Computational spectroscopy of helium-solvated molecules: effective inertia, from small He clusters toward the nanodroplet regime

Accurate computer simulations of the rotational dynamics of linear molecules solvated in He clusters indicate that the large-size (nanodroplet) regime is attained quickly for light rotors (HCN) and slowly for heavy ones (OCS, N2O, and CO2), thus challenging previously reported results. Those results spurred the view that the different behavior of light rotors with respect to heavy ones-including a smaller reduction of inertia upon solvation of the former-would result from the lack of adiabatic following of the He density upon molecular rotation. We have performed computer experiments in which the rotational dynamics of OCS and HCN molecules was simulated using a fictitious inertia appropriate to the other molecule. These experiments indicate that the approach to the nanodroplet regime, as well as the reduction of the molecular inertia upon solvation, is determined by the anistropy of the potential, more than by the molecular weight. Our findings are in agreement with recent infrared and/or microwave experimental data which, however, are not yet totally conclusive by themselves.     

Van der waals interactions and decrease of the rotational barrier of methyl-sized rotators: a theoretical study

Rotational barriers of methyl-sized molecular rotators are investigated theoretically using ab initio and empirical force field calculations in molecular models simulating various environmental conditions experienced by the molecular rotors. Calculations on neopentane surrounded by methyl groups suggest that the neopentane's methyl rotational potential energy barrier can be reduced by up to an order of magnitude by locating satellite functional groups around the rotator at a geometry that destabilizes the staggered conformation of the rotator through van der Waals repulsive interactions and reduces the staggered/eclipsed relative energy difference. Molecular mechanics and molecular dynamics calculations indicate that this barrier-reducing geometry can also be found in molecular rotators surface mounted on graphite surfaces or carbon nanotube models. In these models, molecular dynamics simulations show that the rotation of methyl-sized functional groups can be catalyzed by van der Waals interactions, thus making very rigid rotators become thermally activated at room temperature. These results are discussed in the context of design of nanostructures and use of methyl groups as markers for microenvironmental conditions.     

Probing ground-state single-electron self-exchange across a molecule-metal interface

We have probed single-molecule redox reaction dynamics of hemin (chloride) adsorbed on Ag nanoparticle surfaces by single-molecule surface-enhanced Raman spectroscopy (SMSERS) combined with spectroelectrochemistry. Redox reaction at the molecule/Ag interface is identified and probed by the prominent fluctuations of the Raman frequency of a specific vibrational mode, ν(4), which is a typical marker of the redox state of the iron center in a hemin molecule. On the basis of the autocorrelation and cross-correlation analysis of the single-molecule Raman spectral trajectories and the control measurements of single-molecule spectroelectochemistry and electrochemical STM, we suggest that the single-molecule redox reaction dynamics at the hemin-Ag interface is primarily driven by thermal fluctuations. The spontaneous fluctuation dynamics of the single-molecule redox reaction is measured under no external electric potential across the molecule-metal interfaces, which provides a novel and unique approach to characterize the interfacial electron transfer at the molecule-metal interfaces. Our demonstrated approaches are powerful for obtaining molecular coupling and dynamics involved in interfacial electron transfer processes. The new information obtained is critical for a further understanding, design, and manipulation of the charge transfer processes at the molecule-metal interface or metal-molecule-metal junctions, which are fundamental elements in single-molecule electronics, catalysis, and solar energy conversion.     

Onset of slow dynamics in difluorotetrachloroethane glassy crystal

Complementary neutron spin-echo and x-ray experiments and molecular-dynamics simulations have been performed on difluorotetrachloroethane (CFCl2-CFCl2) glassy crystal. Static, single-molecule reorientational dynamics and collective dynamics properties are investigated. Our results confirm the strong analogy between molecular liquids and plastic crystals. The orientational disorder is characterized at different temperatures and a change in the nature of rotational dynamics is observed. A careful check of the rotational diffusion model is performed using self-angular correlation functions Cl with high l values and compared to results obtained on molecular liquids composed of A-B dumbbells. Below the crossover temperature at which slow dynamics emerge, we show that some scaling predictions of the mode coupling theory hold and that alpha-relaxation times and nonergodicity parameters are controlled by the nontrivial static correlations.     

Electrochemically controlled self-assembled monolayers characterized with molecular and sub-molecular resolution

Self-assembled organization of functional molecules on solid surfaces has developed into a powerful and sophisticated tool for surface chemistry and nanotechnology. A number of reviews on the topic have been available since the mid 1990s. This perspective article aims to focus on recent development in the investigations of electronic structures and assembling dynamics of electrochemically controlled self-assembled monolayers (SAMs) of thiol containing molecules on gold surfaces. A brief introduction is first given and particularly illustrated by a Table summarizing the molecules studied, the surface lattice structures and the experimental operating conditions. This is followed by discussion of two major high-resolution experimental methods, scanning tunnelling microscopy (STM) and single-crystal electrochemistry. In Section 3, we briefly address choice of supporting electrolytes and substrate surfaces, and their effects on the SAM structures. Section 4 constitutes the major body of the article by offering some details of recent studies for the selected cases, including in situ monitoring of assembling dynamics, molecular electronic structures, and the key external factors determining the SAM packing. In Section 5, we give examples of what can be offered by theoretical computations for the detailed understanding of the SAM electronic structures revealed by STM images. A brief summary of the current applications of SAMs in wiring metalloproteins, design and fabrication of sensors, and single-molecule electronics is described in Section 6. In the final two sections (7 and 8), we discuss the current status in understanding of electronic structures and properties of SAMs in electrochemical environments and what could be expected for future perspectives.     

Molecular Rotors in Porous Organic Frameworks

Porous organic frameworks perform a variety of functions, owing to their extremely large surface areas, but the dynamics of the structural elements have never been explored. Our discovery of ultra‐fast molecular rotors (10⁶ Hz at 225 K) in their architectures allows us to look at them from a new perspective. The constructive elements are robust struts and rapid rotors, resulting in a dynamic material whose motion can be frozen or released at will. The rotational motion can be actively regulated in response to guests. As the temperature is increased, the rotors spin ever faster, approaching free‐rotational diffusion at 550 K. The unusual combination of remarkable nanoporosity with fast dynamics is intriguing for engineering oscillating dipoles and producing responsive materials with switchable ferroelectricity, and for applications spanning from sensors to actuators, which capture and release chemicals on command.     

The role of molecular rotation in activated dissociative adsorption on metal surfaces

The role of molecular rotation in dissociative adsorption of H2 on the activated NiAl(110) metal surface is systematically investigated by means of classical dynamics calculations performed on ab initio six-dimensional potential energy surfaces. The calculations show that molecules rotate abruptly when they are close to the surface and that this rotation allows the molecules to adopt the orientation that is more convenient for dissociation (i.e., nearly parallel to the surface). Also, in reactive sectors of the NiAl(110) unit cell, there is an "angular threshold" below which molecules cannot dissociate. This angular threshold goes down as the incidence energy increases, which explains the rise of the dissociation probability and the fact that it reaches a value close to 1 at incidence energies of the order of 2 eV. The fact that switching on molecular rotation favors dissociation establishes a competition between dissociation and rotational excitation of reflected molecules above the dissociation threshold. Measurements on rotational excitation might thus bring indirect evidence on the dissociation dynamics. Sample calculations for nonactivated Pd(111) and activated Cu(110) metal surfaces suggest that some of these conclusions may be of general validity.     

Giant Crystalline Molecular Rotors that Operate in the Solid State

Molecular motion in the solid state is typically precluded by the highly dense environment, and only molecules with a limited range of sizes show such dynamics. Here, we demonstrate the solid-state rotational motion of two giant molecules, i.e., triptycene and pentiptycene, by encapsulating a bulky N-heterocyclic carbene (NHC) Au(I) complex in the crystalline media. To date, triptycene is the largest molecule (surface area: 245 Ų; volume: 219 ų) for which rotation has been reported in the solid state, with the largest rotational diameter among reported solid-state molecular rotors (9.5 Å). However, the pentiptycene rotator that is the subject of this study (surface area: 392 Ų; volume: 361 ų; rotational diameter: 13.0 Å) surpasses this record. Single-crystal X-ray diffraction analyses of both the developed rotors revealed that these possess sufficient free volume around the rotator. The molecular motion in the solid state was confirmed using variable-temperature solid-state ²H spin-echo NMR studies. The triptycene rotor exhibited three-fold rotation, while temperature-dependent changes of the rotational angle were observed for the pentiptycene rotor.     

Translational to rotational energy transfer in molecule-surface collisions

A theoretical approach that combines classical mechanics for treating translational and rotational degrees of freedom and quantum mechanics for describing the excitation of internal molecular modes is applied to the scattering of diatomic molecules from metal surfaces. Calculations are carried out for determining the extent of energy transfer to the rotational degrees of freedom of the projectile molecule. For the case of observed spectra of intensity versus final rotational energy, quantitative agreement with available experimental data for the scattering of NO and N(2) from close packed metal surfaces is obtained. It is shown that such measurements can be used to determine the average rotational energy of the incident molecular beam. Measurements of the exchange of energy between translational and rotational degrees of freedom upon collision are also described by calculations for these same systems.     

Single-molecule microscopy studies of electric-field poling in chromophore-polymer composite materials

One strategy for increasing the efficiency of organic electrooptic devices based on chromophore-polymer composite materials is to improve chromophore ordering. In these materials, ordering is induced through the interaction of the chromophore dipole moment with an external electric field, applied at temperatures near the Tg of the polymer host, a process referred to as "poling". To provide insight into the molecular details of the poling process under conditions representative of device construction, the rotational dynamics of single 4-dicyano-methylene-2-methyl-6-(p-(dimethylamino)styryl)-4H-pyran (DCM) molecules in poly(methyl acrylate) at T = Tg + 11 degrees C in the presence and absence of an electric field are investigated using single-molecule confocal fluorescence microscopy. Single-molecule rotational dynamics are monitored through the time evolution of the fluorescence anisotropy. The anisotropy correlation function demonstrates nonexponential decay, with beta values derived from fits using the Kohlrausch-Williams-Watts law ranging from 0.7 to 1 with beta(KWW) = 0.83. This observation is consistent with previous studies of molecular rotation dynamics in polymer melts and reflects the dynamical heterogeneity provided by the polymer host. The rotational dynamics of DCM are weakly perturbed in the presence of a 50 V/microm electric field, typical of the field strength employed in device construction. The expected perturbation of the rotational dynamics is determined and found to be consistent with the alignment potential created by the electric field relative to the amount of thermal energy available. The relevance of these findings with respect to current models of the poling process is discussed. This work demonstrates the utility of polarization-sensitive single-molecule microscopy in elucidating the details of molecular reorientation during poling.     

Molecular dynamics simulations for CO(2) absorption spectra. I. Line broadening and the far wing of the ν(3) infrared band

Classical molecular dynamics simulations (CMDS) have been carried out for gaseous CO(2) starting from the intermolecular potential energy surface. Through calculations for a large number of molecules treated as rigid rotors, various autocorrelation functions (ACFs) are obtained together with probabilities of rotational changes. Those used in the present paper are the ACFs of the center of mass velocity and of the molecular orientation, and the conditional probability of a change of the angular speed. They enable calculations, respectively, of the mass diffusion coefficient, of the infrared (dipolar) band shape including the wings, and of individual line-broadening coefficients. It is shown that these calculations, free of any adjustable parameter, lead to good agreement with measured values. This is expected from previous studies for the mass diffusion coefficient and line-broadening coefficients, but it is, to our knowledge, the first demonstration of the interest of CMDS for the prediction of band wings. The present results thus open promising perspectives for the theoretical treatment of the difficult problem of far wings profiles.     

Self-Assembly of Highly Stable Zirconium(IV) Coordination Cages with Aggregation Induced Emission Molecular Rotors for Live-Cell Imaging

The self-assembly of highly stable zirconium(IV)-based coordination cages with aggregation induced emission (AIE) molecular rotors for in vitro bio-imaging is reported. The two coordination cages, NUS-100 and NUS-101, are assembled from the highly stable trinuclear zirconium vertices and two flexible carboxyl-decorated tetraphenylethylene (TPE) spacers. Extensive experimental and theoretical results show that the emissive intensity of the coordination cages can be controlled by restricting the dynamics of AIE-active molecular rotors though multiple external stimuli. Because the two coordination cages have excellent chemical stability in aqueous solutions (pH stability: 2–10) and impressive AIE characteristics contributed by the molecular rotors, they can be employed as novel biological fluorescent probes for in vitro live-cell imaging.     

An investigation of water dynamics in binary mixtures of water and dimethyl sulfoxide

The motion of water molecules in mixtures of water and d6-dimethyl sulfoxide (DMSO) has been explored through molecular dynamics (MD) simulations using the SPC/E water model (J. Chem. Phys. 1987, 91, 6269) and the P2 DMSO model (J. Chem. Phys. 1993, 98, 8160). We evaluate the self-intermediate scattering functions, FS(Q,t), which are related by a Fourier transform to the incoherent structure factors, S(Q,omega), measured in quasielastic neutron scattering (QNS) experiments. We compare our results to recent QNS experiments on these mixtures reported by Bordallo et al. (J. Chem. Phys. 2004, 121, 12457). In addition to comparing the MD data to the experimental signals, which correspond to a convolution of S(Q,omega) with a resolution function, we examine the rotational and translational components of FS(Q,t) and investigate to what extent simulation results for the single-molecule dynamics follow the dynamical models that are used in the analysis of the experimental data. We find that the agreement between the experimental signal and the MD data is quite good and that the portion of FS(Q,t) due to translational dynamics is well represented by the jump-diffusion model. The model parameters and their composition dependence are in reasonable agreement with experiment, exhibiting similar trends in water mobility with composition. Specifically, we find that water motion is less hindered in water-rich and water-poor mixtures than it is near equimolar composition. We find that the extent of coupling between rotational and translational motion contributing to FS(Q,t) increases as the equimolar composition of the mixture is approached. Thus, the decoupling approximation, which is used to extract information on rotational relaxation from QNS spectra at higher momentum transfer (Q) values, becomes less accurate than that in water-rich or DMSO-rich mixtures. We also find that rotational relaxation deviates quite strongly from the isotropic rotational diffusion model. We explore this issue further by investigating the behavior of orientational time correlations for different unit vectors and corresponding to Legendre polynomials of orders 1-4. We find that the rotational time correlations of water molecules behave in a way that is more consistent with the extended jump rotation model recently proposed by Laage and Hynes (Science 2006, 311, 832).     

Molecular dynamics of glucose in solution: a quasielastic neutron scattering study

The molecular dynamics of glucose dissolved in heavy water have been investigated at 280 K by the technique of quasielastic neutron scattering. The scattering was described by a dynamic structure factor that accounts for decoupled diffusive jumps and free rotational motions of the glucose molecules. With increasing glucose concentration, the diffusion constant decreases by a factor five and the time between jumps increases considerably. Our observations validate theoretical predictions concerning the impact of concentration on the environment of a glucose molecule and the formation of cages made by neighboring glucose molecules at higher concentrations.     

Aggregation‐Induced Emission Rotors: Rational Design and Tunable Stimuli Response

A novel molecular design strategy is provided to rationally tune the stimuli response of luminescent materials with aggregation‐induced emission (AIE) characteristics. A series of new AIE‐active molecules (AIE rotors) are prepared by covalently linking different numbers of tetraphenylethene moieties together. Upon gradually increasing the number of rotatable phenyl rings, the sensitivity of the response of the AIE rotors to viscosity and temperature is significantly enhanced. Although the molecular size is further enlarged, the performance is only slightly improved due to slightly increased effective rotors, but with largely increased rotational barriers. Such molecular engineering and experimental results offer more in‐depth insight into the AIE mechanism, namely, restriction of intramolecular rotations. Notably, through this rational design, the AIE rotor with the largest molecular size turns out to be the most viscosensitive luminogen with a viscosity factor of up to 0.98.     

Self‐Assembly of Highly Stable Zirconium(IV) Coordination Cages with Aggregation Induced Emission Molecular Rotors for Live‐Cell Imaging

The self‐assembly of highly stable zirconium(IV)‐based coordination cages with aggregation induced emission (AIE) molecular rotors for in vitro bio‐imaging is reported. The two coordination cages, NUS‐100 and NUS‐101, are assembled from the highly stable trinuclear zirconium vertices and two flexible carboxyl‐decorated tetraphenylethylene (TPE) spacers. Extensive experimental and theoretical results show that the emissive intensity of the coordination cages can be controlled by restricting the dynamics of AIE‐active molecular rotors though multiple external stimuli. Because the two coordination cages have excellent chemical stability in aqueous solutions (pH stability: 2–10) and impressive AIE characteristics contributed by the molecular rotors, they can be employed as novel biological fluorescent probes for in vitro live‐cell imaging.     

核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。 结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。 尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。 尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。 本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。     

Photophysics of Fluorescent Contact Sensors Based on the Dicyanodihydrofuran Motif

Fluorescent molecular rotors have been used for measurements of local mobility on molecular length scales, for example to determine viscosity, and for the visualization of contact between two surfaces. In the present work, we deepen our insight into the excited-state deactivation kinetics and mechanics of dicyanodihydrofuran-based molecular rotors. We extend the scope of the use of this class of rotors for contact sensing with a red-shifted member of the family. This allows for contact detection with a range of excitation wavelengths up to ∼600 nm. Steady-state fluorescence shows that the fluorescence quantum yield of these rotors depends not only on the rigidity of their environment, but – under certain conditions – also on its polarity. While excited state decay via rotation about the exocyclic double bond is rapid in nonpolar solvents and twisting of a single bond allows for fast decay in polar solvents, the barriers for both processes are significant in solvents of intermediate polarity. This effect may also occur in other molecular rotors, and it should be considered when applying such molecules as local mobility probes.     

Multiplexed Discrimination of Single Amino Acid Residues in Polypeptides in a Single SERS Hot Spot

The SERS-based detection of protein sequences with single-residue sensitivity suffers from signal dominance of aromatic amino acid residues and backbones, impeding detection of non-aromatic amino acid residues. Herein, we trap a gold nanoparticle in a plasmonic nanohole to generate a single SERS hot spot for single-molecule detection of 2 similar polypeptides (vasopressin and oxytocin) and 10 distinct amino acids that constitute the 2 polypeptides. Significantly, both aromatic and non-aromatic amino acids are detected and discriminated at the single-molecule level either at individual amino acid molecules or within the polypeptide chains. Correlated with molecular dynamics simulations, our results suggest that the signal dominance due to large spatial occupancy of aromatic rings of the polypeptide sidechains on gold surfaces can be overcome by the high localization of the single hot spot. The superior spectral and spatial discriminative power of our approach can be applied to single-protein analysis, fingerprinting, and sequencing.