基于有机功能化碳纳米管的自组装

利用自组装的方法,实现碳纳米管的有序排列可以充分有效的促进碳纳米管在各个领域的应用。本文从自组装所依赖的驱动力着手,介绍了国内外近几年来基于功能化碳纳米管的自组装开展的研究工作及取得的成果,重点介绍了通过配位作用、静电力及氢键、亲水/疏水相互作用等实现的自组装。     

Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers

The reliability of molecular simulations largely depends on the quality of the empirical force field parameters. Force fields used in lipid simulations continue to be improved to enhance the agreement with experiments for a number of different properties. In this work, we have carried out molecular dynamics simulations of neat DMPC bilayers using united‐atom Berger force field and three versions of all‐atom CHARMM force fields. Three different systems consisting of 48, 72, and 96 lipids were studied. Both particle mesh Ewald (PME) and spherical cut‐off schemes were used to evaluate the long‐range electrostatic interactions. In total, 21 simulations were carried out and analyzed to find out the dependence of lipid properties on force fields, system size, and schemes to calculate long‐range interactions. The acyl chain order parameters calculated from Berger and the recent versions of CHARMM simulations have shown generally good agreement with the experimental results. However, both sets of force fields deviate significantly from the experimentally observed P‐C dipolar coupling values for the carbon atoms that link the choline and glycerol groups with the phosphate groups. Significant differences are also observed in several headgroup parameters between CHARMM and Berger simulations. Our results demonstrate that when changes were introduced to improve CHARMM force field using PME scheme, all the headgroup parameters have not been reoptimized. The headgroup properties are likely to play a significant role in lipid–lipid, protein–lipid, and ligand–lipid interactions and hence headgroup parameters in phospholipids require refinement for both Berger and CHARMM force fields. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2010     

The Influence of N‐doped Carbon Materials on Supported Pd: Enhanced Hydrogen Storage and Oxygen Reduction Performance

N‐doped graphene has become an important support for Pd in both hydrogen storage and catalytic reactions. The molecular orbitals of carbon materials (including graphene, fullerene, and small carbon clusters) and those of the supported Pd species will hybrid much stronger as N dopants are introduced, owing to the increased electrostatic attraction at the interface. This enhances the carbon substrates′ catching force for the supported Pd, preventing its leaching and aggregation in many practical applications. The better dispersion and stabilization of Pd nanoparticles, which are induced by various carbon supports with N‐doping, are pleasing to us and could increase their efficiency and facilitate their recycling during various reaction processes in several fields.     

3kA钕电解槽流场中颗粒受力分析

近年来随着NdFeB永磁的应用发展,对金属Nd质量的要求越来越高,而电解过程碳颗粒运动及溶解对金属质量的影响至关重要。通过理论与数值模拟相结合的方式对流场中不溶于电解液的碳固体颗粒的主要受力类型进行梳理,对其运动轨迹进行数值模拟研究,针对稀土电解槽进行了颗粒-流场的计算及模拟,研究发现曳力及重力是颗粒在电解槽中起主要作用的力。曳力是改变颗粒运动轨迹的影响因素,且曳力随粒径的增大而增大。0.07 mm颗粒粒径是区分主要作用力是重力还是曳力的临界值,颗粒粒径越大,越不利于电解槽得到纯净的Nd单质。对进一步改进电解槽槽型,从而得到质量更好、杂质更少的稀土金属,并对后续各物理场对颗粒的影响提供参考意义。     

Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations

With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, in our hands those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for small molecules, proteins, lipids, and lipid bilayers and recently have begun work on carbohydrate force fields. The latter area has been relatively untouched by force field developers with particular focus on polarizable, non-additive interaction potential models. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration method for phase-dependent polarizable force fields, lipid molecules, and small-molecule carbohydrates. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields.     

Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations

Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for CNT-water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ-potential.     

Force fields and vibrational spectroscopy: A discussion on status and future prospects

A start is given for a discussion about the use of force fields for describing and interpreting molecular geometries, relative energies and vibrational spectra. The development of modern, generic force fields, e.g. Class II force fields, has diminished the necessity for specific force fields, and they should be applied in far more cases than they are being used now.     

Synthesis of carbon encapsulated magnetic nanoparticles with giant coercivity by a spray pyrolysis approach

Carbon encapsulated magnetic (metal) nanoparticles (CEMNPs) have wide applications in biomedicine and the magnetic recording industry. However, synthesis of such particles with a high coercive force and good ferromagnetism is still a great challenge. The present study reports a new method for the continuous production of CEMNPs of high purity. This involves the spray pyrolysis of a mixture of iron pentacarbonyl and ethanol at 500-900 degrees C. Results show that the Fe (or Fe3C) particles synthesized at 700 and 900 degrees C were well encapsulated by graphitic layers with rare byproducts such as carbon nanotubes, nanofibers, or bulk amorphous carbon. Those synthesized at 700 degrees C had a particle size of 30-50 nm, a giant coercive force of 867 Oe, and a good magnetic remanence of 33% at room temperature. The present approach based on spray pyrolysis is advantageous over previous ones in suitability for large-scale production, and the synthesized material has wide applications in many fields.     

Molecular dynamics simulations of the interactions between platinum clusters and carbon platelets

Molecular dynamics simulations have been performed with two reactive force fields to investigate the structure of a Pt100 cluster adsorbed on the three distinct sides of a carbon platelet. A revised Reax force field for the carbon-platinum system is presented. In the simulations, carbon platelet edges both with and without hydrogen termination have been studied. It is found that the initial mismatch between the atomic structure of the platelet egde and the adsorbed face of the Pt100 cluster leads to a desorption of a few platinum atoms from the cluster and the subsequent restructuring of the cluster. Consequently, the average Pt-Pt bond length is enlarged in agreement with experimental results. This change in the bond length is supposed to play an important role in the enhancement of the catalytic activity, which is demonstrated by studying the changes in the bond order of the platinum atoms. We found an overall shift to lower values as well as a loss of the well-defined peak structure in the bond-order distribution.     

Biomolecular simulations of membranes: physical properties from different force fields

Phospholipid force fields are of ample importance for the simulation of artificial bilayers, membranes, and also for the simulation of integral membrane proteins. Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all-atom generalized AMBER force field (GAFF) for dioleoylphosphatidylcholine molecules. Only the latter displays the experimentally observed difference in the order of the C2 atom between the two acyl chains. The interfacial water dynamics is smoothly increased between the lipid carbonyl region and the bulk water phase for all force fields; however, the water order and with it the electrostatic potential across the bilayer showed distinct differences between the force fields. Both Berger and GAFF underestimate the lipid self-diffusion. GAFF offers a consistent force field for the atomic scale simulation of biomembranes.     

Empirical force fields for biological macromolecules: overview and issues

Empirical force field-based studies of biological macromolecules are becoming a common tool for investigating their structure-activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of empirical force field-based methods is the quality of the force fields combined with the algorithmic advances that allow for more accurate reproduction of experimental observables. Presented is an overview of the issues associated with the development and application of empirical force fields to biomolecular systems. This is followed by a summary of the force fields commonly applied to the different classes of biomolecules; proteins, nucleic acids, lipids, and carbohydrates. In addition, issues associated with computational studies on "heterogeneous" biomolecular systems and the transferability of force fields to a wide range of organic molecules of pharmacological interest are discussed.     

Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations

Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.     

Molecular structures of acetylene derivatives of tin

The geometry and force fields of the bis(trimethylstannyl)acetylene molecule (a conformer withD _3d symmetry corresponding to a minimum of the total energy of the molecule) were calculated by the RHF and MP2(fc) methods. The effective core potential in SBK form with the optimized 31G^* valence basis set was employed in the case of Sn atoms. The 6–31G^** and 6–311G^** basis sets were used for carbon and hydrogen atoms. Vibrational spectra of the light and perdeuterated isotopomers of bis(trimethylstannyl)acetylene were interpreted using the procedure of scaling the quantum-chemical force fields. For Part 5, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 616–626, April, 2000.     

On the accuracy of force fields for predicting the physical properties of dimethylnitramine

The accuracy of three force fields for predicting the physical properties of dimethylnitramine (DMNA) has been investigated by using molecular dynamics simulations. The Sorescu, Rice, and Thompson (SRT) (J. Phys. Chem. B 1997, 101, 798) rigid-molecule, flexible generalized AMBER (J. Comput. Chem. 2004, 25, 1157), and Smith et al. flexible force fields (J. Phys. Chem. B 1999, 103, 705) were tested. The density, lattice parameters, isotherm, and melting point of DMNA are calculated using classical molecular dynamics. Except for the melting point, the predictions of the three force fields are in reasonable agreement with experimental values. The calculated thermodynamic melting points (Tmp) for the SRT, AMBER, and Smith et al. force fields are 380, 360, and 260 K, respectively. The experimental value is 331 K. Modifications of the torsional barriers in the AMBER force field resulted in Tmp = 346 K, in good agreement with the experimental value of 331 K. The calculated lattice parameters and bulk modulus are also improved with the modifications of the AMBER potential. The results indicate that, although not sufficiently accurate without modifications, the general force fields such as AMBER provide the basis for developing force fields that correctly predict the physical properties of nitramines.     

Force fields of halide-substituted methane derivatives

The paper describes methods for determining the force fields of large sets of molecules which share the common property that in their constituent groups of molecules the equivalent force constants always change monotonically with the properties of substituent atoms belonging to the same subgroup of the periodic table. The force fields of the CH_4−nX_n (n=0–4, X=F, Cl, Br, I) molecules of the methane series are obtained. The applications of these force fields are discussed. In particular, they can serve as a basis for a data bank of the force fields of fragments suitable for constructing the force fields of more complex molecules. Russian Scientific Center “Applied Chemistry”, St. Petersburg. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 250–256, March–April, 1996. Translated by I. Izvekova     

In search of the next Holy Grail of polyoxide chemistry: explicitly correlated ab initio full quartic force fields for HOOH, HOOOH, HOOOOH, and their isotopologues

Explicitly correlated ab initio methods have been used to compute full quartic force fields for the three chain minima for HOOOOH, which are found to lie within 1 kcal mol(-1). The CCSD(T)-F12 method with the cc-pVTZ-F12 basis set was used to compute equilibrium structures, anharmonic vibrational frequencies, and rotational constants for HOOH, HOOOH, and three chain isomers of HOOOOH, with the two former force fields being used as benchmarks for the latter three. The full quartic force fields were computed in such a way as to yield fundamental frequencies for all isotopologues at once. The present research confirms the recent experimental identification of HOOOH and provides reliable force fields in support of future experimental work on the enigmatic bonding paradigms involved in the HOOOOH chain.     

Evaluation of force fields for molecular simulation of polyhedral oligomeric silsesquioxanes

Polyhedral oligomeric silsesquioxanes (POSS) are nanometer-size molecules suitable for the production of organic-inorganic nanocomposite materials. These organic-inorganic nano-building blocks show promise for enabling the production of polymeric materials of exceptional mechanical properties as well as novel composite materials. While the experimental studies of these materials have rapidly evolved in the past decade, their theoretical investigation is still in its infancy. Toward the validation of force fields for the molecular simulation of POSS-containing systems, we present the charge-transfer reactive (CTR) force field for the molecular simulation of polyhedral oligomeric silsesquioxane (POSS) molecules and compare the ability of this, and several force fields taken from the literature, to predict the thermophysical properties of POSS-containing systems. The literature force fields compared include the universal force field (UFF) and the COMPASS and Hybrid-COMPASS force fields. Predictions from molecular dynamics simulations of the structural parameters (unit cell vectors), melting temperature, and FT-IR spectra of crystals of POSS monomers are presented. The POSS monomers investigated are octahydride, octamethyl, and octapropyl POSS. Predicted quantities are compared to experimental results where available and provide molecular-level physical insight into several aspects of the behavior of POSS molecules. While all the force fields tested perform reasonably well, our results indicate that the Hybrid-COMPASS and CTR force fields predict structural properties that are in good agreement with experimental data.     

The formate anion: the harmonic and anharmonic force fields

Harmonic and anharmonic symmetry force constant matrices have been obtained for six isotopically substituted species of the formate anion. The valence force fields derived from the above matrices were used to recalculate the vibrational frequencies. These force fields are compared with others previously reported and obtained via other methods.     

QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal‐organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three‐step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal‐organic frameworks (MOFs), QuickFF is used to determine force fields for MIL‐53(Al) and MOF‐5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc.