Electrostatic field effect on molecular structures at metal surfaces

We report on the structural transitions of molecules on metal surfaces by external electrostatic field. An electrode–molecule–electrode model is considered to quantify the effect of electrostatic forces at the molecule–electrode interface. Within a quasi-parallel-plate capacitor approach, this model reveals how external electrostatic fields change the delicate balance between molecule–substrate and molecule–molecule interactions, leading to substantial changes in the molecular conformation. The predictions are validated by scanning tunneling microscopy (STM) observations of four different molecules and electrode facets. In addition, first-principles simulations verify the results of our model calculations.     

Luminescent properties of thermally activated delayed fluorescence molecule with intramolecular π-π interaction between donor and acceptor

Influence of intramolecular π-π interaction on the luminescent properties of thermally activated delayed fluorescence(TADF) molecule(3, 5-bis(3,6-di-tert-butyl-9 H-carbazol-9-yl)-phenyl)(pyridin-4-yl) methanone(DTCBPY) is theoretically studied by using the density functional theory(DFT) and time-dependent density functional theory(TD-DFT).Four conformations(named as A, B, C, and D) of the DTCBPY can be found by relax scanning, and the configuration C corresponds to the luminescent molecule detected experimentally. Besides, we calculate the proportion of each conformation by Boltzmann distribution, high configuration ratios(44% and 52%) can be found for C and D. Moreover, C and D are found to exist with an intramolecular π-π interaction between one donor and the acceptor; the intramolecular interaction brings a smaller Huang-Rhys factor and reduced reorganization energy. Our work presents a rational explanation for the experimental results and demonstrates the importance of the intramolecular π-π interaction to the photophysical properties of TADF molecules.     

Influence of solvent on the chiral resolution of organic molecules on Au(111): EC-STM study of biphenyl dicarboxylic acid on Au(111) in an aqueous environment

Adsorption-induced chiral resolution of organic molecules is important due to its potential applications in stereo-selective catalysis. We studied the adsorption-induced chiral resolution using a model achiral molecule of 4,4′ biphenyl dicarboxylic acid (BPDA) on Au(111) in 0.1 M perchloric acid (HClO₄) by electrochemical scanning tunneling microscopy (EC-STM). Our experimental data showed that the BPDA molecules formed island structures with distinctive preferred orientations at the length scale of the molecular size. The molecules did not show any orientational ordering above the length scale, indicating that chiral resolution was absent in the aqueous environment. Previously, the molecules were found to have chiral resolution on Au(111) in ultra-high vacuum conditions (UHV). We calculated angle-dependent binding energy between the substrate and a BPDA molecule, the intermolecular interactions between the BPDA molecules, and their interactions with water molecules. The calculations suggest that the absence of chiral resolution in the aqueous environment originated from the decrease in the intermolecular energy of the BPDA molecules due to their hydrogen bonds with the surrounding water molecules. The strength of the hydrogen bonding between BPDA molecules was sufficient to overcome the energy barrier for chiral resolution through rotational motion in UHV, but not in an aqueous environment.     

Calculation of mechanical properties of human red cells based on electrically induced deformation experiments

A mathematical model is presented to calculate the couple of forces elongating a three-axial ellipsoidal cell within a high frequency nonuniform electric field. The force was calculated through numerical integration of the polarisation induced force density as a function of the geometrical parameters of human red blood cells. The parameters were taken from previous experiments using video microscopy. The resulting shear moduli are some what higher than those obtained from mechanical measurements, but are in acceptable agreement. Our approach demonstrates that at high field strength an isotropic membrane tension is reached. A mechanical breakdown of cells at high field strength is not compatible with our calculations.     

Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment

We show that the ionic environment plays a critical role in determining the configurational properties of DNA confined in silica nanochannels. The extension of DNA in the nanochannels increases as the ionic strength is reduced, almost tripling over two decades in ionic strength for channels around 100 x 100 nm in dimension. Surprisingly, we find that the variation of the persistence length alone with ionic strength is not enough to explain our results. The effect is due mainly to increasing self-avoidance created by the reduced screening of electrostatic interactions at low ionic strength. To quantify the increase in self-avoidance, we introduce a new parameter into the de Gennes theory: an effective DNA width that gives the increase in the excluded volume due to electrostatic repulsion.     

Optical conductivity of wet DNA

Motivated by recent experiments, we study the optical conductivity of DNA in its natural environment containing water molecules and counterions. Our density functional theory calculations (using Siesta) for four base pair B-DNA with order 250 surrounding water molecules suggest a thermally activated doping of the DNA by water states which generically leads to an electronic contribution to low-frequency absorption. The main contributions to the doping result from water near DNA ends, breaks, or nicks and are thus potentially associated with temporal or structural defects in the DNA.     

Effects of Ionic Dependence of DNA Persistence Length on the DNA Condensation at Room Temperature

DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA.A series of experiments pointed out that,in the DNA condensation process by multivalent cations,the condensed DNA takes elongated coil or compact globule states and the population of the compact globule states increases with an increase in ionic concentration.At the same time,single molecule experiments carried out in solution with multivalent cations(such as spermidine,spermine)indicated that DNA persistence length strongly depends on the ionic concentration.In order to revolve the effects of ionic concentration dependence of persistence length on DNA condensation,a model including the ionic concentration dependence of persistence length and strong correlation of multivalent cation on DNA is provided.The autocorrelation function of the tangent vectors is found as an effective way to detect the ionic concentration dependence of toroidal conformations.With an increase in ion concentration,the first periodic oscillation contained in the autocorrelation function shifts,the number of segment contained in the first periodic oscillation decreases gradually.According to the experiments,the average long-axis length is defined to estimate the ionic concentration dependence of condensation process further.The relation between long-axis length and ionic concentration matches the experimental results qualitatively.     

Ionic effects on overstretching transition of B-DNA

A three-dimensional model is proposed herein to study the ionic effects of a NaCl solution on the overstretching transition of long B-DNA molecules. In this model, the bending deformations of DNA backbones, cooperativity of base-stacking interactions, electrostatic interactions, and spatial effects of the DNA double-helix structure are taken into account. The energy of electrostatic interactions is given as a function of the ionic strength and of the folding angle based on the Poisson-Boltzmann equation. An expression is derived, which shows that the overstretching force is linear with the natural logarithm of the ionic strength. The analytical results of this model are in good agreement with recently reported experimental results.     

Effect of electroelastic anisotropy of DNA-like molecules on their tertiary structure

Under certain conditions, mechanical forces can cause an anisotropic molecule like DNA to assume a toroidal spatial structure. A simple model describing such a behavior is suggested. The model incorporates anisotropic elastic energy and external electrical forces. The steady-state structures formed by a macromolecule have been studied numerically using this model. There exist ranges of model parameters, namely, the anisotropy of the elastic tensor, magnitude and orientation of forces, and modulation periods, where molecules have toroidal, spherical, or extended structures. Estimates of parameters characteristic of these structures are consistent with experimental data. In particular, the toroidal structure dimension corresponds to experimental dimensions of toroidal globules produced as a result of so-called PSI condensation of DNA molecules. Zh. éksp. Teor. Fiz. 112, 2156–2168 (December 1997)     

Physical Approaches to the Study of DNA

New micromanipulation techniques now enable physicists and biologists to study the behavior of single biomolecules such as DNA. In particular, it is possible to measure the elastic response of individual DNA molecules to changes in the double helix's supercoiling. The force versus extension diagram for torsionally relaxed DNA is continuous and allows one to evaluate the persistence length of the polymer. When the molecule is supercoiled, however, stretching leads to the buildup of torsional stress in the double helix's axis. When the twist energy thus generated increases beyond a critical value, the molecule is locally destabilized and changes conformation. This structural transition occurs at stretching forces which can be exerted in vivo by molecular motors and at degrees of supercoiling found in the cell, and may have implications for DNA structure and function within the nucleus.     

Effect of electrostatics on aggregation of prion protein Sup35 peptide

Self-assembly of misfolded proteins into ordered fibrillar structures is a fundamental property of a wide range of proteins and peptides. This property is also linked with the development of various neurodegenerative diseases such as Alzheimer's and Parkinson's. Environmental conditions modulate the misfolding and aggregation processes. We used a peptide, CGNNQQNY, from yeast prion protein Sup35, as a model system to address effects of environmental conditions on aggregate formation. The GNNQQNY peptide self-assembles in fibrils with structural features that are similar to amyloidogenic proteins. Atomic force microscopy (AFM) and thioflavin T (ThT) fluorescence assay were employed to follow the aggregation process at various pHs and ionic strengths. We also used single molecule AFM force spectroscopy to probe interactions between the peptides under various conditions. The ThT fluorescence data showed that the peptide aggregates fast at pH values approaching the peptide isoelectric point (pI = 5.3) and the kinetics is 10 times slower at acidic pH (pH 2.0), suggesting that electrostatic interactions contribute to the peptide self-assembly into aggregates. This hypothesis was tested by experiments performed at low (11 mM) and high (150 mM) ionic strengths. Indeed, the aggregation lag time measured at pH 2 at low ionic strength (11 mM) is 195 h, whereas the lag time decreases ~5 times when the ionic strength is increased to 150 mM. At conditions close to the pI value, pH 5.6, the aggregation lag time is 12 ± 6 h under low ionic strength, and there is minimal change to the lag time at 150 mM NaCl. The ionic strength also influences the morphology of aggregates visualized with AFM. In pH 2.0 and at high ionic strength, the aggregates are twofold taller than those formed at low ionic strength. In parallel, AFM force spectroscopy studies revealed minimal contribution of electrostatics to dissociation of transient peptide dimers.     

Raman comparison of skin dermis of different ages: focus on spectral markers of collagen hydration

Skin aging is the most visible sign of aging of the body. This complex process involves molecular and structural alterations of the main skin constituents. The major cutaneous constituent is type I collagen that gives strength and resilience to the skin. This macromolecule possesses a particular triple helix structure and is arranged in the form of a fibrous network. Water plays a crucial role for maintaining this molecular assembly which is altered during intrinsic chronological aging. To investigate some of these structural alterations, Raman microspectroscopy was employed since this biophotonic approach permits to probe the biomolecular composition of the skin in a non‐destructive manner. In addition, type I collagen gives specific Raman vibrations; some of which being sensitive to the molecule conformation and to the water environment. In this purpose, Raman spectra of four skin samples of different ages (two samples of 40 year old and two samples of 70 year old) were collected by varying the relative environmental humidity. Our experiments highlighted spectral differences between the four samples. The analysis of the Raman data permitted to suggest a model for the interactions between collagen and water molecules and a decrease in collagen fibers compactness with chronological aging. Our study demonstrates that Raman spectroscopy can be a useful tool to investigate skin aging, with innovative applications in dermatology as well as in cosmetics. Copyright © 2013 John Wiley & Sons, Ltd.     

DNA condensation and size effects of DNA condensation agent

Based on the model of the strong correlation of counterions condensed on DNA molecule, by tailoring interaction potential, interduplex spacing and correlation spacing between condensed counterions on DNA molecule and interduplex spacing fluctuation strength, toroidal configuration, rod-like configuration and two-hole configurations are possible. The size effects of counterion structure on the toroidal structure can be detected by this model. The autocorrelation function of the tangent vectors is found as an effective way to detect the structure of toroidal conformations and the generic pathway of the process of DNA condensation. The generic pathway of all of the configurations involves an initial nucleation loop, and the next part of the DNA chain is folded on the top of the initial nucleation loop with different manners, in agreement with the recent experimental results.     

Entropic compression of interacting DNA loops

We solve a model for the equilibrium folding of DNA via the formation of randomly placed (nonspecific) loops. We find that the loop rearrangement entropy drives a significant reduction in loop size as more loops form. The reduction of the most probable loop size occurs over a wide range of forces and is enhanced by interloop cooperativity, indicating that it should be observable in single DNA experiments.     

Direct immobilization and hybridization of DNA on group III nitride semiconductors

A key concern for group III-nitride high electron mobility transistor (HEMT) biosensors is the anchoring of specific capture molecules onto the gate surface. To this end, a direct immobilization strategy was developed to attach single-stranded DNA (ssDNA) to AlGaN surfaces using simple printing techniques without the need for cross-linking agents or complex surface pre-functionalization procedures. Immobilized DNA molecules were stably attached to the AlGaN surfaces and were able to withstand a range of pH and ionic strength conditions. The biological activity of surface-immobilized probe DNA was also retained, as demonstrated by sequence-specific hybridization experiments. Probe hybridization with target ssDNA could be detected by PicoGreen fluorescent dye labeling with a minimum detection limit of 2 nM. These experiments demonstrate a simple and effective immobilization approach for attaching nucleic acids to AlGaN surfaces which can further be used for the development of HEMT-based DNA biosensors.     

Room-temperature fluctuations in the fluorescence of a single polymer molecule

A theoretical model of light absorption and emission by a polymer molecule has been developed using recent experimental data on the room-temperature fluctuations in the fluorescence intensity of single molecules of a PPV-PPyV copolymer containing several tens of chromophores. An analysis of the experimental data based on the proposed model shows evidence of a change in the conformation of a polymer molecule in the triplet state. By applying the theory to the PPV-PPyV copolymer, it is possible to determine the rate constants of the conformation variation, the rates of the transition from the singlet to the triplet state, and the lifetime of the triplet state of the molecule. The theory also predicts some new effects which can be verified by experiment.     

Aqueous electrolyte surfaces in strong electric fields: molecular insight into nanoscale jets and bridges

Exposing aqueous surfaces to a strong electric field gives rise to interesting phenomena, such as formation of a floating water bridge or an eruption of a jet in electrospinning. In an effort to account for the phenomena at the molecular level, we performed molecular dynamics simulations using several protocols on both pure water and aqueous solutions of sodium chloride subjected to an electrostatic field. All simulations consistently point to the same mechanisms which govern the rearrangement of the originally planar surface. The results show that the phenomena are primarily governed by an orientational reordering of the water molecules driven by the applied field. It is demonstrated that, for pure water, a sufficiently strong field yields a columnar structure parallel to the field with an anisotropic arrangement of the water molecules with their dipole moments aligned along the applied field not only in the surface layer but over the entire cross section of the column. Nonetheless, the number of hydrogen bonds per molecule does not seem to be affected by the field regardless of its strength and molecule’s orientation. In the electrolyte solutions, the ionic charge is able to overcome the effect of the external field tending to arrange the water molecules radially in the first coordination shell of an ion. The ion–water interaction interferes thus with the water–electric field interaction, and the competition between these two forces (i.e., strength of the field versus concentration) provides the key mechanism determining the stability of the observed structures.     

Stretching and relaxation dynamics in double stranded DNA

We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special attention to the opening–closing dynamics of double-stranded DNA molecules which are forced into non-equilibrium conformations. Mechanical stress imposed at one terminal end of the DNA molecule brings it into a partially opened configuration. We examine the subsequent relaxation dynamics connected with energy exchange processes between the various degrees of freedom and structural rearrangements leading to complete recombination to the double-stranded conformation. The similarities and differences between the relaxation dynamics for a planar ladder-like DNA molecule and a twisted one are discussed in detail. In this way we show that the attainment of a quasi-equilibrium regime proceeds faster in the case of the twisted DNA form than for its thus less flexible ladder counterpart. Furthermore we find that the velocity of the complete recombination of the DNA molecule is lower than the velocity imposed by the forcing unit which is in compliance with the experimental observations for the opening–closing cycle of DNA molecules.     

Transverse fluctuation analysis of single extended DNA molecules

We observed fluctuations of elongated DNA molecules by fluorescence microscopy. The molecules are fixed at both ends and undulate. Mode analysis of the thermally excited undulations of the labeled DNA molecules gives access to the spectral density of the amplitude fluctuations. From these measurements we estimate the tension acting on the DNA molecules. We found the forces to be within the entropic elasticity range of a typical DNA molecule (measured on the single-molecule level). Received: 11 November 2002 / Accepted: 12 May 2002 / Published online: 4 June 2003 RID="a" ID="a"Present address: Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. e-mail: zoherg@rockefeller.edu     

Dispersion energies of interaction between asymmetric molecules

A derivation is given of a formula that describes the contribution of electric dipole-dipole forces to the dispersion energy between two unexcited molecules possessing axial symmetry. The symmetry axes may be oriented in any way relative to one another, and the molecules need not be identical. Our result is valid for the case that each molecule belongs to a substance whose optical dispersion curve can be characterized adequately by a pair of resonance frequencies. The method developed in the present paper, forms the basis for an extension of our theory that includes the dipole-quadrupole forces, and which will be expounded in a subsequent paper. A few special orientations of the symmetry axes are treated numerically with the aid of experimental data relating to some diatomic molecules. In this way estimates are made of the sizes of the errors committed in calculations carried out on the assumption that spherical symmetry obtains.