aminoanthracene clusters: an indicator for interstellar dust growth

ABSTRACT Growth of clusters by adduction of monomers – as the first step in dust particle growth – is an area of much interest in astronomy. We focus on the fullerene/9-aminoanthracene cluster species, to illustrate the competition between the van der Waals bonding growth and the covalent bonding growth model versus the charge transfer model in the large cluster formation process. The experimental results show that fullerene-fragment (C56 and C58)/9-aminoanthracene cluster cations, e.g. [(C14H11N)nC56]+ and [(C14H11N)nC58]+, n = [1,7], are efficiently formed, while C$_{60}^+$ is insensitive to the cluster’s formation. With laser irradiation, all the fullerene/9-aminoanthracene clusters dissociate into 9-aminoanthracene and fullerene cations. The mechanisms for the reactions of fullerene cations and 9-aminoanthracene were investigated by theoretical calculations, under the assumption that the molecular geometries found for the formed complexes correspond to the global energy minima: the absence of C$_{60}^+$ clusters is mainly due to the charge transfer channel’s competition; [(C14H11N)C58]+ has three types of isomers, with van der Waals or covalent bonds, mainly depending on the reaction sites of fullerene cations. Importantly, in the size grown process, for the fullerene/9-aminoanthracene cluster there exists a geometry configuration conversion between the van der Waals and covalent bonding modes. The largest fullerene/9-aminoanthracene clusters, e.g. [(C14H11N)7C58]+ (240 atoms, ∼4 nm in size), are likely in a multishelled geometry, i.e. seven 9-aminoanthracene molecules surrounding fullerene cations in two layers, which can directly build the relationship between molecular clusters and carbonaceous grains. Nitrogen matters! The specific side chains (e.g. –NH2) play an important role in the growth of interstellar dust.

Building blocks for autonomous computing materials: Dimers, trimers, and tetramers.

Autonomous computing materials for data storage and computing offer an opportunity for next generation of computing devices. Patchy nanoparticle networks, for example, have been suggested as potential candidates for emulating neuronal networks and performing brain-like computing. Here, we use molecular dynamics (MD) simulations to show that stable dimers, trimers, and tetramers can be built from citrate capped gold nanoparticles (cit-AuNPs) linked by poly(allylamine hydrochloride) (PAH) chains. We use different lengths of PAHs to build polymer-networked nanoparticle assemblies that can emulate a complex neuronal network linked by axons of varying lengths. We find that the tetramer structure can accommodate up to 11 different states when the AuNP pairs are connected by either of two polymer linkers, PAH200 and PAH300. We find that the heavy AuNPs contribute to the assembly's structure stability. To further illustrate the stability, the AuNP-AuNP distances in dimer, trimer, and tetramer structures are reduced by steering the cit-AuNPs closer to each other. At different distances, these steered structures are all locally stable in a 10ns MD simulation time scale because of their connection to the AuNPs. We also find that the global potential energy minimum is at short AuNP-AuNP distances where AuNPs collapse because the -NH3 + and -COO- attraction reduces the potential energy. The stability and application of these fundamental structures remain to be further improved through the use of alternative polymer linkers and nanoparticles.

Physico-chemistry and adhesion kinetics of algal biofilm on polyethersulfone (PES) membrane with different surface wettability

Microalgal biofilm growth on porous substrates has recently garnered extensive attention with the advantage of high biomass productivity with low liquid culture volume. In such cultivation, the surface characteristics of supporting materials play essential role supporting biofilm growth. In view of this, a study on the membrane surface wettability of a commercial polyethersulfone (PES) membrane with two different hydrophilicities was selected in a long-term benthic biofilm cultivation experiment. Findings revealed that both soluble and bounded extracellular polymeric substances (EPS) contributed towards the formation of an adhesive gel layer onto the membrane’s surfaces. The maximum accumulated cell density was achieved by C. fusiformis around 47.64 ± 4.03 × 109 cells m−2 onto phobic PES (79.29°) and the least by N. incerta around 6.40 ± 0.49 × 109 cells m−2 onto philic PES (47.56°). The fact remained that the cell attachment rate was almost similar for both A. coffeaeformis and N. incerta but with gradual reduction after day 12 for phobic PES and day 8 for philic PES for the three benthic species. The change of adhesion ratio was well explained with their respective EPS variation. The XDLVO model employed suggested the dominance of acid-base interactions in high ionic strength liquid, leading to higher global minimum energy occurring on phobic PES. Overall, the findings indicated that biofilm formation is favored on polymer substrate having lower surface energy due to the attractive interaction of the submerged surface with those biomolecules and colloids.

Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers

The functionality of an enzyme depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric α/β-hydrolase enzyme (Tm = 73.5 °C; ΔTm > 23 °C) affected the protein folding energy landscape. The introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded soluble domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations might (i) activate cryptic hinge-loop regions and (ii) establish secondary interfaces, where they make extensive noncovalent interactions between the intertwined protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from small-angle X-ray scattering (SAXS) and cross-linking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain swapping occurs exclusively in vivo. Crucially, the swapped-dimers exhibited advantageous catalytic properties such as an increased catalytic rate and elimination of substrate inhibition. These findings provide additional enzyme engineering avenues for next-generation biocatalysts.

Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking.

We have performed dynamic docking between a prototypic G-protein-coupled receptor (GPCR) system, the β2-adrenergic receptor, and its antagonist, alprenolol, using one of the enhanced conformation sampling methods, multicanonical molecular dynamics (McMD), which does not rely on any prior knowledge for the definition of the reaction coordinate. Although we have previously applied our McMD-based dynamic docking protocol to various globular protein systems, its application to GPCR systems would be difficult because of their complicated design, which include a lipid bilayer, and because of the difficulty in sampling the configurational space of a binding site that exists deep inside the GPCR. Our simulations sampled a wide array of ligand-bound and ligand-unbound structures, and we measured 427 binding events during our 48 μs production run. Analysis of the ensemble revealed several stable and meta-stable structures, where the most stable structure at the global free energy minimum matches the experimental one. Additional canonical MD simulations were used for refinement and validation of the structures, revealing that most of the intermediates are sufficiently stable to trap the ligand in these intermediary states and furthermore validated our prediction results. Given the difficulty in reaching the orthosteric binding site, chemical optimization of the compound for the second ranking configuration, which binds near the pocket's entrance, might lead to a high-affinity allosteric inhibitor. Accordingly, we show that the application of our methodology can be used to provide crucial insights for the rational design of drugs that target GPCRs.

Sulphur-Bridged BAl5S5+ with 17 Counting Electrons: A Regular Planar Pentacoordinate Boron System.

At present, most of the reported planar pentacoordinate clusters are similar to the isoelectronic substitution of CAl5+, with 18 counting electrons. Meanwhile, the regular planar pentacoordinate boron systems are rarely reported. Hereby, a sulphur-bridged BAl5S5+ system with a five-pointed star configuration and 17 counting electrons is identified at the global energy minimum through the particle-swarm optimization method, based on the previous recognition on bridged sulphur as the peripheral tactics to the stable planar tetracoordinate carbon and boron. Its outstanding stability has been demonstrated by thermodynamic analysis at 900 K, electronic properties and chemical bonding analysis. This study provides adequately theoretical basis and referable data for its experimental capture and testing.

Deep reinforcement learning for predicting kinetic pathways to surface reconstruction in a ternary alloy

The majority of computational catalyst design focuses on the screening of material components and alloy composition to optimize selectivity and activity for a given reaction. However, predicting the metastability of the alloy catalyst surface at realistic operating conditions requires an extensive sampling of possible surface reconstructions and their associated kinetic pathways. We present CatGym, a deep reinforcement learning (DRL) environment for predicting the thermal surface reconstruction pathways and their associated kinetic barriers in crystalline solids under reaction conditions. The DRL agent iteratively changes the positions of atoms in the near-surface region to generate kinetic pathways to accessible local minima involving changes in the surface compositions. We showcase our agent by predicting the surface reconstruction pathways of a ternary Ni3Pd3Au2(111) alloy catalyst. Our results show that the DRL agent can not only explore more diverse surface compositions than the conventional minima hopping method, but also generate the kinetic surface reconstruction pathways. We further demonstrate that the kinetic pathway to a global minimum energy surface composition and its associated transition state predicted by our agent is in good agreement with the minimum energy path predicted by nudged elastic band calculations.

Atomic Clusters: Structure, Reactivity, Bonding, and Dynamics.

Atomic clusters lie somewhere in between isolated atoms and extended solids with distinctly different reactivity patterns. They are known to be useful as catalysts facilitating several reactions of industrial importance. Various machine learning based techniques have been adopted in generating their global minimum energy structures. Bond-stretch isomerism, aromatic stabilization, Rener-Teller effect, improved superhalogen/superalkali properties, and electride characteristics are some of the hallmarks of these clusters. Different all-metal and nonmetal clusters exhibit a variety of aromatic characteristics. Some of these clusters are dynamically stable as exemplified through their fluxional behavior. Several of these cluster cavitands are found to be agents for effective confinement. The confined media cause drastic changes in bonding, reactivity, and other properties, for example, bonding between two noble gas atoms, and remarkable acceleration in the rate of a chemical reaction under confinement. They have potential to be good hydrogen storage materials and also to activate small molecules for various purposes. Many atomic clusters show exceptional opto-electronic, magnetic, and nonlinear optical properties. In this Review article, we intend to highlight all these aspects.

Vibratile Dihydrophenazines with Controllable Luminescence Enabled by Precise Regulation of π-Conjugated Wings

Vibratile Dihydrophenazines with Controllable Luminescence Enabled by Precise Regulation of π-Conjugated Wings

Electrowetting-based control of wetting transition of a nanodroplet on pillar-arrayed surfaces

Two extreme wetting states, a highly non-wetting Cassie state and a wetting Wenzel state, can coexist or even mutually convert on patterned surfaces. Such a conversion process may be spontaneous or induced by external stimuli. This work studies the wetting transition of a nanodroplet on pillar-arrayed surfaces induced by an external electric field via an energy-minimization method in conjunction with molecular dynamics (MD) simulations. The simulation results reveal that driven by the electric field, the initial Cassie state could go through a partial wetting state, and eventually converts to the Wenzel state. The free-energy landscape reveals that there are multiple local energy minima, corresponding to multiple metastable states. For the metastable Cassie state, the wetting transition is irreversible, i.e., the droplet would remain in the Wenzel state when the electric field is removed. Conversely, the spontaneous dewetting transition from the Wenzel to the Cassie state can occur, if only the Cassie droplet is in a global energy minimum configuration. Thus, the stable Cassie wetting configuration is essential for triggering the spontaneous dewetting transition.

Crystal structures, DFT calculations and Hirshfeld surface analysis of two (E)-3-(aryl)-1-(naphthalen-1-yl)prop-2-en-1-one chalcone derivatives, potential Mycobacterium tuberculosis Enoyl ACP reductase (InhA) inhibitors and optical materials: conformational differences within the prop-2-en-1-one unit

A combined structural and computational study has been conducted on two chalcone compounds, namely (E)-3-(4-bromophenyl)-1-(4,8-dimethoxynaphthalen-1-yl)prop-2-en-1-one (1), and (E)-3-(3,4-dichlorophenyl)-1-(4,8-dimethoxynaphthalen-1-yl)prop-2-en-1-one (2). These compounds are members of a series of compounds identified from a molecular modelling study as potentially active Mycobacterium tuberculosis Enoyl ACP reductase (InhA) inhibitors. In addition, the computational study indicated that the compounds have potential as optical materials.The combined study revealed that both molecules in the solid state displayed similar overall molecular conformations between a ‘‘T’’ and a ‘‘Y’’ shape, but with different arrangements in the bridging prop-2-en-1-one unit: an anti-periplanar in 1 and a syn-periplanar in 2. The experimental and calculated bond lengths and angles for anti-periplanar1 and syn-periplanar2 were generally in good agreement.Theoretical calculations at the B3LYP/DGTZVP level in the gas phase, DMSO and water media indicated that for both compounds, the syn-periplanar form was the energy local minimum while the anti-periplanar form was the energy global minimum. However, the energy differences are very small, with slight variations when using the different basis sets (0.80 and 0.84 kcal/mol using the B3LYP/DGTVP theory level in gas phase, 0.28 and 0.32 in DMSO and 0.27 and 0.31 kcal/mol in water). The differences in the solid state arrangements within the bridging prop-2-en-1-one unit in 1 and 2 arise from variations in the intermolecular interactions, with halogen bonds being considered to be an important factor in stabilizing a syn-periplanar arrangement in compound 2. PLATON and Hirshfeld surface analyses confirmed the important intermolecular interactions in 1 and 2.Calculations were also carried out on the electronic and vibrational spectra, dipole moments and charge distributions of 1 and 2. The HOMO was located in the dimethoxynaphthalenyl region of the molecule with mild donor character, while the LUMO was located in the propenyl and phenyl regions of each molecule. The energy gaps between these orbitals are 3.35 eV for 1 3.25 eV for 2. The delocalization present in compounds 1 and 2 facilitates the HOMO-LUMO charge transfer process.The total electronic molecular dipolar moments (μTotal) were calculated to be 4.1511 and 5.9316 D for 1 and 2, respectively. The values of μTotal found for 1 and 2 are both larger than reported values for similar compounds, indicating that the compounds studied here should exhibit a good non-linear optical response.

An assessment of phase field fracture: crack initiation and growth.

The phase field paradigm, in combination with a suitable variational structure, has opened a path for using Griffith's energy balance to predict the fracture of solids. These so-called phase field fracture methods have gained significant popularity over the past decade, and are now part of commercial finite element packages and engineering fitness- for-service assessments. Crack paths can be predicted, in arbitrary geometries and dimensions, based on a global energy minimization-without the need for ad hoc criteria. In this work, we review the fundamentals of phase field fracture methods and examine their capabilities in delivering predictions in agreement with the classical fracture mechanics theory pioneered by Griffith. The two most widely used phase field fracture models are implemented in the context of the finite element method, and several paradigmatic boundary value problems are addressed to gain insight into their predictive abilities across all cracking stages; both the initiation of growth and stable crack propagation are investigated. In addition, we examine the effectiveness of phase field models with an internal material length scale in capturing size effects and the transition flaw size concept. Our results show that phase field fracture methods satisfactorily approximate classical fracture mechanics predictions and can also reconcile stress and toughness criteria for fracture. The accuracy of the approximation is however dependent on modelling and constitutive choices; we provide a rationale for these differences and identify suitable approaches for delivering phase field fracture predictions that are in good agreement with well-established fracture mechanics paradigms. This article is part of a discussion meeting issue 'A cracking approach to inventing new tough materials: fracture stranger than friction'.

Optimal Computational Offloading and Content Caching in Wireless Heterogeneous Mobile Edge Computing Systems With Hopfield Neural Networks

This paper explores the problem of joint computational offloading and content caching (OCP) in the wireless heterogeneous mobile edge computing (MEC) system, where each small-cell base station (BS) is equipped with the MEC server having the content caching/processing capabilities. The communication and computing resources of the system are allocated to users requesting or offloading their contents via the BSs to minimize the system-wide computational overhead. Due to the non-deterministic polynomial time hardness of the OCP, it is difficult to solve it with an exact integer-programming (IP) method. Instead, the problem is solved by adopting the Hopfield neural network (HNN) based approach. In particular, the HNN model representing the OCP is constructed. The global energy minimum of the model corresponds to a solution of the OCP. However, because of the negativity of diagonal weights, the convergence of this model to a stable state cannot be guaranteed. Subsequently, a range of “synthetic” HNN models with the global convergence property is developed to replace the original HNN. Based on these models, three different search algorithms are formulated and implemented in a long-term evolution advanced network. The algorithms demonstrate an improved performance when compared to other relevant IP methods in simulations.

Ion dynamics and selectivity of Nav channels from molecular dynamics simulation

The voltage-gated sodium (Nav) channels are crucial in initiating and propagating action potentials in excitable cells. In this work, with atomistic molecular simulations employing conventional and advanced sampling techniques, we investigate the dynamics of a series of Nav channels. The thermodynamic picture along the ion permeation pathway is obtained and the ion dynamics in the channels are analyzed. The ion permeation pathway could be divided into several regions. The cation enters the channel through the selectivity filter, stays in the global free energy minimum at the central cavity, and waits for the open of the activation gate. Exchanges between neighboring ions are also observed. There is an obvious free energy barrier for K+ entering the channel, and the thermodynamic stability of K+ in the central cavity is similar to the extracellular side, while there is no explicit barrier for Na+ and the cation is more stable in the cavity.

DFT Studies of Selected Epoxies with Mesogenic Units-Impact of Molecular Structure on Electro-Optical Response.

Theoretical studies of molecular structure and electric charge distribution were carried out for three epoxy compounds with different mesogenic cores. The compounds exhibit a nematic phase and form polymer networks that are potential bases for various composites. Results were compared to analogous materials with non-polar chains. A customized process involving geometry optimization of a series of conformations was employed to greatly increase likelihood of reaching global energy minimum for each molecule. All computations used Density Functional Theory (DFT) electron correlation model with the B3LYP hybrid functional. Molecular structure calculations yielded several parameters, including the magnitude and direction of the dipole moment, polarizability (α), first hyperpolarizability (β), and highest-occupied/lowest-unoccupied molecular orbital (HOMO-LUMO) energies. These parameters can help predict electronic properties of the nematic phase and the polymer network and assess their predisposition for application in electrooptical devices. In particular, the magnitude and direction of the dipole moment determine molecular alignment of liquid crystal phases in electric field, which enables controlling molecular order also in cured networks. Theoretical results were supplemented with observations of the nematics and their behavior in electric field. It was demonstrated for the studied compounds that a change in aliphatic chain polarity helps preserve and reinforce perpendicular alignment of molecules induced by electric field.

Van der Waals interactions of the disulfide bond revealed: A microwave spectroscopic study of the diethyl disulfide-argon complex.

The van der Waals complex formed between diethyl disulfide (DEDS) and an argon atom was investigated by pulsed-jet Fourier transform microwave spectroscopy in conjunction with quantum chemical computations. One set of transition lines belonging to the configuration of the global potential energy minimum was measured and assigned. The rotational constants A, B, and C were accurately determined to be 1262.5758(1) MHz, 845.402 12(9) MHz, and 574.006 38(8) MHz, respectively. The distance between the argon atom and the center of mass of the DEDS subunit is 4.075(16) Å. Quantum theory of atoms in molecules and non-covalent interaction analyses reveal that the interactions take place between the argon atom and four sites of the DEDS subunit. Furthermore, the usage of the energy decomposition analysis approach provides further understanding of the characteristics of the van der Waals interactions. Additionally, ab initio calculations and symmetry-adapted perturbation theory analysis of the binary complexes of DEDS with He, Ne, Kr, and Xe atoms were carried out to get further insight into the characteristics of the van der Waal interactions of the disulfide bond.