Conformal Mode Research Articles

Three-Dimensional Nanofabrication with Elastomeric Phase Masks

This Feature Article reviews recent work on an optical technique for fabricating, in a single exposure step, three-dimensional (3D) nanostructures with diverse structural layouts. The approach, which we refer to as proximity field nanopatterning, uses conformable, elastomeric phase masks to pattern thick layers of transparent, photosensitive materials in a conformal contact mode geometry. Aspects of the optics, the materials, and the physical chemistry associated with this method are outlined. A range of 3D structures illustrate its capabilities, and several application examples demonstrate possible areas of use in technologies ranging from microfluidics to photonic materials to density gradient structures for chemical release and high-energy density science.

Synthetic, spectroscopic and X-ray crystallographic structural studies on copper(II) complexes of the aminoguanizone of pyruvic acid

Copper(II) complexes of general empirical formula, CuX(Hagpa) · nH 2O and Cu(agpa) · 2H 2O (H 2agpa = aminoguanizone of pyruvic acid, X = Cl −, Br −, NO 3 - , CH 3COO −, 1 / 2 SO 4 2 - , n = 0, 1, 1.5, 2), have been synthesized and characterized by IR, EPR spectroscopy and X-ray crystallography. The IR spectra of the complexes showed the ONN coordination of the ligand to copper(II) ion. The crystal structures of H 2agpa · H 2O and complexes [Cu(Hagpa)Br] and [Cu 2(Hagpa) 2(H 2O) 2(SO 4)] · DMSO showed an invariable conformation and coordination mode for the uninegatively charged tridentate ligand and revealed the formation of linear polymers in which bromide or sulfate anions bridge the copper(II) ions. The EPR spectra for complexes CuX(Hagpa) · nH 2O are described by spin Hamiltonian for S = 1/2, without hyperfine structure. The g-tensor is symmetrical for Cu(agpa) · 2H 2O, has tri-axial anisotropy for sulfate complexes, and exhibits axial symmetry for the other compounds investigated.

Principal-components analysis of shape fluctuations of single DNA molecules

Thermal fluctuations agitate molecules in solution over a broad range of times and distances. By passively watching the shape fluctuations of a thermally driven biomolecule, one can infer properties of the underlying interactions that determine the motion. We applied this concept to single molecules of fluorescently labeled lambda-DNA, a key model system for polymer physics. In contrast to most other single-molecule DNA experiments, we examined the unstretched, equilibrium state of DNA by using an anti-Brownian electrokinetic trap to confine the center of mass of the DNA without perturbing its internal dynamics. We analyze the long-wavelength conformational normal modes, calculate their spring constants, and measure linear and nonlinear couplings between modes. The modes show strong signs of nonlinear hydrodynamics, a feature of the underlying equations of polymer dynamics that has not previously been reported and is neglected in the widely used Rouse and Zimm approximations.

The Crucial Step in Ether Phospholipid Biosynthesis: Structural Basis of a Noncanonical Reaction Associated with a Peroxisomal Disorder

Ether phospholipids are essential constituents of eukaryotic cell membranes. Rhizomelic chondrodysplasia punctata type 3 is a severe peroxisomal disorder caused by inborn deficiency of alkyldihydroxyacetonephosphate synthase (ADPS). The enzyme carries out the most characteristic step in ether phospholipid biosynthesis: formation of the ether bond. The crystal structure of ADPS from Dictyostelium discoideum shows a fatty-alcohol molecule bound in a narrow hydrophobic tunnel, specific for aliphatic chains of 16 carbons. Access to the tunnel is controlled by a flexible loop and a gating helix at the protein-membrane interface. Structural and mutagenesis investigations identify a cluster of hydrophilic catalytic residues, including an essential tyrosine, possibly involved in substrate proton abstraction, and the arginine that is mutated in ADPS-deficient patients. We propose that ether bond formation might be orchestrated through a covalent imine intermediate with the flavin, accounting for the noncanonical employment of a flavin cofactor in a nonredox reaction.

Quantum structure of space near a black hole horizon

We describe a midi-superspace quantization scheme for generic single horizon black holes in which only the spatial diffeomorphisms are fixed. The remaining Hamiltonian constraint yields an infinite set of decoupled eigenvalue equations: one at each spatial point. The corresponding operator at each point is the product of the outgoing and ingoing null convergences, and describes the scale invariant quantum mechanics of a particle moving in an attractive 1/X2 potential. The variable X that is analogous to particle position is the square root of the conformal mode of the metric. We quantize the theory via Bohr quantization, which by construction turns the Hamiltonian constraint eigenvalue equation into a finite difference equation. The resulting spectrum gives rise to a discrete spatial topology exterior to the horizon. The spectrum approaches the continuum in the asymptotic region.

Structural preferences and thermal stability of complexes with the exo-bidentate ligand 1,2-bis(2-methylimidazol-1-ylmethyl)benzene

We describe a series of new coordination polymers of Cd(II), Co(II) and Ag(I) with 1,2-bis(2-methylimidazol-1-ylmethyl)benzene. All complexes were characterized by single crystal X-ray diffraction which reveals polymeric bridging of metal centers by the ligand in all cases. The cadmium center in complex 1 has a slightly irregular octahedral geometry involving two Cl − ions and four N atoms from individual ligands, resulting in the formation of undulated (4,4) layers. In complex 2 the cobalt(II) ion is coordinated by two Cl − ions and two N atoms from separate ligands. This yields a slightly irregular tetrahedral coordination environment around the metal center and the formation of a 1D zigzag-chain structure. Each of the three Ag(I) complexes ( 3– 5) forms an infinite 1D chain. These three complexes are similar both in conformation and packing mode despite modification of the counterions. The size of the counterion appears to affect the thermal stabilities of the resulting networks.

The Role of Protein Kinase C as a Regulator of NG115‐401L Neuronal Cell Calcium Signaling Pathways

The molecular regulation of non-voltage gated calcium influx continues to be an important but poorly characterized signaling pathway in cellular physiology. We have previously characterized unique features of calcium influx in the NG115-401L (401L) neuronal cell line, revealing a phenotype that appears to depend on a conformational coupling mode for the regulation of both calcium influx and release. In this study, we used ratiometric microscope photometry on Fura 2 loaded 401L cells to further probe the apparatus mediating calcium influx when cells are stimulated with pro-inflammatory hormones such as bradykinin. In particular, we have examined the effects of pharmacological modulation of protein kinase C (PKC) on native 401L cells and on cells overexpressing canonical transient receptor potential (TRPC) ion channels. Our preliminary results reveal that inhibitors of PKC augment calcium influx in 401L cells suggesting that PKC activation serves to suppresses the calcium influx mechanism. In contrast, pharmacological activation of PKC using phorbol ester treatment did not significantly influence calcium influx in both native or TRPC overexpressing 401L cells. Intriguingly, we observed that PKC activation in the presence of extracellular calcium elicited discharge from intracellular calcium stores, suggesting a composite target containing PKC activity regulating both calcium release and influx. This work was supported by a grant from the National Institutes of Neurological Disorders and Stroke (1R15 NS048041-01A1) to D.W.T.

Single‐beam CARS spectroscopy applied to low‐wavenumber vibrational modes

AbstractIn single‐beam coherent anti‐Stokes Raman scattering (CARS) spectroscopy, a complete CARS scheme is accomplished with tailored pulses from a fs‐oscillator by coherent control of the nonlinear signal generation. Here, the application of single‐beam CARS to low‐wavenumber vibrational modes in the range of 50–400 cm−1 is demonstrated by investigating pure liquid‐phase samples and molecules in solution. The spectral resolution (17 cm−1) achieved by coherent control of the CARS process is an order of magnitude better than the spectral width of the excitation pulses (150 cm−1 FWHM). At the same time, nonresonant background is suppressed by more than 1 order of magnitude. It is shown that spectral shaping of the excitation spectrum can drastically extend the accessible range of vibrational modes in single‐beam CARS. The implemented scheme is very well suited for CARS microscopy because of its conceptual simplicity and flexibility, and presents the opportunity for spatially resolved studies of conformational modes in biological samples. Copyright © 2006 John Wiley & Sons, Ltd.

Casimir effect: running Newton constant or cosmological term

We argue that the instability of Euclidean Einstein gravity is an indication that the vacuum is non-perturbative and contains a condensate of the metric tensor in a manner reminiscent of Yang–Mills theories. As a simple step toward the characterization of such a vacuum the value of the 1-loop effective action is computed for Euclidean de Sitter spaces as a function of the curvature when the unstable conformal modes are held fixed. Two phases are found, one where the curvature is large and gravitons should be confined and another one which appears to be weakly coupled and tends to be flat. The induced cosmological constant is positive or negative in the strongly or weakly curved phase, respectively. The relevance of the Casimir effect in understanding the UV sensitivity of gravity is pointed out.

Electron–phonon coupling in DNA: a systematic study

The coupling of all twelve possible conformational modes of DNA duplexes and four pair-wise correlations among them to positive charge (hole) motion through these biopolymers has been systematically analysed in regular homogeneous B-DNA trimers and tetramers of adenosine–thymidine (AT) and guanosine–cytidine (GC) Watson–Crick pairs using PM3 semiempirical quantum chemistry. Of these only five modes have been found to be most strongly coupled to the electron motion in DNA, namely stretching of H-bonding both in AT and GC, correlated Buckle–Rise and Stagger–Tilt motions in GC and correlated Shear–Twist motion in AT. The parameters for the corresponding polaronic Hamiltonians have been estimated. The nature of these DNA polarons is discussed taking into account the relevant experimental results currently available.

Twistor actions for non-self-dual fields; a new foundation for twistor-string theory

Twistor space constructions and actions are given for full Yang-Mills and conformal gravity using almost complex structures that are not, in general, integrable. These are used as the basis of a derivation of the twistor-string generating functionals for tree level perturbative scattering amplitudes of Yang-Mills and conformal gravity. The derivation follows by expanding and resumming the classical approximation to the path integral obtained from the twistor action. It provides a basis for exploring whether the equivalence can be made to extend beyond tree level and allows one to disentangle conformal supergravity modes from the Yang-Mills modes.

Vibrational analysis, conformational stability, force constants, barriers to internal rotations, RHF, MP2 and DFT calculations of trans,trans‐2,4‐hexadiene

AbstractSix conformers are proposed for the trans,trans‐2,4‐hexadiene (TTHD) molecule. Utilizing the 6–31G(d) and 6–311 + G(d) basis sets at the levels of RHF, MP2 with full electron correlation and DFT‐B3LYP, five conformers are found to be transition states, due to the calculated imaginary wavenumber(s). Accordingly, the totally symmetric TTT conformer where the two methyl groups are staggered to all trans vinylic hydrogen's (C2h symmetry) is the stable conformer in the gaseous, liquid and crystalline phases. Aided by MP2(full)/6–311 + G(d) geometric parameters, a chosen value of the kinetic parameter F = 6.11284856 was determined. Utilizing the observed band at 148 cm−1 in the far‐infrared spectrum of the gas, a value of 1.41 ± 0.06 kcal mol−1 was obtained for the C3v internal rotor (V3), compared with 1.83 ± 0.07 kcal mol−1 predicted from a potential energy surface scan (1 kcal = 4.184 kJ). Aided by normal coordinate analysis and quantum chemistry (QC) calculations, the scaled quantum mechanical (SQM) force field was obtained employing five scaling factors for different types of vibrational motions. The scaled vibrational wavenumbers from both MP2(full) and B3LYP levels using the 6–31G(d) basis set provides an excellent approach to the observed fundamentals in either infrared or Raman spectra of the TTT conformer. Thus, confident vibrational assignments and potential energy distributions (PEDs) were provided for all fundamental modes of the TTT conformer. Moreover, the conformational stabilities, structural parameters, rotational constants, infrared intensities and Raman scattering activities are also reported. These results are discussed and compared with the experimentally determined values for some related conjugate systems when appropriate. Copyright © 2004 John Wiley & Sons, Ltd.

The discovery of N-(1,3-thiazol-2-yl)pyridin-2-amines as potent inhibitors of KDR kinase

An azo-dye lead was modified to a novel N-(1,3-thiazol-2-yl)pyridin-2-amine series of KDR kinase inhibitors through the use of rapid analog libraries. This new class has been found to be potent, selective, and of low molecular weight. Molecular modeling has postulated an interesting conformational preference and binding mode for these compounds in the active site of the enzyme.

Gating of a Molecular Transistor: Electrostatic and Conformational

We derive a general result that can be used to evaluate and compare the transconductance of different field-effect mechanisms in molecular transistors, both electrostatic and conformational. The electrostatic component leads to the well-known thermal limit in the absence of tunneling. We show that in a standard three-terminal geometry and in the absence of strong electron−phonon coupling, the conformational component can lead to significant advantages only if the molecular dipole moment μ is comparable to etox, tox being the thickness of the oxide. Surprisingly, this conclusion is independent of the “softness” of the conformational modes involved or other geometrical factors. Detailed numerical results for specific examples are presented in support of the analytical results.

Stability issues in the modified starobinsky model

We discuss the stability of the anomaly-induced inflation (modified Starobinsky model) with respect to the arbitrary choice of initial data and with respect to the small perturbations of the conformal factor and tensor modes of the metric in the later period of inflation and, partially, in the present Universe.

Conformational and stereochemical flexibility in cadmium(II) complexes of aza-thioether macrocycles.

The synthesis and crystal structures of four CdII macrocyclic complexes containing mixed N-, O- and S-donors, [Cd(NO3)2([12]aneN2S2)] (1), [Cd(NO3)2([12]aneNS3)] (2), [Cd(NO3)2([15]aneNO2S2)] (3) and [Cd(NO3)([15]aneN2O2S)]NO3 (4), are presented. The metal ion is coordinated outside of the macrocyclic cavity in the complexes of the smaller macrocycles ([12]aneN2S2 and [12]aneNS3) while the flexibility of the larger macrocycles in and allows very different conformations to be adopted with a 'butterfly' geometry in and a flattened geometry in. No correlation between the number of sulfur donors and Cd-S bond distance in these types of complexes is observed, although the number and binding mode of the nitrato ligands is determined by the conformation and binding mode of the macrocycle. The position of the nitrato ligand also influences, through steric conflicts with the macrocyclic donor atoms, the bond distances in both ligand systems.

Conformal Algebra and Physical States in a Non-Critical 3-Brane on R xS3

A world-volume model of non-critical 3-brane is quantized in a strong coupling phase where fluctuations of the conformal mode become dominant. This phase, called the conformal-mode dominant phase, is realized at the very high energy far beyond the Planck mass scale. We separately treat the conformal mode and the traceless mode and quantize the conformal mode "non-perturbatively", while the traceless mode is treated in the perturbation which is renormalizable and asymptotically free. In the conformal-mode dominant phase, the coupling of the traceless mode vanishes and the world-volume dynamics is described as a four dimensional conformal field theory (CFT_4). We canonically quantize this model on R*S^3 where the dynamical metric fields are expanded using spherical tensor harmonics on S^3. Conformal charges and conformal algebra are constructed. They give strong constraints on physical states. We find that all negative-metric modes are related to positive-metric modes through the charges so that they are not independent physical modes themselves. An infinite number of physical states satisfying the conformal invariance conditions are constructed. In appendix, we construct spherical vector, tensor harmonics on S^3 in the useable form using Wigner D-functions and Clebsch-Gordan coefficients and calculate integrals of their products.

Reactive vibrational excitation spectroscopy of formic acid in solid argon: Quantum yield for infrared induced trans→cis isomerization and solid state effects on the vibrational spectrum

Formic acid molecules are trapped in two predominant local environments (sites) when isolated in an argon matrix at 8 K. Using narrowband tunable infrared (IR) radiation, we performed site-selective excitation of various vibrational modes of the lower-energy trans conformer. For all excited modes, ranging from 7000 to 2950 cm−1, we detected site-selective isomerization to the higher-energy cis form. By measuring the IR absorption of a selected band of the cis conformer as a function of the excitation frequency, the reactive vibrational excitation (RVE) spectra were obtained. The trans→cis isomerization quantum yields for the excited modes were determined. Remarkably, very high absolute values were obtained for the quantum yield (up to 40%) at excitation energies above the reaction barrier. The efficiency of the photoinduced isomerization is essentially independent of the excited vibrational mode in a broad energy interval. Even when the excitation energy was below the reaction barrier, IR-induced rotational isomerization was observed, which indicates tunneling from the vibrationally excited trans conformer to the cis form. Using the RVE spectra, phonon sidebands were detected on the high-frequency side of the zero-phonon-line of the OH stretching mode of trans-formic acid. These weak and broad bands were not observed in the absorption spectra. Additionally, a relatively narrow band blueshifted by 6 cm−1 from the OH stretching fundamental mode was assigned to a librational satellite based on simulations using the hindered rotation model for an asymmetric top trapped in an octahedral crystal field.

The vibrational spectra and conformations of ethylbenzene

Infrared spectra (4000–250 cm −1) of the liquid, amorphous, crystalline solids and solutions in liquid krypton and Raman spectra (2500–20 cm −1) of the liquid as well as the amorphous and crystalline solids of ethylbenzene and its deuterated analogue—ethylbenzene- d 10 have been recorded. The spectra indicate that in the liquid and amorphous solids a small amount of a second conformer is present, whereas only one conformer remains in the crystalline phases. Assignments of the observed band wave numbers are discussed by comparison with normal mode wave numbers and IR and RS intensities calculated from ab initio 6-31G force fields and optimised geometries for both conformers for two species. All of the normal modes of conformers have been assigned.

Grand-canonical simulation of 4D simplicial quantum gravity

A thorough numerical examination for the field theory of 41) quantum gravity (QG) with a special emphasis on the conformal mode dependence has been studied. More clearly than before, we obtain the string susceptibility exponent of the partition function by using the Grand-Canonical Monte-Carlo method. Taking thorough care of the update method, the simulation is made for 4D Euclidean simplicial manifold coupled to N x scalar fields and N A U(1) gauge fields. The numerical results suggest that 4D simplicial quantum gravity (SQG) can be reached to the continuum theory of 41) QG. We discuss the significant property of 4D SQG.