Partial Control of an Ion-Molecule Reaction by Selection of the Internal Motion of the Polyatomic Reagent Ion

Spin-Dependent Stereochemistry: A Nonadiabatic Quantum Dynamics Case Study of S + H2 → SH + H Reaction

We study the spin-dependent stereodynamics of the S + H2 → SH + H reaction by using full-dimensional quantum dynamics calculations with zero total nuclear angular momentum along the triplet 3A″ states and singlet 1A' states. We find that the interplay between the electronic spin direction and the molecular geometry has a measurable influence on the singlet-triplet intersystem crossing reaction probabilities. Our results show that for some incident scattering angles in the body-fixed frame, the relative difference in intersystem crossing reaction probabilities (as determined between spin up and spin down initial states) can be as large as 15%. Our findings are an ab initio demonstration of spin-dependent nonadiabatic dynamics, which we hope will shine light as far as understanding the chiral-induced spin selectivity effect.

Proton transfer dynamics modified by CH-stretching excitation

Gaining insight how specific rovibrational states influence reaction kinetics and dynamics is a fundamental goal of physical chemistry. Purely statistical approaches often fail to predict the influence of a specific state on the reaction outcome, evident in a great number of both experimental and theoretical studies. Most detailed insight in atomistic reaction mechanisms is achieved using accurate collision experiments and high level dynamics calculations. For ion-molecule reactions such experiments are scarce. Here we show the influence of symmetric CH-stretching vibration on the rate and dynamics of proton transfer in the reaction of F- + CH3I. We find a pronounced shift in the reaction dynamics for excited reactions from indirect to preferred direct dynamics at higher collision energy. Moreover, excited reactions occur at larger impact parameters. Finally, we compare vibrational excitation with collision energy and find that vibration is overall more efficient in promoting reactivity, which agrees with recent theoretical calculations.

Reactive mode composition factor analysis of transition states: the case of coupled electron-proton transfers

A simple method for the evaluation of the kinetic energy distribution within the reactive mode of a transition state (TS), denoted as the Reactive Mode Composition Factor (RMCF), is presented. It allows one to directly map the barrier properties onto the atomic-motion components of the reaction coordinate at the TS, which has potential to shed light onto some mechanistic features of a chemical process. To demonstrate the applicability of RMCF to reactivity, we link the kinetic energy distribution within a reactive mode with the asynchronicity (η) in C-H bond activation, as they both evolve in a series of coupled proton-electron transfer (CPET) reactions between Fe^IVO oxidants and 1,4-cyclohexadiene. RMCF shows how the earliness or lateness of a process manifests as a redistribution of kinetic energy in the reactive mode as a function of the free energy of reaction (ΔG₀) and η. Finally, the title analysis can be applied to predict H-atom tunneling contributions and kinetic isotope effects in a set of reactions, yielding a transparent rationalization based on the kinetic energy distributions in the reactive mode.

Observation of different reactivities of para and ortho-water towards trapped diazenylium ions

Water is one of the most fundamental molecules in chemistry, biology and astrophysics. It exists as two distinct nuclear-spin isomers, para- and ortho-water, which do not interconvert in isolated molecules. The experimental challenges in preparing pure samples of the two isomers have thus far precluded a characterization of their individual chemical behavior. Capitalizing on recent advances in the electrostatic deflection of polar molecules, we separate the ground states of para- and ortho-water in a molecular beam to show that the two isomers exhibit different reactivities in a prototypical reaction with trapped diazenylium ions. Based on ab initio calculations and a modelling of the reaction kinetics using rotationally adiabatic capture theory, we rationalize this finding in terms of different rotational averaging of ion-dipole interactions during the reaction.

Water molecules exist as two distinct nuclear-spin isomers denoted ortho and para. Here, the authors separate these two isomers in the gas phase to show that they exhibit different reactivities in a prototypical proton-transfer reaction.

CH stretching excitation promotes its cleavage in the F + CHD3(ν1 = 1) → HF + CD3 reaction at low collision energies

The effects of CH stretching excitation on the reactivity of the F + CHD₃ → HF + CD₃ reaction were experimentally studied.

Fine- and hyperfine-structure effects in molecular photoionization. II. Resonance-enhanced multiphoton ionization and hyperfine-selective generation of molecular cations

Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine-structure effects in one-photon ionization of molecules presented in Paper I [M. Germann and S. Willitsch, J. Chem. Phys. 145, 044314 (2016)]. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including the hyperfine structure that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ionization experiments.

How Is C-H Vibrational Energy Redistributed in F + CHD3(ν1 = 1) → HF + CD3?

The effects of CH stretching excitation on the F + CHD3 → HF + CD3 reaction are studied experimentally using crossed-beam and time-sliced velocity map imaging techniques at the collision energy of 9.0 kcal/mol. The fraction of the vibrationally excited CHD3 reagent in the crossed-beam region was determined accurately, allowing us to investigate quantitatively the effects of CH stretching excitation on the title reaction. Experimental data show that the vibrational energy in the excited CH bond of CHD3 is almost exclusively deposited into the HF product vibration, and hence, the HF products from the excited-state reaction are about one vibrational quantum hotter than those of the ground-state reaction, while the vibrational state distribution of the CD3 products is only slightly affected. The reaction is suppressed by the CH stretching excitation, and the overall reactivity of the vibrationally excited reaction is 74 ± 4% of that of the ground-state reaction for CD3(ν2 = 0, 1, 2, 3) product channels.

Electronic state dependence of the ion-molecule reaction CH(3)CN(+) + CH(3)CN → CH(4)CN(+) + CH(2)CN: threshold electron-secondary ion coincidence (TESICO) and direct ab initio molecular dynamics study

The ion-molecule reaction, CH(3)CN(+) + CH(3)CN → CH(3)CNH(+) + CH(2)CN, has been investigated using the threshold electron-secondary ion coincidence (TESICO) technique. Relative reaction cross sections for two microscopic reaction mechanisms, i.e., proton transfer (PT) from the acetonitrile ion CH(3)CN(+) to neutral acetonitrile CH(3)CN and hydrogen atom abstraction (HA) by CH(3)CN(+) from CH(3)CN, have been determined for two low-lying electronic states, (2)E and (2)A(1) of the CH(3)CN(+) primary ion. The cross section for PT of the (2)A(1) state was smaller than that of the (2)E state, whereas that of HA are almost the same in the two states. Ab initio calculations showed that the dissociation of the C-H(+) bond of CH(3)CN(+) is easier in the (2)E state than that in the (2)A(1) state. The direct ab initio molecular dynamics (MD) calculations showed that two mechanisms, direct proton transfer and complex formation, contribute the reaction dynamics.

Single-molecule measurement of the strength of a siloxane bond

Increasing the mechanical stability of artificial polymer materials is an important task in materials science, and for this a profound knowledge of the critical mechanoelastic properties of its constituents is vital. Here, we use AFM-based single-molecule force spectroscopy measurements to characterize the rupture of a single silicon-oxygen bond in the backbone of polydimethylsiloxane as well as the force-extension behavior of this polymer. PDMS is not only a polymer used in a large variety of products but also an important model system for highly flexible polymers. In our experiments, we probe the entire relevant force range from low forces dominated by entropy up to the rupture of the covalent Si-O bonds in the polymer backbone at high forces. The resulting rupture-force histograms are investigated with microscopic models of bond rupture under load and are compared to density functional theory calculations to characterize the free-energy landscape of the Si-O bond in the polymer backbone.

Mapping mouse gamete interaction forces reveal several oocyte membrane regions with different mechanical and adhesive properties

This study focuses on the interaction involved in the adhesion of mouse gametes and on the mechanical properties of the oocyte membrane. The oocyte has an asymmetrical shape, and its membrane is composed of two distinct areas. One is rich in microvilli, and the other is smoother and without microvilli. With a biomembrane force probe (BFP) adapted to cell-cell measurements, we have quantified the separation forces between a spermatozoon and an oocyte. Microvillar and amicrovillar areas of the oocyte surface have been systematically probed and compared. In addition to a substantial difference in the elastic stiffness of these two regions, the experiments have revealed the presence of two types of membrane domains with different mechanical and adhesive properties, both distributed over the entire oocyte surface (i.e., in both microvillar and amicrovillar regions). If gamete contact occurs in the first type of domain, then the oocyte membrane deforms only elastically under traction. The pull-off forces in these domains are higher in the amicrovillar region. For a spermatozoon contact with the other type of domain, there can be a transition from the elastic to viscoelastic regime, and then tethers are extruded from the oocyte membrane.

Vibrational overtone spectroscopy of phenol and its deuterated isotopomers

We have measured the OH- and OD-stretching fundamental and overtone spectra of phenol and its deuterated isotopomers under jet-cooled conditions using nonresonant ionization detection spectroscopy and vapor-phase infrared (IR) and near-infrared (NIR) spectra at room temperature using conventional and photoacoustic spectroscopy. The OH- and OD-stretching bands in the jet-cooled spectra are about 1-10 cm(-1) wide and generally show a few Lorentzian shaped peaks. The bands in the room-temperature spectra have widths of 20-30 cm(-1) and display clear rotational profiles. The band profiles in the jet-cooled spectra arise mostly from nonstatistical intramolecular vibrational redistribution (IVR) with specific coupling to "doorway" states, which are likely to involve CH- and CD-stretching vibrations. The transition dipole moment that determines the rotational structure is found to rotate significantly from the fundamental to the third overtone and is not directed along the OH(D) bond. We use these calculated transition dipole moments to simulate the rotational structure. We determine the rotational temperature in the jet-cooled spectra to be about 0.5 K. Anharmonic oscillator local mode calculations of frequencies and intensities of the OH- and OD-stretching transitions are compared with our measured results. The calculated intensities are in good agreement with the absolute intensities obtained from conventional spectroscopy and with the relative intensities obtained from the room-temperature laser spectroscopy.

Adhesion force studies of Janus nanoparticles

Janus nanoparticles represent a unique nanoscale analogue to the conventional surfactant molecules, exhibiting hydrophobic characters on one side and hydrophilic characters on the other. Yet, direct visualization of the asymmetric surface structures of the particles remains a challenge. In this paper, we used a simple technique based on AFM adhesion force measurements to examine the two distinctly different hemispheres of the Janus particles at the molecular level. Experimentally, the Janus nanoparticles were prepared by ligand exchange reactions at the air-water interface. The particles were then immobilized onto a substrate surface with the particle orientation controlled by the chemical functionalization of the substrate surface, and an AFM adhesion force was employed to measure the interactions between the tip of a bare silicon probe and the Janus nanoparticles. It was found that when the hydrophilic side of the particles was exposed, the adhesion force was substantially greater than that with the hydrophobic side exposed, as the silicon probes typically exhibit hydrophilic properties. These studies provide further confirmation of the amphiphilic nature of the Janus nanoparticles.

Monitoring the activity of tyrosinase on a tyramine/dopamine-functionalized surface by force microscopy

Tyrosinase activity is monitored by pi-donor-acceptor force interactions between a bipyridinium-modified AFM tip and the biocatalytic reaction product generated on a tyramine- (or dopamine-) modified surface. Upon oxidation of the surface to dopaquinone as a result of tyrosinase activity, force interactions are switched "OFF". After reduction of the resulting surface with ascorbic acid, forces are quantitatively reestablished as a result of the formation of the dopamine-functionalized surfaces. The method provides a general approach to design biosensors using force interactions as the readout signal.

The study of state-selected ion-molecule reactions using the vacuum ultraviolet pulsed field ionization-photoion technique

This paper presents the methodology to generate beams of ions in single quantum states for bimolecular ion-molecule reaction dynamics studies using pulsed field ionization (PFI) of atoms or molecules in high-n Rydberg states produced by vacuum ultraviolet (VUV) synchrotron or laser photoexcitation. Employing the pseudocontinuum high-resolution VUV synchrotron radiation at the Advanced Light Source as the photoionization source, PFI photoions (PFI-PIs) in selected rovibrational states have been generated for ion-molecule reaction studies using a fast-ion gate to pass the PFI-PIs at a fixed delay with respect to the detection of the PFI photoelectrons (PFI-PEs). The fast ion gate provided by a novel interleaved comb wire gate lens is the key for achieving the optimal signal-to-noise ratio in state-selected ion-molecule collision studies using the VUV synchrotron based PFI-PE secondary ion coincidence (PFI-PESICO) method. The most recent development of the VUV laser PFI-PI scheme for state-selected ion-molecule collision studies is also described. Absolute integral cross sections for state-selected H2+ ions ranging from v+ = 0 to 17 in collisions with Ar, Ne, and He at controlled translational energies have been obtained by employing the VUV synchrotron based PFI-PESICO scheme. The comparison between PFI-PESICO cross sections for the H2+(HD+)+Ne and H2+(HD+)+He proton-transfer reactions and theoretical cross sections based on quasiclassical trajectory (QCT) calculations and three-dimensional quantum scattering calculations performed on the most recently available ab initio potential energy surfaces is highlighted. In both reaction systems, quantum scattering resonances enhance the integral cross sections significantly above QCT predictions at low translational and vibrational energies. At higher energies, the agreement between experiment and quasiclassical theory is very good. The profile and magnitude of the kinetic energy dependence of the absolute integral cross sections for the H2+(v+ = 0-2,N+ = 1)+He proton-transfer reaction unambiguously show that the inclusion of Coriolis coupling is important in quantum dynamics scattering calculations of ion-molecule collisions.

Specific and nonspecific interaction forces between Escherichia coli and silicon nitride, determined by poisson statistical analysis

The nature of the physical interactions between Escherichia coli JM109 and a model surface (silicon nitride) was investigated in water via atomic force microscopy (AFM). AFM force measurements on bacteria can represent the combined effects of van der Waals and electrostatic forces, hydrogen bonding, steric interactions, and perhaps ligand-receptor type bonds. It can be difficult to decouple these forces into their individual components since both specific (chemical or short-range forces such as hydrogen bonding) and nonspecific (long-range colloidal) forces may be present in the overall profiles. An analysis is presented based on the application of Poisson statistics to AFM adhesion data, to decouple the specific and nonspecific interactions. Comparisons with classical DLVO theory and a modified form of a van der Waals expression for rough surfaces were made in order to help explain the nature of the interactions. The only specific forces in the system were due to hydrogen bonding, which from the Poisson analysis were found to be -0.125 nN. The nonspecific forces of 0.155 nN represent an overall repulsive interaction. These nonspecific forces are comparable to the forces calculated from DLVO theory, in which electrostatic-double layer interactions are added to van der Waals attractions calculated at the distance of closest approach, as long as the van der Waals model for "rough" spherical surfaces is used. Calculated electrostatic-double layer and van der Waals interactions summed to 0.116 nN. In contrast, if the classic (i.e., smooth) sphere-sphere model was used to predict the van der Waals forces, the sum of electrostatic and van der Waals forces was -7.11 nN, which appears to be a large overprediction. The Poisson statistical analysis of adhesion forces may be very useful in applications of bacterial adhesion, because it represents an easy way to determine the magnitude of hydrogen bonding in a given system and it allows the fundamental forces to be easily broken into their components.

Single-Molecule Force Spectroscopy of Bimolecular Reactions: System Homology in the Mechanical Activation of Ligand Substitution Reactions

The mechanochemistry of the bimolecular nucleophilic substitution of DMSO for substituted pyridines at a square-planar pincer Pd(II) center was investigated using single-molecule force spectroscopy (SMFS). The SMFS data are interpreted in terms of the Bell-Evans model, which gives thermal off-rates for two reactions that agree well with previous, stress-free measurements. The characteristic force dependency of the rupture rate, fbeta, is effectively constant for the two reactions examined (22 +/- 2 and 24 +/- 2 pN), and the system homology in the mechanical response is consistent with expected similarities in the reaction potential energy surfaces.

Interaction between poly[(R)-3-hydroxybutyrate] depolymerase and biodegradable polyesters evaluated by atomic force microscopy

Adsorption of PHB depolymerase from Ralstonia pickettii T1 to biodegradable polyesters such as poly[(R)-3-hydroxybutyrate] (PHB) and poly(l-lactic acid) (PLLA) was investigated by atomic force microscopy (AFM). The substrate-binding domain (SBD) with histidines within the N-terminus was prepared and immobilized on the AFM tip surface via a self-assembled monolayer with a nitrilotriacetic acid group. Using the functionalized AFM tips, the force-distance measurements for polyesters were carried out at room temperature in a buffer solution. In the case of AFM tips with immobilized SBD and their interaction with polyesters, multiple pull-off events were frequently recognized in the retraction curves. The single rupture force was estimated at approximately 100 pN for both PLLA and PHB. The multiple pull-off events were recognized even in the presence of a surfactant, which will prevent nonspecific interactions, but reduced when using polyethylene instead of polyesters as a substrate. The present results provide that the PHB depolymerase adsorbs specifically to the surfaces of polyesters and that the single unbinding event evaluated here is mainly associated with the interaction between one molecule of SBD and the polymer surface.

Protein crystals as scanned probes for recognition atomic force microscopy

Lysozyme crystal growth has been localized at the tip of a conventional silicon nitride cantilever through seeded nucleation. After cross-linking with glutaraldehyde, lysozyme protein crystal tips image gold nanoparticles and grating standards with a resolution comparable to that of conventional tips. Force spectra between the lysozyme crystal tips and surfaces covered with antilysozyme reveal an adhesion force that drops significantly upon blocking with free lysozyme, thus confirming that lysozyme crystal tips can detect molecular recognition interactions.

Rupture force between the third strand and the double strand within a triplex DNA

The rupture force to separate the third strand and the duplex within a triplex DNA was measured by means of atomic force spectroscopy. The tip and the sample surfaces were functionalized by oligodeoxyribonucleotides 5'-TTCTTCTTTCTTTTCCTTTTCTTTCTTCTTACTTCTCTCTCTC TCTCTCT-SH-3'. The sample surface was hybridized with 5'-AAGAAGAAAGAAAAGGAAAAGAAAGAAGAA-3' to form a double strand DNA on the surface prior to the force measurements. These sequences form triple helices with 30 base pairs under a pH of 5.8 and in the presence of 2.0 mM spermine. Signals of rupture of single and multiple triplex DNA were observed in the force distance curves. Rupture force histograms revealed a force of 42.6 +/- 1.9 pN from 24 independent measurements at a tip velocity of 400 nm/s to separate the third strand from duplex DNA. The velocity dependence of the rupture force quantum indicates a thermal dissociation process similar to that of rupturing a ds-DNA. The number of rupture events was controlled by adding oligonucleotides 5'-AAGAAGAAAGAAAAGGAAAAGAAAGAAGAA-3' either to reduce or to initiate triplex formation.

Single-molecular Pair Unbinding Studies of Mannuronan C-5 Epimerase AlgE4 and Its Polymer Substrate

Alginate biosynthesis involves C-5-mannuronan epimerases catalyzing the conversion of beta-D-mannuronic acid to alpha-L-guluronic acid at the polymer level. Mannuronan epimerases are modular enzymes where the various modules yield specific sequential patterns of the converted residues in their polymer products. Here, the interaction between the AlgE4 epimerase and mannuronan is determined by dynamic force spectroscopy. The specific unbinding between molecular pairs of mannuronan and AlgE4 as well as its two modules, A and R, respectively, was studied as a function of force loading rate. The mean protein-mannuronan unbinding forces were determined to be in the range 73-144 pN, depending on the protein, at a loading rate of 0.6 nN/s, and increased with increasing loading rate. The position of the activation barrier was determined to be 0.23 +/- 0.04 nm for the AlgE4 and 0.10 +/- 0.02 nm for its A-module. The lack of interaction observed between the R-module and mannuronan suggest that the A-module contains the binding site for the polymer substrate. The ratio between the epimerase-mannuronan dissociation rate and the catalytic rate for epimerization of single hexose residues suggests a processive mode of action of the AlgE4 epimerase yielding the observed sequence pattern in the uronan associated with the A-module of this enzyme.

Active control of the dynamics of atoms and molecules

There has been much progress in the control of chemical reactions since methods of active control were first proposed by Brumer & Shapiro and by Tannor & Rice ten years ago. This chapter reviews both theoretical and experimental advances in the field. Control schemes based on quantum mechanical interference between competing paths and the manipulation of wave packets with tailored laser pulses are discussed. The theory of optimal control, the limitations of control theory applied to many-body dynamics, and the effects of constraints on the trajectory of the controlled observable are presented. Experimental progress in controlling the population of specific quantum states, in manipulating the dynamics of bound wave packets, and in the control of chemical reactions are reviewed, and current problems in the field are summarized.

β-Cyclodextrin Host−Guest Complexes Probed under Thermodynamic Equilibrium: Thermodynamics and AFM Force Spectroscopy

The rupture forces of individual host-guest complexes between beta-cyclodextrin (beta-CD) heptathioether monolayers on Au(111) and several surface-confined guests were measured in aqueous medium by single molecule force spectroscopy using an atomic force microscope. Anilyl, toluidyl, tert-butylphenyl, and adamantylthiols (0.2-1%) were immobilized in mixed monolayers with 2-mercaptoethanol on gold-coated AFM tips. For all guests and for all surface coverages, the force-displacement curves measured between the functionalized tips and monolayers of beta-CD exhibited single, as well as multiple, pull-off events. The histograms of the pull-off forces showed several maxima at equidistant forces, with force quanta characteristic for each guest of 39 +/- 15, 45 +/- 15, 89 +/- 15, and 102 +/- 15 pN, respectively. These force quanta were independent of the loading rate, indicating that, because of the fast complexation/decomplexation kinetics, the rupture forces were probed under thermodynamic equilibrium. The force values followed the same trend as the free binding energy Delta G degrees measured for model guest compounds in solution or on beta-CD monolayers, as determined by microcalorimetry and surface plasmon resonance measurements, respectively. A descriptive model was developed to correlate quantitatively the pull-off force values with the Delta G degrees of the complexes, based on the evaluation of the energy potential landscape of tip-surface interaction.

Specific aptamer-protein interaction studied by atomic force microscopy

Aptamers are a new class of synthetic DNA/RNA oligonucleotides generated from in vitro selection to selectively bind with various molecules. Due to their molecular recognition capability for proteins, aptamers are becoming promising reagents in protein detection and new drug development. In this study, the specific interaction between the protein immunoglobulin E (IgE) and its 37-nt aptamer has been measured directly by atomic force microscopy. The single-molecule unbinding force between IgE and the aptamer is determined using the Poisson statistical method. The individual unbinding force between IgE and its monoclonal antibody has also been obtained and compared to that between IgE and the aptamer. The results reveal the high affinity of the aptamer to protein, which could match or even surpass that of the antibody to its antigen.

A novel single-molecule study to determine protein--protein association constants

Atomic force microscopy (AFM) is traditionally used as an imaging technique to gain qualitative information for a biological system. We have successfully used the imaging capabilities of the AFM to determine protein-protein association constants. We have developed a method to measure the molecular weight of a protein based on its volume determined from AFM images. Our volume determination method allows for rapid, accurate analysis of large protein populations. On the basis of the measured volume, the fraction of monomers as dimers was determined for the DNA helicase UvrD, and the dissociation constant (K(d)) for the helicase was calculated. We determined a K(d) for UvrD of 1.4 microM, which is in good agreement with published K(d) data obtained from analytical ultracentrifugation (AUC) studies. Our method provides a rapid method for determining protein-protein association constants.

Monitoring the conformational fluctuations of DNA hairpins using single-pair fluorescence resonance energy transfer

We present single-pair fluorescence resonance energy transfer (spFRET) observations of individual opening and closing events of surface-immobilized DNA hairpins. Two glass-surface immobilization strategies employing the biotin-streptavidin interaction and a third covalent immobilization strategy involving formation of a disulfide bond to a thiol-derivatized glass surface are described and evaluated. Results from image and time-trace data from surface-immobilized molecules are compared with those from freely diffusing molecules, which are unperturbed by surface interactions. Using a simple two-state model to analyze the open and closed time distributions for immobilized hairpins, we calculate the lifetimes of the two states. For hairpins with a loop size of 40 adenosines and a stem size of either seven or nine bases, the respective closed-state lifetimes are 45 +/- 2.4 and 103 +/- 6.0 ms, while the respective open-state lifetimes are 133 +/- 5.5 and 142 +/- 22 ms. These results show that the open state of the hairpin is favored over the closed state of the hairpin under these conditions, consistent with previous diffusion fluorescence correlation spectroscopy (FCS) experiments on poly(A)-loop hairpins. The measured open-state lifetime is about 30 times longer than the calculated 3 ms open-state lifetime for both hairpins based on a closing rate scaling factor derived from a previous FCS study for hairpins in diffusion with 12-30 thymidines in their loops. As predicted, the closed-state lifetime is dependent on the stem length and is independent of the loop characteristics. Our findings indicate that current models should consider sequence dependence in calculating ssDNA thermostability. The surface immobilization chemistries and other experimental techniques described here should prove useful for studies of single-molecule populations and dynamics.