Single dibenzoterrylene molecules in an anthracene crystal: spectroscopy and photophysics.

We study single dibenzoterrylene molecules in an anthracene single crystal at 1.4 K in two insertion sites at 785.1 and 794.3 nm. The single-molecule zero-phonon lines are narrow (about 30 MHz), intense (the detected fluorescence rates at saturation reach 100,000 counts s(-1)), and very photostable. The intersystem-crossing yield is extremely low (10(-7) or lower). All of these features are hallmarks of an excellent system for high-resolution spectroscopy and nanoscale probing at cryogenic temperatures.     

Imaging of tautomerism in a single molecule

Fluorescence imaging is used to visualize directly the transfer of two inner hydrogen atoms in single porphycene molecules. This reaction leads to a chemically equivalent but differently oriented structure and hence results in a rotation of the transition dipole moments. By probing single immobilized molecules with an azimuthally polarized laser beam in the focal spot of a confocal microscope we observe ring-like emission patterns, possible only for a chromophore with two nearly orthogonal transition dipole moments. Numerical simulations of the observed emission patterns yield a value of 72 degrees for the angle between the S0-S1 transition moments in the two tautomeric forms.     

THE ORIENTATION OF THE TRANSITION DIPOLE MOMENTS OF CHLOROPHYLL a and PHEOPHYTIN a IN THEIR MOLECULAR FRAME

Abstract— In this paper we describe the determination of the orientation of the absorption and emission transition dipoles of chlorophyll a and pheophytin a in their molecular frame. For this purpose we have embedded the pigments in anhydrous nitrocellulose films with a concentration of 2 × 10^-7 mol/g. We have shown previously that under these conditions the pigments are in a purely monomeric state, are distributed uniformly both before and after stretching and that no intermolecular energy transfer among the molecules takes place.
Using a combination of steady-state anisotropy experiments on unstretched films and angle-resolved fluorescence depolarization measurements on stretched films, we obtain the orientation of the transition dipole moments of both pigments in their molecular frame and the orientational distribution function of the molecules relative to the stretching direction of the film.
The steady-state anisotropy measurements indicate that chlorophyll a has two distinct emission dipole moments and that excitation in the Soret-region results in simultaneous excitation of two or more absorption transition dipole moments. On the other hand, excitation in the Q_Y-band involves only a single dipole moment. The directions of the transition dipole moments in the molecular frame are obtained from the angle-resolved measurements. Pheophytin a also exhibits two emission dipole moments, but the angle between them is much smaller than that between the corresponding dipoles for chlorophyll a . As a consequence the dipole moments contributing to the Soret-region could not be resolved and only an effective absorption transition dipole moment in the Soret-region is extracted.     

Spectral Diffusion of Single Dibenzoterrylene Molecules in 2,3‐Dimethylanthracene

We study single dibenzoterrylene molecules embedded in the dipolar disordered crystal 2,3‐dimethylanthracene at 1.25 K. Broad linewidths (about 1 GHz, ～30 times broader than in the anthracene crystal), high saturation excitation intensities (～1000 times larger than in anthracene), as well as strong spectral diffusions are observed. Additionally, spectral jumping is studied by varying the excitation intensity and the temperature. We propose that the spectral diffusion and dynamic disorder in this system arise from the combination of a static disorder with slight reorientations of the methyl groups of the host molecules.     

Structural and optical properties of DNA layers covalently attached to diamond surfaces

Label-free detection of DNA molecules on chemically vapor-deposited diamond surfaces is achieved with spectroscopic ellipsometry in the infrared and vacuum ultraviolet range. This nondestructive method has the potential to yield information on the average orientation of single as well as double-stranded DNA molecules, without restricting the strand length to the persistence length. The orientational analysis based on electronic excitations in combination with information from layer thicknesses provides a deeper understanding of biological layers on diamond. The pi-pi* transition dipole moments, corresponding to a transition at 4.74 eV, originate from the individual bases. They are in a plane perpendicular to the DNA backbone with an associated n-pi* transition at 4.47 eV. For 8-36 bases of single- and double-stranded DNA covalently attached to ultra-nanocrystalline diamond, the ratio between in- and out-of-plane components in the best fit simulations to the ellipsometric spectra yields an average tilt angle of the DNA backbone with respect to the surface plane ranging from 45 degrees to 52 degrees . We comment on the physical meaning of the calculated tilt angles. Additional information is gathered from atomic force microscopy, fluorescence imaging, and wetting experiments. The results reported here are of value in understanding and optimizing the performance of the electronic readout of a diamond-based label-free DNA hybridization sensor.     

Thermally induced polarizabilities and dipole moments of small tin clusters

We study the influence of thermal excitation on the electric susceptibilities for Sn(6) and Sn(7) clusters by molecular beam electric deflection and Monte-Carlo simulations in conjunction with quantum-chemical calculations. At low temperatures (40 K), no field-induced broadening of the Sn(6) and Sn(7) cluster beams are observed, in agreement with vanishing permanent electric dipole moments due to their centro-symmetrical ground states. The electric polarizabilities of Sn(6) and Sn(7), as inferred from the field-induced molecular beam deflection, are in good agreement with the quantum-chemical predictions. At elevated temperatures of 50-100 K, increased polarizabilities of about 2-3 ?(3) are obtained. Also, we found indications of a field-induced beam broadening which points to the existence of permanent dipole moments of about 0.01-0.02 D per atom at higher temperatures. These results cannot be explained by thermal excitations within a harmonic oscillator model, which would yield a temperature-independent polarizability and fluxional, but not permanent, dipole moments. We analyze this behavior by Monte-Carlo simulations in order to compute average temperature-induced electric dipole moments. For that purpose, we developed a novel technique for predicting observables sampled on the quantum-chemical potential energy surface by an umbrella sampling correction of Monte-Carlo results obtained from simulations utilizing an empirical potential. The calculated, fluxional dipole moments are in tune with the observed beam broadenings. The cluster dynamics underlying the polarizability appear to be intermediate between rigid and floppy molecules which leads to the conclusion that the rotational, not the vibrational temperature seems to be the key parameter that determines the temperature dependence of the polarizability.     

Spectroscopy of Single Dibenzoterrylene Molecules in para‐Dichlorobenzene

We study single dibenzoterrylene (DBT) molecules embedded in 1,4‐dichlorobenzene (para‐dichlorobenzene, pDCB) at 1.2 K. Due to the relatively low melting point of pDCB (53 °C), this host‐guest system can be easily prepared from the molten phase. Narrow linewidths, stable molecular lines and high saturation count rates of single DBT molecules were observed. For this reason, we consider this host‐guest system a promising candidate for the study of interactions of single molecules with other small objects such as waveguides or nanoparticles.     

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites,solvent density,and solvent dipole

The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.     

A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy

We present an approach for calculating nonlinear spectroscopic observables, which overcomes the approximations inherent to current phenomenological models without requiring the computational cost of performing molecular dynamics simulations. The trajectory mapping method uses the semi-classical approximation to linear and nonlinear response functions, and calculates spectra from trajectories of the system's transition frequencies and transition dipole moments. It rests on identifying dynamical variables important to the problem, treating the dynamics of these variables stochastically, and then generating correlated trajectories of spectroscopic quantities by mapping from the dynamical variables. This approach allows one to describe non-Gaussian dynamics, correlated dynamics between variables of the system, and nonlinear relationships between spectroscopic variables of the system and the bath such as non-Condon effects. We illustrate the approach by applying it to three examples that are often not adequately treated by existing analytical models--the non-Condon effect in the nonlinear infrared spectra of water, non-Gaussian dynamics inherent to strongly hydrogen bonded systems, and chemical exchange processes in barrier crossing reactions. The methods described are generally applicable to nonlinear spectroscopy throughout the optical, infrared and terahertz regions.     

Assignment of aluminum corroles absorption bands to electronic transitions by femtosecond polarization resolved VIS-pump IR-probe spectroscopy

We combine femtosecond polarization resolved VIS-pump IR-probe spectroscopy with DFT and TD-DFT calculations to identify and assign absorption bands to electronic transitions for corroles. These macrocycles and their corresponding metal complexes are receiving great attention because of their utility in many fields, while many of their spectroscopic features have not yet been fully described. Analysis of the perturbed free induction decay provides information about the bleaching signal at time zero and allows for determination of overlapping excited state and bleaching signal amplitudes. The S(0) → S(1) and S(0) → S(2) transitions in the Q-band of the hexacoordinated Al(tpfc)(py)(2) and Br(8)Al(tpfc)(py)(2) absorption spectra are explicitly assigned. Angles between these electronic transition dipole moments (tdms) with a single vibrational transition dipole moment of (53 ± 2)° and (34 ± 2)° when excited at 580 and 620 nm for hexacoordinated Al(tpfc)(py)(2) and (51 ± 2)° and (43 ± 2)° when excited at 590 and 640 nm for hexacoordinated Br(8)Al(tpfc)(py)(2) were determined. The relative angles between the two lowest electronic tdms are (90 ± 8)° and (94 ± 3)° for Al(tpfc)(py)(2) and Br(8)Al(tpfc)(py)(2), respectively. Angles are determined before time zero by polarization resolved perturbed free induction decay and after time zero by polarization resolved transients. Comparison of corrole's wave functions with those of porphine show that the reduced symmetry in the corrole molecules results in lifting of Q-band degeneracy and major reorientation of the electronic transition dipole moments within the molecular scaffold. This information is necessary in designing optimal corrole-based electron and energy transfer complexes.     

Electrostatic properties of cyano-containing mesogens

We analyse the electrostatic properties of a set of cyano-containing mesogen molecules with different rigid cores and variable alkyl chain lengths, computing the molecular charge distributions. Using the simple prototype benzonitrile, we analyse the reliability of the quantum chemical methods used to estimate the electrostatic dipole moments of polar conjugated molecules. We show that the electronic properties of the long mesogenic molecules can be treated by combining HF geometry optimization procedures with single point MP2 calculations. We compare the results of these computations with the available experimental phase transition data of mesogens and discuss some examples of how the non-trivial mesomorphic behaviour, which is usually observed in these cyano compounds, can be qualitatively explained by the molecular electrostatic interaction potential.     

Electrostatic properties of cyano-containing mesogens

We analyse the electrostatic properties of a set of cyano-containing mesogen molecules with different rigid cores and variable alkyl chain lengths, computing the molecular charge distributions. Using the simple prototype benzonitrile, we analyse the reliability of the quantum chemical methods used to estimate the electrostatic dipole moments of polar conjugated molecules. We show that the electronic properties of the long mesogenic molecules can be treated by combining HF geometry optimization procedures with single point MP2 calculations. We compare the results of these computations with the available experimental phase transition data of mesogens and discuss some examples of how the non-trivial mesomorphic behaviour, which is usually observed in these cyano compounds, can be qualitatively explained by the molecular electrostatic interaction potential.     

When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration

In order to test the validity of the cluster ansatz approach as well as of the continuum model approach and to learn about the solvation shell, we carried out first-principles molecular dynamics simulations of the alanine hydration. Our calculations contained one alanine molecule dissolved in 60 water molecules. Dipole moments of individual molecules were derived by means of maximally localized Wannier functions. We observed an average dipole moment of about 16.0 D for alanine and of about 3.3 D for water. In particular, the average water dipole moment in proximity of alanine's COO(-) group decayed continously with increasing distance, while, surprisingly, close to the CH3 and NH3+ group, the dipole moment first rose before its value dropped. In a cluster ansatz approach, we considered snapshots of alanine surrounded by different water molecule shells. The dipole moments from the cluster approaches utilizing both maximally localized Wannier functions as well as natural population analysis served to approximate the dipole moments of the total trajectory. Sufficient convergence of the cluster ansatz approach is found for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dieletric continuum.     

Can octupolar molecules be poled by an external electric field?

Octupolar molecules are generally believed to be of potential use in developing nonlinear optical materials owing to the fact that they do not easily form molecular aggregates. This is often put against the conjectured drawback that electric fields have no poling, or ordering, effect for this class of molecules because of the lack of a permanent ground state dipole moment. In this paper, we analyze this notion in some detail and present results from molecular dynamics computer simulations of an ensemble of a prototypical octupolar molecule, the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) molecule, dissolved in chloroform. It is found that TATB molecules indeed show rather significant dipole moments in solutions because of the dual action of the thermal motions of the atoms and the strong intermolecular interactions. Applied electric fields accordingly show significant effects on the orientations of the molecular dipole moments. We also find that TATB molecules can aggregate because of the strong hydrogen-bonding interactions between the molecules, though they lack a static permanent dipole moment. Thus, the simulation results for TATB molecules in solution present us with a totally different notion about the collective properties of octupolar molecules. Taking account of quantum chemistry results, we found that the collective molecular nonlinear optical (NLO) properties are enhanced after the onset of the electric field, showing significant anisotropic characteristics.     

Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model

The solution conformation of alpha-conotoxin GI and its two single disulfide analogues are simulated using a polarizable force field in combination with the molecular fragmentation quantum chemical calculation. The polarizability is explicitly described by allowing the partial charges and fragment dipole moments to be variables, with values coming from the linear-scaling energy-based molecular fragmentation calculations at the B3LYP/6-31G(d) level. In comparison with the full quantum chemical calculations, the fragmentation approaches can yield precise ground-state energies, dipole moments, and static polarizabilities for peptides. The B3LYP/6-31G(d) charges and fragment-centered dipole moments are introduced in calculations of electrostatic terms in both AmberFF03 and OPLS force fields. Our test calculations on the gas-phase glucagon (PDB code: 1gcn) and solvated alpha-conotoxin GI (PDB code: 1not) demonstrate that the present polarization model is capable of describing the structural properties (such as the relative conformational energies, intramolecular hydrogen bonds, and disulfide bonds) with accuracy comparable to some other polarizable force fields (ABEEM/MM and OPLS-PFF) and the quantum mechanics/molecular mechanics (QM/MM) hybrid model. The employment of fragment-centered dipole moments in calculations of dipole-dipole interactions can save computational time in comparison with those polarization models using atom-centered dipole moments without much loss of accuracy. The molecular dynamics simulations using the polarizable force field demonstrate that two single disulfide GI analogues are more flexible and less structured than the native alpha-conotoxin GI, in agreement with NMR experiments. The polarization effect is important in simulations of the folding/unfolding process of solvated proteins.     

Molecular ion LiHe: ab initio study

High level ab initio calculations are performed on the molecular ion LiHe⁺. Potential energy curves for the low-lying singlet and triplet electronic states are calculated using the multi-reference configuration interaction and single-reference coupled cluster methods with large basis sets. The corresponding dipole moments and transition dipole moments functions are also determined. The basic spectroscopic properties and excitation energies of the electronic states are derived from rovibrational bound state calculations.     

Relativistic effective potential SCF calculations of AgH and AuH

Relativistic effective potentials (REP) are now widely used in molecular electronic structure calculations. Tests of these REP are needed to assess their accuracy. This can now be done for AgH and AuH since Lee and McLean have published Dirac-Fock calculations for these molecules. Comparative SCF calculations have been performed for two types of effective potential. Satisfactory agreement between the effective potential results and Dirac-Fock values is found for spectroscopic constants and dipole moments, which supports the use of these potentials for heavy atom containing molecules.     

Theoretical investigation of the coexistence of α and β-nitric acid trihydrates (NAT) molecular conformations

In this letter we document the possibility of the existence of a second molecular configuration for nitric acid trihydrates. Density functional theory (DFT) methods have been used for studying the nitric acid trihydrates α and β-NAT conformations, their spectroscopic and thermodynamics properties and dipole moments have been calculated. This study describes the gas–solid phase transition of the NAT and provides two possible pathways for the molecular structure transformation between α and β-NAT.     

First-order model potential for optical dipole transitions: Application to the lithium isoelectronic sequence

We have constructed two first-order model potentials which were designed to yield dipole transition moments, and have applied them to the lithium isoelectronic sequence. The models contain two or three adjustable parameters, chosen so as to reproduce selected transition moment data on a single ion of the sequence. With negligible computational effort, they both yield other transition moments of high accuracy.     

Optical imaging of excited-state tautomerization in single molecules

Tautomerism process of single fluorescent molecules was studied by means of confocal microscopy in combination with azimuthally or radially polarized laser beams. During a tautomerism process the transition dipole moment (TDM) of a molecule changes its orientation which can be visualized by the fluorescence excitation image of the molecule. We present experimental and theoretical studies of two porphyrazine-type molecules and one type of porphyrin molecule: a symmetrically substituted metal-free phthalocyanine and porphyrin, and nonsymmetrically substituted porphyrazine. In the case of phthalocyanine the fluorescence excitation patterns show that the angle between the transition dipole moments of the two tautomeric forms is near 90°, in agreement with quantum chemical calculations. For porphyrazine we find that the orientation change of the TDM is less than 60° or larger than 120°, as theoretically predicted. Most of the porphyrin molecules show no photoinduced tautomerization, while for 7% of the total number of investigated molecules we observed excitation patterns of two different trans forms of the same single molecule. We demonstrate for the first time that a molecule, undergoing a tautomerism process stays in one tautomeric trans conformation during a time comparable with the acquisition time of one excitation pattern. This allowed us to visualize the existence of each of the two trans forms of one single porphyrin molecule, as well as the sudden switching between these tautomers.