Molecular Modeling of the Chain Structures of Polybenzoxazines

IntroductionThe benzoxazine polymer could be deemed asan alternative to traditional phenolics because ofthe similar main chain structures.A Novolac typeof phenolic resin has the unit,Ar—CH2 — withsome Ph—CH2 N( R)—CH2 — structure,where Phdenotes the phenolic group.In addition to theadvantages owned by ordinary phenolics,such ashigh temperature resistance,dimensional stability,good electrical properties,flame retardance,andlow smoke generation,this family ofpolybenzoxazines provides t…     

Synthesis and X-ray Crystal Structure of a New Molecular Clip

The synthesis and X-ray crystal structure of a new molecular clip 2 was reported. It （C24H24N4O2, Mr = 400.47） crystallizes in the space group C2/c with a = 15.587（2）, b = 8.5805（12）, c = 15.259（2） A, β = 102.448（3）°, V= 1992.9 （5）A63, Z = 4, Dc = 1.335 g/cm63,μ = 0.087 mm^-1 and F（000） = 848. It remains monomeric in the crystal and a tape-like structure is formed in the crystal structure of molecular clip. The most unusual structural feature of 2 is the boat conformation of its cyclohexyl ring imposed by the ring fusion at C（9）-C（9a）.     

Tetranitromethane: A Nightmare of Molecular Flexibility in the Gaseous and Solid States

After numerous attempts over the last seven decades to obtain a structure for the simple, highly symmetric molecule tetranitromethane (C(NO₂)₄, TNM) that is consistent with results from diffraction experiments and spectroscopic analysis, the structure has now been determined in the gas phase and the solid state. For the gas phase, a new approach based on a four‐dimensional dynamic model for describing the correlated torsional dynamics of the four C−NO₂ units was necessary to describe the experimental gas‐phase electron diffraction intensities. A model describing a highly disordered high‐temperature crystalline phase was also established, and the structure of an ordered low‐temperature phase was determined by X‐ray diffraction. TNM is a prime example of molecular flexibility, bringing structural methods to the limits of their applicability.     

Impact of finite-temperature and condensed-phase effects on theoretical X-ray absorption spectra of transition metal complexes

The impact of condensed-phase and finite-temperature effects on the theoretical X-ray absorption spectra of transition metal complexes is assessed. The former are included in terms of the all-electron Gaussian and augmented plane-wave approach, whereas the latter are taken into account by extensive ensemble averaging along second-generation Car–Parrinello ab initio molecular dynamics trajectories. We find that employing the periodic boundary conditions and including finite-temperature effects systematically improves the agreement between our simulated X-ray absorption spectra and experimental measurements. © 2018 Wiley Periodicals, Inc.     

分子束中生物分子的光谱与结构

研究分子束中的生物分子有助于探讨生物分子的固有性质和由于生物环境而引起的其他性质之间的区别。本文首先介绍了一种可将生物分子在气相中"孤立"的实验技术,即激光解吸并分子束冷却技术,同时还介绍了与该研究方向相关的光谱方法,即UV/UV和IR/UV烧孔光谱等。并回顾了近年来人们应用这些实验技术对分子束中的氨基酸和短肽、核酸碱基、糖类和神经递质类分子以及它们的团簇最新研究进展。文中还简要介绍了一种新的应用于构象异构动力学研究的光谱方法,即激励辐射泵浦-注孔(SEP-HF)和激励辐射泵浦-布居转移(SEP-PT)。最后,综述了短肽离子光解离动力学和短肽离子中发生的电荷快速转移动力学过程的研究进展。     

Oxazolidinone Antibiotics: Chemical,Biological and Analytical Aspects

This review covers the main aspects concerning the chemistry, the biological activity and the analytical determination of oxazolidinones, the only new class of synthetic antibiotics advanced in clinical use over the past 50 years. They are characterized by a chemical structure including the oxazolidone ring with the S configuration of substituent at C5, the acylaminomethyl group linked to C5 and the N-aryl substituent. The synthesis of oxazolidinones has gained increasing interest due to their unique mechanism of action that assures high antibiotic efficiency and low susceptibility to resistance mechanisms. Here, the main features of oxazolidinone antibiotics licensed or under development, such as Linezolid, Sutezolid, Eperezolid, Radezolid, Contezolid, Posizolid, Tedizolid, Delpazolid and TBI-223, are discussed. As they are protein synthesis inhibitors active against a wide spectrum of multidrug-resistant Gram-positive bacteria, their biological activity is carefully analyzed, together with the drug delivery systems recently developed to overcome the poor oxazolidinone water solubility. Finally, the most employed analytical techniques for oxazolidinone determination in different matrices, such as biological fluids, tissues, drugs and natural waters, are reviewed. Most are based on HPLC (High Performance Liquid Chromatography) coupled with UV-Vis or mass spectrometer detectors, but, to a lesser extent are also based on spectrofluorimetry or voltammetry.     

Crystallographic and Dynamic Aspects of Solid‐State NMR Calibration Compounds: Towards ab Initio NMR Crystallography

The excellent results of dispersion‐corrected density functional theory (DFT‐D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT‐D calculations is a target, especially for the field of molecular NMR crystallography. Four ¹³C ss‐NMR calibration compounds are investigated by single‐crystal X‐ray diffraction, molecular dynamics and DFT‐D calculations. The crystal structure of 3‐methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated ¹³C chemical shifts of these compounds are in excellent agreement with experiment, with a root‐mean‐square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT‐D chemical shift calculation improves the accuracy of calculated chemical shifts.     

Energy Aspects of Thermal Molecular Switching: Molecular Thermal Hysteresis of Helicene Oligomers

Molecular switching is a phenomenon by which a molecule reversibly changes its structure and state in response to external stimuli or energy. Herein, molecular switching is discussed from thermodynamic and kinetic aspects in terms of energy supply with an emphasis on the thermal switching exhibited by helicene oligomers. It includes the inversion of relative thermodynamic stability induced by temperature changes and molecular thermal hysteresis in a closed system. The thermal phenomenon associated with the oligomers involves population/concentration changes between metastable states under nonequilibrium thermodynamic control.     

Molecular structure of 2-Amino-5-(1-methyl-5-nitro-2-imidazolyl)-1,3,4-thiadiazol (Megazol) and related compounds: A concerted study using X-ray crystallography,molecular mechanics,and semiempirical methods

A structural study of three nitroimidazoles was carried out using molecular mechanics, semiempirical methods, and X-ray crystallography. Structural features which might account for the high efficiency of1 (Megazol) as an antiparasitic drug and its opposite, the inactivity of its regiomers2 and3 were examined, i.e., coplanarity of the two rings, preferred conformations, and rotational barriers around the pivot bond between the two rings. For the three compounds an antiperiplanar conformation is preferred for the N(CH₃) and C-S bonds. For compounds1 and3, the rings are coplanar, with2 being somewhat twisted. The geometry obtained by molecular mechanics for compound1 is in excellent agreement with the X-ray structure, and greater confidence can be placed in this method than in semiempirical ones. Similarities observed on the LUMO positions, as well as rotational barriers lead to the conclusion that the differences in biological activity of these compounds do not rely on their ground state properties but rather on their subsequent reactions with oxygen. In addition, the calculations revealed significant structural information of a family of biological importance (nitroimidazoles) and constitute a comparative test for the MM2, AM1, and PM3 methods.     

Dynamics of a Spreading Nanodroplet: A Molecular Dynamic Simulation

The spreading of polymer nanodroplets upon a sudden change from partial to complete wetting on an ideally flat and structureless solid substrate has been studied by molecular dynamic simulations using a coarse‐grained bead‐spring model of flexible macromolecules. Tanner's law for the growth of the lateral droplet radius {R(t) ∝ t^0.1} is found to hold as long as the droplet does not disintegrate into individually moving chains. The data for the contact angle θ following from Tanner's law correspond to a dependence on time {θ(t) ∝ t^−0.3}. Our analysis of the mean square displacements of the polymer centers of mass reveals several dynamic regimes during the process of spreading. PACS numbers: 68.10.Gw, 05.70.Ln, 61.20.Ja, 8.45.Gd.

Molecular dynamics results for the average mean square displacement of all polymer chains plotted vs. time for a broad range of values for ε_wall.     

X-ray Crystal Structure and Molecular Mechanics Calculations of (2,6-iso-dipropyl-phenylamide) Dimethyl ( tetra-methylcyclopenta-dienyl ) Silane Titanium Dichloride

Crystal and molecular structure of (2,6-dipropylphenylamide) dimethyl (tetra-methyl cyclopentadienyl) silane titanium dichloride (I) was fully characterized by X-ray diffraction. The crystal is obtained from a mixture of ether/hexane as orthorhombic, with a = 12.658 (3) (A), b = 16.62 (3)(A), c = 11.760 (2)(A), V = 2474.2 (9)(A) 3, Z = 4, space group Pnma, R = 0.0399. Componud I compose of the π-bounded ring with its dimethylsilyl-dipropyl phenyl amido group and the two terminal chloride atoms coordinated to central metal to form a so-called constrained geometry catalyst (CGC) structure. The result of molecular mechanics (MM) calculations on compound I shows that bond lengths and bond angles from the MM calculation are comparable to the data obtained from the X-ray diffraction study. The relation of the structure of CGCs and their catalytic activity by MM calculations is also discussed.     

Molecular Dynamic Simulation of Side-Chain Liquid Crystalline Elastomer

Summary: Molecular dynamic simulation of side chain liquid crystalline elastomer has been carried out. As an initial state a flexible polymer network in a low molecular liquid-crystal (LC) solvent was used. The LC solvent comprises of anisotropic rod-like semiflexible linear molecules (mesogens) composed of particles bonded into the chain by FENE potential. Rigidity of LC molecules was induced by a bending potential. All interactions between nonbonded particles are described by a repulsive Lennard-Jones potential. For the systems with different values of density and order parameter obtained after sufficiently long trajectory the attachment of ends of mesogens to the polymer network was simulated. The kinetic of the process of mesogens attachment to network was studied as well as morphology of attachment. The structural and dynamical behaviour of side chain LC elastomer was studied and compared with systems of polymer network in low molecular LC solvent.     

手性酞菁的合成及其绝对构型

在锂存在的条件下在正戊醇中回流环化四聚相应的光学活性的前驱体联二萘[2,1-e:1',2'-g][1,4]二羟基-5,6-邻苯二氰, 然后用醋酸酸化处理, 合成了一对对映的四个联二萘酚基团取代的手性自由酞菁四(联二萘[1,2-e:1',2'-g]-1,4-二羟基)[2,3-b;2',3'-k;2',3'-t;2'',3''-c']酞菁(1), 并利用一系列的光谱学方法以及元素分析表征了这种新型的手性酞菁化合物. 单晶X衍射分析确定了两种对映体的绝对构型, 从而阐明了自由酞菁(1)的手性分配.     

Crystal and Molecular Structures of Phosphonolactone Derivatives of Chromone

The crystal structure of chromone hydrazonium salt (±)-1-hydroxy-1-oxo-3-phenyl-1,3-dihydro-1λ⁵-2,1-oxaphospholo[4,5-b]-4H-1-benzopyran-4-one (2) and its acid (±)-1-hydroxy-1-oxo-3-phenyl-1,3-dihydro-1λ⁵-2,1-oxaphospholo[4,5-b]-4H-1-benzopyran-4-one (3) have been solved. Condensed rings are almost planar, the P atom adopts nearly tetragonal geometry. The molecular packing is influenced by inter- and intramolecular contacts, which can be recognized as hydrogen bonds.     

X-ray Crystal Structure and Molecular Mechanics Calculations of (2,6-iso-dipropyl-phcnylamidc) Dimethyl (tetra-methylecyclopenta- dienyl)Silane Titanium Dichloride

ExperimentalSynthesisofitToI.sg(4mmol.)TiCI,.THFin25mLTHFwasaddedI.sg(4mmol.)dilithium(2,6-propylphenylamide)dimethyl(tetra-methylcyclopentadienyl)silaneandthemixturewasallowedtostirforIhour,then0.639AgCI(4mmol.)wasadded.After4hoursstirring,thesolventwasmovedandtheresiduewasextractedwithdiethylether.Theetherextractwasfilteredandevaporatedtodrynesstogive0.409yellowcrystallinesolid,yield41%.'H-NMR(C,D,)f0.48(6H),l.I2(6H),l.49(6H),l.98(6H).2.18(6H),and3.04(2H).Asuitablesinglecrystalwa…     

Molecular and electronic structure of halogen-substituted phosphaalkenes

Peculiarities of the molecular and electronic structure of P- and C-halogen-substituted phosphaalkenes have been considered on the basis of results of X-ray diffraction studies and quantumchemical calculations. Introduction of an electronegative halogen atom is shown to have an insignificant effect on the intramolecular bond angle distribution, whereas the influence on the P=C bond length is noticeable. Thus, in P-substituted phosphaalkenes it substantially increases the polarization of the P=C bond (which causes its noticeable shortening). In C-substituted phosphaalkenes the effect of halogen atoms is less pronounced: decreasing the P=C bond polarization leads only to its slight elongation. In addition, a considerable elongation of the phosphorus-halogen bond in comparison with three-coordination phosphorus compounds is a peculiarity of the molecular structure of P-halogen-substituted phosphaalkenes.     

Molecular modeling for Cu(II)‐aminopolycarboxylate complexes: Structures,conformational energies,and ligand binding affinities

A ligand field molecular mechanics (LFMM) force field (FF) has been developed for d⁹ copper(II) complexes of aminopolycarboxylate ligands. Training data were derived from density functional theory (DFT) geometry optimizations of 14 complexes comprising potentially hexadentate N₂O₄, tetrasubstituted ethylenediamine (ed), and propylenediamine cores with various combinations of acetate and propionate side arms. The FF was validated against 13 experimental structures from X‐ray crystallography including hexadentate N₂O₄ donors where the nitrogens donors are forced to be cis and bis‐tridentate ONO ligands which generate complexes with trans nitrogen donors. Stochastic conformational searches for [Cu{ed(acetate)_n (propionate)_4‐n}]^2?, n = 0–4, were carried out and the lowest conformers for each system reoptimized with DFT. In each case, both DFT and LFMM predict the same lowest‐energy conformer and the structures and energies of the higher‐energy conformers are also in satisfactory agreement. The relative interaction energies for n = 0, 2, and 4 computed by molecular mechanics correlate with the experimental log β binding affinities. Adding in the predicted log β values for n = 1 and 3 suggest for this set of complexes a monotonic decrease in log β as the number of propionate arms increases. © 2013 Wiley Periodicals, Inc.