DANPY (dimethylaminonaphthylpyridinium): an economical and biocompatible fluorophore.

Dyes with nonlinear optical (NLO) properties enable new imaging techniques and photonic systems. We have developed a dye (DANPY-1) for photonics applications in biological substrates such as nucleic acids; however, the design specification also enables it to be used for visualizing biomolecules. It is a prototype dye demonstrating a water-soluble, NLO-active fluorophore with high photostability, a large Stokes shift, and a favorable toxicity profile. A practical and scalable synthetic route to DANPY salts has been optimized featuring: (1) convergent Pd-catalyzed Suzuki coupling with pyridine 4-boronic acid, (2) site-selective pyridyl N-methylation, and (3) direct recovery of crystalline intermediates without chromatography. We characterize the optical properties, biocompatibility, and biological staining behavior of DANPY-1. In addition to stability and solubility across a range of polar media, the DANPY-1 chromophore shows a first hyperpolarizability similar to common NLO dyes such as Disperse Red 1 and DAST, a large two-photon absorption cross section for its size, substantial affinity to nucleic acids in vitro, an ability to stain a variety of cellular components, and strong sensitivity of its fluorescence properties to its dielectric environment.

Detection of mucopolysaccharidosis III-A (Sanfilippo Syndrome-A) in dried blood spots (DBS) by tandem mass spectrometry.

BACKGROUND: With ongoing efforts to develop improved treatments for Sanfilippo Syndrome Type A (MPS-IIIA), a disease caused by the inability to degrade heparan sulfate in lysosomes, we sought to develop an enzymatic activity assay for the relevant enzyme, sulfamidase, that uses dried blood spots (DBS). METHODS: We designed and synthesized a new sulfamidase substrate that can be used to measure sulfamidase activity in DBS using liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS: Sulfamidase activity was readily detected in DBS using the new substrate and LC-MS/MS. Sulfamidase activity showed acceptable linearity proportional to the amount of enzyme and reaction time. Sulfamidase activity in 238 random newborns was well elevated compared to the range of activities measured in DBS from 8 patients previously confirmed to have MPS-IIIA. CONCLUSIONS: This is the first report of an assay capable of detecting sulfamidase in DBS. The new assay could be useful in diagnosis and potentially for newborn screening of MPS-IIIA.

Optimizing calculations of electronic excitations and relative hyperpolarizabilities of electrooptic chromophores.

CONSPECTUS: Organic glasses containing chromophores with large first hyperpolarizabilities (ß) are promising for compact, high-bandwidth, and energy-efficient electro-optic devices. Systematic optimization of device performance requires development of materials with high acentric order and enhanced hyperpolarizability at operating wavelengths. One essential component of the design process is the accurate calculation of optical transition frequencies and hyperpolarizability. These properties can be computed with a wide range of electronic structure methods implemented within commercial and open-source software packages. A wide variety of methods, especially hybrid density-functional theory (DFT) variants have been used for this purpose. However, in order to provide predictions useful to chromophore designers, a method must be able to consistently predict the relative ordering of standard and novel materials. Moreover, it is important to distinguish between the resonant and nonresonant contribution to the hyperpolarizabiliy and be able to estimate the trade-off between improved ß and unwanted absorbance (optical loss) at the target device's operating wavelength. Therefore, we have surveyed a large variety of common methods for computing the properties of modern high-performance chromophores and compared these results with prior experimental hyper-Rayleigh scattering (HRS) and absorbance data. We focused on hybrid DFT methods, supplemented by more computationally intensive Møller-Plesset (MP2) calculations, to determine the relative accuracy of these methods. Our work compares computed hyperpolarizabilities in chloroform relative to standard chromophore EZ-FTC against HRS data versus the same reference. We categorized DFT methods used by the amount of Hartree-Fock (HF) exchange energy incorporated into each functional. Our results suggest that the relationship between percentage of long-range HF exchange and both ßHRS and λmax is nearly linear, decreasing as the fraction of long-range HF exchange increases. Mild hybrid DFT methods are satisfactory for prediction of λmax. However, mild hybrid methods provided qualitatively incorrect predictions of the relative hyperpolarizabilities of three high-performance chromophores. DFT methods with approximately 50% HF exchange, and especially the Truhlar M062X functional, provide superior predictions of relative ßHRS values but poorer predictions of λmax. The observed trends for these functionals, as well as range-separated hybrids, are similar to MP2, though predicting smaller absolute magnitudes for ßHRS. Frequency dependence for ßHRS can be calculated using time-dependent DFT and HF methods. However, calculation quality is sensitive not only to a method's ability to predict static hyperpolarizability but also to its prediction of optical resonances. Due to the apparent trade-off in accuracy of prediction of these two properties and the need to use static finite-field methods for MP2 and higher-level hyperpolarizability calculations in most codes, we suggest that composite methods could greatly improve the accuracy of calculations of ß and λmax.

Design and synthesis of chromophores with enhanced electro-optic activities in both bulk and plasmonic-organic hybrid devices.

This study demonstrates enhancement of in-device electro-optic activity via a series of theory-inspired organic electro-optic (OEO) chromophores based on strong (diarylamino)phenyl electron donating moieties. These chromophores are tuned to minimize trade-offs between molecular hyperpolarizability and optical loss. Hyper-Rayleigh scattering (HRS) measurements demonstrate that these chromophores, herein described as BAH, show >2-fold improvement in ß versus standard chromophores such as JRD1, and approach that of the recent BTP and BAY chromophore families. Electric field poled bulk devices of neat and binary BAH chromophores exhibited significantly enhanced EO coefficients (r33) and poling efficiencies (r33/Ep) compared with state-of-the-art chromophores such as JRD1. The neat BAH13 devices with charge blocking layers produced very large poling efficiencies of 11.6 ± 0.7 nm2 V-2 and maximum r33 value of 1100 ± 100 pm V-1 at 1310 nm on hafnium dioxide (HfO2). These results were comparable to that of our recently reported BAY1 but with much lower loss (extinction coefficient, k), and greatly exceeding that of other previously reported OEO compounds. 3 : 1 BAH-FD : BAH13 blends showed a poling efficiency of 6.7 ± 0.3 nm2 V-2 and an even greater reduction in k. 1 : 1 BAH-BB : BAH13 showed a higher poling efficiency of 8.4 ± 0.3 nm2 V-2, which is approximately a 2.5-fold enhancement in poling efficiency vs. JRD1. Neat BAH13 was evaluated in plasmonic-organic hybrid (POH) Mach-Zehnder modulators with a phase shifter length of 10 µm and slot widths of 80 and 105 nm. In-device BAH13 achieved a maximum r33 of 208 pm V-1 at 1550 nm, which is ∼1.7 times higher than JRD1 under equivalent conditions.

Electro-Optic Activity in Excess of 1000 pm V-1 Achieved via Theory-Guided Organic Chromophore Design.

High performance organic electro-optic (OEO) materials enable ultrahigh bandwidth, small footprint, and extremely low drive voltage in silicon-organic hybrid and plasmonic-organic hybrid photonic devices. However, practical OEO materials under device-relevant conditions are generally limited to performance of ≈300 pm V-1 (10× the EO response of lithium niobate). By means of theory-guided design, a new series of OEO chromophores is demonstrated, based on strong bis(4-dialkylaminophenyl)phenylamino electron donating groups, capable of EO coefficients (r33 ) in excess of 1000 pm V-1 . Density functional theory modeling and hyper-Rayleigh scattering measurements are performed and confirm the large improvement in hyperpolarizability due to the stronger donor. The EO performance of the exemplar chromophore in the series, BAY1, is evaluated neat and at various concentrations in polymer host and shows a nearly linear increase in r33 and poling efficiency (r33 /Ep , Ep is poling field) with increasing chromophore concentration. 25 wt% BAY1/polymer composite shows a higher poling efficiency (3.9 ± 0.1 nm2 V-2 ) than state-of-the-art neat chromophores. Using a high-ε charge blocking layer with BAY1, a record-high r33 (1100 ± 100 pm V-1 ) and poling efficiency (17.8 ± 0.8 nm2 V-2 ) at 1310 nm are achieved. This is the first reported OEO material with electro-optic response larger than thin-film barium titanate.

Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation.

Rigid spin-labeled nucleoside C, an analog of deoxycytidine that base-pairs with deoxyguanosine, was incorporated into DNA oligomers by chemical synthesis. Thermal denaturation experiments and circular dichroism (CD) measurements showed that C has a negligible effect on DNA duplex stability and conformation. Nucleoside C was incorporated into several positions within single-stranded DNA oligomers that can adopt two hairpin conformations of similar energy, each of which contains a four-base loop. The relative mobility of nucleotides in the alternating C/G hairpin loops, 5'-d(GCGC) and 5'-d(CGCG), was determined by electron paramagnetic resonance (EPR) spectroscopy. The most mobile nucleotide in the loop is the second one from the 5'-end, followed by the third, first and fourth nucleotides, consistent with previous NMR studies of DNA hairpin loops of different sequences. The EPR hairpin data were also corroborated by fluorescence spectroscopy using oligomers containing reduced C (C(f)), which is fluorescent. Furthermore, EPR spectra of duplex DNAs that contained C at the end of the helix showed features that indicated dipolar coupling between two spins. These data are consistent with end-to-end duplex stacking in solution, which was only observed when G was paired to C, but not when C was paired with A, C or T.

Conformational equilibria of bulged sites in duplex DNA studied by EPR spectroscopy.

Conformational flexibility in nucleic acids provides a basis for complex structures, binding, and signaling. One-base bulges directly neighboring single-base mismatches in nucleic acids can be present in a minimum of two distinct conformations, complicating the examination of the thermodynamics by calorimetry or UV-monitored melting techniques. To provide additional information about such structures, we demonstrate how electron paramagnetic resonance (EPR) active spin-labeled base analogues, base-specifically incorporated into the DNA, are monitors of the superposition of different bulge-mismatch conformations. EPR spectra provide information about the dynamic environments of the probe. This information is cast in terms of "dynamic signatures" that have an underlying basis in structural variations. By examining the changes in the equilibrium of the different states across a range of temperatures, the enthalpy and entropy of the interconversion among possible conformations can be determined. The DNA constructs with a single bulge neighboring a single-base mismatch ("bulge-mismatches") may be approximately modeled as an equilibrium between two possible conformations. This structural information provides insight into the local composition of the bulge-mismatch sequences. Experiments on the bulge-mismatches show that basepairing across the helix can be understood in terms of purine and pyrimidine interactions, rather than specific bases. Measurements of the enthalpy and entropy of formation for the bulge-mismatches by differential scanning calorimetry and UV-monitored melting confirm that the formation of bulge-mismatches is in fact more complicated than a simple two-state process, consistent with the base-specific spectral data that bulge-mismatches exist in multiple conformations in the premelting temperature region. We find that the calculations with the nearest-neighbor (NN) model for the two likely conformations do not correlate well with the populations of structures and thermodynamic parameters inferred from the base-specific EPR dynamics probe. We report that the base-specific spin probes are able to identify a bistable, temperature dependent, switching between conformations for a particular complex bulged construct.

The Importance of Assay Imprecision near the Screen Cutoff for Newborn Screening of Lysosomal Storage Diseases.

For newborn screening (NBS) of lysosomal storage diseases, programs measure enzymatic activities in dried blood spots (DBS) and, in most cases, act on samples where the measurement is below a specific cutoff value. The rate of false positives and negatives in any NBS program is of critical importance. The measured values across a population of newborns are governed by many factors, and in this article we focus on assay imprecision. Assay parameters including the Analytical Range and the Z-Factor have been discussed as a way to compare assay performance for NBS of lysosomal storage diseases. Here we show that these parameters are not rigorously connected to the rate of false positives and negatives. Rather, it is the assay imprecision near the screen cutoff that is the most important parameter that determines the rate of false positives and negatives. We develop the theoretical treatment of assay imprecision and how it is linked to screen performance. What emerges is a useful type of parametric plot that allows for rigorous assessment of the effect of assay imprecision on the rate of false positives and false negatives that is independent of the choice of screen cutoff value. Such plots are useful in choosing cutoff values. They also show that a high assay imprecision cannot be overcome by changing the cutoff value or by use of postanalysis, statistical tools. Given the importance of assay imprecision near the cutoff, we propose that quality control DBS are most useful if they span a range of analyte values near the cutoff. Our treatment is also appropriate for comparing the performance of multiple assay platforms that each measure the same quantity (i.e., the enzymatic activity in DBS). The analysis shows that it is always best to use the assay platform that gives the lowest imprecision near the cutoff.

Molecular Engineering of Structurally Diverse Dendrimers with Large Electro-Optic Activities.

To boost electro-optic (EO) performance, a series of multichromophore dendrimers have been developed based on higher hyperpolarizability (CLD-type) chromophore cores that have been used previously (FTC-type dendrimers). The multichromophore dendrimers were molecularly engineered to have either three arms, two arms, or one arm; long or short linkers; and a fluorinated dendron (FD) or tert-butyldiphenylsilyl (TBDPS) shell. The EO performance obtained by FDSD (poling efficiency = 1.60 nm2 V-2), based on succinic diester linkers, was higher than the analogue with longer adipic diester linkers and higher than the analogs with fewer chromophore moieties. Due to the shorter succinic diester linker and improved site isolation, the dendrimer chromophore with TBDPS groups exhibited enhanced glass-transition temperature ( Tg = 108 °C) and comparable poling efficiency (1.62 nm2 V-2) to the FD-containing version. These neat EO dendrimers have a higher index of refraction ( n = 1.75-1.84 at 1310 nm) than guest-host polymeric EO materials ( n ≈ 1.6, 1310 nm) and FTC-type EO dendrimers ( n = 1.73, 1310 nm), which is important, because a key metric for Mach-Zehnder modulators is proportional to n3. In addition, binary chromophore organic glasses (BCOGs) were prepared by doping a secondary EO chromophore at 25 wt % into neat dendrimers. Enhancements of EO performance were found in all BCOG materials compared with neat dendrimers due to the effect of blending. As a result of increased chromophore density, the n values of the BCOGs improved to 1.81-1.92. One BOCG, in particular, displayed the highest poling efficiency (2.35 nm2 V-2) and largest EO coefficient ( r33) value of 275 pm V-1 at 1310 nm, which represents a high n3 r33 figure-of-merit of 1946 pm V-1. The high poling efficiencies and n3 r33 figure-of-merit combined with excellent film forming confirm these neat dendrimers and BCOGs based on them as promising candidates for incorporation into photonic devices.

Rational enhancement of second-order nonlinearity: bis-(4-methoxyphenyl)hetero-aryl-amino donor-based chromophores: design, synthesis, and electrooptic activity.

Two new highly hyperpolarizable chromophores, based on N,N- bis-(4-methoxyphenyl) aryl-amino donors and phenyl-trifluoromethyl-tricyanofuran (CF3-Ph-TCF) acceptor linked together via pi-conjugation through 2,5-divinylenethienyl moieties as the bridge, have been designed and synthesized successfully for the first time. The aryl moieties on the donor side of the chromophore molecules were varied as to be thiophene and 1-n-hexylpyrrole. The linear and nonlinear optical (NLO) properties of all compounds were evaluated in addition to recording relevant thermal and electrochemical data. The properties of the two new molecules were comparatively studied. These results are critically analyzed along with two other compounds, reported earlier from our laboratories and our collaborator's, that contain (i) aliphatic chain-bearing aniline and (ii) dianisylaniline as donors, keeping the bridge (2,5-divinylenethienyl-), and the acceptor (CF3-Ph-TCF), constant. Trends in theoretically (density functional theory, DFT) predicted, zero-frequency gas-phase hyperpolarizability [beta(0;0,0)] values are shown to be consistent with the trends in beta HRS(-2omega;omega,omega), as measured by Hyper-Rayleigh Scattering (HRS), when corrected to zero-frequency using the two-level model (TLM) approximation. Similarly, trends in poling efficiency data (r33/E(p)) and wavelength dispersion measured by reflection ellipsometry (using a Teng-Man apparatus) and attenuated total reflection (ATR) are found to fit the TLM and DFT predictions. A 3-fold enhancement in bulk nonlinearity (r33) is realized as the donor subunits are changed from alkylaniline to dianisylaminopyrrole donors. The results of these studies provide insight into the complicated effects on molecular hyperpolarizability of substituting heteroaromatic subunits into the donor group structures. These studies also demonstrate that, when frequency dependence and electric-field-induced ordering behavior are correctly accounted for, ab initio DFT generated beta(0;0,0) is effective as a predictor of changes in r33 behavior based on chromophore structure modification. Thus DFT can provide valuable insight into the electronic structure origin of complex optical phenomena in organic media.

Theory for spin-lattice relaxation of spin probes on weakly deformable DNA.

The weakly bending rod (WBR) model of double-stranded DNA (dsDNA) is adapted to analyze the internal dynamics of dsDNA as observed in electron paramagnetic resonance (EPR) measurements of the spin-lattice relaxation rate, R(1e), for spin probes rigidly attached to nucleic acid-bases. The WBR theory developed in this work models dsDNA base-pairs as diffusing rigid cylindrical discs connected by bending and twisting springs whose elastic force constants are kappa and alpha, respectively. Angular correlation functions for both rotational displacement and velocity are developed in detail so as to compute values for R(1e) due to four relaxation mechanisms: the chemical shift anisotropy (CSA), the electron-nuclear dipolar (END), the spin rotation (SR), and the generalized spin diffusion (GSD) relaxation processes. Measured spin-lattice relaxation rates in dsDNA under 50 bp in length are much faster than those calculated for the same DNAs modeled as rigid rods. The simplest way to account for this difference is by allowing for internal flexibility in models of DNA. Because of this discrepancy, we derive expressions for the spectral densities due to CSA, END, and SR mechanisms directly from a weakly bending rod model for DNA. Special emphasis in this development is given to the SR mechanism because of the lack of such detail in previous treatments. The theory developed in this paper provides a framework for computing relaxation rates from the WBR model to compare with magnetic resonance relaxation data and to ascertain the twisting and bending force constants that characterize DNA.

Simple Model for the Benzene Hexafluorobenzene Interaction.

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. The simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions, and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.

Identification of amino acids that promote specific and rigid TAR RNA-tat protein complex formation.

The Tat protein and the transactivation responsive (TAR) RNA form an essential complex in the HIV lifecycle, and mutations in the basic region of the Tat protein alter this RNA-protein molecular recognition. Here, EPR spectroscopy was used to identify amino acids, flanking an essential arginine of the Tat protein, which contribute to specific and rigid TAR-Tat complex formation by monitoring changes in the mobility of nitroxide spin-labeled TAR RNA nucleotides upon binding. Arginine to lysine N-terminal mutations did not affect TAR RNA interfacial dynamics. In contrast, C-terminal point mutations, R56 in particular, affected the mobility of nucleotides U23 and U38, which are involved in a base-triple interaction in the complex. This report highlights the role of dynamics in specific molecular complex formation and demonstrates the ability of EPR spectroscopy to study interfacial dynamics of macromolecular complexes.

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.

Linear and nonlinear optical properties of a macrocyclic trichromophore bundle with parallel-aligned dipole moments.

A macrocyclic trichromophore bundle 1 with parallel-aligned dipole moments has been synthesized to study the influence of aggregation and orientation of a nonlinear optical (NLO) chromophore on its optical properties. The linear and nonlinear optical properties of 1 and a single chromophore standard 2 have been studied by UV-vis absorption, fluorescence, solvatochromic spectrometry, and hyper-Rayleigh scattering (HRS). Reduced first-order hyperpolarizability beta, hypsochromic shift, enhanced solvatochromic shifts, and fluorescence quenching for individual chromophores were observed when 1 was compared with 2. Analysis of the data showed that the transition dipole moment changes only slightly when the chromophores are parallel aligned in the bundle architecture. However, the apparent hyperpolarizability of the individual chromophores decreased significantly by about 20%. The reduction in beta for the individual chromophores in 1 is largely due to the hypsochromic shift, i.e., excitation energy increase of the interband (charge-transfer) energy gap and the reduced difference between the ground-state and excited-state dipole moments. The hypsochromic shift and fluorescence quenching are consistent with exciton theory. Possible reasons for the enhanced solvatochromic shift are discussed.

Systematic Generation of Anisotropic Coarse-Grained Lennard-Jones Potentials and Their Application to Ordered Soft Matter.

We have developed an approach to coarse-grained (CG) modeling of the van der Waals (vdW) type of interactions among molecules by representing groups of atoms within those molecules in terms of ellipsoids (rather than spheres). Our approach systematically translates an arbitrary underlying all-atom (AA) representation of a molecular system to a multisite ellipsoidal potential within the family of Gay-Berne type potentials. As the method enables arbitrary levels of coarse-graining, or even multiple levels of coarse-graining within a single simulation, we describe the method as a Level of Detail (LoD) model. The LoD model, as integrated into our group's Metropolis Monte Carlo computational package, is also capable of reducing the complexity of the molecular electrostatics by means of a multipole expansion of charges obtained from an AA force field (or directly from electronic structure calculations) of the charges within each ellipsoid. Electronic polarizability may additionally be included. The present CG representation does not include transformation of bonded interactions; ellipsoids are connected at the fully atomistic bond sites by freely rotating links that are constrained to maintain a constant distance. The accuracy of the method is demonstrated for three distinct types of self-assembling or self-organizing molecular systems: (1) the interaction between benzene and perfluorobenzene (dispersion interactions), (2) linear hydrocarbon chains (a system with large conformational flexibility), and (3) the self-organization of ethylene carbonate (a highly polar liquid). Lastly, the method is applied to the interaction of large (∼100 atom) molecules, which are typical of organic nonlinear optical chromophores, to demonstrate the effect of different CG models on molecular assembly.

Relation of system dimensionality and order parameters.

Orientational order parameters are useful metrics for characterizing the probability distribution for vector-valued quantities such as the dipole moment or optical axis of molecules in materials such as liquid crystals and organic glasses. These parameters are the moments of the underlying orientational probability distribution. Many molecular systems can be characterized using a single centrosymmetric (even) moment. For dipolar systems, an applied electric or magnetic field can break the symmetry of the system, leading to nonzero acentric (odd) moments. For complex systems, it is difficult to characterize the nature of the bulk structures and to quantitatively understand the relationship between acentric and centrosymmetric moments. We have found that it is useful to relate the moments of the distribution in terms of an apparent dimensionality of the ordering process. Here we show that the idea of noninteger dimensionality, originally introduced by Stillinger, provides a useful method to characterize the relation between centrosymmetric and acentric orientational order parameters. Applying dimensional constraints is equivalent to removing rotational degrees of freedom or constraining rotation within a restricted volume. Simulations based on simple examples­using restoring potentials on arrays of independent dipoles­and on complex many-body Monte Carlo simulations of dipolar spheroids are described. An analysis of the results illustrates the utility of fractional dimensionality to describe ordering in materials.

Dielectric and phase behavior of dipolar spheroids.

The Stockmayer fluid, composed of dipolar spheres, has a well-known isotropic-ferroelectric phase transition at high dipole densities. However, there has been little investigation of the ferroelectric transition in nearly spherical fluids at dipole densities corresponding to those found in many polar solvents and in guest-host organic electro-optic materials. In this work, we examine the transition to ordered phases of low-aspect-ratio spheroids under both unperturbed and poled conditions, characterizing both the static dielectric response and thermodynamic properties of spheroidal systems. Spontaneous ferroelectric ordering was confined to a small region of aspect ratios about unity, indicating that subtle changes in sterics can have substantial influence on the behavior of coarse-grained liquid models. Our results demonstrate the importance of molecular shape in obtaining even qualitatively correct dielectric responses and provide an explanation for the success of the Onsager model as a phenomenological representation for the dielectric behavior of polar organic liquids.

Comparing continuous wave progressive saturation EPR and time domain saturation recovery EPR over the entire motional range of nitroxide spin labels.

The measurement of spin-lattice relaxation rates from spin labels, such as nitroxides, in the presence and absence of spin relaxants provides information that is useful for determining biomolecular properties such as nucleic acid dynamics and the interaction of proteins with membranes. We compare X-band continuous wave (CW) and pulsed or time domain (TD) EPR methods for obtaining spin-lattice relaxation rates of spin labels across the entire range of rotational motion to which relaxation rates are sensitive. Model nitroxides and spin-labeled biological species are used to illustrate the potential complications that arise in extracting relaxation data under conditions typical to biological experiments. The effect of super hyperfine (SHF) structure is investigated for both CW and TD spectra. First and second harmonic absorption and dispersion CW spectra of the nitroxide spin label, TEMPOL, are all fit simultaneously to a model of SHF structure over a range of microwave amplitudes. The CW spectra are novel because all harmonics and microwave phases were acquired simultaneously using our homebuilt CW/TD spectrometer. The effect of the SHF structure on the pulsed free induction decay (FID) and pulsed saturation recovery spectrum is shown for both protonated and deuterated TEMPOL. We present novel pulsed saturation recovery measurements on biological molecules, including spin-lattice relaxation rates of spin-labeled proteins and spin-labeled double-stranded DNA. The impact of structure and dynamics on relaxation rates are discussed in the context of each of these examples. Collisional relaxation rates with oxygen and transition metal paramagnetic relaxants are extracted using both continuous wave and time domain methods. The extent of the errors inherent in the CW method and the advantages of pulsed methods for unambiguously measuring collisional relaxation rates are discussed. Spin-lattice relaxation rates, determined by both CW and pulsed methods, are used to determine the electrostatic potential on the surface of a protein.

Formulation of Zeeman modulation as a signal filter.

The Bloch equation containing a Zeeman modulation field is solved analytically by treating the Zeeman modulation frequency as a perturbation. The absorption and dispersion signals at both 0 degrees and 90 degrees modulation phase are obtained. The solutions are valid to first order in the modulation frequency, but are otherwise valid for any value of modulation amplitude or microwave amplitude. A first order treatment of modulation frequency is shown to be a valid approximation over a wide range of typical experimental EPR conditions. The solutions derived from the Bloch equation suggest that the effect of over-modulation on first and second harmonic EPR spectra can be formulated as a mathematical filter that smoothes and broadens the under-modulated signal. The only adjustable filter parameter is a width that is equivalent to the applied peak-to-peak modulation amplitude. The true spin-spin and spin-lattice relaxation rates are completely determined from the under-modulated spectrum. The filters derived from the analytic solutions of the Bloch equation in the linear limit of modulation frequency are tested against numerical solutions of the Bloch equation that are valid for any modulation frequency to show their applicability. The filters are further tested using experimental EPR spectra. Experimental under-modulated spectra are mathematically filtered and compared with the experimental over-modulated spectra. The application of modulation filters to STEPR spectra is explored and limitations are discussed.