Large Energy Barrier Research Articles

Characterizing the Molecular Mechanisms for Flipping Charged Peptide Flanking Loops across a Lipid Bilayer.

The cell membrane largely prevents the passive diffusion of charged molecules due to the large free energy barrier associated with translocating charged groups across the hydrophobic lipid bilayer core. Despite this barrier, some peptides can interconvert between transmembrane and surface-adsorbed states by "flipping" charged flanking loops across the bilayer on a surprisingly rapid second-minute time scale. The transmembrane helices of some multispanning membrane proteins undergo similar reorientation processes, suggesting that loop-flipping may be a mechanism for regulating membrane protein topology; however, the molecular mechanisms underlying this behavior remain unknown. In this work, we study the loop-flipping behavior exhibited by a peptide with a hydrophobic transmembrane helix, charged flanking loops, and a central, membrane-exposed aspartate residue of varying protonation state. We utilize all-atom temperature accelerated molecular dynamics simulations to predict the likelihood of loop-flipping without predefining specific loop-flipping pathways. We demonstrate that this approach can identify multiple possible flipping pathways, with the prevalence of each pathway depending on the protonation state of the central residue. In particular, we find that a charged central residue facilitates loop-flipping by stabilizing membrane water defects, enabling the "self-catalysis" of charge translocation. These findings provide detailed molecular-level insights into charged loop-flipping pathways that may generalize to other charge translocation processes, such as lipid flip-flop or the large-scale conformational rearrangements of multispanning membrane proteins.

Adsorption of dimethyl sulfoxide on blue phosphorene

Dimethyl sulfoxide (DMSO) is widely used in industrial, medical, and other applications. However, it has been demonstrated that DMSO is toxic at low concentrations. Therefore, it is important to find a way to trap/reduce it. It has been shown that two dimensional materials can be used for environmental protection. In this work, we have studied the adsorption of a DMSO molecule on blue phosphorene, a new material with promising properties. Our first principles calculations find stable physisorbed and chemisorbed states. In the first case, the DMSO stays on top of the phosphorene layer, while in the second, the molecule is reduced into dimethyl sulfide (DMS), a less toxic molecule. However, a large energy barrier has to be overcome to reach this final state. These results indicate that phosphorene is a good substrate to trap DMSO but not to inactivate it.

Effect of constructive rehybridization on transverse conductivity of aligned single-walled carbon nanotube films

Alignment of densely packed single-walled carbon nanotubes (SWNTs) largely preserves the extraordinary electronic properties of individual SWNTs in the alignment direction, while in transverse direction the films are very resistive due to large energy barriers for tunneling between adjacent SWNTs. We demonstrate that chromium atoms inserted between the sidewalls of parallel SWNTs effectively coordinate to the benzene rings of the nanotubes via hexahapto bonds that preserve the nanotube-conjugated electronic structure and serve as a conduit for electron transfer. The atomically interconnected aligned SWNTs exhibit enhanced transverse conductivity, which increases by ∼2100% as a result of the photoactivated organometallic functionalization with Cr. The hexahapto mode of bonding the graphitic surfaces of carbon nanotubes with transition metal atoms offers an attractive route to the reversible chemical engineering of the transport properties of aligned carbon nanotube thin films. We demonstrate that a device fabricated with aligned SWNTs can be reversibly switched between a state of high electrical conductivity (ON) by light and low electrical conductivity (OFF) by applied potential. This study provides a route to the design of novel nanomaterials for applications in electrical atomic switches, optoelectronic and spintronic devices.

Structure and single-molecule magnet behavior of a rhombus-shaped Dy4 cluster

The reaction of the lanthanide(III) β-diketonate salt (Dy(beac)3·2H2O) with a bidentate chelating ligand 5-(2-hydroxy-5-methylbenzylidene)-8-hydroxylquinoline (HL) afforded the tetranuclear Dy(III) cluster, [Dy4(μ3-OH)2L6(beac)4]·10CH3CN (1). The elemental analysis (EA), powder X-ray diffraction (PXRD), single-crystal X-ray diffraction and magnetic properties of 1 have been characterized. The X-ray structural analysis reveals that cluster 1 contains one Dy4 center with a rhombus-shaped arrangement, and each Dy(III) ion of 1 is located in a distorted square antiprism geometrical configuration. Magnetic properties study indicate that 1 shows single-molecule magnet behavior with larger energy barrier (ΔE/kB) of 78.3 K and τ0 = 4.4 × 10−7 s.

Supersonic jet spectroscopy of parent hemiporphycene: Structural assignment and vibrational analysis for S0 and S1 electronic states.

Hemiporphycene (HPc), a constitutional isomer of porphyrin, is studied under supersonic expansion conditions by means of laser-induced fluorescence, visible-visible hole-burning experiments, single vibronic level fluorescence techniques, and quantum chemical calculations. Only one trans form of jet-cooled HPc is observed, in contrast to solution studies that evidence a mixture of two trans tautomeric forms separated in energy by ∼1 kcal/mol. Reliable structural assignment is provided by simulating absorption and emission patterns at the density functional theory and time-dependent density functional theory levels of theory. The vibronic spectra are nicely reproduced for both electronic ground and lowest excited singlet states for the most stable trans form. In contrast to another porphyrin isomer, porphycene (Pc), no tunneling or photo-induced hydrogen transfer is detected. The lower symmetry of HPc compared with Pc and the concomitant non-equivalent positions of the inner-cavity nitrogen atoms result in a non-symmetric double minimum potential for tautomerization, larger energy barrier, and a longer tunneling distance, with the average intramolecular hydrogen bond length larger in HPc than in Pc. HPc readily forms hydrates that show red-shifted absorption relative to the bare molecule.

Stone-Wales like defects formation, stability and reactivity in black phosphorene

During the synthesis of ultra-thin materials with a hexagonal lattice structure, Stone-Wales (SW) type of defects are quite likely to be formed that can result in dramatic changes in their electronic and mechanical properties. Here we investigated the formation and reactivity of SW-like defects in Phosphorene. Our calculations show that the energy barrier for the formation of SW-like defects in phosphorene is significantly lower than in graphene. Moreover, the nature of phosphorene provides a large energy barrier for the healing of the SWL defect, therefore defective phosphorene is stable. SWL-defect phosphorene are semiconductors with bandgap wider than pristine phosphorene that depends on the density of defects. Furthermore, nitrogen substitution in SWL defected phosphorene shows that defect lattice sites are the least preferable substitution locations for the N atoms. Easy formation of SWL defects in phosphorene provides a guideline for bandgap engineering in phosphorene based materials through such defects.

Rapid Desorption of Polyelectrolytes from Solid Surfaces Induced by Changes of Aqueous Chemistry.

The short-term desorption induced by changes of aqueous chemistry of predeposited polyelectrolyte layers on solid surfaces was studied with reflectometry. The behavior of a strong polycation, polydiallydimethylammonium chloride (PDADMAC), interacting with flat silica was investigated in detail. Results showed that partial desorption of preadsorbed polymer chains can be quickly triggered by changes in ionic strength and pH. When lowering these parameters in the PDADMAC-silica system, the increased lateral repulsive potential of neighboring chains drove the desorption of some of the polymer. Furthermore, layer desorption was favored when electrostatic interactions between a polyelectrolyte and the underlying surface became less attractive or switched to being repulsive. At the investigated timescales (<1 h), adlayer desorption was always partial and often incomplete. When initiating desorption from a condition of large adsorbed mass, desorption effects did not result in the plateau mass obtained by adsorption on a clean surface: an excess mass remained deposited. The results thus suggest that a relatively large energy barrier needs to be overcome to induce redissolution of predeposited chains and that this barrier may be a function of the number of polymer-surface interactions, which are in turn correlated with polymer molecular mass. These mechanisms have important implications for environmental processes and colloidal systems because they imply that, once adsorbed, polymeric chains may be redissolved but only to a limited degree at typical engineering timescales.

Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.

Interest in atomically detailed simulations has grown significantly with recent advances in computational hardware and Markov state modeling (MSM) methods, yet outstanding questions remain that hinder their widespread adoption. Namely, how do alternative sampling strategies explore conformational space and how might this influence predictions generated from the data? Here, we seek to answer these questions for four commonly used sampling methods: (1) a single long simulation, (2) many short simulations run in parallel, (3) adaptive sampling, and (4) our recently developed goal-oriented sampling algorithm, FAST. We first develop a theoretical framework for analytically calculating the probability of discovering select states on simple landscapes, where we uncover the drastic effects of varying the number and length of simulations. We then use kinetic Monte Carlo simulations on a variety of physically inspired landscapes to characterize the probability of discovering particular states and transition pathways for each of the four methods. Consistently, we find that FAST simulations discover each target state with the highest probability, while traversing realistic pathways. Furthermore, we uncover the potential pathology that short parallel simulations sometimes predict an incorrect transition pathway by crossing large energy barriers that long simulations would typically circumnavigate. We refer to this pathology as "pathway tunneling". To protect against this phenomenon when using adaptive-sampling and FAST simulations, we introduce the FAST-string method. This method enhances sampling along the highest-flux transition paths to refine an MSMs transition probabilities and discriminate between competing pathways. Additionally, we compare the performance of a variety of MSM estimators in describing accurate thermodynamics and kinetics. For adaptive sampling, we recommend simply normalizing the transition counts out of each state after adding small pseudocounts to avoid creating sources or sinks. Lastly, we evaluate whether our insights from simple landscapes hold for all-atom molecular dynamics simulations of the folding of the λ-repressor protein. Remarkably, we find that FAST-contacts predicts the same folding pathway as a set of long simulations but with orders of magnitude less simulation time.

Benzoxazine Atropisomers: Intrinsic Atropisomerization Mechanism and Conversion to High Performance Thermosets

Atropisomers have inspired chemists and biologists for decades due to their chiral structures and associated biological properties. However, most of atropisomers reported so far arise in highly substituted biaryls and related compounds, and other types have been rarely observed. Here we report a new type of atropisomerism in ortho-tetrahydrophthalimide functional 1,3-benzoxazine family, where the atropisomerism is evident from NMR spectra, with the branching ratio of the atropisomeric configurations invariant with the measurement temperatures. Density functional theory calculations suggested that the reaction intermediate, ortho-tetrahydrophthalimide phenol, is key to the atropisomerism, which creates a large energy barrier after deprotonation and thus determines the branching ratios of the benzoxazine atropisomers. In addition, the ring-opening polymerization of benzoxazine atropisomers has also been investigated. The benzoxazine atropisomers bearing acetylene exhibit unexpectedly low polymerization temp...

Theoretical Calculations for the 1,4-Hydrogen Shift of 1-Hydroxyallyl Radicals Leading to α-Keto Radicals; Prediction of Facilitation by 1-Amino and 3-Tin Substituents

DFT calculations were carried out to elucidate the 1,4-hydrogen shift of 1-hydroxyallyl radicals to give α-keto radicals. The 1,4-H shift is predicted to be exothermic with large energy barriers. H...

Relation between switching time distribution and damping constant in magnetic nanostructure

It is widely known that the switching time is determined by the thermal stability parameters and external perturbations such as magnetic field and/or spin polarized current in magnetic nano-structures. Since the thermal stability parameter and switching time are crucial values in the design of spin-transfer torque magnetic random access memory, the measurement of the switching time is important in the study of the switching behavior of ferromagnetic nano-structures. In this study, we focus on the distribution of the switching time. Within the limit of a large energy barrier, a simple analytical expression between damping constant and anisotropy field with switching time distribution is obtained and confirmed by numerically solving the Fokker-Planck equation. We show that the damping constant and anisotropy field can be extracted by measuring the full width half maximum of the switching time distribution in the magnetic nano-structure devices. Furthermore, the present method can be applied to not only single nano-structure, but also inhomogeneous nano-structure arrays.

Element-specific magnetic properties of mixed 3d−4f metallacrowns

Single molecule magnets comprising rare earth metals are of high interest due to the unquenched orbital moments of the rare earth ions that result in a large energy barrier for magnetization reversal. We investigate the magnetic properties of polynuclear $3d\text{\ensuremath{-}}4f15$-MC-5 metallacrowns using x-ray magnetic circular dichroism of powder samples at a temperature of 7 K in a magnetic field of 7 T. The sum rule analysis reveals element-specific spin and orbital moments. The magnetic moments of the $3d$ transition metal Ni(II) ions are coupled antiferromagnetically to each other and contribute only little to the total molecular moment. The spin and orbital moments of the rare earth ions are unexpectedly smaller than the ionic values resulting from Hund's rules. We explain the reduction of the orbital magnetic moment by a finite magnetic anisotropy. Considering an energy functional including magnetic anisotropy and Zeeman energy the powder average reveals a magnetic anisotropy of 28 meV (340 K) in the case of Dy(III) and 7 meV (85 K) in the case of Tb(III). The spin moments agree with the ionic value, too, when the expectation values of the dipole operator are considered.

Large Intercalation Pseudocapacitance in 2D VO2 (B): Breaking through the Kinetic Barrier.

VO2 (B) features two lithiation/delithiation processes, one of which is kinetically facile and has been commonly observed at 2.5 V versus Li/Li+ in various VO2 (B) structures. In contrast, the other process, which occurs at 2.1 V versus Li/Li+ , has only been observed at elevated temperatures due to large interaction energy barrier and extremely sluggish kinetics. Here, it is demonstrated that a rational design of atomically thin, 2D nanostructures of VO2 (B) greatly lowers the interaction energy and Li+ -diffusion barrier. Consequently, the kinetically sluggish step is successfully enabled to proceed at room temperature for the first time ever. The atomically thin 2D VO2 (B) exhibits fast charge storage kinetics and enables fully reversible uptake and removal of Li ions from VO2 (B) lattice without a phase change, resulting in exceptionally high performance. This work presents an effective strategy to speed up intrinsically sluggish processes in non-van der Waals layered materials.

Exploring different reaction mechanisms for oxidation of CO over a single Pd atom incorporated nitrogen-doped graphene: A DFT study

Single-metal catalysts have attracted particular interests in recent years due to their outstanding catalytic activity in CO oxidation reaction. In the present study, periodic DFT calculations are performed to investigate possible reaction mechanisms for oxidation of CO over a single Pd atom incorporated nitrogen-doped graphene. According to our results, the formation energy of a single-vacancy decreases by incorporation of pyridinic nitrogen atoms in graphene. The Pd atom can be stably anchored over the vacancy site, as evidenced by the large energy barriers for diffusion of the Pd atom to its neighboring sites. It is found that the incorporation of nitrogen atoms makes a significant increase in the adsorption energy of O2 and CO molecules over the supported Pd atom. The latter can be attributed to the shift in the bonding states of the Pd towards the Fermi level, which facilitates the charge-transfer from the 4d orbitals of this atom to the 2π∗ orbitals of O2 and CO molecules. The CO oxidation over the Pd atom supported nitrogen-doped graphene can proceed via three different mechanisms; namely, Eley-Rideal (ER), Langmuir-Hinshelwood (LH) and termolecular Eley-Rideal (TER) mechanisms. Our calculations reveal that the TER mechanism is preferred over the LH and ER, due to its smaller activation energy. The CO oxidation via the TER mechanism is a thermodynamically favorable process over the supported Pd atom, due to a large negative change in the Gibbs free energy of this reaction. The findings of this study can be useful to design more efficient single-atom catalysts to remove toxic CO molecules.

Hydrophobic gating in BK channels

The gating mechanism of transmembrane ion channels is crucial for understanding how these proteins control ion flow across membranes in various physiological processes. Big potassium (BK) channels are particularly interesting with large single-channel conductance and dual regulation by membrane voltage and intracellular Ca2+. Recent atomistic structures of BK channels failed to identify structural features that could physically block the ion flow in the closed state. Here, we show that gating of BK channels does not seem to require a physical gate. Instead, changes in the pore shape and surface hydrophobicity in the Ca2+-free state allow the channel to readily undergo hydrophobic dewetting transitions, giving rise to a large free energy barrier for K+ permeation. Importantly, the dry pore remains physically open and is readily accessible to quaternary ammonium channel blockers. The hydrophobic gating mechanism is also consistent with scanning mutagenesis studies showing that modulation of pore hydrophobicity is correlated with activation properties.

Graphdiyne Electrocatalyst

Graphdiyne Electrocatalyst

Intrinsic Origin of Enhancement of Ferroelectricity in SnTe Ultrathin Films.

Previous studies showed that, as ferroelectric films become thinner, their Curie temperature (T_{c}) and polarization below T_{c} both typically decrease. In contrast, a recent experiment [Chang etal., Science 353, 274 (2016)SCIEAS0036-807510.1126/science.aad8609] observed that atomic-thick SnTe films have a higher T_{c} than their bulk counterpart, which was attributed to extrinsic effects. We find, using first-principles calculations, that the 0-K energy barrier for the polarization switching (which is a quantity directly related to T_{c}) is higher in most investigated defect-free SnTe ultrathin films than that in bulk SnTe, and that the 5-unit-cell (UC) SnTe thin film has the largest energy barrier as a result of an interplay between hybridization interactions and Pauli repulsions. Further simulations, employing a presently developed effective Hamiltonian, confirm that freestanding, defect-free SnTe thin films have a higher T_{c} than bulk SnTe, except for the 1-UC case. Our work, therefore, demonstrates the possibility to intrinsically enhance ferroelectricity of ultrathin films by reducing their thickness.

An ab initio study on stacking and stability of TiAl3 phases

TiAl3 persists in many Al alloys and plays a detrimental role in solidification of related melts. Knowledge about TiAl3 phases and phase relations is of importance to get some insight into the solidification processes, the microstructures and the properties of Al alloys. In this manuscript, we present a systematic study of the basic structures of TiAl3 with aid from ab initio density functional theory (DFT) calculations. The study confirms that the ground state of TiAl3 has the D023 structure, whereas the observed D022 type is a metastable phase. The calculations have identified the stability of a series of stacking composed of both D022- and D023-TiAl3 units. At elevated temperature, the equilibrium configuration contains neither pure D023 nor pure D022 but will consist of a combination of the TiAl3 cubes arranged to minimise its Gibbs energy. Stacking default investigation reveals a large energy barrier for the D022 ↔ D023 transition. The obtained information sheds some light on the rich variety of the experimental observations in Al alloys, and further to understand the complex titanium aluminides and their thermo-structural properties.

Reservoir pH replica exchange.

We present the reservoir pH replica exchange (R-pH-REM) method for constant pH simulations. The R-pH-REM method consists of a two-step procedure; the first step involves generation of one or more reservoirs of conformations. Each reservoir is obtained from a standard or enhanced molecular dynamics simulation with a constrained (fixed) protonation state. In the second step, fixed charge constraints are relaxed, as the structures from one or more reservoirs are periodically injected into a constant pH or a pH-replica exchange (pH-REM) simulation. The benefit of this two-step process is that the computationally intensive part of conformational search can be decoupled from constant pH simulations, and various techniques for enhanced conformational sampling can be applied without the need to integrate such techniques into the pH-REM framework. Simulations on blocked Lys, KK, and KAAE peptides were used to demonstrate an agreement between pH-REM and R-pH-REM simulations. While the reservoir simulations are not needed for these small test systems, the real need arises in cases when ionizable molecules can sample two or more conformations separated by a large energy barrier, such that adequate sampling is not achieved on a time scale of standard constant pH simulations. Such problems might be encountered in protein systems that exploit conformational transitions for function. A hypothetical case is studied, a small molecule with a large torsional barrier; while results of pH-REM simulations depend on the starting structure, R-pH-REM calculations on this model system are in excellent agreement with a theoretical model.

High Interfacial Barriers at Narrow Carbon Nanotube-Water Interfaces.

Water displays anomalous fast diffusion in narrow carbon nanotubes (CNTs), a behavior that has been reproduced in both experimental and simulation studies. However, little is reported on the effect of bulk water-CNT interfaces, which is critical to exploiting the fast transport of water across narrow carbon nanotubes in actual applications. Using molecular dynamics simulations, we investigate here the effect of such interfaces on the transport of water across arm-chair CNTs of different diameters. Our results demonstrate that diffusion of water is significantly retarded in narrow CNTs due to bulk regions near the pore entrance. The slowdown of dynamics can be attributed to the presence of large energy barriers at bulk water-CNT interfaces. The presence of such intense barriers at the bulk-CNT interface arises due to the entropy contrast between the bulk and confined regions, with water molecules undergoing high translational and rotational entropy gain on entering from the bulk to the CNT interior. The intensity of such energy barriers decreases with increase in CNT diameter. These results are very important for emerging technological applications of CNTs and other nanoscale materials, such as in nanofluidics, water purification, nanofiltration, and desalination, as well as for biological transport processes.