[show abstract][hide abstract] ABSTRACT: The linear and two-dimensional infrared (2DIR) responses of the amide I vibrational mode in liquid formamide are investigated experimentally and theoretically using molecular dynamics simulations. The recent method based on the numerical integration of the Schrödinger equation is employed to calculate the 2DIR spectra. Special attention is devoted to the interplay of the structural dynamics and the excitonic nature of the amide I modes in determining the optical response of the studied system. In particular, combining experimental data, simulated spectra and analysis of the simulated atomic trajectory in terms of a transition dipole coupling model, we provide a convincing explanation of the peculiar features of the 2DIR spectra, which show a substantial increase of the antidiagonal bandwidth with increasing frequency. We point out that, at variance with liquid water, the 2DIR spectral profile of formamide is determined more by the excitonic nature of the vibrational states than by the fast structural dynamics responsible for the frequency fluctuations.
Physical Chemistry Chemical Physics 06/2011; 13(23):11351-8. · 3.83 Impact Factor
[show abstract][hide abstract] ABSTRACT: The association of peptides to phospholipid membranes through the insertion of an anchoring hydrocarbon tail is common to some viruses and to several anticancer drugs. We investigate the association of an anchor dipeptide, N-myristoylated methyl glycine (MrG), to phospholipid membrane fragments made of 1-palmitoyl-2-linoleyl phosphatidylcholine (PLPC). Here we report on the experimental findings of two-dimensional infrared spectroscopy of an MrG backbone in the 6 μm wavelength region. The experimental outcomes are supported by ab initio calculations and by a molecular dynamics simulation accomplished with the replica exchange method. We find that the guest molecule has a preferential unfolded conformation, with dihedral angles Φ = -90 ± 20° and Ψ = -180 ± 20°, while the average orientational distribution of the amide I transition dipole moments with respect to the neighbor PLPC carbonyls is peaked at angles in the range 21-33°. The depth of penetration of MrG inside the membrane corresponds rather well to the one estimated in our previous paper [J. Phys. Chem. B, 2009, 113, 16246], where we found that the backbone moieties of MrG are localized slightly above the carbonyl groups of PLPC. According to the simulation results, the anchor tail is completely inserted in the hydrophobic region of the bilayer, with a largely prevalent extended conformation and a preferential alignment along the average direction of the PLPC hydrocarbon tails.
The Journal of Physical Chemistry B 03/2011; 115(18):5294-303. · 3.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: Being largely driven by electrostatic interactions, hydration compensates hydrophobic repulsion and, thus, contributes decisively in structural expressions of molecules in a phospholipid membrane environment. Here, we explore the nature of the aqueous state associated with carbonyl moieties of a phospholipid bilayer. The task is of an obvious difficulty, since water clustering at a membrane interface implies the presence of various aqueous states giving rise to spectral inhomogeneity. The resultant frequency overlap of the optical response from states of differing nature obscures the structural analysis. We extract the information on water next to phospholipid carbonyls by monitoring the O-D stretch perturbation upon direct infrared excitation of lipid carbonyl groups. Modelling the signal with the help of quantum computations and molecular dynamics simulation, we extract the geometry for the optimal placement of water next to carbonyl moieties, and anticipate the time scale of the water molecule displacement, leading to the disruption of the hydrogen bond, upon direct excitation of the C=O group. The picture we provide here is of general and applied value. The practical importance stems from the necessity of experimentally characterizing the hydration of polar moieties in polypeptides (of pharmacological significance) when in a phospholipid environment, a task not yet achieved.
Physical Chemistry Chemical Physics 11/2009; 11(43):9979-86. · 3.83 Impact Factor
[show abstract][hide abstract] ABSTRACT: We explore the localization of a guest N-myristoylated methyl glycine anchor dipeptide in a phospholipid environment. The dipeptide is part of a conservative sequence, which ensures proper association of a wide group of proteins in living organisms with a cellular phospholipid membrane. Using linear and two-color anharmonic infrared spectroscopy, we measure relative degrees of hydration of the amide I modes of the dipeptide and of phospholipid carbonyls. The atomic density of water in dependence of the distance from the hydrophobic center of the bilayer (a result of an independent Neutron scattering experiment) allows us to determine the relative altitudes of the peptide carbonyls with respect to those of the phospholipid ones. Considering this, and the dimensions of the dipeptide molecular frame, we anticipate the average angle between the backbone of the dipeptide and the normal to the membrane surface. The results provide a descriptive picture of the depth and geometry of partitioning of a guest N-myristoylated methyl glycine anchor dipeptide into a phospholipid membrane.
The Journal of Physical Chemistry B 11/2009; 113(50):16246-50. · 3.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: Vibrational dynamics of liquid formamide is studied in the spectral region of the amide I mode by means of linear and two-dimensional infrared spectroscopies. The two-dimensional spectrum has a complex structure to be connected to the partially excitonic nature of the vibrational states. The measurements performed on a 1:10 (12)C:(13)C formamide isotopic mixture allow separating the broadening contribution due to the inhomogeneous frequency distribution of the local oscillators from that of excitonic origin. A model based on the Kubo picture of the line broadening is used, together with the dynamic information obtained from a molecular dynamics simulation, to fit the spectra of the (12)C formamide impurity in the isotopic mixture. The relevant dynamical information, such as the amplitude of the frequency fluctuations, lifetime of the second vibrational excited state, and anharmonicity, is thus recovered. By appropriately combining the outcomes of experiments and molecular dynamics simulation, we demonstrate that motional narrowing determines the line shape of the amide I resonance to a large extent. The same analysis provides an estimate of the transition dipole moment of formamide, which results in good agreement with an ab initio calculation. The calculated frequency fluctuation correlation time is found to be comparable to the hydrogen-bond lifetime, which defines the basic structural relaxation rate of the networked liquid.
The Journal of Chemical Physics 06/2009; 130(20):204518. · 3.16 Impact Factor
[show abstract][hide abstract] ABSTRACT: We explore the two-dimensional infrared response of D(2)O and of OD impurity at the interface of phospholipid membrane fragments. The spectra of the two aqueous states are inhomogeneously broadened due to the absorption of water molecule associated with the membrane interface in different structural sites. The nonlinear spectra of the two species allow disentangling of the spectral contributions of the aqueous states of two types: where the stretching modes are under effective mixing and where the stretching modes are uncoupled. By reviewing the results of the experimental studies with the support of molecular dynamic simulation we identify the spectral signatures of the main structural motives responsible for the inhomogeneous distribution of resonances in the infrared OD stretching region. Our analysis provides a quantitative estimate of the statistical population of the different aqueous species at the polar interface of the bilayer.
The Journal of Physical Chemistry B 03/2009; 113(13):4119-24. · 3.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: We have developed a fitting algorithm able to extract spectral and dynamic properties of a three level oscillator from a two-dimensional infrared spectrum (2D-IR) detected in time resolved nonlinear experiments. Such properties go from the frequencies of the ground-to-first and first-to-second vibrational transitions (and hence anharmonicity) to the frequency-fluctuation correlation function. This last is represented through a general expression that allows one to approach the various strategies of modeling proposed in the literature. The model is based on the Kubo picture of stochastic fluctuations of the transition frequency as a result of perturbations by a fluctuating surrounding. To account for the line-shape broadening due to pump pulse spectral width in double-resonance measurements, we supply the fitting algorithm with the option to perform the convolution of the spectral signal with a Lorentzian function in the pump-frequency dimension. The algorithm is tested here on 2D-IR pump-probe spectra of a Gly-Ala dipeptide recorded at various pump-probe delay times. Speedup benchmarks have been performed on a small Beowulf cluster. The program is written in FORTRAN language for both serial and parallel architectures and is available free of charge to the interested reader.
Journal of Computational Chemistry 08/2008; 29(9):1507-16. · 3.84 Impact Factor
[show abstract][hide abstract] ABSTRACT: The inter- and intramolecular interactions of the carbonyl moieties at the polar interface of a phospholipid membrane are probed by using nonlinear femtosecond infrared spectroscopy. Two-dimensional IR correlation spectra separate homogeneous and inhomogeneous broadenings and show a distinct cross-peak pattern controlled by electrostatic interactions. The inter- and intramolecular electrostatic interactions determine the inhomogeneous character of the optical response. Using molecular dynamics simulation and the nonlinear exciton equations approach, we extract from the spectra short-range structural correlations between carbonyls at the interface.
Proceedings of the National Academy of Sciences 10/2007; 104(39):15323-7. · 9.74 Impact Factor
[show abstract][hide abstract] ABSTRACT: The physics of confined water has stimulated extensive research in recent years, in particular, regarding the role of hydrogen bonding as a significant factor in the observed dynamics. In this work, two-dimensional infrared spectroscopy was employed to investigate the response of the OH moiety of water in phospholipid membrane samples. The results show strong evidence for three distinct hydrogen bonding motifs (H2O with zero, one, or both OH moieties hydrogen bonded), whose relative proportions at the membrane interface are estimated.
[show abstract][hide abstract] ABSTRACT: Femtosecond infrared (IR) two-color pump-probe experiments were used to investigate the nonlinear response of the D2O stretching vibration in weakly hydrated dimyristoyl-phosphatidylcholine (DMPC) membrane fragments. The vibrational lifetime is comparable to or longer than that in bulk D2O and is frequency dependent, as it decreases with increasing probe frequency. Also, the lifetime increases when the water content of the sample is lowered. The measured lifetimes range between 903 and 390 fs. A long-lived spectral feature grows in following the excitation and is attributed to photoinduced D-bond breaking. The photoproduct spectrum differs from the steady state difference Fourier transform infrared (FTIR) spectrum, showing that the full thermalization of the excitation energy happens on a much longer time scale than the time interval considered (12 ps). Further evidence of the inhomogeneous character of the water residing in the polar region of the bilayer comes from the spectral anisotropy. The water molecules absorbing on the low frequency side of the absorption band show no decay at all of the anisotropy, while an ultrafast partial decay appears when the high frequency side of the spectrum is probed. The overall behavior differs remarkably from that observed with similar experiments in bulk water and in water segregated in inverse micelles. In weakly hydrated phospholipid membranes, water molecules are present mostly as isolated species, prevalently involved in strong, rigid, and persistent hydrogen bonds with the polar groups of the bilayer molecules. This specific character appears to have a direct effect on the structural stability and thermal properties of the membrane.
The Journal of Physical Chemistry B 03/2007; 111(6):1377-83. · 3.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: We combine two-color ultrafast infrared spectroscopy and molecular dynamics simulation to investigate the hydration of carbonyl moieties in a dimyristoyl-phosphatidylcholine bilayer. Excitation with femtosecond infrared pulses of the OD stretching mode of heavy water produces a time dependent change of the absorption band of the phospholipid carbonyl groups. This intermolecular vibrational coupling affects the entire C=O band, thus suggesting that the optical inhomogeneity of the infrared response of carbonyl in phospholipid membranes cannot be attributed to the variance in hydration. Both the experimental and the theoretical results demonstrate that sn-1 carbonyl has a higher propensity to form hydrogen bonds with water in comparison to sn-2. The time-resolved experiment allows following the evolution of the system from a nonequilibrium localization of energy in the OD stretching mode to a thermally equilibrated condition and provides the characteristic time constants of the process. The approach opens a new opportunity for investigation of intermolecular structural relations in complex systems, like membranes, polymers, proteins, and glasses.
Journal of the American Chemical Society 08/2006; 128(29):9466-71. · 10.68 Impact Factor
[show abstract][hide abstract] ABSTRACT: Two-dimensional infrared (2D-IR) spectroscopy has been used to probe structure and dynamics in binary sphingomyelin/phospholipid liposomes. The liposomes consist of 1-palmitoyl-2-linoleyl phosphatidylcholine (PLPC) and sphingomyelin (SPM) in the ratio 1:1. The diagonal part of the 2D-IR spectra shows two bands which are due to amide I of SPM and to the carbonyl moieties of PLPC. The diagonal components of the 2D-IR spectra reveal a difference in the molecular dynamics. The presence of off-diagonal cross-peaks indicates the occurrence of intermolecular structural correlation. The intensity of the cross-peaks is consistent with segregation of two lipid components into PLPC and SPM molecular domains.
The Journal of Physical Chemistry B 03/2006; 110(4):1499-501. · 3.61 Impact Factor