Fast multipole method for three-dimensional systems with periodic boundary condition in two directions

We derived a new expression for the electrostatic interaction of three-dimensional charge-neutral systems with two-dimensional periodic boundary conditions (slab geometry) using a fast multipole method (FMM). Contributions from all the image cells are expressed as a sum of real and reciprocal space terms, and a self-interaction term. The reciprocal space contribution consists of two parts: zero and nonzero terms of the absolute value of the reciprocal lattice vector. To test the new expressions, electrostatic interactions were calculated for a randomly placed charge distribution in a cubic box and liquid water produced by molecular dynamics calculation. The accuracy could be controlled by the degree of expansion of the FMM. In the present expression, the computational complexity of the electrostatic interaction of N-particle systems is order N, which is superior to that of the conventional two-dimensional periodic Ewald method for a slab geometry and the particle mesh Ewald method with a large empty space at an interface of the unit cell. © 2020 Wiley Periodicals, Inc.     

Algorithms for GPU‐based molecular dynamics simulations of complex fluids: Applications to water,mixtures, and liquid crystals

A custom code for molecular dynamics simulations has been designed to run on CUDA‐enabled NVIDIA graphics processing units (GPUs). The double‐precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse‐grained and atomistic models, holonomic constraints, Nosé–Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard‐Jones and Gay‐Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n‐hexane/2‐propanol mixture; and a liquid crystal mesogen, 2‐(4‐butyloxyphenyl)‐5‐octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33–119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69–287 fold improvement and three GPUs yield a 101–377 fold speedup. © 2015 Wiley Periodicals, Inc.     

An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions

Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component. For short distances from the point of interest, the HCP uses the full set of atomic charges available. For long‐distance interactions, the approximate charge distributions with smaller sets of charges are used instead. For a structure consisting of N charges, the computational cost of computing the pairwise interactions via the HCP scales as O(N log N), under assumptions about the structural organization of biomolecular structures generally consistent with reality. A proof‐of‐concept implementation of the HCP shows that for large structures it can lead to speed‐up factors of up to several orders of magnitude relative to the exact pairwise O(N²) all‐atom computation used as a reference. For structures with more than 2000–3000 atoms the relative accuracy of the HCP (relative root‐mean‐square force error per atom), approaches the accuracy of the particle mesh Ewald (PME) method with parameter settings typical for biomolecular simulations. When averaged over a set of 600 representative biomolecular structures, the relative accuracies of the two methods are roughly equal. The HCP is also significantly more accurate than the spherical cutoff method. The HCP has been implemented in the freely available nucleic acids builder (NAB) molecular dynamics (MD) package in Amber tools. A 10 ns simulation of a small protein indicates that the HCP based MD simulation is stable, and that it can be faster than the spherical cutoff method. A critical benefit of the HCP approximation is that it is algorithmically very simple, and unlike the PME, the HCP is straightforward to use with implicit solvent models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Melting behaviors of icosahedral metal clusters studied by Monte Carlo simulations

We present an atom‐resolved analysis method that traces physical quantities such as the root‐mean‐square bond length fluctuation and coordination number for individual atoms as functions of temperature or time. This method is applied to explain the temperature‐dependent behaviors of three types of Ni_N (N=12,13,14) clusters. The detailed studies for the three types of clusters reveal characteristics as follows: (a) as the temperature increases, all three types of clusters undergo two‐stage melting, irrespective of the existence of vacancy or adatom on the icosahedral surfaces, (b) the melting of icosahedral clusters with vacancy starts with vacancy hopping, which has not been observed for any type of small clusters (N<34), (c) the melting of the icosahedral clusters with adatom (N=14) is initiated by adatom hopping, followed by the site exchange between the adatom and surface atoms. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 380–387, 2000     

The Synthesis and One‐ and Two‐Photon Optical Properties of Dipolar,Quadrupolar and Octupolar Donor–Acceptor Molecules Containing Dimesitylboryl Groups

Two series of related donor–acceptor conjugated dipolar, pseudo‐quadrupolar (V‐shaped) and octupolar molecular systems based on the p‐dimesitylborylphenylethynylaniline core, namely, 4‐(4‐dimesitylborylphenylethynyl)‐N,N‐dimethylaniline, 4‐[4‐(4‐dimesitylborylphenylethynyl)phenylethynyl]‐N,N‐dimethylaniline, 3,6‐bis(4‐dimesitylborylphenylethynyl)‐N‐n‐butylcarbazole and tris[4‐(4‐dimesitylborylphenylethynyl)phenyl]amine, and on the E‐p‐dimesitylborylethenylaniline motif, namely, E‐4‐dimesitylborylethenyl‐N,N‐di(4‐tolyl)aniline, 3,6‐bis(E‐dimesitylborylethenyl)‐N‐n‐butylcarbazole and tris(E‐4‐dimesitylborylethenylphenyl)amine have been synthesised by palladium‐catalyzed cross‐coupling and hydroboration routes, respectively. Their absorption and emission maxima, fluorescence lifetimes and quantum yields have been obtained and their two‐photon absorption (TPA) spectra and TPA cross‐sections have been examined. Of these systems, the octupolar compound tris(E‐4‐dimesitylborylethenylphenyl)amine has been shown to exhibit the largest TPA cross‐section among the two series of approximately 1000 GM at 740 nm. Its TPA performance is comparable to those of other triphenylamine‐based octupoles of similar size. The combination of such large TPA cross‐sections and high emission quantum yields, up to 0.94, make these systems attractive for applications involving two‐photon excited fluorescence (TPEF).     

Exploring the similarities between potential smoothing and simulated annealing

Simulated annealing and potential function smoothing are two widely used approaches for global energy optimization of molecular systems. Potential smoothing as implemented in the diffusion equation method has been applied to study partitioning of the potential energy surface (PES) for N‐Acetyl‐Ala‐Ala‐N‐Methylamide (CDAP) and the clustering of conformations on deformed surfaces. A deformable version of the united‐atom OPLS force field is described, and used to locate all local minima and conformational transition states on the CDAP surface. It is shown that the smoothing process clusters conformations in a manner consistent with the inherent structure of the undeformed PES. Smoothing deforms the original surface in three ways: structural shifting of individual minima, merging of adjacent minima, and energy crossings between unrelated minima. A master equation approach and explicit molecular dynamics trajectories are used to uncover similar features in the equilibrium probability distribution of CDAP minima as a function of temperature. Qualitative and quantitative correlations between the simulated annealing and potential smoothing approaches to enhanced conformational sampling are established. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 531–552, 2000     

Development and rheological investigation of novel alginate/N‐succinylchitosan hydrogels

In the present article alginate hydrogels and novel hydrogels based on blends of alginate/N‐succinylchitosan have been realized in water solution at neutral conditions. The gels have been obtained by crosslinking via the internal setting method using calcium carbonate (CaCO₃) as calcium ions source. A rheological investigation of both the plain alginate and the alginate/N‐succinylchitosan blend hydrogels has been performed by means of oscillatory dynamic measurements. The effect of the inclusion of different amounts of CaCO₃ on the critical deformation (γ_c) characterizing the limit of the linear viscoelastic regime has been studied for the plain alginate gels. The frequency response in small amplitude oscillatory experiments of the plain alginate gels has been investigated in terms of the storage (G′) and loss (G″) modulus behavior. The dynamic data have been interpreted in terms of the Friedrich and Heymann model. The inclusion of the N‐succinylchitosan, in the range 10–50% w/w, had no effect on the γ_c values. On the contrary, when the 10% w/w of the N‐succinylchitosan is added to the plain alginate gels, a significant increase in the storage modulus values is recorded for all the systems analyzed. The gelation kinetics has been investigated and the results indicate that the kinetics process can be accelerated increasing the percentage of Ca⁺² ions and/or including the N‐succinylchitosan in the plain alginate systems. Finally, the morphological analysis of scaffolds obtained from the hydrogels through freeze‐drying revealed an interconnected porous structure. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1167–1182, 2008     

SPE–HPLC–MS/MS method for the trace analysis of tobacco‐specific N‐nitrosamines and 4‐(methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanol in rabbit plasma using tetraazacalix[2]arene[2]triazine‐modified silica as a sorbent

Tobacco‐specific N‐nitrosamines (TSNAs), including N′‐nitrosonornicotine, 4‐(methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanone, N′‐nitrosoanatabine, and N′‐nitrosoanabasine, have been implicated as a source of carcinogenicity in tobacco and cigarette smoke. We present a rapid and effective method comprising SPE based on tetraazacalix[2]arene[2]triazine‐modified silica as sorbent and analysis with HPLC–MS/MS for the determination of TSNAs and 4‐(methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanol (NNAL), a metabolite of 4‐(methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanone, in rabbit plasma. The linear dynamic ranges were 10–2000 pg/mL for NNAL and 4–2000 pg/mL for the four TSNAs with good correlation coefficients (>0.9965). The LODs were in the range of 0.9–3.7 pg/mL, and the LOQs were between 2.9 and 12.3 pg/mL. The accuracies of the method were also evaluated and found to be in the range of 90.1–113.3%. This method is promising to be applied to the preconcentration and determination of TSNAs and NNAL in smoke and human body fluids.     

Synthesis and polarized light‐induced birefringence of new polymethacrylates containing carbazolyl and azobenzene pendant groups

Low T_g copolymers of [11(N‐carbazolyl)undecylmethacrylate] and [2,5‐dimethylphenyl‐[(4‐nitrophenyl)azo]‐phenoxyalkylmethacrylate] have been synthesized and the polarized light‐induced birefringence of thick films (70 μm) has been investigated at a constant deducted temperature relative to T_g (T − T_g = 10 °C). The optical properties of these copolymers have been studied in relation to the azo‐dye content and the length of the alkyl spacer between the azo‐dye and the methacrylic backbone. They have been compared with the dispersion of (4‐methoxy‐2,5‐dimethylphenyl)‐(4‐nitrophenyl)diazene (DMNPAA) within a poly[11(N‐carbazolyl)undecyl‐methacrylate] and a poly[N‐vinylcarbazole] (PVK) matrix. The experimental curves have been fitted by biexponentials, so emphasizing the effects of the copolymer structure on the kinetics of the writing process. The photoinduced orientation is more than three orders of magnitude higher in a grafted material compared to the dispersion version. The azo‐dye concentration also has an important role in both the amplitude and the dynamics of the photo‐orientation. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 205–213, 2000     

N‐phenyl‐substituted pyrrolidines,piperidines and azabicyclics by a tandem reduction‐double reductive amination reaction

N‐Phenyl‐substituted pyrrolidines and piperidines have been synthesized by catalytic reduction of nitrobenzene in the presence of 4‐ and 5‐oxoaldehydes, respectively. The process involves reduction of the aromatic nitro group to give the N‐phenylhydroxylamine or aniline followed by reductive amination with the two carbonyl functional groups. Monocyclic systems are generally formed in high yield and are easily purified. The method has also been extended to the synthesis of fused N‐phenylazabicyclics from 2‐(3‐oxo‐propyl)cycloalkanones. A high degree of diastereoselectivity for the trans‐fused product is observed in substrates having an ester group α to the cycloalkanone carbonyl. Bicyclic precursors lacking this ester group give mixtures of cis and trans products. Finally, contrary to previous reports, we have demonstrated that aniline can be substituted for nitrobenzene in these reactions.     

己内酰胺一步法氢化烷基化合成N-烷基环己亚胺

A new synthetic method for the preparation of N-alkylhexahydroazepine by one-step catalytic alkylation and hydrogenation of caprolactam has been developed. Alkylated caprolactam was firstly synthesized by catalytic alkylation of caprolactam with alcohol and then directly hydrogenated into N-alkylhexahydroazepine over Cu-ZnO/γ-Al2O3 catalyst.     

Postgel properties in the statistical crosslinking of heterochains. II. Free‐radical crosslinking copolymerization

The heterochain crosslinking theory is applied to postgel behavior in the free‐radical crosslinking copolymerization of vinyl and divinyl monomers. In this context, the crosslinked polymer formation can be viewed as a system in which the primary chains formed at different times are combined in accordance with the statistical chain‐connection rule governed by the chemical reaction kinetics. Because the primary chains are formed consecutively, the number of chain types N must be extrapolated to infinity, N → ∞. Practically, such extrapolation can be conducted with the calculated values for only three different N values. The analytical expressions for the weight fraction and average molecular weights of the sol fraction are derived for the general primary chain length distribution function in free‐radical polymerization. Illustrative calculations show that the obtained results agree with those from the Monte Carlo method, and that the postgel properties in free‐radical crosslinking copolymerization systems could be significantly different from those in randomly crosslinked systems. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 2342–2350, 2000     

New Lipophilic 2‐Amino‐N,N′‐dialkyl‐4,5‐dimethylimidazolium Cations: Synthesis,Structure, Properties,and Outstanding Thermal Stability in Alkaline Media

A series of new N,N′‐dialkyl‐4,5‐dimethylimidazolium cations possessing electron‐rich 2‐imidazolylidene‐ or phosphoranylidene‐amino substituents has been efficiently synthesized from common precursors, N,N′‐dialkyl‐4,5‐dimethylimidazol‐2‐ylidenes. The new lipophilic salts obtained have been found to be highly stable towards strong alkali under both biphasic and homogeneous conditions. Their exceptional aqueous base resistance, which has hitherto only been seen with peralkylated polyaminophosphazenium cations, may be attributed to three factors: aromatic stabilization, efficient resonance charge delocalization, and steric protection of the exocyclic nitrogen linkage due to bulky lipophilic N‐alkyl substituents.     

Postgel properties in the statistical crosslinking of heterochains. I. Systems with N types of chains

The heterochain crosslinking model describes nonrandom crosslinking of polymer chains and is an extension of the classical Flory/Stockmayer gelation theory. We consider the postgelation relationship for the system consisting of N types of polymer chains, in which the probability that a crosslink point on an i‐type chain is connected to a j‐type chain is explicitly given by p_ij. The analytical solutions for the weight fraction of the sol, the number‐average and weight‐average molecular weights within the sol fraction, and the crosslinking density within the sol and gel fractions are derived for the systems, with each type of chain conforming to the Schulz–Zimm distribution. Illustrative calculations are shown for the systems consisting of two and three types of chains, and the obtained results agree with those from the Monte Carlo method. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 2333–2341, 2000     

Synergistic interaction of epoxides and N‐vinylcarbazole during photoinitiated cationic polymerization

A kinetic study was conducted of the independent photoinitiated cationic polymerization of a number of epoxide monomers and mixtures of these monomers with N‐vinylcarbazole. The results show that these two different classes of monomers undergo complex synergistic interactions with one another during polymerization. It was demonstrated that N‐vinylcarbazole as well as other carbazoles are efficient photosensitizers for the photolysis of both diaryliodonium and triarylsulfonium salt photoinitiators. In the presence of large amounts of N‐vinylcarbazole, the rates of the cationic ring‐opening photopolymerization of epoxides are markedly accelerated. This effect has been ascribed to a photoinitiated free‐radical chain reaction that results in the oxidation of monomeric and polymeric N‐vinylcarbazole radicals by the onium salt photoinitiators to generate cations. These cations can initiate the ring‐opening polymerization of the epoxides, leading to the production of copolymers. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 3697–3709, 2000     

One‐pot Synthesis of 2,5‐Disubstituted‐1,3,4‐oxadiazoles Based on the Reaction of N,N‐Dimethyl Amides with Acid Hydrazides

Convenient and efficient one pot method for the synthesis of 2,5‐disubstituted‐1,3,4‐oxadiazoles based on the reaction of N,N‐dimethyl amides with acid hydrazides has been developed. The methodology is applied to a wide range of difference aryl hydrazide and difference N,N‐dimethyl amides to 2,5‐disubstituted‐1,3,4‐oxadiazoles yield the in good to excellent yields. It will be possible wide useful application in synthesis.     

Determination of N‐nitrosamines in cosmetic products by vortex‐assisted reversed‐phase dispersive liquid–liquid microextraction and liquid chromatography with mass spectrometry

A new analytical method for the simultaneous determination of trace levels of seven prohibited N‐nitrosamines (N‐nitrosodimethylamine, N‐nitrosoethylmethylamine, N‐nitrosopyrrolidine, N‐nitrosodiethylamine, N‐nitrosopiperidine, N‐nitrosomorpholine, and N‐nitrosodiethanolamine) in cosmetic products has been developed. The method is based on vortex‐assisted reversed‐phase dispersive liquid–liquid microextraction, which allows the extraction of highly polar compounds, followed by liquid chromatography with mass spectrometry. The variables involved in the extraction process were studied to obtain the highest enrichment factor. Under the selected conditions, 75 μL of water as extraction solvent was added to 5 mL of n‐hexane sample solution and assisted by vortex mixing during 30 s to form the cloudy solution. The method was successfully validated showing good linearity (0.5–50 ng/mL), enrichment factors up to 65 depending on the target compound, limits of detection values of 1.8–50 ng/g, and good repeatability (RSD < 9.8%). Finally, the proposed method was applied to different cosmetic samples. Quantitative relative recovery values (80–113%) were obtained, thus showing that matrix effects were negligible. The achieved analytical features of the proposed method, besides of its simplicity and affordability, make it useful to perform the quality control of cosmetic products to ensure the safety of consumers.     

Efficient and Eco‐friendly Syntheses of 1,5‐Benzothiazepines and 1,5‐Benzodiazepines Catalyzed by [Hmim][NO3] under Mild Conditions

This article presents a synthetic method and reaction mechanism of the 1,5‐benzothiazepines and 1,5‐benzodiazepines derivatives. In this research, 36 thiazepines and diazepines (mostly new) with a new method have been prepared and their structures have been characterized by spectroscopic methods. Crystal structures of a new thiazepine and diazepine (seven‐membered rings) have also been determined and compared with thiazine (six‐membered ring). In this method, N‐methylimidazolium nitrate [Hmim][NO₃] has been used as a catalyst that acts as an environmental friendly system.     

Generation and Rearrangement of N,O‐Dialkenylhydroxylamines for the Synthesis of 2‐Aminotetrahydrofurans

A new diastereoselective route to 2‐aminotetrahydrofurans has been developed from N,O‐dialkenylhydroxylamines. These intermediates undergo a spontaneous C?C bond‐forming [3,3]‐sigmatropic rearrangement followed by a C?O bond‐forming cyclization. A copper‐catalyzed N‐alkenylation of an N‐Boc‐hydroxylamine with alkenyl iodides, and a base‐promoted addition of the resulting N‐hydroxyenamines to an electron‐deficient allene, provide modular access to these novel rearrangement precursors. The scope of this de novo synthesis of simple nucleoside analogues has been explored to reveal trends in diastereoselectivity and reactivity. In addition, a base‐promoted ring‐opening and Mannich reaction has been discovered to covert 2‐aminotetrahydrofurans to cyclopentyl β‐aminoacid derivatives or cyclopentenones.     

Living radical photopolymerization induced grafting on thiol–ene based substrates

The formation of reactive substrates with iniferter‐mediated living radical photopolymerization is a powerful technique for surface modification, which can readily be used to facilitate the incorporation of a variety of surface functionalities. In this research, the photopolymerization kinetics of novel bulk thiol–ene systems have been compared with those of typical acrylate and methacrylate systems when polymerized in the presence of the photoiniferter p‐xylene bis(N,N‐diethyl dithiocarbamate) (XDT). In the presence of XDT, the thiol–ene systems photopolymerize more quickly than the traditional acrylate and methacrylate systems by one to two orders of magnitude. Fourier transform infrared spectroscopy has been used to monitor the photografting kinetics of various monomers on dithiocarbamate‐functionalized surfaces. Furthermore, this technique has been used to evaluate surface‐initiation kinetics and to emphasize the influence of bulk substrate properties on grafting kinetics. Finally, photopatterning has been demonstrated on a dithiocarbamate‐incorporated thiol–ene substrate with conventional photolithographic techniques. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2134–2144, 2005