Point interactions for 3D sub-Laplacians

In this paper we show that, for a sub-Laplacian Δ on a 3-dimensional manifold M, no point interaction centered at a point $q_0\in M$ exists. When M is complete w.r.t. the associated sub-Riemannian structure, this means that Δ acting on $C_0^{\infty }(M?\{q_0\})$ is essentially self-adjoint in $L^2(M)$. A particular example is the standard sub-Laplacian on the Heisenberg group. This is in stark contrast with what happens in a Riemannian manifold N, whose associated Laplace-Beltrami operator acting on $C_0^{\infty }(N?\{q_0\})$ is never essentially self-adjoint in $L^2(N)$, if $\dim ?N\le 3$. We then apply this result to the Schrödinger evolution of a thin molecule, i.e., with a vanishing moment of inertia, rotating around its center of mass.     

[Nb@Ge13/14]3−: New Family Members of Ge-Based Intermetalloid Clusters

During the past two decades, single-atom-centered medium-sized germanium clusters [M@Ge_n] (M=transition metals, n>12) have been extensively explored, both from theoretical perspectives and experimental gas-phase syntheses. However, the actual structural arrangements of the Ge₁₃ and Ge₁₄ endohedral cages are still ambiguous and have long remained an unresolved problem for experimental implementation. In this work, we successfully synthesize 13-/14-vertex Ge clusters [Nb@Ge₁₃]³⁻ ( 1 ) and [Nb@Ge₁₄]³⁻ ( 2 ), which are structurally characterized and exhibit unprecedented topologies, neither classical deltahedra nor 3-connected polyhedral structures. Theoretical analysis indicates that the major stabilization of the Ge backbones arises due to the substantial interaction of Ge 4p-AOs with the endohedral Nb 4d-AOs through three/four-center two-electron bonds with an enhanced electron density accumulated over the shortest Nb−Ge13 contact in 1 . Low occupancies of the direct two-center two-electron (2c–2e) Nb−Ge and Ge−Ge σ bonds point to a considerable degree of electron delocalization over the Ge cages revealing their electron deficiency.     

Recent progress on pure organic room temperature phosphorescence materials based on host-guest interactions

Pure organic room temperature phosphorescence (RTP) has been attracting a lot interest recently. So far, many strategies have succeeded in achieving efficient organic RTP materials by increasing the rate of intersystem crossing (ISC) and suppressing non-radiative transitions. In supramolecular chemistry, the control and regulation of molecular recognition based on the role of the host and guest in supramolecular polymers matrix, has attracted much attention. Recently, researchers have successfully achieved room temperature phosphorescence of pure organic complexes through host-guest interactions. The host molecule specifically includes the phosphorescent guest to reduce non-radiative transitions and enhance room temperature phosphorescence emission. This review aims to describe the developments and achievements of pure organic room temperature phosphorescence systems through the mechanism of host-guest interactions in recent years, and demonstrates the exploration and pursuit of phosphorescent materials of researchers in different fields.     

Experimental and Theoretical Insights into the Optical Properties and Intermolecular Interactions in Push-Pull Bromide Salts

Experimental and theoretical insights into the nature of intermolecular interactions and their effect on optical properties of 1-allyl-4-(1-cyano-2-(4-dialkylaminophenyl)vinyl)pyridin-1-ium bromide salts ( I and II ) are reported. A comparison of optical properties in solution and in the solid-state of the salts ( I and II ) with their precursors ( Ia and IIa ) is made. The experimental absorption maxima (λ_max) in CHCl₃ is at 528 nm for I and at 542 nm for II , and a strong bathochromic shift of ∼110 nm is observed for salts I and II compared with their precursors. The absorption bands in solid-state at ∼627 nm for I and at ∼615 nm for II that are assigned to charge transfer (CT) effect. The optical properties and single crystal structural features of I and II are explored by experimental and computational tools. The calculated λ_max and the CT are in good agreement with the experimental results. The intermolecular interactions existing in the crystal structures and their energies are quantified for various dimers by PIXEL, QTAIM and DFT approaches. Three types of interactions, (i) the cation⋅⋅⋅cation interactions, (ii) cation⋅⋅⋅anion interactions and (iii) anion⋅⋅⋅anion interactions are observed. The cationic moiety is mainly destabilized by C−H⋅⋅⋅N/π and π⋅⋅⋅π interactions whereas the cation and anion moiety is predominantly stabilized by strong C−H⋅⋅⋅Br⁻ interactions in both structures. The existence of charge transfer between cation and anion moieties in these structures is established through NBO analysis.     

Modeling halogen bonding with planewave density functional theory: Accuracy and challenges

Inspired by the recent interest of halogen bonding (XB) in the solid state, we detail a comprehensive benchmark study of planewave DFT geometry and interaction energy of lone-pair (LP) type and aromatic (AR) type halogen bonded complexes, using PAW and USPP pseudopotentials. For LP-type XB dimers, PBE-PAW generally agrees with PBE/aug-cc-pVQZ(−pp) geometries but significantly overbinds compared to CCSD(T)/aug-cc-pVQZ(-pp). Grimme's D3 dispersion corrections to PBE-PAW gives better agreement to the MP2/cc-pVTZ(-pp) results for AR-type dimers. For interaction energies, PBE-PAW may overbind or underbind for weaker XBs but clearly overbinds for stronger XBs. D3 dispersion corrections exacerbate the overbinding problem for LP-type complexes but significantly improves agreement for AR-type complexes compared to CCSD(T)/CBS. Finally, for periodic XB crystals, planewave PBE methods slightly underestimate the XB lengths by 0.03 to 0.05 Å. © 2019 Wiley Periodicals, Inc.     

A new sequence based encoding for prediction of host–pathogen protein interactions

Pathogen–host interactions are very important to figure out the infection process at the molecular level, where pathogen proteins physically bind to human proteins to manipulate critical biological processes in the host cell. Data scarcity and data unavailability are two major problems for computational approaches in the prediction of pathogen–host interactions. Developing a computational method to predict pathogen–host interactions with high accuracy, based on protein sequences alone, is of great importance because it can eliminate these problems. In this study, we propose a novel and robust sequence based feature extraction method, named Location Based Encoding, to predict pathogen–host interactions with machine learning based algorithms. In this context, we use Bacillus Anthracis and Yersinia Pestis data sets as the pathogen organisms and human proteins as the host model to compare our method with sequence based protein encoding methods, which are widely used in the literature, namely amino acid composition, amino acid pair, and conjoint triad. We use these encoding methods with decision trees (Random Forest, j48), statistical (Bayesian Networks, Naive Bayes), and instance based (kNN) classifiers to predict pathogen–host interactions. We conduct different experiments to evaluate the effectiveness of our method. We obtain the best results among all the experiments with RF classifier in terms of F1, accuracy, MCC, and AUC.     

Strong Pancake 2e/12c Bond in π-Stacking Phenalenyl Derivatives Avoiding Bond Conversion

The nature of the 2e/12c bond and its conversion to a carbon-carbon single bond in phenalenyl dimers have prompted a great deal of interests recently. In this work, we theoretically investigated a series of π-stacking phenalenyl derivatives with 2e/12c bonding character by density functional theory (DFT) calculations to elucidate origin of this unusual bond conversion. Results show that bond-conversion of the phenalenyl dimer easily occurs at room-temperature both dynamically and thermodynamically. However, bond-conversion of hetero π-stacking adducts, in which the two center carbon atoms were substituted by boron and nitrogen atoms, respectively, is much more difficult, because the 2e/12c bond is stabilized by its charge transfer character. Consequently, the bond-conversion is an endothermic process, albeit with a low conversion barrier. Interestingly, Lewis acid-base interactions would be induced by substitution of the center nitrogen atom to phosphorus atom. The 2e/12c bond is further stabilized by 5.9 kcal mol⁻¹ and its conversion is also thermodynamically unfavorable.     

In silico structure-based design of enhanced peptide inhibitors targeting RNA polymerase PAN-PB1C interaction

Developing antivirals for influenza A virus (FluA) has become more challenging due to high range of antigenic mutation and increasing numbers of drug-resistant viruses. Finding a selective inhibitor to target highly conserved region of protein-protein interactions interface, thereby increasing its efficiency against drug resistant virus could be highly beneficial. In this study, we used in silico approach to derive FluAPep1 from highly conserved region, PA_N-PB1_C interface and generated 121 FluAPep1 analogues. Interestingly, we found that the FluAPep1 interaction region in the PA_N domain are highly conserved in many FluA subtypes. Especially, FluAPep1 targets two pandemic FluA strains, H1N1/avian/2009 and H3N2/Victoria/1975. All of these FluA subtypes PA_N domain (H1N1/H3N2CAN/H3N2VIC/H7N1/H7N2) were superimposed with PA_N domain from H17N10 and the calculated root mean standards deviations were less than 3 Å. FlexPepDock analysis revealed that FluAPep1 exhibited higher binding affinity (score -246.155) with the PA_N domain. In addition, around 86% of non-hot spot mutated peptides (FluAPep28-122) showed enhanced binding affinity with PA_N domain. ToxinPred analysis confirmed that designed peptides were non-toxic. Thus, FluAPep1 and its analogues has potential to be further developed into an antiviral treatment against FluA infection.     

Differences and similarities among hypoxanthinium nitrate hydrate structures

Crystals of hypoxanthinium (6‐oxo‐1H,7H‐purin‐9‐ium) nitrate hydrates were investigated by means of X‐ray diffraction at different temperatures. The data for hypoxanthinium nitrate monohydrate (C₅H₅N₄O⁺·NO₃^?·H₂O, Hx1 ) were collected at 20, 105 and 285 K. The room‐temperature phase was reported previously [Schmalle et al. (1990). Acta Cryst. C 46 , 340–342] and the low‐temperature phase has not been investigated yet. The structure underwent a phase transition, which resulted in a change of space group from Pmnb to P2₁/n at lower temperature and subsequently in nonmerohedral twinning. The structure of hypoxanthinium dinitrate trihydrate (H₃O⁺·C₅H₅N₄O⁺·2NO₃^?·2H₂O, Hx2 ) was determined at 20 and 100 K, and also has not been reported previously. The Hx2 structure consists of two types of layers: the `hypoxanthinium nitrate monohydrate' layers (HX) observed in Hx1 and layers of Zundel complex H₃O⁺·H₂O interacting with nitrate anions (OX). The crystal can be considered as a solid solution of two salts, i.e. hypoxanthinium nitrate monohydrate, C₅H₅N₄O⁺·NO₃^?·H₂O, and oxonium nitrate monohydrate, H₃O⁺(H₂O)·NO₃^?.     

Uncertainty quantification for dynamics of geometrically nonlinear structures coupled with internal acoustic fluids in presence of sloshing and capillarity

In this paper, we propose an uncertainty quantification analysis, which is the continuation of a recent work performed in a deterministic framework. The fluid–structure system under consideration is the one experimentally studied in the sixties by Abramson, Kana, and Lindholm from the Southwest Research Institute under NASA contract. This coupled system is constituted of a linear acoustic liquid contained in an elastic tank that undergoes finite dynamical displacements, inducing geometrical nonlinear effects in the structure. The liquid has a free surface on which sloshing and capillarity effects are taken into account. The problem is expressed in terms of the acoustic pressure field in the fluid, of the displacement field of the elastic structure, and of the normal elevation field of the free surface. The nonlinear reduced-order model constructed in the recent work evoked above is reused for implementing the nonparametric probabilistic approach of uncertainties. The objective of this paper is to present a sensitivity analysis of this coupled fluid–structure system with respect to uncertainties and to use a classical statistical inverse problem for carrying out the experimental identification of the hyperparameter of the stochastic model. The analysis show a significant sensitivity of the displacement of the structure, of the acoustic pressure in the liquid, and of the free-surface elevation to uncertainties in both linear and geometrically nonlinear simulations.