Interactions between solid surfaces with adsorbed polyelectrolytes of opposite charge

Adsorption of polyelectrolytes to surfaces of opposite charge typically leads to charge neutralization and subsequent charge reversal. As can be shown by direct force measurements and stability studies, the interaction forces are dominated by repulsive forces originating from diffuse layer overlap and attractive van der Waals forces, in line with the classical theory of Derjaguin, Landau, Verwey, and Overbeek (DLVO). Recently, the existence of an additional attractive non-DLVO force was demonstrated, and its likely origin is the attraction between patch-charge heterogeneities. With novel single molecule pulling experiments with the atomic force microscope (AFM) polymer bridging forces could be shown to represent the most important contribution to the adhesion of surfaces coated by polyelectrolytes.     

Self-localization of polyacrylic acid molecules on polar ZnO(0001)-Zn surfaces

The adsorption of single polyacrylic acid (PAAc) molecules was investigated on stepped hydroxide-stabilized polar ZnO(0001)-Zn surfaces using atomic force microscope (AFM) topography and force distance spectroscopy. Stepped surfaces of ZnO(0001)-Zn were prepared by a wet chemical etching procedure and PAAc molecules were adsorbed from aqueous NaClO(4) solutions. AFM single molecule topography studies could be utilized to show that polyacrylic acid molecules specifically adsorb on the non-polar (10-10) step edge faces at low ionic strengths. The radius of gyration of the dissolved PAAc in aqueous solution was measured by means of static light scattering experiments yielding a radius of gyration of R(g)=136 nm at pH 7.4 in 50 mM NaClO(4)/NaOH solution, which is in good agreement with the size of the adsorbed PAAc molecules as measured using AFM. The obtained results could be rationalized in terms of binding-site configurations at step edges and the effect of the chemical environment on both local electric double layer charge and molecular conformation of the PAAc molecules. The point of zero charge of the ZnO(10-10) surface was measured with chemical force microscopy to be pH(PZC)=10.2 ± 0.2. The specific adsorption of polyacrylic acid at non-polar ZnO step-edges can be explained by coordinative bonds formed between the carboxylic acid group and the Zn-surface atoms. On the hydroxide stabilized polar surface only weak hydrogen bonds can be formed in addition to van-der-Waals forces. Thus a "diffusion and trapping" mechanism keeps the adsorbed PAAc molecules mobile on the ZnO(0001)-Zn surface terraces due to small interaction forces until they are trapped at the (10-10) step faces by stronger coordinative bonds from the carboxylic groups to zinc atoms located in the first atomic layer of the crystal structure.     

Short-range forces between glass surfaces in aqueous solutions

We found that the force between glass surfaces measured with an atomic force microscope (AFM) has universal character in the short range, less than approximately 1 nm or about 3-4 water molecules, independent of solution conditions, that is, electrolyte ion size, charge and concentration and pH. Our results suggest that the excess DLVO force, obtained by subtracting the DLVO theory with a charge regulation model from the AFM force data, essentially does not change with the electrolytes Na, Ca, and Al, in the range of concentration from 10(-6) to 10(-2) M and the range of pH from 3.1 to 7.9. Single force curves for a glass-silica system in a 10-4 M aqueous NaCl solution at pH approximately 5.1 show oscillations with a period of about 0.25 nm, roughly the diameter of a water molecule. We postulate that the excess force between glass surfaces arises from a surface-induced solvent effect, from the creation of a hydrogen-bonding network at the surface level, rather than from a solvent-induced surface steric hindrance.     

Molecular morphology of modified partially hydrolyzed polyacrylamide (MHPAM) on mica substrates and Langmuir-Blodgett films of MHPAM/CTAB complexes as observed by AFM

Direct observation of molecular morphology of modified partially hydrolyzed polyacrylamide (MHPAM) has been studied in this paper by atomic force microscopy (AFM). The MHPAM molecule chains are stretched forming worm-like coils due to the electrostatic repulsion between randomly distributed positive charges along the chain at pH 3. The further data analysis demonstrates single MHPAM molecules are being imaged. In addition, morphology of Langmuir-Blodgett films of MHPAM/CTAB complexes on mica surfaces also investigated as a function of the subphase pH. At pH 6, MHPAM/CTAB molecules covered on mica surfaces adopted the worm-like nanostructures, and at pH 7, conformational transition of polymer complexes appeared, showing the morphology of bump-like to some extent owing to aggregation of intrachains and interchains. Eventually, more compact globule morphology was formed at pH 12.     

Single molecule force spectroscopy of asphaltene aggregates

Asphaltene aggregation and deposition cause severe problems in nearly all phases of petroleum processing. To resolve those problems, understanding the aggregation mechanisms is a prerequisite and has attracted the interest of a great number of investigators. However, to date, the nature and extent of asphaltene aggregation remain widely debated. In the present study, we attempt to investigate asphaltene aggregation from a completely new perspective. The technique of single molecule force spectroscopy (SMFS) was used to investigate the response of single asphaltene aggregates under an external pulling force. Force curves representing the stretching of single asphaltene aggregates were obtained in simple electrolyte solutions (KCl and calcium) and organic solvents (toluene and heptane). These force curves were well-fitted by the modified worm-like chain model, indicating that those asphaltene aggregates acted like long-chain polymers under pulling by an external force. It was found that lower solution pH values and the presence of divalent cations resulted in a lower bending rigidity of the formed aggregates. The information retrieved from the force curves suggests that asphaltene molecules with a structure featuring small aromatic clusters connected by aliphatic chains do exist and that asphaltene aggregation could occur through a linear polymerization mechanism. The current study extends the application scope of SMFS.     

Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules

The folding and unfolding kinetics of single molecules, such as proteins or nucleic acids, can be explored by mechanical pulling experiments. Determining intrinsic kinetic information, at zero stretching force, usually requires an extrapolation by fitting a theoretical model. Here, we apply a recent theoretical approach describing molecular rupture in the presence of force to unfolding kinetic data obtained from coarse-grained simulations of ubiquitin. Unfolding rates calculated from simulations over a broad range of stretching forces, for different pulling directions, reveal a remarkable "turnover" from a force-independent process at low force to a force-dependent process at high force, akin to the "roll-over" in unfolding rates sometimes seen in studies using chemical denaturant. While such a turnover in rates is unexpected in one dimension, we demonstrate that it can occur for dynamics in just two dimensions. We relate the turnover to the quality of the pulling direction as a reaction coordinate for the intrinsic folding mechanism. A novel pulling direction, designed to be the most relevant to the intrinsic folding pathway, results in the smallest turnover. Our results are in accord with protein engineering experiments and simulations which indicate that the unfolding mechanism at high force can differ from the intrinsic mechanism. The apparent similarity between extrapolated and intrinsic rates in experiments, unexpected for different unfolding barriers, can be explained if the turnover occurs at low forces.     

Atomic Force Microscopy for Molecular Structure Elucidation

Using scanning probe microscopy techniques, at low temperatures and in ultrahigh vacuum, individual molecules adsorbed on surfaces can be probed with ultrahigh resolution to determine their structure and details of their conformation, configuration, charge states, aromaticity, and the contributions of resonance structures. Functionalizing the tip of an atomic force microscope with a CO molecule enabled atomic‐resolution imaging of single molecules, and measurement of their adsorption geometry and bond‐order relations. In addition, by using scanning tunneling microscopy and Kelvin probe force microscopy, the density of the molecular frontier orbitals and the electric charge distribution within molecules can be mapped. Combining these techniques yields a high‐resolution tool for the identification and characterization of individual molecules. The single‐molecule sensitivity and the possibility of atom manipulation to induce chemical reactions with the tip of the microscope open up unique applications in chemistry, and differentiate scanning probe microscopy from conventional methods for molecular structure elucidation. Besides being an aid for challenging cases in natural product identification, atomic force microscopy has been shown to be a powerful tool for the investigation of on‐surface reactions and the characterization of radicals and molecular mixtures. Herein we review the progress that high‐resolution scanning probe microscopy with functionalized tips has made for molecular structure identification and characterization, and discuss the challenges it will face in the years to come.     

Single‐Molecule Sensing of Environmental pH—an STM Break Junction and NEGF‐DFT Approach

Sensors play a significant role in the detection of toxic species and explosives, and in the remote control of chemical processes. In this work, we report a single‐molecule‐based pH switch/sensor that exploits the sensitivity of dye molecules to environmental pH to build metal–molecule–metal (m‐M‐m) devices using the scanning tunneling microscopy (STM) break junction technique. Dyes undergo pH‐induced electronic modulation due to reversible structural transformation between a conjugated and a nonconjugated form, resulting in a change in the HOMO–LUMO gap. The dye‐mediated m‐M‐m devices react to environmental pH with a high on/off ratio (≈100:1) of device conductivity. Density functional theory (DFT) calculations, carried out under the non‐equilibrium Green’s function (NEGF) framework, model charge transport through these molecules in the two possible forms and confirm that the HOMO–LUMO gap of dyes is nearly twice as large in the nonconjugated form as in the conjugated form.     

Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments

The nonequilibrium work relation allows for the calculation of equilibrium free energy differences between states based on the exponential average of accumulated work from irreversible transitions. Here, we compare two distinct approaches of calculating free energy surfaces from unidirectional single-molecule pulling experiments: the stiff spring approximation and the Hummer-Szabo method. First, we perform steered molecular dynamics simulations to mechanically stretch the model peptide deca-alanine using harmonic potentials with different spring stiffnesses and at various constant pulling velocities. We then calculate free energy surfaces based on the two methods and their variants, including the first and second cumulant expansion of the exponentially weighted work and the Gaussian position approximation for the delta function in Hummer and Szabo's expression. We find that with large harmonic force constants, the second cumulant expansion performs well in conjunction with either the stiff spring approximation or the Hummer-Szabo method. When interpreting dynamic force spectroscopy (pullings at different speeds), the second cumulant expansion of the stiff spring approximation performs the best when pulling velocities are similar, but variants of the Hummer-Szabo perform the best when they are spread over a large spectrum. While these conclusion are not definitive for all systems, the insights should prove useful for scientists interpreting nonequilibrium pulling experiments.     

The currant bun model of simple molecules

The model of a molecule previously introduced by the authors, in which most of the electronic charge is represented by point charges on the nuclei, in the lone pairs and bonds, and the remainder is in a diffuse function which represents the outer electrons, is here extended. Molecules with several heavy atoms require several diffuse functions, one for each heavy atom, in addition to one at the centre of nuclear charge. In an electric field the centre of each diffuse function moves against a harmonic restoring force and this gives rise to the polarizability of the molecule. When two molecules interact the movement of this function produces the dispersion force. The model thus embodies all the long range forces between molecules in a more accurate and simpler way than was possible earlier.     

Nanoscale repulsive forces between mica and silica surfaces in aqueous solutions

Nanoscale repulsive forces between mineral surfaces in aqueous solutions were measured for the asymmetric mica-silica system. The force measured with an atomic force microscope (AFM) has universal character in the short range, less than ～1 nm or about 3-4 water molecules, independent of solution conditions, that is, electrolyte ion (Na, Ca, Al), concentration (10(-6)-10(-2)M), and pH (3.9-8.2). Notably, the force is essentially the same as for the glass-silica system. Single force curves for a mica-silica system in a 10(-4)M aqueous NaCl solution at pH ～ 5.1 show oscillations with a period of about 0.25 nm, roughly the diameter of a water molecule, a consequence of a layer-by-layer dehydration of the surfaces when pushed together. This result provides additional support to the idea that nanoscale repulsive forces between mineral surfaces in aqueous solutions arise from a surface-induced water effect; the water between two mineral plates that are pushed together becomes structured and increasingly anchored to the surface of the plates by the creation of a hydrogen-bonding network that prevents dehydration of the surfaces.     

Implementation and performance of the artificial force induced reaction method in the GRRM17 program

This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC‐AFIR), single‐component algorithm (SC‐AFIR), and double‐sphere algorithm (DS‐AFIR), are available, where the MC‐AFIR was the only algorithm which has been available in the previous 2014 version. The MC‐AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC‐AFIR performs automated generation of global or semiglobal reaction path network. The DS‐AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Grafting of single, stimuli-responsive poly(ferrocenylsilane) polymer chains to gold surfaces

Redox-responsive poly(ferrocenylsilane) (PFS) polymer molecules were attached individually to gold surfaces for force spectroscopy experiments on the single molecule level. By grafting ethylenesulfide-functionalized PFS into the defects of preformed self-assembled monolayers (SAMs) of different omega-mercaptoalkanols on Au(111), the surface coverage of PFS macromolecules could be conveniently controlled. Atomic force microscopy (AFM), contact angle, as well as cyclic and differential pulse voltammetry measurements were carried out to characterize the morphology, wettability, and surface coverage of the grafted layers. The values of the PFS surface coverage were found to depend on the chain length of the omega-mercaptoalkanol molecules and on the concentration of the PFS solution but not on the insertion time or on the molar mass of PFS. The equilibrium surface coverages were successfully described by Langmuir adsorption isotherms. For low-surface coverage values (< 6.2 x 10(-4) chain/nm2), achieved by PFS insertion from very dilute solutions (8 x 10(-6) M) into long-chain SAMs, AFM and differential pulse voltammetry showed that surfaces exposing isolated individual polymer chains were obtained. The isolated PFS macromolecules were subjected to in situ AFM-based single molecule force spectroscopy (SMFS) measurements. The single chain elasticity of PFS in isopropanol (and ethanol) was fitted with the modified freely jointed chain (m-FJC) model. This procedure yielded a Kuhn segment length of 0.33 +/- 0.05 nm and a segment elasticity of 32 +/- 5 nN/nm.     

Viscoelastic measurements of single molecules on a millisecond time scale by magnetically driven oscillation of an atomic force microscope cantilever

The dynamical nature of biomolecular systems means that knowledge of their viscoelastic behavior is important in fully understanding function. The linear viscoelastic response can be derived from an analysis of Brownian motion. However, this is a slow measurement and technically demanding for many molecular systems of interest. To address this issue, we have developed a simple method for measuring the full linear viscoelastic response of single molecules based on magnetically driven oscillations of an atomic force microscope cantilever. The cantilever oscillation frequency is periodically swept through the system resonance in less than 200 ms allowing the power spectrum to be obtained rapidly and analyzed with a suitable model. The technique has been evaluated using dextran, a polysaccharide commonly used as a test system for single molecule mechanical manipulation experiments. The monomer stiffness and friction constants were compared with those derived from other methods. Excellent agreement is obtained indicating that the new method accurately and, most importantly, rapidly provides the viscoelastic response of a single molecule between the tip and substrate. The method will be a useful tool for studying systems that change their structure and dynamic response on a time scale of 100-200 ms, such as protein folding and unfolding under applied force.     

Determination of anisotropic surface characteristics of different phyllosilicates by direct force measurements

To fundamentally understand the electrokinetic behavior of clay minerals, it is necessary to study the anisotropic surface charge properties of clay surfaces. In this study, two 2:1 layer natural minerals, talc and muscovite, were chosen as representatives of magnesium and aluminum phyllosilicate minerals, respectively. The molecularly smooth basal planes of both platy minerals were obtained by cleavage along the basal planes, while suitable edge surfaces were prepared by an ultramicrotome cutting technique. Silicon nitride atomic force microscopy tip was used as a probe to study the interaction forces between the tip and clay basal/edge surfaces in aqueous solutions of various pH values. The measured interaction force profiles between the tip and clay basal/edge surfaces were fitted with the classical DLVO (Derjaguin-Landau-Verwey-Overbeek) theory, which allows direct determination of electrical surface potential of talc and muscovite surfaces. The surface potential of muscovite basal planes was found to be significantly more negative than the basal plane of talc, both being pH insensitive. In contrast, the surface potential of edge surfaces was highly pH-dependent, exhibiting a point of zero charge (PZC) at pH 7.5 and 8.1 for edges of muscovite and talc, respectively. The observed differences in surface potential of basal planes and edge surfaces for both talc and muscovite are closely related to their crystal structure and ionization characteristics. The protonation reactivity and the contribution of each surface group to the surface charging behavior are modeled using their protonation constants.     

Conductivity in alkylamine/gold and alkanethiol/gold molecular junctions measured in molecule/nanoparticle/molecule bridges and conducting probe structures

Charge transport through alkane monolayers on gold is measured as a function of molecule length in a controlled ambient using a metal/molecule/nanoparticle bridge structure and compared for both thiol and amine molecular end groups. The current through molecules with an amine/gold junction is observed to be more than a factor of 10 larger than that measured in similar molecules with thiol/gold linkages. Conducting probe atomic force microscopy is also used to characterize the same monolayer systems, and the results are quantitatively consistent with those found in the nanoparticle bridge geometry. Scaling of the current with contact area is used to estimate that approximately 100 molecules are probed in the nanoparticle bridge geometry. For both molecular end groups, the room-temperature conductivity at low bias as a function of molecule length shows a reasonable fit to models of coherent nonresonant charge tunneling. The different conductivity is ascribed to differences in charge transfer and wave function mixing at the metal/molecule contact, including possible effects of amine group oxidation and molecular conformation. For the amine/Au contact, the nitrogen lone pair interaction with the gold results in a hybrid wave function directed along the molecule bond axis, whereas the thiol/Au contact leads to a more localized wave function.     

Influence of the Number of Anchoring Groups on the Electronic and Mechanical Properties of Benzene‐, Anthracene‐ and Pentacene‐Based Molecular Devices

One of the central issues of molecular electronics (ME) is the study of the molecule–metal electrode contacts, and their implications for the conductivity, charge‐transport mechanism, and mechanical stability. In fact, stochastic on/off switching (blinking) reported in STM experiments is a major problem of single‐molecule devices, and challenges the stability and reliability of these systems. Surprisingly, the ambiguous STM results all originate from devices that bind to the metallic electrode through a one‐atom connection. In the present work, DFT is employed to study and compare the properties of a set of simple acenes that bind to metallic electrodes with an increasing number of connections, in order to determine whether the increasing numbers of anchoring groups have a direct repercussion on the stability of these systems. The conductivities of the three polycyclic aromatic hydrocarbons are calculated, as well as their transmission spectra and current profiles. The thermal and mechanical stability of these systems is studied by pulling and pushing the metal–molecule connection. The results show that molecules with more than one connection per electrode exhibit greater electrical efficiency and current stability.     

Controlling Single Molecule Conductance by a Locally Induced Chemical Reaction on Individual Thiophene Units

Among the prerequisites for the progress of single‐molecule‐based electronic devices are a better understanding of the electronic properties at the individual molecular level and the development of methods to tune the charge transport through molecular junctions. Scanning tunneling microscopy (STM) is an ideal tool not only for the characterization, but also for the manipulation of single atoms and molecules on surfaces. The conductance through a single molecule can be measured by contacting the molecule with atomic precision and forming a molecular bridge between the metallic STM tip electrode and the metallic surface electrode. The parameters affecting the conductance are mainly related to their electronic structure and to the coupling to the metallic electrodes. Here, the experimental and theoretical analyses are focused on single tetracenothiophene molecules and demonstrate that an in situ‐induced direct desulfurization reaction of the thiophene moiety strongly improves the molecular anchoring by forming covalent bonds between molecular carbon and copper surface atoms. This bond formation leads to an increase of the conductance by about 50 % compared to the initial state.     

Titration of ionizable monolayers by measurement of the electric double-layer force

We have determined the pKa of surface-bound primary amine groups by determining the surface potential as a function of solution pH from the magnitude of the electric double-layer force. Using colloid-probe atomic force microscopy (AFM), we measured the force as a function of separation between a particle of radius R = 10 microm and a planar surface, each coated with a self-assembled monolayer of HS(CH2)2CONH((CH2)2O)8(CH2)2NH2. The force was measured from pH 3 to 7, and the surface potential was determined by fitting the results to solutions of the nonlinear Poisson-Boltzmann equation. The surface pKa of the primary amine group was found to be 5.0 +/- 0.2, in agreement with the results of contact-angle and chemical-force titrations on similar surfaces with primary amine groups. The surface charge density indicates that less than 1% of the NH2 groups are dissociated at pH 3, suggesting that ionization is very unfavorable in the local environment of the ethylene oxide chains. This noncontact method should be of general applicability to surfaces with ionizable groups and avoids the possible complications of large contact forces on the surfaces under study.     

In situ Surface Charge Density Visualization of Self-assembled DNA Nanostructures after Ion Exchange

The charge density of DNA is a key parameter in strand hybridization and for the interactions occurring between DNA and molecules in biological systems. Due to the intricate structure of DNA, visualization of the surface charge density of DNA nanostructures under physiological conditions was not previously possible. Here, we perform a simultaneous analysis of the topography and surface charge density of DNA nanostructures using atomic force microscopy and scanning ion conductance microscopy. The effect of in situ ion exchange using various alkali metal ions is tested with respect to the adsorption of DNA origami onto mica, and a quantitative study of surface charge density reveals ion exchange phenomena in mica as a key parameter in DNA adsorption. This is important for structure-function studies of DNA nanostructures. The research provides an efficient approach to study surface charge density of DNA origami nanostructures and other biological molecules at a single molecule level.