Bond connectivity measured via relaxation-assisted two-dimensional infrared spectroscopy

The relaxation-assisted two-dimensional infrared (RA 2DIR) method is a novel technique for probing structures of molecules, which relies on vibrational energy transport in molecules. In this article we demonstrate the ability of RA 2DIR to detect the bond connectivity patterns in molecules using two parameters, a characteristic intermode energy transport time (arrival time) and a cross-peak amplification coefficient. A correlation of the arrival time with the distance between the modes is demonstrated. An 18-fold amplification of the cross-peak amplitude for the modes separated by approximately 11 A is shown using RA 2DIR; larger cross-peak amplifications are expected for the modes separated by larger distances. The RA 2DIR method enhances the applicability of 2DIR spectroscopy by making practical the long-range measurements using a variety of structural reporters, including weak IR modes. The data presented demonstrate the analytical power of RA 2DIR which permits the speedy structural assessments of the bond connectivity patterns.     

Sulfoxide stretching mode as a structural reporter via dual-frequency two-dimensional infrared spectroscopy

The S=O stretching mode in sulfoxides, having a frequency in the 950-1150?cm(-1) range, is tested as a structural label via dual-frequency two-dimensional infrared (2DIR) spectroscopy. The properties of this structural reporter are studied in several compounds, including (4,4(')-dimethyl-2,2(')-bipyridyl)(o-methylsulfinylbenzoate) ruthenium II, [Ru(dmb)(2)(BzSO)](+), (RuBzSO), octylsulfinylpropionic acid (OSPA), and o- and p-methylsulfinyl-benzoic acid (oMSBA and pMSBA). The mode assignment in the fingerprint region for these compounds is made using a combination of density functional theory calculations and 2DIR and relaxation-assisted 2DIR (RA 2DIR) spectroscopies. The SO stretching mode frequency and IR intensity demonstrate substantial sensitivity to the molecular structure. Multiple cross peaks of the C=O and S=O stretching modes with modes in the fingerprint region (930-1450?cm(-1)) were recorded. The 2DIR and RA 2DIR spectra focusing at interactions of a high-frequency mode of a ligand with the modes in the fingerprint region provide a spectral fingerprint of a compound and help mode assignment in the often congested fingerprint region. The cross-peak amplitudes in oMSBA, pMSBA, and OSPA were compared with the theoretical predictions based on the computed values for the off-diagonal anharmonicities and a reasonable match is found. The SO stretching mode provides means for assigning other modes in the fingerprint region and constitutes a promising structural reporter for the 2DIR and RA 2DIR spectroscopy measurements.     

Discrimination between coupling networks of glucopyranosides varying at a single stereocenter using two-dimensional vibrational correlation spectroscopy

A combination of two-dimensional infrared (2DIR) correlation spectroscopy, linear absorption spectroscopy, and density functional theory quantum calculations was used to identify characteristic spectral features of two anomers of acetylated 2-azido-2-deoxy-D-glucopyranose. While the linear absorption spectra for the α and β anomers were distinctive, a substantial difference between them was observed only in the spectral region below 1200 cm(-1). The infrared correlation spectra of the two anomers differed significantly, even in regions where their linear absorption spectra were similar. Very substantial differences were found for the N≡N/C=O stretch mode region of the 2DIR correlation spectrum, indicating differences in the anharmonic coupling of the N≡N stretching mode of the equatorially oriented N(3) group with the CO modes when the C(1) ester was either in the axial (α anomer) or equatorial (β anomer) orientation. In addition, the energy transport patterns originating from the excited N≡N stretching mode were found to be different for the two anomers; up to a 1.8-fold difference in the energy transport times was observed for the probed modes of the same type in the two anomers. The results demonstrate the capability of 2DIR and relaxation-assisted 2DIR (RA 2DIR) spectroscopies to provide unique spectroscopic data specific to sugar anomers that vary at a single stereochemical center. These methods identify unique coupling networks within individual sugar stereochemical units and demonstrate the potential to identify a number of stereochemical differences among them.     

Decongestion of methylene spectra in biological and non-biological systems using picosecond 2DIR spectroscopy measuring electron-vibration–vibration coupling

Methylene is found in the repeat units of many polymers including proteins. In some cases it appears to be a useful reporter of variation in local environment whilst in other contexts average behaviour seems to dominate. In this paper we apply a particular 2DIR technique to a range of systems containing methylene groups, showing that mode frequencies, linewidths and splittings can be easily extracted even when the infrared absorption bands are too congested to allow reliable analysis. 2DIR spectra of polyethylene and several liquid alkanes are compared and it is shown for the case of l-arginine that the methylene scissor modes are split and that this can be resolved by tracking the 2DIR spectrum as a function of time. Calculations from first principles reveal that for most of the methylene modes studied, electrical anharmonicity is the dominant contributor to the 2DIR cross-peak intensity, with the mechanical anharmonicity making only a small contribution.     

Transition from IVR limited vibrational energy transport to bulk heat transport

In a previous paper [M. Schade, P. Hamm, Vibrational energy transport in the presence of intrasite vibrational energy redistribution, J. Chem. Phys. 131 (2009) 044511], it has been shown that on ultrashort length and time scales, the speed of vibrational energy transport along a molecular chain is limited by intrasite vibrational relaxation rather than the actual intersite propagation. However, since intrasite vibrational relaxation is length independent, the intersite propagation rate is expected to become rate-limiting at some length scale, where propagation approaches the bulk limit. In the present paper, we investigate the transition between both regimes. The response of different types of modes may be very different at early times, depending on how much they contribute directly to energy transport. Surprisingly though, when averaging the energy content over all vibrational modes of the various chain sites, the complexity of the intrasite vibrational relaxation process is completely hidden so that energy transport on the nanoscale can be described by an effective propagation rate, that equals the bulk value, even at short times.     

Assessment and prediction of thermal transport at solid-self-assembled monolayer junctions

Self-assembled monolayers (SAMs) have recently garnered much interest due to their unique electrical, chemical, and thermal properties. Several studies have focused on thermal transport across solid-SAM junctions, demonstrating that interface conductance is largely insensitive to changes in SAM length. In the present study, we have investigated the vibrational spectra of alkanedithiol-based SAMs as a function of the number of methylene groups forming the molecular backbone via Hartree-Fock methods. In the case of Au-alkanedithiol junctions, it is found that despite the addition of nine new vibrational modes per added methylene group, only one of these modes falls below the maximum phonon frequency of Au. In addition, the alkanedithiol one-dimensional density of normal modes (modes per unit energy per unit length) is nearly constant regardless of chain length, explaining the observed insensitivity. Furthermore, we developed a diffusive transport model intended to predict interface conductance at solid-SAM junctions. It is shown that this predictive model is in an excellent agreement with prior experimental data available in the literature.     

Stretching and compression of a macromolecule under different modes of mechanical manupulations

This review is concerned with the response of an isolated polymer chain subjected to the action of the two different modes of the mechanical impact on the chain ends. In one mode, the end-to-end distance is changed in a controlled fashion and the fluctuating response force is measured; in the second case, an external stress field is applied to the chain end, and the measured response of the system is the fluctuating end-to-end distance. The main attention is focused on the results of the computer-aided simulation experiments and theoretical results. Upon stretching of an ideal chain, a real chain in a good solvent, or a globule, the resultant strain-force and force-strain dependences are shown to be different for chains with finite length L; however, this difference diminishes with an increase in the length of a molecule. When the anchored Gaussian chain is separated from the adsorbing surface, this difference disappears in the limit of high L; however, in the neighborhood of the phase transition, some characteristics (fluctuations, distribution functions) appear to be critically different under different impact modes even in the thermodynamic limit. The example of an abnormal system is discussed: The behavior of a polymer chain compressed by a small piston is different in the conjugated ensembles, and, as the system increases in size, this difference becomes even more pronounced.     

Picosecond IR-UV pump-probe spectroscopic study on the vibrational energy flow in isolated molecules and clusters

Intramolecular vibrational energy redistribution (IVR) and vibrational predissociation (VP) from the XH stretching vibrations, where X refers to O or C atom, of aromatic molecules and their hydrogen(H)-bonded clusters are investigated by picosecond time-resolved IR-UV pump probe spectroscopy in a supersonic beam. For bare molecules, we mainly focus on IVR of the OH stretch of phenol. We describe the IVR of the OH stretch by a two-step tier model and examine the effect of the anharmonic coupling strength and the density of states on IVR rate and mechanism by using isotope substitution. In the H-bonded clusters of phenol, we show that the relaxation of the OH stretching vibration can be described by a stepwise process and then discuss which process is sensitive to the H-bonding strength. We discuss the difference/similarity of IVR/VP between the "donor" and the "acceptor" sites in phenol-ethylene cluster by exciting the CH stretch vibrations. Finally, we study the vibrational energy transfer in the isolated molecules having the alkyl chain, namely phenylalcanol (PA). In this system, we measure the rate constant of the vibrational energy transfer between the OH stretch and the vibrations of benzene ring which are connected at the both ends of the alkyl chain. This energy transfer can be called "through-bond IVR". We investigate the three factors which are thought to control the energy transfer rate; (1) "OH <--> next CH(2)" coupling, (2) chain length and (3) conformation. We discuss the energy transfer mechanism in PAs by examining these factors.     

Intermolecular vibrational modes and orientational dynamics of cooperative hydrogen-bonding dimer of 7-azaindole in solution

We observed the low-frequency Raman-active intermolecular vibrational modes of 7-azaindole in CCl(4) by femtosecond Raman-induced Kerr effect spectroscopy. To understand the dynamical aspects and vibrational modes of 7-azaindole in the solution, the ultrafast dynamics of 1-benzofuran in CCl(4) was also examined as a reference and ab initio quantum chemistry calculations were performed for 7-azaindole and 1-benzofuran. The cooperative hydrogen-bonding vibrational bands of 7-azaindole dimer in CCl(4) appeared at 89 cm(-1) and 105 cm(-1) represent the overlap of stagger and wheeling modes and the intermolecular stretching mode, respectively. They are almost independent of the concentration in the solution. We further found from the low-frequency differential Kerr spectra of the solutions with neat CCl(4) that the intermolecular motion in the low frequency region below 20 cm(-1) was less active in the case of 7-azaindole/CCl(4) than in the case of 1-benzofuran/CCl(4). The slow orientational relaxation time in 7-azaindole/CCl(4) is ~3.5 times that in 1-benzofuran/CCl(4) because of the nature of the dimerization of 7-azaindole.     

Two-dimensional infrared spectral signatures of 3(10)- and alpha-helical peptides

Two-dimensional infrared (2D IR) spectra of Calpha-alkylated model octapeptides Z-(Aib)8-OtBu, Z-(Aib)5-L-Leu-(Aib)2-OMe, and Z-[L-(alphaMeVal)]8-OtBu have been measured in the amide I region to acquire 2D spectral signatures characteristic of 3(10)- and alpha-helical conformations. Phase-adjusted 2D absorptive spectra recorded with parallel polarizations are dominated by intense diagonal peaks, whereas 2D rephasing spectra obtained at the double-crossed polarization configuration reveal cross-peak patterns that are essential for structure determination. In CDCl3, all three peptides are of the 3(10)-helix conformation and exhibit a doublet cross-peak pattern. In 1,1,1,3,3,3-hexafluoroisopropanol, Z-[L-(alphaMeVal)]8-OtBu undergoes slow acidolysis and 3(10)-to-alpha-helix transition. In the course of this conformational change, its 2D rephasing spectrum evolves from an elongated doublet, characteristic of a distorted 3(10)-helix, to a multiple-peak pattern, after becoming an alpha-helix. The linear IR and 2D absorptive spectra are much less informative in discerning the structural changes. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model. The through-bond and through-space vibrational couplings are modeled by ab initio coupling maps and transition dipole interactions. The local amide I frequency is evaluated by a new approach that takes into account the effects of hydrogen-bond geometry and sites. The static diagonal and off-diagonal disorders are introduced into the Hamiltonian through statistical models to account for conformational fluctuations and inhomogeneous broadening. The sensitivity of cross-peak patterns to different helical conformations and the chain length dependence of the spectral features for short 3(10)- and alpha-helices are discussed.     

Infrared study of 6-methylcoumarin in binary solvent mixtures

The infrared absorption spectra of the carbonyl stretching vibrations of 6-methylcoumarin (6MC) have been investigated in CCl4/ROH mixtures (CCl4/C2H5OH, CCl4/n-C3H7OH, CCl4/i-C3H7OH, and CCl4/t-C5H11OH). Two types of carbonyl stretching vibration bands for 6MC are found with the change of the mole fraction of the aprotic solvent CCl4(X CCl4 in binary solvent mixtures. The dependencies of the frequencies of carbonyl stretching vibrations upsilon(C=O) on X CCl4 allow a distinction and assignment of all species resulting from the solvent-solute interactions. Linear correlations between the upsilon(C=O) of each species and X CCl4 are found. The influence on the transformation of some species caused by the self-associated alcohols is discussed.     

Synthesis, structure, and magnetic properties of three new one-dimensional nickel(II) complexes: new magnetic model for the first one-dimensional S = 1 complex with alternating ferro-ferromagnetic coupling

Three new one-dimensional nickel(II) complexes with the formulas trans-[Ni(N-Eten)2(mu1.3-N3)]n(ClO4)n (1), trans-[Ni(N-Eten)2(mu1.3-N3)]n(PF6)n (2), and cis-[Ni(N-Eten)(mu1.1-N3)2]n (3) (N-Eten = N-Ethylethylenediamine) were synthesized and characterized. Complex 1 has the P2(1)/c space group and consists of a structurally and magnetically alternating one-dimensional antiferromagnetic system with end-to-end azido bridges. Compound 2 has the P1 space group and has alternate units in its structure but consists of a magnetically uniform one-dimensional antiferromagnetic system with end-to-end azido bridges. Complex 3 has the I2/a space group and may be described as a structurally and magnetically alternating one-dimensional ferromagnetic system with double azido bridged ligands in an end-on coordination mode. The chi(M)T versus T plots for compound 3 suggest an intramolecular ferromagnetic interaction between adjacent NiII ions and metamagnetism at low temperature (below 10 K). The magnetization measurements versus applied field confirm this metamagnetic ordering. In order to describe the magnetic data of this compound we developed a general formula for the magnetic susceptibility of the isotropic ferro-ferromagnetic S = 1 Heisenberg chain in terms of the alternation parameter alpha (= J2/J1); this assumed a variation of chi(M)T versus the length N.     

The Mechanism of Flex-Activation in Mechanophores Revealed By Quantum Chemistry

Flex-activated mechanophores can be used for small-molecule release in polymers under tension by rupture of covalent bonds that are orthogonal to the polymer main chain. Using static and dynamic quantum chemical methods, we here juxtapose three different mechanical deformation modes in flex-activated mechanophores (end-to-end stretching, direct pulling of the scissile bonds, bond angle bendings) with the aim of proposing ways to optimize the efficiency of flex-activation in experiments. It is found that end-to-end stretching, which is a traditional approach to activate mechanophores in polymers, does not trigger flex-activation, whereas direct pulling of the scissile bonds or displacement of adjacent bond angles are efficient methods to achieve this goal. Based on the structural, energetic and electronic effects responsible for these observations, we propose ways of weakening the scissile bonds experimentally to increase the efficiency of flex-activation.     

Pentachlorocyclopropane/base complexes: matrix isolation infrared spectroscopic and density functional study of C-H- - -N hydrogen bonds

Hydrogen-bonded complexes of pentachlorocyclopropane with the bases acetonitrile, ammonia, monomethylamine, and dimethylamine have been isolated and characterized for the first time in argon matrices at 16 K. Coordination of the proton of pentachlorocyclopropane (Pccp) to the electron donor (N) of the base was evidenced by red shifts of the CH stretching mode. These shifts, which range from 22 to 170 cm(-1), increase in the order CH3CN, NH3, (CH3)NH2, and (CH3)2NH. Density functional theory (DFT) calculations at the B3LYP level agree well with experiment and support the formation of 1:1 complexes of Pccp/base. Distinct changes were observed in ring modes as well as CCl and CCl2 modes. The hydrogen bond energy of the complexes varies from 2.95 to 4.22 kcal/mol and is stronger than our previously studied bromocyclopropane-ammonia complex (2.35 kcal/mol, MP2).     

Beta-azidoalanine as an IR probe: application to amyloid Abeta(16-22) aggregation

Beta-azidoalanine dipeptide 1 was synthesized, and its azido stretching vibration in H2O and dimethyl sulfoxide (DMSO) was studied by using Fourier transform (FT) IR spectroscopy. The dipole strength of the azido stretch mode is found to be about 19 and 5 times larger than those of the CN and SCN stretch modes, respectively, which have been used as local environmental IR sensors. The azido stretch band in H2O is blue-shifted by about 14 cm(-1) in comparison to that in DMSO, indicative of its sensitivity to the electrostatic environment. To test the utility of beta-azidoalanine as an IR probe of the local electrostatic environment in proteins, azidopeptide 4 was prepared by its incorporation into Abeta(16-22) peptide of the Alzheimer's disease amyloid beta-protein at position Ala21. The amide I IR spectrum of 4 in D2O suggests that the azidopeptide thus modified forms in-register beta-sheets in aggregates as observed for normal Abeta(16-22). The azido peak frequency of 4 in aggregates is almost identical to that in DMSO, indicating that the azido group is not exposed to water but to the hydrophobic environment. We believe that beta-azidoalanine will be used as an effective IR probe for providing site-specific information about the local electrostatic environments of proteins.     

Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy

We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.     

Rotational relaxation in simple chain models

The rotational dynamics of chemically similar systems based on freely jointed and freely rotating chains are studied. The second Legendre polynomial of vectors along chain backbones is used to investigate the rotational dynamics at different length scales. In a previous study, it was demonstrated that the additional bond-angle constraint in the freely rotating case noticeably perturbs the character of the translational relaxation away from that of the freely jointed system. Here, it is shown that differences are also apparent in the two systems' rotational dynamics. The relaxation of the end-to-end vector is found to display a long time, single-exponential tail and a stretched exponential region at intermediate times. The stretching exponents beta are found to be 0.75+/-0.02 for the freely jointed case and 0.68+/-0.02 for the freely rotating case. For both system types, time-packing-fraction superposition is seen to hold on the end-to-end length scale. In addition, for both systems, the rotational relaxation times are shown to be proportional to the translational relaxation times, demonstrating that the Debye-Stokes-Einstein law holds. The second Legendre polynomial of the bond vector is used to probe relaxation behavior at short length scales. For the freely rotating case, the end-to-end relaxation times scale differently than the bond relaxation times, implying that the behavior is non-Stokes-Einstein, and that time-packing-fraction superposition does not hold across length scales for this system. For the freely jointed case, end-to-end relaxation times do scale with bond relaxation times, and both Stokes-Einstein and time-packing-fraction-across-length-scales superposition are obeyed.     

Physical polymerization and liquid crystallization of RNA oligomers

Ultrashort complementary RNA oligomers, as short as six base pairs in length, are found to exhibit chiral nematic and columnar liquid crystal phases in aqueous solution, through end-to-end adhesion into physically bound, but chemically segmented, polymers. Geometrical constraints indicate that the phosphate helix is continuous along the aggregated chain. The end-to-end adhesion is due to a base-staking type interaction, whose energy and temperature dependence are determined.     

Investigation of coherence transfer between “CH3” and “CH2” groups in ethanol with time-resolved multiplex CARS technique

The coherence transfer between stretching vibration modes of C–H bonds in the ethanol is detected by time-resolved multiplex CARS technique and it occurs via “through-bond transfer” pathway. The time scale and velocity of coherence transfer are estimated at 90 fs and 1670 m/s. Moreover, coherence transfer process requires vibrational modes of acceptor and donor are different.     

Elastic Behavior of Polymer Chains

The elastic behavior of the polymer chain was investigated in a three-dimensional off-lattice model. We sample more than 109 conformations of each kind of polymer chain by using a Monte Carlo algorithm, then analyze them with the non-Gaussian theory of rubberlike elasticity, and end with a statistical study. Through observing the effect of the chain flexibility and the stretching ratio on the mean-square end-to-end distance, the average energy, the average Helmholtz free energy, the elastic force, the contribution of energy to the elastic force, and the entropy contribution to elastic force of the polymer chain, we find that a rigid polymer chain is much easier to stretch than a flexible polymer chain. Also, a rigid polymer chain will become difficult to stretch only at a quite high stretching ratio because of the effect of the entropy contribution. These results of our simulation calculation may explain some of the macroscopic phenomena of polymer and biomacromolecular elasticity.