AFM observation of cation complexation of dibenzocrown ethers adsorbed on highly oriented pyrolytic graphite

The cation complexation behavior of dibenzocrown ethers adsorbed on highly oriented pyrolytic graphite substrates was investigated by means of atomic force microscopy using probe tips modified chemically with ammonium ion by silane coupling. The specific adhesion force based on the intermolecular force between dibenzocrown ether and ammonium ion was observed via force curve measurements in ethanol at the interface between the substrate and tip. The observed specific force decreased in the presence of the alkali metal ion in solution, indicating that the cation in solution interferes with the complexation of the crown ethers adsorbed on the substrate with the ammonium ion immobilized on the tip. The blocking effect of metal ions in solution on the observed force depended on the sizes of both the blocking cation and crown ether ring, suggesting that the surface-adsorbed dibenzocrown ethers possess a selective cation-complexing ability similar to that in their bulk state and that the adhesion force measurements using cation-modified tips allow evaluation of the cation-complexing ability of crown ethers under cation-competitive conditions.     

Direct measurement of hydrophobic particle–bubble interactions in aqueous solutions by atomic force microscopy: Effect of particle hydrophobicity

Direct measurements of the interaction forces between a spherical silica particle and a small air bubble have been conducted in aqueous electrolyte solutions by using an atomic force microscope (AFM). The silica particle was hydrophobized with a silanating reagent, and the interaction forces were measured by using several particles with different surface hydrophobicities. In the measured force curves, a repulsive force was observed at large separation distances as the particle moved towards the bubble. The origin of the repulsive force was attributed to an electrostatic double-layer force because both the particle and bubble were negatively charged. After the repulsive force, an extremely long-range attractive force acted between the surfaces. These results indicate that the intervening thin water film between the particle and bubble rapidly collapsed, resulting in the particle penetrating the bubble.

The instability of the thin water film between the surfaces suggests the existence of an additional attractive force. By comparing the repulsive forces of the obtained force curves with the DLVO theory, the rupture thickness was estimated. The hydrophobicity of the particle did not significantly change the rupture thickness, whereas the pH of the solution is considered to be a critical factor.     

Investigations of heterogeneous ultrathin blends using lateral force microscopy

In order to study the glass transition of thin film polymer blends, high spatial resolution and temperature sensitivity is needed. In this paper, we emphasize the importance of the calibration of scanning parameters such as load and speed when measuring the glass transition temperature of polymers using lateral force microscopy. Once calibrated, this method is ideal for investigations of heterogeneous samples such as blends and co‐polymers. We present an analysis technique for lateral force imaging using a fast and stable cooling/heating stage. This approach involves mapping the friction forces over a certain area and identifying regions of different frictional properties. The difference in the average friction force can then be plotted as a function of temperature. The friction force is expected to vary around the glass transition. Therefore, the glass transition temperature can be defined as the temperature at which the difference in the average friction force undergoes a slope change. We present investigations of blends using polystyrene mixed with poly(butylmethacrylate). The transition temperatures obtained are in good agreement with the bulk values of corresponding homopolymeric films.     

Harmonic dynamics of beta-D-fructopyranose

The vibrational spectra of beta-D-fructopyranose crystals have been recorded in the 4000-400 cm(-1) region using the infrared and in the 4000-20 cm(-1) region using the Raman. These spectra are used as an experimental basis in order to establish a force field for the beta-D-fructopyranose molecule in the crystalline state through a normal co-ordinates analysis. For this purpose, a modified Urey-Bradley-Shimanoushi force field was combined with an intermolecular potential energy function that includes the van-der-Walls interactions, the electrostatic terms, and an explicit hydrogen bond function. The force field parameters are derived from those of beta-D-glucose and are fitted so as to obtain a good agreement between the calculated and the observed frequencies. The results obtained demonstrate the reliability and the transferability of the set of parameters constituting the initial force field. The fitted force field reproduces the experimental spectra to a marked degree of accuracy.     

Force field parameters for the simulation of modified histone tails

We describe the development of force field parameters for methylated lysines and arginines, and acetylated lysine for the CHARMM all‐atom force field. We also describe a CHARMM united‐atom force field for modified sidechains suitable for use with fragment‐based docking methods. The development of these parameters is based on results of ab initio quantum mechanics calculations of model compounds with subsequent refinement and validation by molecular mechanics and molecular dynamics simulations. The united‐atom parameters are tested by fragment docking to target proteins using the MCSS procedure. The all‐atom force field is validated by molecular dynamics simulations of multiple experimental structures. In both sets of calculations, the computational predictions using the force field were compared to the corresponding experimental structures. We show that the parameters yield an accurate reproduction of experimental structures. Together with the existing CHARMM force field, these parameters will enable the general modeling of post‐translational modifications of histone tails. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Molecular dynamics simulations of the melting of 1,3,3-trinitroazetidine

Physical properties of condensed-phase 1,3,3-trinitroazetidine (TNAZ) have been computed with molecular dynamics (MD) and a nonreactive, fully flexible force field formulated by combining the intramolecular interactions obtained from the Generalized AMBER Force Field and the rigid-molecule force field developed by Sorescu-Rice-Thompson [J. Phys. Chem. B 1997, 101, 798] (AMBER-SRT). The results are compared with MD calculations, using the AMBER force field. The predicted densities of crystalline TNAZ from both force fields are about 10% lower than the experimental value. The calculated thermodynamic melting point at 1 atm from the AMBER-SRT force field is 390 K, in good agreement with the measured value of 374 K, while the AMBER force field predicts a thermodynamic melting point of 462 K. The lattice parameters and the molecular and crystal structures calculated with the AMBER-SRT force field are in excellent agreement with experiment. Simulations with the AMBER-SRT force field were also used to generate the isotherm of TNAZ up to 4 GPa and the bulk modulus and its pressure derivative.     

2-氟-5-溴吡啶分子振动光谱的密度泛涵理论研究

用密度泛函理论方法B3LYP以及6-311++G(2df,2pd)基组对2-氟-5-溴吡啶分子 的平衡几何构型进行了优化并计算了该分子的振动谐力场。使用Pulay的标度方法 对理论力场进行了标度。采用Wilson的GF矩阵方法,根据标度后的理论力场进行了 简正坐标分析,对2-氟-5-溴吡啶分子的振动基频进行了理论研究,得到了势能分 布和红外振动频率。与红外频率的实验值相比较,理论频率的均方差为24 cm~(-1) 。此外,根据振动模式的势能分布对此分子的振动基频进行了理论归属,并对前人 的指认进行了修正和补充。     

Effects of hydration on scale factors for ab initio force constants

Experimentally measured vibrational frequencies from the polar groups of peptides in aqueous solutions do not agree with frequencies calculated from scaled quantum mechanical force fields (SQMFF) using differential scale factors developed for molecules in the vapor phase. Measured stretching frequencies for carbonyl groups are more than 50 wavenumbers lower than the calculated values. On the other hand, frequencies for non-polar groups calculated using these scale factors are relatively accurate. Our goal is to develop a SQMFF that yields accurate calculated frequencies for peptides in aqueous solutions. To this end, we have calculated scale factors for ab initio force constants for formic acid, acetic acid, and acetone using a least squares fit of calculated and experimental frequencies. We compare these scale factors with changes observed in the ab initio force constants calculated for these molecules at various states of hydration. These force constants are calculated using fully optimized geometries for these hydrated molecules using the 4-31G basis. We present a comparison of the experimental and calculated frequencies, along with their potential energy distributions, for both vapor and aqueous phases. The results indicate that scale factors can simulate the effects of solvation on molecular force constants to yield accurate scaled ab initio force fields.     

Effect of contact geometry on the pull-off force evaluated under high-vacuum and humid atmospheric conditions

The effect of condensed water on pull-off forces under high vacuum (HV) and 0 to 83% relative humidity (RH) N2 atmospheric conditions was evaluated for different contact geometries using atomic force microscopy (AFM). The pull-off force was measured using two types of contact geometry: contact between hemispherical asperities and a flat silicon probe on an AFM cantilever (called a spherical-flat contact) and between a flat silicon substrate and a flat nickel probe on an AFM cantilever (called a flat-flat contact). The hemispherical asperities were fabricated using a focused ion beam (FIB) system, and each peak had a radius of curvature of between 70 and 610 nm. The flat nickel probe was fabricated by friction-induced wear. Measurement results showed that for the spherical-flat contact the pull-off force was proportional to the radius of curvature of the asperity peak and was slightly lower in HV than in humid 14% RH N2. For the flat-flat contact in HV, with increasing contact time, the pull-off force increased in HV but decreased in humid 62 and 83% RH N2. The pull-off force in HV was lower than that in humid N2 when the contact time was less than 10 s but was higher when the contact time was longer than 30 s. The estimated adhesion force based on the Laplace pressure from the contact geometry agreed reasonably well with the measured pull-off force.     

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.     

Molecular dynamics simulations of methane hydrate using polarizable force fields

Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are found between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane only.     

Optimization of clamping force for low-viscosity polymer injection molding

Due to its low cost and high efficiency, injection molding is used for the mass production of many plastic products nowadays. However, when processing low-viscosity plastic materials, i.e., materials with an excellent fluidity, an inappropriate setting of the clamping force often results in a poor appearance and dimensional accuracy of the final product. Thus, operators usually take the upper limit of the clamping force as a default in setting up the machine in an attempt to improve the quality of the molded parts. However, such an approach shortens the machine and mold life, increases the energy consumption, and leads to poor air venting. Consequently, more scientific methods for determining the clamping force setting are required. To meet this demand, the present study proposes a clamping force search methodology for determining the optimal clamping force setting of a hydraulic cylinder clamping injection molding machine in the processing of low-viscosity plastics such as thermoplastic polyurethane (TPU) and polypropylene (PP). Based on the characteristic extracted from the sensing tie-bar elongation profile under different clamping force settings, a regression analysis on these data points is implemented to seek for an optimal clamping force. The experimental results show that for an injection molding machine with a hydraulic cylinder clamping mechanism, the effect of the mold temperature on the clamping force is sufficiently small to be ignored, which has an impact on the toggle type clamping unit. Furthermore, compared to traditional methods, the optimal clamping force obtained using the method proposed in the present study results in a significant improvement in the yield rate. Overall, the results confirm that for low-viscosity polymer resins, the optimal clamping force determined using the proposed method results in a higher and more consistent quality of the molded parts than that achieved using the proper clamping force setting for ordinary-viscosity resins.     

Chemical force titrations of functionalized Si(111) surfaces

Chemical force titrations-plots of the adhesive force between an atomic force microscope tip and sample as a function of pH-were acquired on alkyl monolayer-derivatized Si(111) surfaces. Gold-coated AFM tips modified with thioalkanoic acid self-assembled monolayers (SAM) were employed. Alkyl monolayer-derivatized Si(111) surfaces terminated with methyl, carboxyl, and amine groups were produced via hydrosilylation reactions between 1-alkene reagents and H-terminated silicon. The functionalized surfaces were characterized using standard surface science techniques (AFM, FTIR, and XPS). Titration of the methyl-terminated surface using the modified (carboxyl-terminated) atomic force microscope tip resulted in a small pH-independent hydrophobic interaction. Titration of the amine-terminated surface using the same tip resulted in the determination of a surface pKa of 5.8 for the amine from the pH value from the maximum in the force titration curve. A pK(1/2) of 4.3 was determined for the carboxyl-terminated Si(111) in a similar way. These results will be discussed in relation to the modified Si(111) surface chemistry and organic layer structure, as well as with respect to existing results on Au surfaces modified with SAMs bearing the same functional groups.     

Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations

The free energy landscapes of peptide conformations were calibrated by ab initio quantum chemical calculations, after the enhanced conformational diversity search using the multicanonical molecular dynamics simulations. Three different potentials of mean force for an isolated dipeptide were individually obtained by the multicanonical molecular dynamics simulations using the conventional force fields, AMBER parm94, AMBER parm96, and CHARMm22. Each potential of mean force was then calibrated based upon the umbrella sampling algorithm from the adiabatic energy map that was calculated separately by the ab initio molecular orbital method, and all of the calibrated potentials of mean force coincided well. The calibration method was also applied to the simulations of a peptide dimer in explicit water models, and it was shown that the calibrated free energy landscapes did not depend on the force field used in the classical simulations, as far as the conformational space was sampled well. The current calibration method fuses the classical free energy calculation with the quantum chemical calculation, and it should generally make simulations for biomolecular systems much more reliable when combining with enhanced conformational sampling.     

Influence of solvent environment and tip chemistry on the contact mechanics of tip-sample interactions in friction force microscopy of self-assembled monolayers of mercaptoundecanoic Acid and dodecanethiol

Friction force microscopy measurements have been made for self-assembled monolayers of mercaptoundecanoic acid (C10COOH) and dodecanethiol (C11CH3) in different liquid media. In perfluorodecalin, the friction-load relationship was nonlinear and consistent with adhesion-controlled sliding. The effective range of the attractive force was controlled by using AFM tips functionalized with alkanethiols (chemical force microscopy). Like pairs of interacting molecules yielded data that were characterized by the Johnson-Kendall-Roberts model of contact mechanics, whereas the interaction between dissimilar pairs of molecules fitted the behavior predicted by the Derjaguin-Muller-Toporov model. In ethanol, the adhesive force was much smaller, and sliding was not adhesion-controlled. Under this condition of low adhesion, the friction force varied linearly with the applied load.     

Origin of adhesion in humid air

The origin of adhesion in humid air is investigated by pull-off force measurements between nanoscale contacts using atomic force microscopes in controlled environments from ultrahigh vacuum through various humidity conditions to water. An equivalent work of adhesion (WOA) model with a simplified interface stress distribution is developed, combining the effects of screened van der Waals and meniscus forces, which describes adhesion in humid air and which self-consistently treats the contact stress and deformation. Although the pull-off force is found to vary significantly with humidity, the equivalent WOA is found to be invariant. Increasing humidity alters the nature of the surface adhesion from a compliant contact with a localized, intense meniscus force to a stiff contact with an extended, weak meniscus force.     

运用功能化修饰的碳纳米管针尖测量配体-受体的作用力

电弧法自制碳纳米管原子力显微镜针尖,对其末端进行功能化修饰,然后测量配体-受体之间的作用力。运用没有功能化修饰的碳纳米管针尖与修饰有亲和素分子的基底进行接触测量时,没有粘滞力出现;而运用末端修饰生物素分子的碳纳米管针尖测量时,有粘滞力产生。功能化的碳纳米管针尖直接测得的粘滞力均大约200pN,此值符合一对配体生物素和受体亲和素之间的作用力。这一结果很难用传统的针尖获得,功能化修饰的碳纳米管针尖能够克服传统针尖在力测量中的局限,在生物学和化学领域有着广泛的应用前景。     

An overlay calculation of the molecular force field of 2- and 3-halogeno derivatives of thiophene

A normal mode calculation, which includes force constants, vibration mean amplitudes, Coriolis parameters and thermodynamic properties, has been performed on a series of six halogenated thiophenes. The zeroth-order force field we have used is that of the thiophene parent molecule, and some specific force constants and interaction constants have been refined using the overlay technique. Results show that the halogen substitution acts upon the heterocyclic ring motion frequencies as an isotopic substitution, viz. with small electronic effects but with remarkable mass effects.     

Single complexation force of 18-crown-6 with ammonium ion evaluated by atomic force microscopy

The cation complexation force of 18-crown-6 has been measured in ethanol by means of atomic force microscopy using probe tips and mica substrates modified chemically with 18-crown-6 and ammonium ion, respectively. The specific complexation force was suppressed by free potassium ion in the measurement solution, indicating a blocking effect based on the competitive complexation of the 18-crown-6 moiety between the free ion and the ammonium ion bound to the substrate. The single complexation force of 18-crown-6 with ammonium ion was evaluated to be about 60 pN in ethanol by autocorrelation analyses of the histograms for observed forces.     

Chemical force microscopy: applications in surface characterisation of natural hydroxyapatite

Detailed mapping of surface chemistry with nanometer resolution has application throughout the physical and life sciences. The atomic force microscope (AFM) has provided a tool that, when using functionalised probes, is capable of providing chemical information with this level of spatial resolution. Here, we describe the technique of chemical force microscopy (CFM) and demonstrate the sensitivity of the technique using chemical force titrations against pH. We describe in detail the specific application of mapping the surface charge on natural hydroxyapatite from skeletal tissue and show that this new information leads to a better understanding of the binding of matrix proteins to the mineral surface.