Showing papers in "Chemical Physics in 2006"

The J- and H-bands of organic dye aggregates

Abstract: Certain molecular aggregates consisting of organic dyes are remarkable in exhibiting an intense and very narrow absorption peak, known as a J-band, which is red-shifted away from the region of monomer absorption Apart from those dyes showing the J-band on aggregation, there are also dyes where the absorption maximum is shifted to higher energies The width of the resulting absorption band (called an H-band) is comparable to that of the monomeric dyes and shows a complicated vibrational structure Following our analysis of the J-band spectra of polymer aggregates using the CES approximation [A Eisfeld, JS Briggs, Chem Phys 281 (2002) 61], a theory that includes vibrations explicitly, we show that the same approximation can account for measured H-band spectra Using simple analytical forms of the monomer spectrum the origin of the widely different shapes of H- and J-bands is explained within the CES approximation

Measuring orbital interaction using quantum information theory

Abstract: Quantum information theory gives rise to a straightforward definition of the interaction of electrons Ip,q in two orbitals p,q for a given many-body wave function. A convenient way to calculate the von Neumann entropies needed is presented in this work, and the orbital interaction Ip,q is successfully tested for different types of chemical bonds. As an example of an application of Ip,q beyond the interpretation of wave functions, Ip,q is then used to investigate the ordering problem in the density-matrix renormalization group.

Absorption in regio-regular poly(3-hexyl)thiophene thin films: Fermi resonances, interband coupling and disorder

Abstract: Absorption in conjugated polymer aggregates is studied theoretically, taking into account excitonic (intermolecular) coupling, exciton–phonon (EP) coupling and site-energy disorder, all treated on equal footing within a generalized Holstein Hamiltonian with numerically generated eigenmodes and energies. The analysis deals primarily with the weak excitonic coupling regime, which for polymers, corresponds to J 0 ≲ 0.4 ω 0 where J 0 is the nearest neighbor excitonic coupling and ω 0 (≈1400 cm −1 ) is the frequency of the ring breathing/stretching mode coupled to the molecular electronic transition with Huang–Rhys factor, λ 2 ≈ 1. Disorder is characterized by a Gaussian distribution of molecular transition frequencies of width σ . Absorption spectra are calculated under the two-particle approximation (TPA) as well as the less accurate, but computationally more efficient single-particle approximation (SPA). Fermi resonances (FRs) arise due to the coupling between the optically allowed single-particle states (vibronic excitons) and the dark two-particle states. In the motional narrowing limit FRs are clearly resolved. Further increases in σ cause the FRs to merge into a single peak for each vibronic band. At this point the SPA becomes accurate for the entire spectrum. The SPA also provides the basis for simplified analytical expressions for the peak intensity ratios, from which the free exciton bandwidth, W , can be determined. Analytical expressions are also obtained for the peak-positions within the vibronic progression. Application to regio-regular poly(3-hexyl)thiophene films shows the exciton bandwidth, W , to be in the range 0.8 ω 0 – ω 0 . The model also accounts for the irregular peak spacings observed in experiment.

A short-range gradient-corrected spin density functional in combination with long-range coupled-cluster methods: Application to alkali-metal rare-gas dimers

Abstract: We extend our recently published short-range gradient-corrected density functional from the closed-shell to the open-shell case, combine it with long-range coupled-cluster methods (CCSD, CCSD(T)), and apply it to the weakly bound alkali-metal rare-gas dimers AmRg (Am = Li–Cs; Rg = Ne–Xe). The results are shown to be superior, with medium-size basis sets, to pure DFT and pure coupled-cluster calculations.

Accurate ab initio prediction of propagation rate coefficients in free-radical polymerization : Acrylonitrile and vinyl chloride

Abstract: A systematic methodology for calculating accurate propagation rate coefficients in free-radical polymerization was designed and tested for vinyl chloride and acrylonitrile polymerization. For small to medium-sized polymer systems, theoretical reaction barriers are calculated using G3(MP2)-RAD. For larger systems, G3(MP2)-RAD barriers can be approximated (to within 1 kJ mol −1 ) via an ONIOM-based approach in which the core is studied at G3(MP2)-RAD and the substituent effects are modeled with ROMP2/6-311+G(3df,2p). DFT methods (including BLYP, B3LYP, MPWB195, BB1K and MPWB1K) failed to reproduce the correct trends in the reaction barriers and enthalpies with molecular size, though KMLYP showed some promise as a low cost option for very large systems. Reaction rates are calculated via standard transition state theory in conjunction with the one-dimensional hindered rotor model. The harmonic oscillator approximation was shown to introduce an error of a factor of 2–3, and would be suitable for “order-of-magnitude” estimates. A systematic study of chain length effects indicated that rate coefficients had largely converged to their long chain limit at the dimer radical stage, and the inclusion of the primary substituent of the penultimate unit was sufficient for practical purposes. Solvent effects, as calculated using the COSMO model, were found to be relatively minor. The overall methodology reproduced the available experimental data for both of these monomers within a factor of 2.

The Herman–Kluk approximation: Derivation and semiclassical corrections

Abstract: The Herman–Kluk (HK) approximation for the propagator is derived semiclassically for a multidimensional system as an asymptotic solution of the Schrodinger equation. The propagator is obtained in the form of an expansion in ℏ , in which the lowest-order term is the HK formula. Thus, the result extends the HK approximation to higher orders in ℏ . Examination of the various terms shows that the expansion is a uniform asymptotic series and establishes the HK formula as a uniform semiclassical approximation. Successive terms in the series should allow one to improve the accuracy of the HK approximation for small ℏ in a systematic and purely semiclassical manner, analogous to a higher-order WKB treatment of time-independent wave functions.

Redox-gated electron transport in electrically wired ferrocene molecules

Abstract: We have synthesized cysteamine-terminated ferrocene molecules and determined the dependence of the electron transport properties of the molecules on their redox states by measuring the current through the molecules as a function of the electrode potential. The current fluctuates over a large range, but its average value increases with the potential. We attribute the current fluctuation and its increase with the potential to the switching of the molecules from low-conductance reduced state to high-conductance oxidized state.

VUV photoabsorption in CF3X (X = Cl, Br, I) fluoro-alkanes

Abstract: A new ultraviolet beam line has been constructed at the Institute of Storage Rings, University of Aarhus (ISA) to study the Photoabsorption of aeronomic molecules. In this paper, visible-UV spectra of CF3Cl and CF3Br are reported at high-resolution in the energy range 3.9-10.8 eV (320-115 nm). For both molecules, the present work provides the most reliable absolute cross-sections available at energies above the lowest lying electronic transition, the dissociative A band. Results are compared with earlier data including the recently published photoabsorption spectrum of CF3I [N.J. Mason, P. Limao-Vieira, S. Eden, P. Kendall, S. Pathak, A. Dawes, J. Tennyson, P. Tegeder, M. Kitajima, M. Okamoto, K. Sunohara, H. Tanaka, H. Cho, S. Samukawa, S.V. Hoffmann, D. Newnham, S.M. Spyrou, Int. J. Mass Spectrom. 223-224 (2003) 647]. The CF3I spectrum is revisited and new assignments made, including the extension of previously proposed its Rydberg series. A detailed description of the ASTRID photoabsorption apparatus at ISA is provided for the first time. (c) 2005 Elsevier B.V. All rights reserved.

Comparison of the electronic structure of PPV and its derivative DIOXA-PPV

Abstract: Electronic structure of two conjugated polymers, PPV and its derivative DIOXA-PPV, are studied by quantum-chemistry methods. Good agreement between the calculations and available experimental data validates the applied methods and enables us to draw conclusions about properties of excitons and polarons in these polymers. In particular, simultaneous use of different correlation plots in atomic site representation and transition densities in real space representation reveals electronic structure and spatial localization of the elementary excitations. The properties of the DIOXA-PPV are discussed in context of possible applications in molecular electronics devices.

Enhanced nucleation, smoothness and conformality of ultrananocrystalline diamond (UNCD) ultrathin films via tungsten interlayers

Abstract: Extremely smooth (6 nm RMS roughness over 4 μm 2 ), thin (100 nm), and continuous ultrananocrystalline diamond (UNCD) films were synthesized by microwave plasma chemical vapor deposition using a 10 nm tungsten (W) interlayer between the silicon substrate and the diamond film. These UNCD films possess a high content of sp 3 -bonded carbon. The W interlayer significantly increased the initial diamond nucleation density, thereby lowering the surface roughness, eliminating interfacial voids, and allowing thinner UNCD films to be grown. This structural optimization enhances the films’ properties and enables its integration with a wide variety of substrate materials.

Study of gas-phase O–H bond dissociation enthalpies and ionization potentials of substituted phenols – Applicability of ab initio and DFT/B3LYP methods

Abstract: In this paper, the study of phenol and 37 compounds representing various ortho-, para-, and meta-substituted phenols is presented. Molecules and their radical structures were studied using ab initio methods with inclusion of correlation energy and DFT in order to calculate the O–H bond dissociation enthalpies (BDEs) and vertical ionization potentials (IPs). Calculated BDEs and IPs were compared with available experimental values to ascertain the suitability of used methods, especially for the description of the substituent induced changes in BDE and IP. MP2, MP3, and MP4 methods do not give reliable results, since they significantly underestimate substituent induced changes in BDE and do not reflect distinct effect of substituents related to para and meta position correctly. DFT/B3LYP method reflects the effect of substituents on BDE satisfactorily, though ΔBDEs are in narrower range than experimental values. BDE of phenol was calculated also using CCSD(T) method in various basis sets. Both, DFT and HF methods describe the effect of substituents on IP identically. However, DFT considerably underestimates individual values. HF method gives IPs in very good agreement with experimental data. Obtained results show that dependences of BDEs and IPs on Hammett constants of the substituents are linear. Linearity of DFT BDE vs. IP dependence is even better than the dependences on Hammett constants and obtained equations allow estimating of O–H BDEs of meta- and para-substituted phenols from calculated IPs.

Doping-induced realignment of molecular levels at organic–organic heterojunctions

Abstract: This article examines how the concept of alignment of charge neutrality levels (CNL) can be used to explain and predict interface dipole and molecular level offset at organic–organic (OO) heterojunctions. The application of the model of CNL alignment to interfaces between undoped materials is reviewed first. The model is then extended to explain the shift of the CNL upon electrical doping of an organic material, and the resulting change in interface dipole and molecular level alignment. This approach provides, at this point, the first comprehensive prediction of energetics at OO heterojunctions.

On a correct description of a multi-temperature dissociating CO2 flow

Abstract: In the present paper, a strongly non-equilibrium reacting CO 2 flow is studied on the basis of the kinetic theory methods. An accurate description of kinetics, gas dynamics and transport properties taking into account complex internal structure of carbon dioxide molecules as well as different rates of vibrational energy exchanges and dissociation is proposed. The expressions for all transport coefficients are derived in the final form. The model, while taking into account multiple CO 2 vibrational modes and main features of intra- and inter-mode energy transitions, is sufficiently simple and suitable for practical realization.

Algebraic-diagrammatic construction propagator approach to molecular response properties

Abstract: A polarization propagator method, referred to as algebraic-diagrammatic construction (ADC), is extended to the treatment of static and dynamic response properties of molecules. The recent intermediate state representation (ISR) concept of the ADC theory, giving direct access to excited states wave functions and properties, allows us to derive simple closed-form expressions for linear and higher response functions. The use of the band-Lanczos algorithm is proposed to evaluate efficiently the resolvent type ADC expressions. The performance of the method is tested in computations of static and dynamic polarizabilities of several small molecules at the second-order (ADC(2)) level of the theory. The ADC(2) results are compared with those of full configuration interaction (FCI), coupled cluster (CC), and SOPPA (second-order polarization propagator approximation) treatments.

χ(3) measurements and optical limiting in dibenzylideneacetone and its derivatives

Abstract: We investigated the third order nonlinear optical properties of dibenzylidene acetone (1,5-diphenyl-1, 4-pentadeine-3-one) and its derivatives. The nonlinear measurements were performed by using single beam Z-scan technique with Q-switched Nd:YAG nanosecond laser pulses at 532 nm. Open aperture data for dibenzylidene and its derivatives demonstrate the presence of two-photon absorption at this wavelength. The dependence of χ (3) on donor/acceptor type substituents to the basic compound clearly shows the electronic origin of nonlinearity and hence demonstrates that the mechanism by which the third order nonlinear response enhanced is not by the thermal effects, but instead due to the strong nonlinear absorption and nonlinear refraction of the compounds. The derivatives of the basic compound show very good optical limiting behavior.

New approach for the electronic energies of the hydrogen molecular ion

Abstract: Herein, we present analytical solutions for the electronic energy eigenvalues of the hydrogen molecular ion H 2 + , namely the one-electron two-fixed-center problem. These are given for the homonuclear case for the countable infinity of discrete states when the magnetic quantum number m is zero, i.e., for 2Σ+ states. In this case, these solutions are the roots of a set of two coupled three-term recurrence relations. The eigensolutions are obtained from an application of experimental mathematics using Computer Algebra as its principal tool and are vindicated by numerical and algebraic demonstrations. Finally, the mathematical nature of the eigenenergies is identified.

Unimolecular rectifiers: Present status

Abstract: Many experimental issues presented here must be resolved before we can really understand unimolecular rectification. Nevertheless, at the University of Alabama six unimolecular rectifiers have been studied (Fig. 1, 1 – 6 ). Langmuir–Blodgett (LB) or Langmuir–Schaefer (LS) monolayer films of these molecules show asymmetric electrical conductivity between Au and Al electrodes. When the films are very compact (LS of 4 , LB of 5 ), and if there is finite intramolecular charge transfer (ICT, or intervalence transfer, IVT), then the electrical behavior persists for many cycles of measurement.

Distance dependence of heterogeneous electron transfer through the nonadiabatic and adiabatic regimes

Abstract: The Landau–Zener formalism, which is strictly valid for a two-state system, is extended to multistate systems by assuming that the electronic interaction between the redox moiety and a given energy level in the electrode is independent of the energy of the level and of the neighboring levels. The resultant electron transmission coefficient, κel,m, over the full range (nonadiabatic to adiabatic regimes) is defined by κ el , m = 2 ( 1 - exp [ - ( ν el , m 0 / 2 ν n ) exp [ - β ( r - r 0 ) ] ] ) / ( 2 - exp [ - ( ν el , m 0 / 2 ν n ) exp [ - β ( r - r 0 ) ] ] ) where r (cm) is the distance between the electrode and the redox moiety, r0 (cm) is the distance between the electrode and the plane of closest approach for the redox moieties, νn (s−1) is the effective nuclear vibration frequency, ν el , m 0 ( s - 1 ) is the energy-independent electron-hopping frequency when r = r0 and when the reactants and products have the same nuclear configurations and energies, and β (cm−1) is the decay constant for electronic coupling. This relationship is shown to be an adequate approximation of the more rigorously derived results of Kuznetsov et al. [J. Electroanal. Chem. 532 (2002) 171] which is valid from weakly coupled (nonadiabatic, ν el , m 0 / ν n ≪ 1 ) to strongly coupled (adiabatic, ν el , m 0 / ν n ≫ 1 ) regimes. We also show that the distance dependence of κel,m is consistent with the experimental observations of Smalley et al. [J. Am. Chem. Soc. 125 (2003) 2004]. The expression for κel,m also leads to a remarkably simple description of khet (units: cm s−1), the rate constant for heterogeneous electron transfer between an electrode and redox species in solution: k het = ( ν n κ n , m / β ) ln ( 1 + ν el , m 0 / ν n ) where κn,m is the nuclear reorganization factor.

Influence of substrate morphology on organic layer growth: PTCDA on Ag(111)

Abstract: By UV-excited photoelectron emission microscopy (UV-PEEM) we investigated the microscopic growth behavior of organic thin films using 3,4,9,10-perylene-tetracarboxylicacid dianhydride (PTCDA) on a Ag(1 1 1) single crystal substrate as example. Direct, real time observation allows to correlate the initial growth modes and the related kinetic parameters with substrate properties like terrace width, step density, and step bunches from the submonolayer range up to 5 layers or more. Above room temperature PTCDA grows in a Stranski–Krastanov fashion: after completion of the first two stable layers three-dimensional islands are formed. The nucleation density strongly depends on the temperature and the substrate morphology thus affecting the properties of the organic film.

Chemical approach to neutral-ionic valence instability, quantum phase transition, and relaxor ferroelectricity in organic charge-transfer complexes

Abstract: Neutral–ionic (NI) phase transition is a reversible switching of organic charge-transfer complexes between distinct valence states by external stimuli. This phase transformation in the low-dimensional system is demonstrated to provide a variety of novel dielectric, structural, and electronic properties. Importantly, ionization of the electron donor–acceptor pairs is usually accompanied by a ferroelectric or antiferroelectric order of the molecular lattice, leading to huge dielectric response near the transition point. Although these characteristics are potentially useful for future electronic and optical applications, the thermally accessible NI transition (TINIT) is still an extremely rare case. The TINIT compounds including some new materials are overviewed in order to provide convenient guides to their design and experimental identifications. The phase transition and dielectric properties can be closely controlled in various ways depending on chemical and physical modifications of the crystals. Among them, a quantum phase transition and relaxor ferroelectricity, both of which are currently attracting subjects from both scientific and practical perspectives, are highlighted as the first achievements in organic charge-transfer complexes.

On the role of dissociative πσ* states in the photochemistry of protonated tryptamine and tryptophan: An ab initio study

Abstract: In very recent experiments, the excited-state lifetimes of protonated aromatic amino acids have been recorded by means of the pump–probe photodissociation technique. The excited-state decays are fast (picosecond time scale), leading to an extensive fragmentation of the protonated species. The calculations presented here for protonated tryptamine and tryptophan using a coupled-cluster method are meant to unravel the complex behavior of these systems.

Structural and morphological properties of silver nanoparticles-phosphate glass composites

Abstract: New types of composite materials belonging to the (100 − x ) [50P 2 O 5 · 30CaO · 20Na 2 O] x Ag 2 O glasses system with 0 ⩽ x ⩽ 0.25 are obtained. Their local structure is analyzed with the help of Raman and infrared spectroscopy and it was found that the glasses structure is built up from predominantly ionic phosphate units. UV–VIS absorption measurements performed on the samples reveal the existence of silver nanoparticles within the soda–calcium-phosphate glass matrix. The electronic absorption spectra and TEM pictures analyses indicate the presence of silver nanoparticles of almost spherical shapes and various sizes inside the glass matrix, depending on the Ag 2 O content. By using the experimental UV–VIS data and a theoretical approach important structural and morphological parameters, such as the radius of the silver nanospheres and the volume fraction of the spheres are determined for one of the investigated composites ( x = 0.05 mol%).

Two-photon absorption of a supramolecular pseudoisocyanine J-aggregate assembly

Abstract: Linear spectral properties, including excitation anisotropy, of pseudoisocyanine or 1,1′-diethyl-2,2′-cyanine iodide (PIC) J-aggregates in aqueous solutions with J-band position at 573 nm were investigated. Two-photon absorption of PIC J-aggregates and monomer molecules was studied using an open aperture Z -scan technique. A strong enhancement of the two-photon absorption cross-section of PIC in the supramolecular J-aggregate assembly was observed in aqueous solution. This enhancement is attributed to a strong coupling of the molecular transition dipoles. No two-photon absorption at the peak of the J-band was detected.

On the integration of the multi-configurational time-dependent Hartree (MCTDH) equations of motion

Abstract: The multi-configurational time-dependent Hartree approach facilitates multi-dimensional wave packet calculations studying polyatomic reaction processes. The efficiency of the approach results from the use of an optimally adapted time-dependent basis of single-particle functions employed in the wavefunction representation. As a consequence, the equations of motion are non-linear. An efficient integration scheme for these equations has been developed by Beck and Meyer [Z. Phys. D 42 (1997) 113]. The scheme is optimally suited for studies of systems where the Hamiltonian can be represented as a sum of products of single-particle operators. Employing the same basic ideas, the present work now introduces and discusses revised integration schemes which are more efficient for systems, where the Hamiltonian includes a general potential energy function. The H + CH 4 → H 2 + CH 3 reaction is employed as an example to test the efficiency of the different schemes.

A theoretical study of uranyl solvation: Explicit modelling of the second hydration sphere by quantum mechanical methods

Abstract: The inclusion of an explicit second sphere in the hydration of the uranyl ion is investigated by DFT. We study model complexes that contain two water molecules in the second sphere hydrogen-bonded to each water molecule in the first. Compared with single-sphere models, significant changes are observed for the uranium–water first-sphere distance, the uranium-“yl” oxygen distance and the uranyl stretching vibrational frequencies. For each of these observables, agreement with experiment is improved with our new model. Charge transfer to uranyl is substantially enhanced when the second hydration sphere is present. Effects of third and subsequent hydration spheres appear to be small, but the influence of water molecules linked to the apical oxygens by a hydrogen-bonding network is probably not negligible. Models based on a polarizable continuum are less satisfactory, particularly for the vibrational frequencies. The uranyl stretching frequencies are highly correlated with charge transfer from water molecules to the “yl” oxygen atoms and with the uranyl bond length.

Growth kinetics of tin oxide nanocrystals in colloidal suspensions under hydrothermal conditions

Abstract: Colloidal suspensions of tin oxide nanocrystals were synthesized at room temperature by the hydrolysis reaction of tin chloride (II), in an ethanolic solution. The coarsening kinetics of such nanocrystals was studied by submitting the as-prepared suspensions to hydrothermal treatments at temperatures of 100, 150 and 200 °C for periods between 60 and 12,000 min. Transmission electron microscopy (TEM) was used to characterize the samples (i.e. distribution of nanocrystal size, average particle radius and morphology). The results show that the usual Ostwald ripening coarsening mechanism does not fit well the experimental data, which is an indicative that this process is not significant for SnO 2 nanocrystals, in the studied experimental conditions. The morphology evolution of the nanocrystals upon hydrothermal treatment indicates that growth by oriented attachment (OA) should be significant. A kinetic model that describes OA growth is successfully applied to fit the data.

Electron transfer across α-helical peptides: Potential influence of molecular dynamics

Abstract: Three hydrophobic leucine-rich peptides Fc18L, Ac18L and 18LAc were prepared. These peptides are equipped with a cystein sulfhydryl group which enables the formation of thin films on gold surfaces. Using these peptides, two types of films of α-helical peptides have been prepared, in which the redox-active peptide Fc18L is diluted by Ac18L (SAM1) or by a mixture of Ac18L and 18LAc (SAM2). In SAM1, the dipole moments of the peptides are aligned in the same direction, whereas in SAM2, they are opposite. Reflection absorption infrared spectroscopy (RAIRS) revealed that the peptides are more vertically oriented in SAM2 compared to those in SAM1. The interaction among the macroscopic helix dipoles gives tighter packing of the peptides in SAM2. Importantly, the electron transfer properties in the two films are significantly different, which is rationalized by differences in the molecular dynamics of the two films.

Solvent effect on indocyanine dyes: A computational approach

Abstract: The solvatochromic behaviour of a series of indocyanine dyes (Dyes I–VIII) was investigated by quantum chemical calculations. The effect of the polymethine chain length and of the indolenine structure has been satisfactorily reproduced by semiempirical Pariser–Parr–Pople (PPP) calculations. The solvatochromism of 3,3,3′,3′-tetramethyl- N , N ′-diethylindocarbocyanine iodide (Dye I) has been deeply investigated within the ab initio time-dependent density functional theory (TD-DFT) approach. Dye I undergoes non-polar solvation and a linear correlation has been individuated between absorption shifts and refractive index. Computed absorption λ max and oscillator strengths obtained by TD-DFT are in good agreement with the experimental data.

DFT modeling and spectroscopic study of metal-ligand bonding in La(III) complex of coumarin-3-carboxylic acid

Abstract: The binding mode of coumarin-3-carboxylic acid (HCCA) to La(III) is elucidated at experimental and theoretical level. The complexation ability of the deprotonated ligand (CCA−) to La(III) is studied using elemental analysis, DTA and TGA data as well as FTIR, 1H NMR and 13C NMR spectra. The experimental data suggest the complex formula La(CCA)2(NO3)(H2O)2. B3LYP, BHLYP, B3P86, B3PW91, PW91P86 and MPW1PW91 functionals are tested for geometry and frequency calculations of the neutral ligand and all of them show bond length deviations bellow 1%. B3LYP/6-31G(d) level combined with large quasi-relativistic effective core potential for lanthanum is selected to describe the molecular, electronic and vibrational structures as well as the conformational behavior of HCCA, CCA− and La–CCA complex. The metal–ligand binding mode is predicted through molecular modeling and energy estimation of different La–CCA structures. The calculated atomic charges and the bonding orbital polarizations point to strong ionic metal–ligand bonding in La–CCA complex and insignificant donor acceptor interaction. Detailed vibrational analysis of HCCA, CCA− and La(CCA)2(NO3)(H2O)2 systems based on both calculated and experimental frequencies confirms the suggested metal–ligand binding mode.

Nonequilibrium protein folding dynamics : laser-induced pH-jump studies of the helix-coil transition

Abstract: The kinetics of the helix–coil transition of poly- l -glutamate were measured in the range of 40 ns to 10 s using a laser-induced pH-jump coupled with time-resolved infrared spectroscopy. Folding of the polypeptide in D 2 O was initiated by photolyzing o -nitrobenzaldehyde, which releases a deuteron, creating a rapid decrease in pD. Side-chain deuteration and conformational changes were monitored independently by varying the IR probe wavelength. The kinetics of the peptide conformational changes observed in the amide I region depended on the initial fraction of helical residues. With essentially no initial helix, amide I absorption changes were indistinguishable from those of instrument response, leading to the conclusion that helix initiation occurs in less than 40 ns. When the initial helix fraction is 0.13, the folding lifetime is lengthened to 625 ns, as predicted by helix–coil theory. We also observe evidence for a kinetically-trapped, nonproductive intermediate formed as the result of rapid deuteration of the unfolded state.