Vibrational Properties of (8,8) and (10,10) SWCNTs before and after Albumin Fragment Adsorption: A Molecular Dynamics Study

Abstract

Single-walled carbon nanotubes (SWNTs) have received great attention for their mechanical, electronic properties, and possible interesting technological applications. Raman spectroscopy has proven to be a sensitive tool for studying the vibrational properties of carbon nanotubes. The frequency of the radial breathing mode (RBM) in the region of 100-350 cm -1 is found to be inversely proportional to the diameter of the nanotube. Using Molecular Mechanics (MM) and Molecular Dynamics (MD) methods conformational and vibrational properties of pure armchair SWCNTs having different diameters and the (10,10) NT after adsorption of an albumin fragment are studied. The distances between carbon atoms in the central part of the nanotube cavity change during MD run at constant temperature (T = 300 K), and the frequencies of this periodic motion are calculated. The conformational and vibrational properties of armchair (10,10) and (8,8) SWCNT, having the diameter equal to 13.56 and 10.85 Å respectively, are here reported. The distances between carbon atoms from opposite sites in the central cavity of the nanotube are calculated during MD runs. Interestingly, for the (10,10) SWCNT the frequency of Raman vibrational mode E 2g around 17 cm -1 is correctly calculated. The frequency of motion due to this motion increases with a decreasing curvature of the armchair CNT. After the adsorption process of an albumin fragment on the (10,10) NT, lower frequencies of motion and lower intensities are calculated. This theoretical work can useful to study possible periodic motion in pure nanomaterials or when they interact with protein fragments, water, or molecules.

Different Conformational Properties and Frequencies of Periodic Motion in the β‐ and γ‐Cyclodextrin

“…This theoretical study is based on MM and MD methods adopting the same simulation protocol proposed in previous work. [20][21][22] The hydrated structure of 𝛽-CD and 𝛾-CD were previously studied. [22] The aim of this work is to study possible periodic motion of 𝛽-CD compared to 𝛾-CD macrocycle [20] after energy minimization, MD run at constant temperature (300 K) lasting 200 ps and, final geometry optimization in vacuo, mimicking an apolar solvent.…”

“…Using a simulation protocol proposed in previous work, [20,21] starting from these optimized geometries, two MD runs lasting 200 ps were carried out, and the distances between two opposite glycosidic oxygens during the MD run and its Fourier transform are calculated both for the 𝛽and 𝛾-CD. All MD simulations are performed at temperature T = 300 K controlled through the Berendsen thermostat.…”

“…[16] In the past 20 years, molecular mechanics (MM) and molecular dynamics (MD) simulations have demonstrated to be a powerful tool for studying at atomistic level the CDs conformational properties, inclusion complexes, aggregates, and drug release process. [13,14,[17][18][19] Using a simulation protocol proposed in previous work, [20][21][22] possible periodic motions in 𝛽-CD are investigated during an MD run and compared with those in 𝛾-CD [20] considering glycosidic oxygens in the macrocycle, forming a flat plane in the former case, and a curved arrangement in the latter one. The results of the present study will be discussed in Section 2.…”