Annealing contour Monte Carlo algorithm for structure optimization in an off-lattice protein model

We present a space annealing version for a contour Monte Carlo algorithm and show that it can be applied successfully to finding the ground states for an off-lattice protein model. The comparison shows that the algorithm has made a significant improvement over the pruned-enriched-Rosenbluth method and the Metropolis Monte Carlo method in finding the ground states for AB models. For all sequences, the algorithm has renewed the putative ground energy values in the two-dimensional AB model and set the putative ground energy values in the three-dimensional AB model.     

Electrochemistry and electrogenerated chemiluminescence of twisted anthracene-functionalized bimesitylenes

The electrochemistry, spectroscopy, and electrogenerated chemiluminescence (ECL) of a variety of 2- and 4-fold anthracene-functionalized tetraarylbimesityls, AB1-4, were investigated. AB1-4 compounds contain a bimesityl core with 2- and 4-fold anthracene functionalities, which generate a rigid D(2d)-symmetric structure. Cyclic voltammetry of AB1 and AB2 showed two reversible, closely spaced one-electron transfers for both oxidation and reduction, and that of AB3 and AB4 showed four reversible, closely spaced one-electron transfers for oxidation and reduction in a benzene/acetonitrile solution. The multielectron transfer properties of all four compounds were confirmed by chronoamperometric experiments with an ultramicroelectrode and digital simulations. These serve as models to probe how interacting groups on a molecule affect the energies of successive electron transfers. AB1-4 compounds are highly fluorescent in nonaqueous solvents and display blue-green emission. They produce very strong ECL with emission at 480 nm, near that of the photoluminescence spectra that can be assigned to emission by direct formation of the singlet via the S-route.     

The condensation and ordering of models of empty liquids

We consider a simple model consisting of particles with four bonding sites ("patches"), two of type A and two of type B, on the square lattice, and investigate its global phase behavior by simulations and theory. We set the interaction between B patches to zero and calculate the phase diagram as the ratio between the AB and the AA interactions, ε(AB)*, varies. In line with previous work, on three-dimensional off-lattice models, we show that the liquid-vapor phase diagram exhibits a re-entrant or "pinched" shape for the same range of ε(AB)*, suggesting that the ratio of the energy scales--and the corresponding empty fluid regime--is independent of the dimensionality of the system and of the lattice structure. In addition, the model exhibits an order-disorder transition that is ferromagnetic in the re-entrant regime. The use of low-dimensional lattice models allows the simulation of sufficiently large systems to establish the nature of the liquid-vapor critical points and to describe the structure of the liquid phase in the empty fluid regime, where the size of the "voids" increases as the temperature decreases. We have found that the liquid-vapor critical point is in the 2D Ising universality class, with a scaling region that decreases rapidly as the temperature decreases. The results of simulations and theoretical analysis suggest that the line of order-disorder transitions intersects the condensation line at a multi-critical point at zero temperature and density, for patchy particle models with a re-entrant, empty fluid, regime.     

Binary nanoparticle superlattices in the semiconductor-semiconductor system: CdTe and CdSe

We report binary nanoparticle superlattices obtained by self-assembly of two different semiconductor quantum dots. Such a system is a means to include two discretized, quantum-confined, and complimentary semiconductor units in close proximity, for purposes of band gap matching and/or energy transfer. From a range of possible structures predicted, we observe an exclusive preference for the formation of Cuboctahedral AB13 and AB5 (isostructural with CaCu5) obtained in the system of 8.1 nm CdTe and 4.4 nm CdSe nanoparticles. For this system, a possible ionic origin for the formation of structures with lower packing densities was ruled out on the basis of electrophoretic mobility measurements. To understand further the principles of superlattice formation, we constructed space-filling curves for binary component hard spheres over the full range of radius ratio. In addition, the pair interaction energies due to core-core and ligand-ligand van der Waals (VDW) forces are estimated. The real structures are believed to form under a combined influence of entropic driving forces (following hard-sphere space filling principles) and the surface (due to ligand-ligand VDW).     

Ordered binary crystal phases of Lennard-Jones mixtures

The lattice energies at zero temperature are calculated, using Lennard-Jones interactions, for a large number of crystal structures associated with ordered binary compounds. In units of the AA interaction length and strength (i.e., sigmaAA= epsilonAA= 1.0) we examine the lowest energy structures, including coexisting phases, across the space of cross-species interactions 0.6< or = sigmaAB< or = 1.1 and 1.0< or = epsilonAB< or = 2.0. The remaining parameters sigmaBB= 0.88 and epsilonBB= 0.5 are chosen so that the parameter space studied includes the space of binary glass-forming alloys. In addition to some large unit cell structures such as Ni3P and PuBr3 appearing among the lowest lattice energies, a number of low-energy structures based on close-packed lattices are found that do not correspond to any experimentally observed crystals. The prevalence and stability of metastable crystal phases at the compositions AB, A2B, and A3B is examined.     

Nanoconfinement effects on the reversibility of hydrogen storage in ammonia borane: a first-principles study

We investigate atomistic mechanisms governing hydrogen release and uptake processes in ammonia borane (AB) within the framework of the density functional theory. In order to determine the most favorable pathways for the thermal inter-conversion between AB and polyaminoborane plus H(2), we calculate potential energy surfaces for the corresponding reactions. We explore the possibility of enclosing AB in narrow carbon nanotubes to limit the formation of undesirable side-products such as the cyclic compound borazine, which hinder subsequent rehydrogenation of the system. We also explore the effects of nanoconfinement on the possible rehydrogenation pathways of AB and suggest the use of photoexcitation as a means to achieve dehydrogenation of AB at low temperatures.     

Prediction of peptide conformation using a scale-transformed entropy sampling algorithm

An algorithm for predicting the lowest energy structure of a peptide has been developed. High-energy barriers on an energy surface can be easily overcome by logarithmically transforming the energy space. For efficient optimizations, the energy space is searched using a scale-transformed entropy sampling method, and conformations specific to a primary structure of the peptide are sampled with large weights. The efficiency of the present method is demonstrated by calculations on cholecystokinin octapeptide (CCK-8).     

Un modèle de transfert énergétique rotation-translation lors de dissociations unimoléculaires à trois atomes

A model of rotational-translational energy transfer in the exit-channel of a three-atom unimolecular reaction. For a three-atom unimolecular reaction of the type ABC → AB + C performed in a supersonic molecular beam experiment, we propose an analytical model to describe how the rotational angular momentum of AB varies from the transition state onto the separated products. This model is compared with quasiclassical trajectory calculations on a model potential energy surface and the agreement found is very satisfying. Including this model in a statistical treatment could possibly extend its ability to describe processes involving non-negligible exit-channel rotational-translational energy transfers.     

Adsorption Behavior and Dynamic Interactions of Anionic Acid Blue 25 on Agricultural Waste

In this study, adsorption characteristics of a negatively charged dye, Acid Blue 25 (AB25), on pomelo pith (PP) was studied by varying the adsorption parameters, with the aim of evaluating the adsorption mechanism and establishing the role of hydrogen bonding interactions of AB25 on agricultural wastes. The kinetics, intraparticle diffusion, mechanism, and thermodynamics of the AB25 adsorption were systematically evaluated and analyzed by pseudo-first-order and pseudo-second-order kinetic models, the Weber–Morris intraparticle and Boyd mass transfer models, the Langmuir, Freundlich, Dubinin–Radushkevich, and Temkin isotherm models, and the Van’t Hoff equation. It was found that AB25 adsorption followed pseudo-second-order kinetics, governed by a two-step pore-volume intraparticle diffusion of external mass transfer of AB25 onto the PP surface. The adsorption process occurred spontaneously. The adsorption mechanism could be explained by the Langmuir isotherm model, and the maximum adsorption capacity was estimated to be 26.9 mg g⁻¹, which is comparable to many reported adsorbents derived from agricultural wastes. Changes in the vibrational spectra of the adsorbent before and after dye adsorption suggested that AB25 molecules are bound to the PP surface via electrostatic and hydrogen bonding interactions. The results demonstrated that the use of pomelo pith, similar to other agricultural wastes, would provide a basis to design a simple energy-saving, sustainable, and cost-effective approach to remove negatively charged synthetic dyes from wastewater.     

Monte Carlo sampling algorithm for searching a scale-transformed energy space of polypeptides

A Monte Carlo sampling algorithm for searching a scale-transformed conformational energy space of polypeptides is presented. This algorithm is based on the assumption that energy barriers can be overcome by a uniform sampling of the logarithmically transformed energy space. This algorithm is tested with Met-enkephalin. For comparison, the entropy sampling Monte Carlo (ESMC) simulation is performed. First, the global minimum is easily found by the optimization of a scale-transformed energy space. With a new Monte Carlo sampling, energy barriers of 3000 kcal/mol are frequently overcome, and low-energy conformations are sampled more efficiently than with ESMC simulations. Several thermodynamic quantities are calculated with good accuracy.     

Highly Symmetric Patchy Multicompartment Nanoparticles from the Self-Assembly of ABC Linear Terpolymers in C-Selective Solvents

Multicompartment micelles, especially those with highly symmetric surfaces such as patchy-like, patchy, and Janus micelles, have tremendous potential as building blocks of hierarchical multifunctional nanomaterials. One of the most versatile and powerful methods to obtain patchy multicompartment micelles is by the solution-state self-assembly of linear triblock copolymers. In this article, we applied the simulated annealing method to study the self-assembly of ABC linear terpolymers in C-selective solvents. Simulations predict a variety of patchy and patchy-like multicompartment micelles with high symmetry and also yield a detailed phase diagram to reveal how to control the patchy multicompartment micelle morphologies precisely. The phase diagram demonstrates that the internal segregated micellar structure depends on the ratio between the volume fractions of the two solvophobic blocks and their incompatibility, whereas the overall micellar shape depends on the copolymer concentration. The relationship between the interfacial energy, stretching energy of chains and the micellar morphology, micellar morphological transition are elucidated by computing the average contact number among the species, the mean square end-to-end distances of the whole terpolymers, the AB blocks in the terpolymers, the AB diblock copolymers, and angle distribution of terpolymers. The anchoring effect of the solvophilic C block on micellar structures is also examined by comparing the morphologies formed from ABC terpolymers and AB diblock copolymers.     

A fluorescent, shape-persistent dendritic host with photoswitchable guest encapsulation and intramolecular energy transfer

A fluorescent and photoresponsive host based on rigid polyphenylene dendrimers (PPDs) has been synthesized. The key building block for the divergent dendrimer buildup is a complex tetracyclone 12 containing azobenzenyl, pyridyl, and ethynyl entities. The rigidity of polyphenylenes is of crucial importance for a site-specific placement of different functions: eight azobenzene (AB) moieties into the rigid scaffold, a fluorescent perylenetetracarboxdiimide (PDI) into the core, and eight pyridin functions into the interior cavities. AB moieties of host-1 undergo reversible cis-trans photoisomerization and are photostable, as confirmed by various techniques: UV-vis, (1)H NMR, size exclusion chromatography, and fluorescence correlation (FCS). In this system, AB moieties act as photoswitchable hinges and enable control over (i) molecular size, (ii) intramolecular energy transfer between AB and PDI, and (iii) encapsulation and release of guest molecules. The presence of PDI allows not only following the effect of cis-trans photoisomerization on molecular size with highly sensitive FCS but also monitoring the efficiency of the intramolecular energy transfer process (from AB to PDI) by time-resolved optical spectroscopy. Pyridyl functions were incorporated to facilitate guest uptake via hydrogen bonds between the host and guests. Also, we have demonstrated that the photoswitchability of the host can be utilized to actively encapsulate guest molecules into its interior cavities. This novel, light-driven encapsulation mechanism could enable the design of new drug delivery systems.     

Theoretical insight into the solvent effect on the stoichiometric reduction of carbonyl compounds by ammonia borane and N-methyl amine borane

For the traditional reduction of ketones and aldehydes, NH₃BH₃ ( AB ) and N-methyl amine borane ( M _n AB ) have been effective reducing agents. However, the reaction process is indefinite and different mechanisms have been proposed; also the solvent effect, which is closely related to the mechanism, has not been considered seriously. Here we employ density functional theory to carry out a comprehensive study on the mechanism. The calculated free energy of the concerted double hydrogen transfer process is lower than the hydroboration mechanism by 4.7 kcal/mol, which indicates that reduction of carbonyl by AB is likely due to be the concerted double hydrogen transfer in both aprotic (tetrahydrofuran) and protic (MeOH) solvents. For the reduction by M _n AB , the corresponding free energies of all reactions are higher than those of AB . Meanwhile, the reduction of benzaldehyde by M _n AB (n = 1, 2) also favors a concerted double hydrogen transfer rather than hydroboration.     

Computational study of the release of H2 from ammonia borane dimer (BH3NH3)2 and its ion pair isomers

High-level electronic structure calculations have been used to map out the relevant portions of the potential energy surfaces for the release of H2 from dimers of ammonia borane, BH3NH3 (AB). Using the correlation-consistent aug-cc-pVTZ basis set at the second-order perturbation MP2 level, geometries of stationary points were optimized. Relative energies were computed at these points using coupled-cluster CCSD(T) theory with the correlation-consistent basis sets at least up to the aug-cc-pVTZ level and in some cases extrapolated to the complete basis set limit. The results show that there are a number of possible dimers involving different types of hydrogen-bonded interactions. The most stable gaseous phase (AB)2 dimer results from a head-to-tail cyclic conformation and is stabilized by 14.0 kcal/mol with respect to two AB monomers. (AB)2 can generate one or two H2 molecules via several direct pathways with energy barriers ranging from 44 to 50 kcal/mol. The diammoniate of diborane ion pair isomer, [BH4-][NH3BH2NH3+] (DADB), is 10.6 kcal/mol less stable than (AB)2 and can be formed from two AB monomers by overcoming an energy barrier of approximately 26 kcal/mol. DADB can also be generated from successive additions of two NH3 molecules to B2H6 and from condensation of AB with separated BH3 and NH3 molecules. The pathway for H2 elimination from DADB is characterized by a smaller energy barrier of 20.1 kcal/mol. The alternative ion pair [NH4+][BH3NH2BH3-] is calculated to be 16.4 kcal/mol above (AB)2 and undergoes H2 release with an energy barrier of 17.7 kcal/mol. H2 elimination from both ion pair isomers yields the chain BH3NH2BH2NH3 as product. Our results suggest that the neutral dimer will play a minor role in the release of H2 from ammonia borane, with a dominant role from the ion pairs as observed experimentally in ionic liquids and the solid state.     

Photon Harvesting in Sunscreen‐Based Functional Nanoparticles

The ultraviolet light component in the solar spectrum is known to cause several harmful effects, such as allergy, skin ageing, and skin cancer. Thus, current research attention has been paid to the design and fundamental understanding of sunscreen‐based materials. One of the most abundantly used sunscreen molecules is Avobenzone (AB), which exhibits two tautomers. Here, we highlight the preparation of spherically shaped nanoparticles from the sunscreen molecule AB as well as from sunscreen‐molecule‐encapsulated polymer nanoparticles in aqueous media and study their fundamental photophysical properties by steady‐state and time‐resolved spectroscopy. Steady‐state studies confirm that the AB molecule is in the keto and enol forms in tetrahydrofuran, whereas the enol form is stable in the case of both AB nanoparticles and AB‐encapsulated poly(methyl methacrylate) (PMMA) nanoparticles. Thus, the keto–enol transformation of AB molecules is restricted to a nanoenvironment. An enhancement of photostability in both the nanoparticle and PMMA‐encapsulated forms under UV light irradiation is observed. The efficient excited energy transfer (60 %) from AB to porphyrin molecules opens up further prospects in potential applications as light‐harvesting systems.     

A machine learning technique toward generating minimum energy structures of small boron clusters

The search for a global minimum related to molecular electronic structure and chemical bonding has received wide attention based on some theoretical calculations at various levels of theory. Particle swarm optimization (PSO) algorithm and modified PSO have been used to predict the energetically stable/metastable states associated with a given chemical composition. Out of a variety of techniques such as genetic algorithm, basin hopping, simulated annealing, PSO, and so on, PSO is considered to be one of the most suitable methods due to its various advantages over others. We use a swarm‐intelligence based parallel code to improve a PSO algorithm in a multidimensional search space augmented by quantum chemical calculations on gas phase structures at 0 K without any symmetry constraint to obtain an optimal solution. Our currently employed code is interfaced with Gaussian software for single point energy calculations. The code developed here is shown to be efficient. Small population size (small cluster) in the multidimensional space is actually good enough to get better results with low computational cost than the typical larger population. But for larger systems also the analysis is possible. One can try with a large number of particles as well. We have also analyzed how arbitrary and random structures and the local minimum energy structures gravitate toward the target global minimum structure. At the same time, we compare our results with that obtained from other evolutionary techniques.     

量子化学MNDO法中键强度的描述

1 前言以CNDO 法为基础建立的键函数方法,把量子化学的成键强度与传统的成键和非成键相互作用的有关项直接联系了起来.它对σ、π体系都能作定量描述,并且有旋转不变性,满足对称性要求,能很好地随键长变化反映键强度情况,并作了很好的尝试.按照同样原理,本文用理论上已作了许多改进的MNDO 法建立原子对作用能E_(AB)来量度成键强度.理论上可以证明,MNDO 法的原子     

Controlled-advancement rigid-body optimization of nanosystems

In this study, we propose a novel optimization algorithm, with application to the refinement of molecular complexes. Particularly, we consider optimization problem as the calculation of quasi-static trajectories of rigid bodies influenced by the inverse-inertia-weighted energy gradient and introduce the concept of advancement region that guarantees displacement of a molecule strictly within a relevant region of conformational space. The advancement region helps to avoid typical energy minimization pitfalls, thus, the algorithm is suitable to work with arbitrary energy functions and arbitrary types of molecular complexes without necessary tuning of its hyper-parameters. Our method, called controlled-advancement rigid-body optimization of nanosystems (Carbon), is particularly useful for the large-scale molecular refinement, as for example, the putative binding candidates obtained with protein–protein docking pipelines. Implementation of Carbon with user-friendly interface is available in the SAMSON platform for molecular modeling at https://www.samson-connect.net . © 2019 Wiley Periodicals, Inc.     

A theoretical study on the structures and energetics of hypothetical TiM(NCN)3 compounds of the 3d transition metals

Quasi-ternary cyanamides and carbodiimides of general formula AB(NCN)(3) with A not equal B have neither been predicted nor synthesized. Thus, hypothetical compounds of that kind containing 3d transition metals were considered (A = Ti, B = Mn, Fe, Co, Ni, Cu) by means of density-functional calculations on 34 structural models, most of which were derived from chemically related phases. After performing structure optimizations based on the local-density approximation, the relative energetic orderings are rationalized in terms of geometrical factors such as molar volumes and polyhedral connections. Total-energy generalized-gradient calculations evidence that the most stable models are enthalpically favored with respect to the elements. Even at ambient temperatures, the ternary phases are predicted as being thermodynamically stable in terms of their Gibbs free formation energies, especially if energetically competing and low-lying binaries (TiC, TiN) can be excluded by a kinetic reaction control. The best models are characterized by low-spin magnetic transition metals found in octahedral coordination, and the TiN(6) and MN(6) polyhedra either share faces or edges.     

关于副本交换分子动力学模拟复杂化学反应的研究

本文研究用温度副本交换分子动力学(T-REMD)和哈密顿副本交换分子动力学(H-REMD)方法模拟复杂化学反应的问题。使用具有不同活化能和反应能的简单置换反应模型,我们检验了上述两种方法用来预测反应平衡产物的效率和应用范围。T-REMD方法对具有适度活化能(约< 20 kcal·mol^-1)或者反应能量(< 3 kcal·mol^-1)的放热反应是有效的。由于在相空间的不完整采样,对于同时具有高活化能和反应能量的反应其模拟效率有严重障碍,并且对于吸热反应问题更为显着。另一方面,H-REMD对一系列具有不同活化能的反应能的模型表现出色,与T-REMD相比,H-REMD可以使用更少的副本获得优异的结果。