Two-dimensional infrared spectroscopy of neat ice Ih

The OH stretch line shape of ice Ih exhibits distinct peaks, the assignment of which remains controversial. We address this longstanding question using two dimensional infrared (2D IR) spectroscopy of the OH stretch of H(2)O and the OD stretch of D(2)O of ice Ih at T = 80 K. The isotropic response is dominated by a 2D line shape component which does not depend on the pump pulse frequency. The decay time of the component that does depend on the pump frequency is calculated using singular value decomposition (bi-exponential decay H(2)O: 30 fs, 490 fs; D(2)O: 40 fs, 690 fs). The anisotropic contribution exhibits on-diagonal peaks, which decay on a very fast timescale (H(2)O: 85 fs; D(2)O: 65 fs), with no corresponding anisotropic cross-peaks. Both isotropic and anisotropic results indicate that randomization of excited dipoles occurs with a very rapid rate, just like in neat liquid water. We conclude that the underlying mechanism relates to the complex interplay between exciton migration and exciton-phonon coupling.     

Quantum effects in ice Ih

Quantum and classical simulations are carried out on ice Ih over a range of temperatures utilizing the TIP4P water model. The rigid-body centroid molecular dynamics method employed allows for the investigation of equilibrium and dynamical properties of the quantum system. The impact of quantization on the local structure, as measured by the radial and spatial distribution functions, as well as the energy is presented. The effects of quantization on the lattice vibrations, associated with the molecular translations and librations, are also reported. Comparison of quantum and classical simulation results indicates that shifts in the average potential energy are equivalent to rising the temperature about 80 K and are therefore non-negligible. The energy shifts due to quantization and the quantum mechanical uncertainties observed in ice are smaller than the values previously reported for liquid water. Additionally, we carry out a comparative study of melting in our classical and quantum simulations and show that there are significant differences between classical and quantum ice.     

Two-dimensional infrared spectroscopy of antiparallel beta-sheet secondary structure

We investigate the sensitivity of femtosecond Fourier transform two-dimensional infrared spectroscopy to protein secondary structure with a study of antiparallel beta-sheets. The results show that 2D IR spectroscopy is more sensitive to structural differences between proteins than traditional infrared spectroscopy, providing an observable that allows comparison to quantitative models of protein vibrational spectroscopy. 2D IR correlation spectra of the amide I region of poly-l-lysine, concanavalin A, ribonuclease A, and lysozyme show cross-peaks between the IR-active transitions that are characteristic of amide I couplings for polypeptides in antiparallel hydrogen-bonding registry. For poly-l-lysine, the 2D IR spectrum contains the eight-peak structure expected for two dominant vibrations of an extended, ordered antiparallel beta-sheet. In the proteins with antiparallel beta-sheets, interference effects between the diagonal and cross-peaks arising from the sheets, combined with diagonally elongated resonances from additional amide transitions, lead to a characteristic "Z"-shaped pattern for the amide I region in the 2D IR spectrum. We discuss in detail how the number of strands in the sheet, the local configurational disorder in the sheet, the delocalization of the vibrational excitation, and the angle between transition dipole moments affect the position, splitting, amplitude, and line shape of the cross-peaks and diagonal peaks.     

Molecular-dynamics studies of surface of ice Ih

We performed molecular dynamics calculations of surface of ice Ih in order to investigate formation mechanism of melting layer on the surface. The results showed that the vibrational amplitude of the atoms in the surface layer greatly depends on the crystal orientation, whereas that in the ice bulk is isotropic. The anisotropy of the vibration is due to a dangling motion of the free O-H bonds exist at the surface layer. The dangling motion enhances the rotational motion of the water molecules. The vibrational density of state showed a coupling between the rotational vibration and the lattice vibration of the water molecules in the surface layer. The coupling of the vibrations causes a distortion of ice lattice. Through the hydrogen-bonding network, the distortion transmits to the interior of the crystal. We conclude that the dangling motion of the free O-H bonds exist at the surface layer is one of the dominant factors governing the surface melting of ice crystal.     

Two-dimensional infrared spectroscopy of azido-nicotinamide adenine dinucleotide in water

Mid-IR active analogs of enzyme cofactors have the potential to be important spectroscopic reporters of enzyme active site dynamics. Azido-nicotinamide adenine dinucleotide (NAD(+)), which has been recently synthesized in our laboratory, is a mid-IR active analog of NAD(+), a ubiquitous redox cofactor in biology. In this study, we measure the frequency-frequency time correlation function for the antisymmetric stretching vibration of the azido group of azido-NAD(+) in water. Our results are consistent with previous studies of pseudohalides in water. We conclude that azido-NAD(+) is sensitive to local environmental fluctuations, which, in water, are dominated by hydrogen-bond dynamics of the water molecules around the probe. Our results demonstrate the potential of azido-NAD(+) as a vibrational probe and illustrate the potential of substituted NAD(+)-analogs as reporters of local structural dynamics that could be used for studies of protein dynamics in NAD-dependent enzymes.     

Transient absorption of vibrationally excited ice Ih

The ultrafast dynamics of HDO:D2O ice Ih at 180 K is studied by midinfrared ultrafast pump-probe spectroscopy. The vibrational relaxation of HDO:D2O ice is observed to proceed via an intermediate state, which has a blueshifted absorption spectrum. Polarization resolved measurements reveal that the intermediate state is part of the intramolecular relaxation pathway of the HDO molecule. In addition, slow dynamics on a time scale of the order of 10-100 ps is observed, related to thermally induced collective reorganizations of the ice lattice. The transient absorption line shape is analyzed within a Lippincott-Schroeder model for the OH-stretch potential. This analysis identifies the main mechanism behind the strong spectral broadening of the v(OH)=1-->2 transition.     

Two-dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution

The linear-infrared and two-dimensional infrared (2D IR) spectra in the amide-I' region of the alanine dipeptide and its (13)C isotopomers in aqueous solution (D(2)O) are reported. The two amide-I' IR transitions have been assigned unambiguously by using (13)C isotopic substitution of the carbonyl group; the amide unit at the acetyl end shows a lower transition frequency in the unlabeled species. The ratio of their transition dipole strengths remains almost unchanged upon (13)C substitution, indicating the absence of intensity transfer between two vibrators. The 2D IR cross peaks directly associated with intramode coupling in this case show a small off-diagonal anharmonicity (0.2 +/- 0.2 cm(-1)), leading to a small coupling constant (1.5 +/- 0.5 cm(-1)). The coupling and the 2D IR spectra in two different polarizations (zzzz and zxxz) are as expected for a polyproline-II (PP(II))-like conformation for dialanine, with the backbone dihedral angles (phi, psi) determined to be in the range of (-70 degrees +/- 25 degrees, +120 degrees +/- 25 degrees). Ab initio DFT calculations and normal mode decoupling analysis in the Ramachandran subspace in the neighborhood of PP(II) conformation confirm the presence of a region where the coupling is vanishingly small and support these experimental findings. The relationship between the coupling and off-diagonal anharmonicity is consolidated by examining the distribution of the latter from an ensemble averaged Hamiltonian incorporating uncorrelated diagonal frequency distributions and a small coupling (<2 cm(-1)); it is found that the most probable value for the off-diagonal anharmonicity falls into the range of experimental observations. Further, incorporating DFT results, the simulated linear-IR and 2D IR can reproduce the essential features of the measurements, including the transition frequency positions and apparent peak intensities. All the experimental results and simulations are consistent with a PP(II)-like conformation for the alanine dipeptide in aqueous solution, in which two amide-I' modes are highly localized and whose frequency distributions are uncorrelated.     

Simulations of proton order and disorder in ice Ih

Computer simulations of ice Ih with different proton orientations are presented. Simulations of proton disordered ice are carried out using a Monte Carlo method which samples over proton degree of freedom, allowing for the calculation of the dielectric constant and for the examination of the degree of proton disorder. Simulations are also presented for two proton ordered structures of ice Ih, the ferroelectric Cmc2(1) structure or ice XI and the antiferroelectric Pna2(1) structure. These simulations indicate that a transition to a proton ordered phase occurs at low temperatures (below 80 K). The symmetry of the ordered phase is found to be dependent on the water potential. The stability of the two proton ordered structures is due to a balance of short-ranged interactions which tend to stabilize the Pna2(1) structure and longer-range interactions which stabilize the Cmc2(1) structure.     

Two-dimensional Fourier-transform infrared correlation spectroscopy study of the high-pressure tuning of proteins

2D FTIR gives new information about the pressure effect on the structure and dynamics of macromolecular systems. Application of this analysis to proteins can unravel the relation of conformational changes and H/D exchange processes. For lipoxygenase, a pressure of 6.5 kbar induces irreversible conformational changes resulting in an increased exposure of interior parts of the protein to the solvent. At the transition pressure the spectral changes indicate a correlation between conformational changes and H/D exchange. Below and above this pressure, the effects of H/D exchange on the spectral changes are predominant.     

Isotope effects in ice Ih: a path-integral simulation

Ice Ih has been studied by path-integral molecular dynamics simulations, using the effective q-TIP4P/F potential model for flexible water. This has allowed us to analyze finite-temperature quantum effects in this solid phase from 25 to 300 K at ambient pressure. Among these effects we find a negative thermal expansion of ice at low temperatures, which does not appear in classical molecular dynamics simulations. The compressibility derived from volume fluctuations gives results in line with experimental data. We have analyzed isotope effects in ice Ih by considering normal, heavy, and tritiated water. In particular, we studied the effect of changing the isotopic mass of hydrogen on the kinetic energy and atomic delocalization in the crystal as well as on structural properties such as interatomic distances and molar volume. For D(2)O ice Ih at 100 K we obtained a decrease in molar volume and intramolecular O-H distance of 0.6% and 0.4%, respectively, as compared to H(2)O ice.     

A van der Waals density functional study of ice Ih

Density functional theory with the van der Waals density functional (vdW-DF) is used to calculate equilibrium crystal structure, binding energy, and bulk modulus of ice Ih. It is found that although it overestimates the equilibrium volume, vdW-DF predicts accurate binding energy of ice Ih, as compared with high level quantum chemistry calculations and experiment. Inclusion of the nonlocal correlation, i.e., van der Waals interaction, leads to an overall improvement over the standard generalized gradient approximation in describing water ice.     

Melting temperature of ice Ih calculated from coexisting solid-liquid phases

We carried out molecular-dynamics simulations by using the two-phase coexistence method with the constant pressure, particle number, and enthalpy ensemble to compute the melting temperature of proton-disordered hexagonal ice I(h) at 1-bar pressure. Four models of water were considered, including the widely used TIP4P [W. L. Jorgensen, J. Chandrasekha, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys.79, 926 (1983)] and TIP5P [M. W. Mahoney and W. L. Jorgensen J. Chem. Phys.112, 8910 (2000)] models, as well as recently improved TIP4P and TIP5P models for use with Ewald techniques-the TIP4P-Ew [W. Horn, W. C. Swope, J. W. Pitera, J. C. Madura, T. J. Dick, G. L. Hura, and T. Head-Gordon, J. Chem. Phys.120, 9665 (2004)] and TIP5P-Ew [S. W. Rick, J. Chem. Phys.120, 6085 (2004)] models. The calculated melting temperature at 1 bar is T(m) = 229 +/- 1 K for the TIP4P and T(m) = 272.0 +/- 0.6 K for the TIP5P ice I(h), both are consistent with previous simulations based on free-energy methods. For the TIP4P-Ew and TIP5P-Ew models, the calculated melting temperature is T(m) = 257.0 +/- 1.1 K and T(m) = 253.9 +/- 1.1 K, respectively.     

Two-dimensional infrared (2D IR) spectroscopy. A new tool for interpreting infrared spectra

Two-dimensional infrared (2D IR) spectroscopy is used to study atactic polystyrene. 2D IR is a technique based on time-resolved detection of IR signals in response to an external perturbation, such as mechanical strain. Since different chemical functional groups respond to the applied perturbation at unique and often different rates, characteristic time-dependent variations of the IR-band intensities are observed. Correlation analysis of the dynamic variation of the IR signals yields a new spectrum defined by two independent wave numbers. Peaks located on a 2D IR spectral plane imply interactions and connectivities among chemical functional groups. By spreading convoluted IR bands over two dimensions, the spectral resolution is also greatly enhanced.     

Two-dimensional correlation infrared spectroscopy studies on the thermal-induced mesophase of 4-nitrobenzohydrazide derivative

Two-dimensional (2D) correlation infrared (IR) spectroscopy has been applied to explore the effect of hydrogen bondings (HBs) on the structure of mesophase in the dissymmetrical 4-nitrobenzohydrazide derivative, N-(4-cetyloxybenzoyl)-N′-(4′-nitrobenzoyl) hydrazine (C16-NO₂). The strength and species of HBs as well as the heat-induced structural variations in mesophase have been investigated. It has been found from 2D correlation IR spectroscopy that the sequential order of changes in the different functionalities in the course of liquid crystalline formation is that, firstly, the alkyl chain changes from the significant population of the trans conformation to the significant population of gauche conformation; then, the intermolecular HB between CO and NH groups is weakened, some even being broken, and consequently, the intermolecular distance is enlarged; finally, the skeleton of phenyl ring has enough space to change their conformation to weaken the π–π stacking interaction. In addition, besides a few free and some medium bonded NH and CO groups, strongly bonded NH and CO groups still predominantly exist in the mesophase.     

Direct dynamics study of ultrafast vibrational energy relaxation in ice Ih

Car-Parrinello molecular dynamics (CPMD) and a previously developed wave packet model are used to study ultrafast relaxation in water clusters. Water clusters of 15 water molecules are used to represent ice Ih. The relaxation is studied by exciting a symmetric or an asymmetric stretch mode of the central water molecule. The CPMD results suggest that relaxation occurs within 100 fs. This is in agreement with experimental work by Woutersen and Bakker and the earlier wave packet calculations. The CPMD results further indicate that the excitation energy is transferred both intramolecularly and intermolecularly on roughly the same time scale. The intramolecular energy transfer occurs predominantly between the symmetric and asymmetric modes while the bend mode is largely left unexcited on the short time scale studied here.     

Adsorption of acetaldehyde on ice as seen from computer simulation and infrared spectroscopy measurements

Detailed investigation of the adsorption of acetaldehyde on I(h) ice is performed under tropospheric conditions by means of grand canonical Monte Carlo computer simulations and compared to infrared spectroscopy measurements. The experimental and simulation results are in a clear accordance with each other. The simulations indicate that the adsorption process follows Langmuir behavior in the entire pressure range of the vapor phase of acetaldehyde. Further, it was found that the adsorption layer is strictly monomolecular, and the adsorbed acetaldehyde molecules are bound to the ice surface by only one hydrogen bond, typically formed with the dangling H atoms at the ice surface, in agreement with the experimental results. Besides this hydrogen bonding, at high surface coverages dipolar attraction between neighboring acetaldehyde molecules also contributes considerably to the energy gain of the adsorption. The acetaldehyde molecules adopt strongly tilted orientations relative to the ice surface, the tilt angle being scattered between 50° and 90° (i.e., perpendicular orientation). The range of the preferred tilt angles narrows, and the preference for perpendicular orientation becomes stronger upon saturation of the adsorption layer. The CH(3) group of the acetaldehyde molecules points as straight away from the ice surface within the constraint imposed by the tilt angle adopted by the molecule as possible. The heat of adsorption at infinitely low coverage is found to be -36 ± 2 kJ/mol from the infrared spectroscopy measurement, which is in excellent agreement with the computer simulation value of -34.1 kJ/mol.     

Two-dimensional infrared spectroscopy study on phase transition and structural variations of a hydrogen-bonded liquid crystal

Infrared (IR) spectra have been measured for a liquid crystal (LC) consisting of one trans-butene diacid (BD) molecule as a proton donor and two 4-(2,3,4-tridecyloxybenzoyloxy)-4'-stilbazoles (DBS) molecules as a proton acceptor (DBS:BD:DBS) linked together with each other by inter-molecular hydrogen bonds over a temperature range from 20 to 120 degrees C to explore its phase transition and heat-induced structural variations. The temperature-dependent IR spectra have shown that the inter-molecular hydrogen bonds are stable in the liquid crystalline phase but become slightly decoupled with temperature increasing. Two kinds of two-dimensional (2D) correlation spectroscopy, variable-variable (VV) and sample-sample (SS) 2D spectroscopy, have been employed to analyze the observed temperature-dependent spectral variations more efficiently. The SS 2D correlation analysis in the spectral range of 2700-1800 cm(-1) has demonstrated that a change in hydrogen bonds in the LC starts from 40 degrees C, which is not clarified by differential scanning calorimetry (DSC) and conventional IR and Raman spectroscopic analyses. On the other hand, the phase transition of LC revealed by SS 2D spectroscopy in the specific spectral regions of 1750-1650 and 3000-2700 cm(-1) is in a good agreement with that revealed by DSC for the heating process. The VV 2D correlation spectroscopy analysis has provided information about the structural variations of inter-molecular hydrogen bonds. The different species of hydrogen-bonded and free -COOH and -COO- groups in the LC have been clarified by the VV 2D correlation analysis. It has also elucidated the specific order of the temperature-induced structural changes in the intra- and inter-molecular hydrogen bonds concerning with the -COOH and/or -COO- groups in the LC.     

Lattice match in density functional calculations: ice Ih vs. beta-AgI

Density functional optimizations of the crystal parameters of ice Ih and beta-AgI imply lattice mismatches of 4.2 to 7.9%, in a survey of eight common, approximate (non-hybrid) functionals, too large to allow a meaningful contribution from Density Functional Theory to the discussion of the significance of lattice match in ice nucleation.     

Two-dimensional ultraviolet spectroscopy of proteins

Two-dimensional ultraviolet (2DUV) spectroscopy is a novel technology for probing molecular structure. We have developed a generalized quantum mechanics/molecular mechanics (QM/MM) approach to simulate the electronic transitions of protein backbones and aromatic amino acids in aqueous solution. These transitions, which occur in the ultraviolet (UV) region, provide a sensitive probe of molecular structure. The features of 2DUV spectra are accurately characterized and enable us to trace small variations in the structure and dynamics as well as evolution propensity with high accuracy. Various structures and dynamic phenomena are investigated to construct a systematic framework for 2DUV simulation mechanisms, so as to explore further applications of this technique. In this feature article, we summarize the theory and applications of 2DUV spectroscopy we have engaged in recently, present the important roles of 2DUV spectroscopy, and outline directions for future development. We hope this article can offer a platform for more scientists in different research fields to gain a clear overview of 2DUVand further attract more people to explore this promising field.