Simulations of the Temperature Dependence of Amide I Vibration

Aquaphotomics investigation of the state of water in oral liquid formulation of traditional Chinese medicine and its dynamics during temperature perturbation

Three types of bound water with different hydrogen bonding strengths were identified and elucidated by aquaphotomics.

Double Hydrogen Bonding Dimerization Propensity of Aqueous Hydroxy Acids Investigated Using Vibrational Optical Activity

Lactic and malic acids are key substances in a number of biochemical processes in living cells and are also utilized in industry. Vibrational spectroscopy represents an efficient and sensitive way to study their structure and interactions. Since water is the natural environment, proper understanding of their molecular dynamics in aqueous solutions is of critical importance. To this end, we employed Raman spectroscopy and Raman optical activity (ROA) to study the conformation of l-lactic and l-malic acids in water (while varying pH, temperature, and concentration), with special emphasis on their double hydrogen bonding dimerization propensity. Raman and ROA experimental data were supported by extensive theoretical calculations of the vibrational properties and by additional experiments (IR absorption, vibrational circular dichroism, and NMR). Conformational behavior of the acids in water was described by molecular dynamics simulations. Reliability of the results was verified by calculating the vibrational properties of populated conformers and by comparing thus obtained spectral features with the experimental data. Calculations estimated the incidence of H-bonded dimers in water to be low in lactic acid and comparable to monomers in malic acid. The "hybrid" approach presented here reveals limitations of relying on the experimental spectra alone to study dimer formation.

Thermoplasmonic Study of a Triple Band Optical Nanoantenna Strongly Coupled to Mid IR Molecular Mode

We report the first thermal study of a triple band plasmonic nanoantenna strongly coupled to a molecular mode at mid IR wavelength (MW IR). The hybrid plasmonic structure supports three spatially and spectrally variant resonances of which two are magnetic and one is dipolar in nature. A hybridized mode is excited by coupling the structure’s plasmonic mode with the vibrational mode of PMMA at 5.79 μm. Qualitative agreement between the spectral changes in simulation and experiment clearly indicates that resistive heating is the dominant mechanisms behind the intensity changes of the dipolar and magnetic peaks. The study also unveils the thermal insensitivity of the coupled mode intensity as the temperature is increased. We propose a mechanism to reduce the relative intensity change of the coupled mode at elevated temperature by mode detuning and surface current engineering and demonstrate less than 9% intensity variation. Later, we perform a temperature cycling test and investigate into the degradation of the Au-PMMA composite device. The failure condition is identified to be primarily associated with the surface chemistry of the material interface rather than the deformation of the nanopatterns. The study reveals the robustness of the strongly coupled hybridized mode even under multiple cycling.

Calculation of Raman parameters of real-size zigzag (n, 0) single-walled carbon nanotubes using finite-size models

Structural and selected Raman features of real-size single-walled carbon nanotubes (SWCNTs) were studied using finite-size pristine SWCNT models at the DFT level.

Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region

Studies of structural changes in peptides and proteins using IR spectroscopy often rely on subtle changes in the amide I' band as a function of temperature. However, these changes can be obscured by the overlap with other absorptions, namely the side-chain and terminal carboxylic groups. The former were the subject of our previous report (Anderson et al., 2014). In this paper we investigate the IR spectra of the asymmetric stretch of α-carboxylic groups for amino acids representing all major types (Gly, Ala, Val, Leu, Ser, Thr, Asp, Glu, Lys, Asn, His, Trp, Pro) as well as the C-terminal groups of three dipeptides (Gly-Gly, Gly-Ala, Ala-Gly) in D₂O at neutral pH. Experimental temperature dependent IR spectra were analyzed by fitting of both symmetric and asymmetric pseudo-Voigt functions. Qualitatively the spectra exhibit shifts to higher frequency, loss in intensity and narrowing with increased temperature, similar to that observed previously for the side-chain carboxylic groups of Asp. The observed dependence of the band parameters (frequency, intensity, width and shape) on temperature is in all cases linear: simple linear regression is therefore used to describe the spectral changes. The spectral parameters vary between individual amino acids and show systematic differences between the free amino acids and dipeptides, particularly in the absolute peak frequencies, but the temperature variations are comparable. The relative variations between the dipeptide spectral parameters are most sensitive to the C-terminal amino acid, and follow the trends observed in the free amino acid spectra. General rules for modeling the α-carboxylic IR absorption bands in peptides and proteins as the function of temperature are proposed.

The non-uniform early structural response of globular proteins to cold denaturing conditions: a case study with Yfh1

The mechanism of cold denaturation in proteins is often incompletely understood due to limitations in accessing the denatured states at extremely low temperatures. Using atomistic molecular dynamics simulations, we have compared early (nanosecond timescale) structural and solvation properties of yeast frataxin (Yfh1) at its temperature of maximum stability, 292 K (Ts), and the experimentally observed temperature of complete unfolding, 268 K (Tc). Within the simulated timescales, discernible "global" level structural loss at Tc is correlated with a distinct increase in surface hydration. However, the hydration and the unfolding events do not occur uniformly over the entire protein surface, but are sensitive to local structural propensity and hydrophobicity. Calculated infrared absorption spectra in the amide-I region of the whole protein show a distinct red shift at Tc in comparison to Ts. Domain specific calculations of IR spectra indicate that the red shift primarily arises from the beta strands. This is commensurate with a marked increase in solvent accessible surface area per residue for the beta-sheets at Tc. Detailed analyses of structure and dynamics of hydration water around the hydrophobic residues of the beta-sheets show a more bulk water like behavior at Tc due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.

Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations

New sets of parameters (maps) for calculating amide I vibrational spectra for proteins through a vibrational exciton model are proposed. The maps are calculated as a function of electric field and van der Waals forces on the atoms of peptide bonds, taking into account the full interaction between peptide bonds and the surrounding environment. The maps are designed to be employed using data obtained from standard all-atom molecular simulations without any additional constraints on the system. Six proteins representing a wide range of sizes and secondary structure complexity were chosen as a test set. Spectra calculated for these proteins reproduce experimental data both qualitatively and quantitatively. The proposed maps lead to spectra that capture the weak second peak observed in proteins containing β-sheets, allowing for clear distinction between α-helical and β-sheet proteins. While the parametrization is specific to the CHARMM force field, the methodology presented can be readily applied to any empirical force field.