van der Waals potential barrier for cobaltocene encapsulation into single-walled carbon nanotubes: classical molecular dynamics and ab initio study

In this work, we carried out geometry optimisations and classical molecular dynamics for the problem of cobaltocene (CC) encapsulation into different carbon nanotubes (CNTs) ((7,7), (8,8), (13,0) and (14,0) tubes were used). CCs are molecules composed of two aromatic pentagonal rings (C5H5) sandwiching one cobalt atom. From our simulation results, we observed that CC was encapsulated into CNTs (8,8), (13,0) and (14,0). However, for CNT (7,7), the encapsulation could not occur, in disaggrement with some previous works in the literature. Our results show that the encapsulation process is mainly governed by van der Waals potential barriers.     

Mixed Valence Tin Oxides as Novel van der Waals Materials: Theoretical Predictions and Potential Applications

Van der Waals (vdW) heterostructures, which can be assembled by combining 2D atomic crystals in a precisely chosen sequence, enable a wide range of potential applications in optoelectronics, photovoltaics, and photocatalysis. However, the difficulty of peeling isolated atomic planes and the lattice mismatch between different materials is the main obstacle to hinder vdW materials from more practical applications. In this work, the mixed valence tin oxides, Sn_xO_y (0.5 < x/y < 1), are proposed as a new member of vdW materials and these mixed valence tin oxides show promise to overcome the above‐mentioned obstacle. Density‐functional theory calculations are combined with an evolutionary algorithm to predict the crystal structures of a series of previously reported tin oxides (Sn₂O₃, Sn₃O₄, Sn₄O₅, and Sn₅O₆), unreported compositions (Sn₇O₈, Sn₉O₁₀, and Sn₁₁O₁₂), and a new β ‐ SnO phase. These structures consist of β‐SnO, Sn₂O₃, and Sn₃O₄ monolayers. Their band gaps can be engineered in the 1.56–3.25 eV range by stacking the monolayers appropriately. The band gap depends linearly on the interlayer distance, as understood from interlayer Sn²⁺–Sn²⁺ and intralayer Sn²⁺–O interactions. Sn_xO_y structures exhibit high photoabsorption coefficients and suitable band‐edge positions for photoexcited H₂ evolution; this indicates potential for environmentally benign solar energy conversion in photovoltaic and photocatalytic applications.     

Calibration of effective van der Waals atomic contact radii for proteins and peptides

Effective van der Waals radii were calibrated in such a way that molecular models built from standard bond lengths and bond angles reproduced the amino acid conformations observed by crystallography in proteins and peptides. The calibrations were based on the comparison of the Ramachandran plots prepared from high-resolution X-ray data of proteins and peptides with the allowed phi, psi torsional angle space for the dipeptide molecular models. The calibrated radii are useful as criteria with which to filter energetically improbable conformations in molecular modeling studies of proteins and peptides.     

Computing van der Waals energies in the context of the rotamer approximation

The rotamer approximation states that protein side-chain conformations can be described well using a finite set of rotational isomers. This approximation is often applied in the context of computational protein design and structure prediction to reduce the complexity of structural sampling. It is an effective way of reducing the structure space to the most relevant conformations. However, the appropriateness of rotamers for sampling structure space does not imply that a rotamer-based energy landscape preserves any of the properties of the true continuous energy landscape. Specifically, because the energy of a van der Waals interaction can be very sensitive to small changes in atomic separation, meaningful van der Waals energies are particularly difficult to calculate from rotamer-based structures. This presents a problem for computational protein design, where the total energy of a given structure is often represented as a sum of precalculated rigid rotamer self and pair contributions. A common way of addressing this issue is to modify the van der Waals function to reduce its sensitivity to atomic position, but excessive modification may result in a strongly nonphysical potential. Although many different van der Waals modifications have been used in protein design, little is known about which performs best, and why. In this paper, we study 10 ways of computing van der Waals energies under the rotamer approximation, representing four general classes, and compare their performance using a variety of metrics relevant to protein design and native-sequence repacking calculations. Scaling van der Waals radii by anywhere from 85 to 95% gives the best performance. Linearizing and capping the repulsive portion of the potential can give additional improvement, which comes primarily from getting rid of unrealistically large clash energies. On the other hand, continuously minimizing individual rotamer pairs prior to evaluating their interaction works acceptably in native-sequence repacking, but fails in protein design. Additionally, we show that the problem of predicting relevant van der Waals energies from rotamer-based structures is strongly nonpairwise decomposable and hence further modifications of the potential are unlikely to give significant improvement.     

Nature of Novel 2D van der Waals Heterostructures for Superior Potassium Ion Batteries

Novel 2D van der Waals heterostructures with innovative bimetallic oxychloride (Bi‐ and Sb‐based oxychloride) nanosheets that are well dispersed on reduced graphene oxide nanosheets, are established through element engineering for superior potassium ion battery (PIBs) anodes. This material displays an exceptional electrochemical performance, obtaining a discharge capacity as high as 360 mAh g^?1 at 100 mA g^?1 after running 1000 cycles for over 9 months with a capacity preservation percentage of 88.5% and achieving a discharge capacity as high as 319 mAh g^?1 at 1000 mA g^?1, in addition to the low charge/discharge plateaus for anodes and promising full cell performance. More significantly, the nature of such 2D van der Waals heterostructures, including the element engineering for morphology control, the function of each component of heterostructures, the mechanism of potassium ion storage, and the process of K⁺ intercalation accompanied with the lattice distortion and chemical bond breakages, is explored in depth. This study is critical for not only paving the way for the practical application of PIBs but also shedding light on fundamentals of potassium ion storage in 2D van der Waals heterostructures.     

General van der Waals potential for common organic molecules

This work presents a systematic development of a new van der Waals potential (vdW2016) for common organic molecules based on symmetry-adapted perturbation theory (SAPT) energy decomposition. The Buf-14-7 function, as well as Cubic-mean and Waldman–Hagler mixing rules were chosen given their best performance among other popular potentials. A database containing 39 organic molecules and 108 dimers was utilized to derive a general set of vdW parameters, which were further validated on nucleobase stacking systems and testing organic dimers. The vdW2016 potential is anticipated to significantly improve the accuracy and transferability of new generations of force fields for organic molecules.     

Structural modification of indomethacin toward selective inhibition of COX-2 with a significant increase in van der Waals contributions

We have synthesized a fluorinated analogue of indomethacin bearing a 3,3,3-trifluoroprop-1-enyl group at its 2-position and evaluated its inhibitory activity towards the COX-1 and COX-2 enzymes in vitro. The results revealed that this fluorinated analogue exhibited much greater inhibitory activity and selectivity towards COX-2 than indomethacin. The increased affinity between the fluorinated analogue and COX-2 was attributed to a significant increase in van der Waals contacts (i.e. van der Waals contributions in ΔG were ?13.80?kcal/mol for COX-1 and ?18.46?kcal/mol for COX-2), explaining an effect of the fluorine substituent in enzyme selectivity. This newly synthesized fluorinated analogue therefore represents a potent and selective COX-2 inhibitor.     

Importance of van der Waals contact between Glu 35 and Trp 109 to the catalytic action of human lysozyme.

The importance of van der Waals contact between Glu 35 and Trp 109 to the active-site structure and the catalytic properties of human lysozyme (HL) has been investigated by site-directed mutagenesis. The X-ray analysis of mutant HLs revealed that both the replacement of Glu 35 by Asp or Ala, and the replacement of Trp 109 by Phe or Ala resulted in a significant but localized change in the active-site cleft geometry. A prominent movement of the backbone structure was detected in the region of residues 110 to 120 and in the region of residues 100 to 115 for the mutations concerning Glu 35 and Trp 109, respectively. Accompanied by the displacement of the main-chain atoms with a maximal deviation of C alpha atom position ranging from 0.7 A to 1.0 A, the mutant HLs showed a remarkable change in the catalytic properties against Micrococcus luteus cell substrate as compared with native HL. Although the replacement of Glu 35 by Ala completely abolished the lytic activity, HL-Asp 35 mutant retained a weak but a certain lytic activity, showing the possible involvement of the side-chain carboxylate group of Asp 35 in the catalytic action. The kinetic consequence derived from the replacement of Trp 109 by Phe or Ala together with the result of the structural change suggested that the structural detail of the cleft lobe composed of the residues 100 to 115 centered at Ala 108 was responsible for the turnover in the reaction of HL against the bacterial cell wall substrate. The results revealed that the van der Waals contact between Glu 35 and Trp 109 was an essential determinant in the catalytic action of HL.     

Unveiling the Unique Phase Transformation Behavior and Sodiation Kinetics of 1D van der Waals Sb2S3 Anodes for Sodium Ion Batteries

Carbon‐coated van der Waals stacked Sb₂S₃ nanorods (SSNR/C) are synthesized by facile hydrothermal growth as anodes for sodium ion batteries (SIBs). The sodiation kinetics and phase evolution behavior of the SSNR/C anode during the first and subsequent cycles are unraveled by coupling in situ transmission electron microscopy analysis with first‐principles calculations. During the first sodiation process, Na⁺ ions intercalate into the Sb₂S₃ crystals with an ultrafast speed of 146 nm s^?1. The resulting amorphous Na_x Sb₂S₃ intermediate phases undergo sequential conversion and alloying reactions to form crystalline Na₂S, Na₃Sb, and minor metallic Sb. Upon desodiation, Na⁺ ions extract from the nanocrystalline phases to leave behind the fully desodiated Sb₂S₃ in an amorphous state. Such unique phase evolution behavior gives rise to superb electrochemical performance and leads to an unexpectedly small volume expansion of ≈54%. The first‐principles calculations reveal distinctive phase evolution arising from the synergy between the extremely low Na⁺ ion diffusion barrier of 190 meV and the sharply increased electronic conductivity upon the formation of amorphous Na_x Sb₂S₃ intermediate phases. These findings highlight an anomalous Na⁺ ion storage mechanism and shed new light on the development of high performance SIB anodes based on van der Waals crystals.     

Van der Waals Forces Between Plasmonic Nanoparticles

We propose a new approach to calculate van der Waals forces between nanoparticles where the van der Waals energy can be reduced to the energy of localized plasmons in nanoparticles. The general theory is applied to describe the interaction between two metallic nanoparticles and between a nanoparticle and a perfectly conducting plane. Our results could be used to prove experimentally the existence of new, recently predicted type of plasmon oscillation (Klimov and Guzatov, Phys Rev B 75:024303, 2007a; Klimov and Guzatov, Quantum Electron 37:209, 2007b) and to elaborate new control mechanisms for the adherence of nanoparticles between each other or onto surfaces.     

The volume of cavities in proteins and virus capsids

An improved algorithm for the calculation of the volume of internal cavities within protein structures and virus capsids as well as the volumes occupied by single amino acid residues were presented. The geometrical approach was based on atomic van der Waals radii. The results obtained with two sets of the radii, those proposed by Pauling and those determined by Tsai et al were compared. The main improvement compared with our previous approach is a more elaborate treatment of the regions at the very boundary of the cavities, which yields a more accurate volume estimate. The cavity volume of a number of Plant Pathogenesis‐Related proteins of class 10 (PR‐10) were reevaluated and the volumes and other geometrical parameters for about 400 capsids of icosahedral viruses were reported. Using the same approach the volumes of amino acid residues in polypeptides as mean values averaged over multiple conformations of the side chain were also estimated. Proteins 2016; 84:1275–1286. © 2016 Wiley Periodicals, Inc.     

On the existence of MHn species with M=Al, Ga and n=4, 5, 6. Computational study of structures, stabilities and bonding

Based on second-order perturbation theory (MP2) predictions with large 6-311++G(3df, 3pd) basis set we have reviewed the possible structures and stabilities of a series of neutral MH_n(M=Al, Ga; n=4, 5, 6) species. For AlH₄ and AlH₅, our results confirm the previous theoretical findings, which indicate the dihydrogen C_s complexes (²A′) AlH₂(H₂) and (¹A′) AlH₃(H₂), respectively, as the lowest energy isomers. We found, similarly, C_s (²A′) GaH₂(H₂) and (¹A′) GaH₃(H₂) van der Waals complexes as the most stable species of the gallium analogues GaH₄ and GaH₅. The calculated H₂ dissociation energies (D_e) for AlH₂(H₂) and AlH₃(H₂) are of the order 1.8–2.5 kcalmol¹, whereas this range of values for GaH₂(H₂) and GaH₃(H₂) is 1.4–1.8 kcalmol¹ . Symmetry-adapted perturbation theory (SAPT) was used to analyze the interaction energies of these dihydrogen complexes (for n=5) to determine why the Ga species show a smaller binding energy than the Al species. The SAPT partitioning of the interaction energy showed significant differences between AlH₃(H₂) and GaH₃(H₂), resulting from the much stronger “hydride” character of the aluminum species. The experimental observation of AlH₂(H₂) and AlH₃(H₂), and likely GaH₃(H₂), via low-temperature matrix isolation has been reported recently by Pullumbi et al. and Andrews et al., supporting the theoretical predictions. For n=6, we found the degenerate C₂(²A) and C_s(²A′) MH₂(H₂)₂ “double H₂” type van der Waals complexes as the lowest energy species for both M=Al and Ga.Electronic Supplementary Material Supplementary material is available for this article at     

A novel approach to the van der pol oscillator: Natural frequency and entrainment

Abstract

The physics of the van der Pol oscillator as realized by the Meissner circuit is discussed by analogy to the beat phenomenon and by a consequent analysis of current balance. The current balance method leads to a new, very accurate equation for the dependence of the oscillator frequency on the feedback parameter. Several aspects of entrainment (existence, limited frequency range, dependence on parameters, phase shift) can be explained, too. Numerical results are presented which have been obtained by solving the homogeneous and inhomogeneous van der Pol equation with a Runge‐Kutta method.     

Sequence structure of van der Waals locks in proteins

Recent works has suggested that proteins in early evolution have gone through a stage of closed loop elements with a typical contour size of 25-35 residues. These closed loops are still the elementary protein units to these days, and can be used to spell out protein sequence/structure relationship through a relatively small number of protein prototypes. In this study we aimed to identify the sequences that are used to lock the loop ends to one another, and to show how an extensive dictionary of such locking pairs can be created using positional correlation data from a large proteome database, and structural data from PDB databases. Such a dictionary can be used in reconstructing the evolutionary pathway the modern proteins have gone through, and in identifying closed loop elements in modern proteins with yet unknown 3D structure.     

Discrete structure of van der Waals domains in globular proteins

Most globular proteins are divisible by domains, distinct substructures of the globule. The notion of hierarchy of the domains was introduced earlier via van der Waals energy profiles that allow one to subdivide the proteins into domains (subdomains). The question remains open as to what is the possible structural connection of the energy profiles. The recent discovery of the loop-n-lock elements in the globular proteins suggests such a structural connection. A direct comparison of the segmentation by van der Waals energy criteria with the maps of the locked loops of nearly standard size reveals a striking correlation: domains in general appear to consist of one to several such loops. In addition, it was demonstrated that a variety of subdivisions of the same protein into domains is just a regrouping of the loop-n-lock elements.     

Analysis of the interactions of sulfur‐containing amino acids in membrane proteins

The interactions of Met and Cys with other amino acid side chains have received little attention, in contrast to aromatic–aromatic, aromatic–aliphatic or/and aliphatic–aliphatic interactions. Precisely, these are the only amino acids that contain a sulfur atom, which is highly polarizable and, thus, likely to participate in strong Van der Waals interactions. Analysis of the interactions present in membrane protein crystal structures, together with the characterization of their strength in small‐molecule model systems at the ab‐initio level, predicts that Met–Met interactions are stronger than Met–Cys ≈ Met–Phe ≈ Cys–Phe interactions, stronger than Phe–Phe ≈ Phe–Leu interactions, stronger than the Met–Leu interaction, and stronger than Leu–Leu ≈ Cys–Leu interactions. These results show that sulfur‐containing amino acids form stronger interactions than aromatic or aliphatic amino acids. Thus, these amino acids may provide additional driving forces for maintaining the 3D structure of membrane proteins and may provide functional specificity.     

Filling small, empty protein cavities: structural and energetic consequences

Most proteins contain small cavities that can be filled by replacing cavity-lining residues by larger ones. Since shortening mutations in hydrophobic cores tend to destabilize proteins, it is expected that cavity-filling mutations may conversely increase protein stability. We have filled three small cavities in apoflavodoxin and determined by NMR and equilibrium unfolding analysis their impact in protein structure and stability. The smallest cavity (14 A3) has been filled, at two different positions, with a variety of residues and, in all cases, the mutant proteins are locally unfolded, their structure and energetics resembling those of an equilibrium intermediate of the thermal unfolding of the wild-type protein. In contrast, two slightly larger cavities of 20 A3 and 21 A3 have been filled with Val to Ile or Val to Leu mutations and the mutants preserve both the native fold and the equilibrium unfolding mechanism. From the known relationship, observed in shortening mutations, between stability changes and the differential hydrophobicity of the exchanged residues and the volume of the cavities, the filling of these apoflavodoxin cavities is expected to stabilize the protein by approximately 1.5 kcal mol(-1). However, both urea and thermal denaturation analysis reveal much more modest stabilizations, ranging from 0.0 kcal mol(-1) to 0.6 kcal mol(-1), which reflects that the accommodation of single extra methyl groups in small cavities requires some rearrangement, necessarily destabilizing, that lowers the expected theoretical stabilization. As the size of these cavities is representative of that of the typical small, empty cavities found in most proteins, it seems unlikely that filling this type of cavities will give rise to large stabilizations.