scholarly journals Intermolecular vibrational modes of crystalline Poly-(r)-3-Hydroxybutyrate observed at Terahertz frequencies investigated by molecular dynamics

2020 ◽  
Vol 26 (2) ◽  
pp. 21-31
Author(s):  
Md Khorshed Alam ◽  
Md Saif Ishtiaque ◽  
Md Imran Hossain ◽  
Hiromitsu Takaba
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Absorption Spectra ◽  
Md Simulation ◽  
Vibrational Transition ◽  
Vibrational Modes ◽  
Temperature Dependent ◽  
Terahertz Frequencies ◽  
Thz Absorption ◽  
Oriented Parallel

Terahertz (THz) absorption spectra of poly 3-hydroxyalkanoates (PHB) for different conformations were investigated using molecular dynamics (MD) method. Temperature-dependent THz absorption spectra of PHB were measured over a temperature range of 10 K to 200 K. Peaks around (2.4-2.6THz) and (3.1-3.2THz) were observed due to vibrational transition of PHB, 1stpeaks are polarized perpendicular to c(┴)axis (along a, b axis) and next peaks are oriented parallel to the c(//) axis. The peak around (2.4-2.6THz) was assigned due to vibrational transition of PHB and C-H…O=C hydrogen bonds are oriented perpendicular to the c(┴) axis. We have also investigated orientation of the intermolecular hydrogen bonds by MD simulation and confirmed that it was mainly along the b axis of PHB. THz absorption spectra shifted to the lower frequencies and noticed widening of the absorption peaks that visualized from characteristics of peaks within creasing temperature, which is well reproduce of experimental observation. Bangladesh Journal of Physics, 26(2), 21-31, December 2019

scholarly journals Temperature dependent poly(L-lactide) crystallization investigated by Fourier transform terahertz spectroscopy

2021 ◽  
Author(s):  
Seiichiro Ariyoshi ◽  
Satoshi Ohnishi ◽  
Hikaru Mikami ◽  
Hideto Tsuji ◽  
Yuki Arakawa ◽  
...  
Keyword(s):  
Fourier Transform ◽  
Absorption Spectra ◽  
Terahertz Spectroscopy ◽  
Thz Spectroscopy ◽  
Frequency Range ◽  
Temperature Dependent ◽  
Thz Absorption

Poly(L-lactide) (PLLA) was investigated by Fourier transform terahertz (THz) spectroscopy over the frequency range of 1.0 – 8.5 THz. THz absorption spectra were acquired for PLLA samples isothermally crystallized at...

Influence of a Combined Low Dosage Gas Hydrate Inhibitor on Methane Hydrate Surface

2014 ◽  
Vol 1008-1009 ◽  
pp. 300-306
Author(s):  
Cui Ping Tang ◽  
Dong Liang Li ◽  
De Qing Liang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Gas Hydrate ◽  
Methane Hydrate ◽  
Md Simulation ◽  
Side Group ◽  
Large Space ◽  
Surface Molecules ◽  
Low Dosage

According to analysis of the gas hydrate cage and structure of the inhibitor and simulation of molecular dynamics, the interaction between GHI1 and hydrates was discussed. The structure analysis indicated the side group of PVP can insert into the open hydrate cage, and force the hydrate growing along the polymer chain, which results in a large space resistance and inhibits gas hydrate agglomerating. The results of MD simulation show GHI1 can damage the surface cage in hydrate lattice; the hydrogen and oxygen in GHI1 can form hydrogen bonds respectively with oxygen and hydrogen in hydrates, which makes the surface molecules of the cages unstable and distorts the cages; Synergist diethylene glycol ether increases strength and range of length of hydrogen bond.

A Theoretical Study Of The Energetics And Vibrational Spectra Of Oxygenated (100) Diamond Surfaces

1995 ◽  
Vol 416 ◽  
Author(s):  
S. Skokov ◽  
B. Weiner ◽  
M. Frenklach
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Vibrational Spectra ◽  
Theoretical Study ◽  
Local Environment ◽  
Hydroxyl Groups ◽  
Vibrational Modes ◽  
Diamond Surfaces ◽  
Molecular Dynamics Calculations

ABSTRACTStatic quantum ab initio and quantum semiempirical molecular dynamics calculations were employed to study reconstructions of (100) diamond surfaces in presence of hydrogen and oxygen. The results indicate that the energetically most favorable structures of oxygenated surfaces are those with chemisorbed hydroxyl groups. It was found that hydrogen bonds are formed among chemisorbed oxygenated species. The formation of these hydrogen bonds is shown to be an important factor in stabilization of adlayers. A number of important vibrational modes characteristic of oxygenated diamond surfaces were identified. The analysis of surface vibrational spectra demonstrates the influence of the local environment on the position of vibrational modes and can be useful for interpretation of experimental data.

Specific osteogenesis imperfecta-related Gly substitutions in type I collagen induce distinct structural, mechanical, and dynamic characteristics

2021 ◽  
Author(s):  
Haoyuan Shi ◽  
Liming Zhao ◽  
Chenxi Zhai ◽  
Jingjie Yeo
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Osteogenesis Imperfecta ◽  
Dynamic Characteristics ◽  
Type I Collagen ◽  
Type I ◽  
Vibrational Modes ◽  
Wild Type ◽  
Triple Helices ◽  
Dynamics Simulations

The stiffnesses, β-structures, hydrogen bonds, and vibrational modes of wild-type collagen triple helices are compared with osteogenesis imperfecta-related mutants using integrative structural and dynamic analysis via molecular dynamics simulations and...

scholarly journals Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Fancui Meng
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Md Simulation ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Dynamics Simulations ◽  
Simulation Time ◽  
Dynamics Method

The binding mode of sorafenib with VEGFR2 was studied using molecular docking and molecular dynamics method. The docking results show that sorafenib forms hydrogen bonds with Asp1046, Cys919, and Glu885 of VEGFR2 receptor. Molecular dynamics simulation suggests that the hydrogen bond involving Asp1046 is the most stable one, and it is almost preserved during all the MD simulation time. The hydrogen bond formed with Cys919 occurs frequently after 6 ns, while the bifurcated hydrogen bonds involving Glu885 occurs occasionally. Meantime, molecular dynamics simulations of VEGFR2 with 11 other urea-substituted aryloxy compounds have also been performed, and the results indicate that a potent VEGFR2 inhibitor should have lower interaction energy with VEGFR2 and create at least 2 hydrogen bonds with VEGFR2.

Sub-THz specific relaxation times of hydrogen bond oscillations in E.coli thioredoxin. Molecular dynamics and statistical analysis

2014 ◽  
Vol 171 ◽  
pp. 179-193 ◽  
Author(s):  
Tatiana Globus ◽  
Igor Sizov ◽  
Boris Gelmont
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Relaxation Time ◽  
Hydrogen Bonds ◽  
Spectral Resolution ◽  
Relaxation Times ◽  
Low Frequency ◽  
Thz Spectroscopy ◽  
Vibrational Modes ◽  
Covalent Bonds

Hydrogen bonds (H-bonds) in biological macromolecules are important for the molecular structure and functions. Since interactions via hydrogen bonds are weaker than covalent bonds, it can be expected that atomic movements involving H-bonds have low frequency vibrational modes. Sub-Terahertz (sub-THz) vibrational spectroscopy that combines measurements with molecular dynamics (MD) computational prediction has been demonstrated as a promising approach for biological molecule characterization. Multiple resonance absorption lines have been reported. The knowledge of relaxation times of atomic oscillations is critical for the successful application of THz spectroscopy for hydrogen bond characterization. The purpose of this work is to use atomic oscillations in the 0.35–0.7 THz range, found from molecular dynamic (MD) simulations of E.coli thioredoxin (2TRX), to study relaxation dynamics of two intra-molecular H-bonds, O⋯H–N and O⋯H–C. Two different complimentary techniques are used in this study, one is the analysis of the statistical distribution of relaxation time and dissipation factor values relevant to low frequency oscillations, and the second is the analysis of the autocorrelation function of low frequency quasi-periodic movements. By studying hydrogen bond atomic displacements, it was found that the atoms are involved in a number of collective oscillations, which are characterized by different relaxation time scales ranging from 2–3 ps to more than 150 ps. The existence of long lasting relaxation processes opens the possibility to directly observe and study H-bond vibrational modes in sub-THz absorption spectra of bio-molecules if measured with an appropriate spectral resolution. The results of measurements using a recently developed frequency domain spectroscopic sensor with a spectral resolution of 1 GHz confirm the MD analysis.

scholarly journals EXPLORING RELATIONSHIP BETWEEN LOCAL DYNAMICS AND RELAXATION PROCESSES ON THE TERAHERTZ FREQUENCIES IN POLYMERS WITH HYDROGEN BONDS

2021 ◽  
pp. 109-118
Author(s):  
Валерий Александрович Рыжов
Keyword(s):  
Glass Transition ◽  
Hydrogen Bonds ◽  
Low Frequency ◽  
Far Infrared ◽  
Polyamide 6 ◽  
Relaxation Processes ◽  
Temperature Dependent ◽  
Disordered Solids ◽  
Common Features ◽  
Terahertz Frequencies

На терагерцовых частотах либрационно-колебательное движение связано с диэлектрической релаксацией в неупорядоченных твердых телах с водородными связями. Взаимодействие между этими процессами ещё мало изучено, особенно при температурах ниже температуры стеклования, что особенно существенно для молекулярной подвижности в полимерах. Изучены полимеры с водородными связями (полиамид-6 и поливинилхлорид) при температурах от 90 до 4000К в диапазоне 0,25 - 4 ТГц с использованием дальней ИК-спектроскопии. Три общих особенностей наблюдались в спектре диэлектрических потерь, Ɛ"(ν):(а) при температурах значительно ниже стеклования (T) эти потери представлены низкочастотным крылом пика поглощения, обусловленного либрацией мономерных звеньев полимеров. (б) При 0.7 T < T < T наблюдаются дополнительные температурно-зависимые потери, которые могут быть связаны с проявлением вторичных релаксационных процессов. (с) При температурах выше T преобладающим вкладом в терагерцовые потери становятся первичные процессы α-релаксации. Полученные результаты показывают, что эволюция терагерцовых потерь с температурой вызвана изменением структуры водородных связей, которое, по-видимому, является универсальным для систем с подобными межмолекулярными взаимодействиями At terahertz frequencies, torsional-vibrational motion is associated with dielectric relaxation in disordered solids with hydrogen bonds. The interaction between these processes has not been studied much, especially at temperatures below the glass transition temperature, which is especially important for molecular mobility in polymers. Polymers with hydrogen bonds (polyamide-6 and polyvinyl chloride) were studied at temperatures from 90 to 4000 K in the range 0.25 - 4 THz using far-infrared spectroscopy. Three common features were observed in the spectrum of dielectric losses, Ɛ"(ν):(А)at temperatures well below glass transition (T), these losses are represented by the low-frequency wing of the absorption peak due to libration of the monomer units of the polymers. (B) At 0.7 T < T < T , additional temperature-dependent losses are observed, which may be associated with the manifestation of secondary relaxation processes. (C) At temperatures above T, the primary relaxation processes become the dominant contribution to terahertz losses. The results show that the evolution of terahertz losses with temperature is caused by a change in the structure of hydrogen bonds, which, apparently, is universal for systems with similar intermolecular interactions.

scholarly journals Plasticity through De-Twinning in Twinned BCC Nanowires

Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 366 ◽  
Author(s):  
G. Sainath ◽  
Sunil Goyal ◽  
A. Nagesha
Keyword(s):  
Molecular Dynamics ◽  
Shear Stress ◽  
Md Simulation ◽  
Deformation Behaviour ◽  
Compressive Loading ◽  
Md Simulations ◽  
Deformation Mechanisms ◽  
Loading Direction ◽  
Simulation Results ◽  
Oriented Parallel

The deformation behaviour of twinned FCC nanowires has been extensively investigated in recent years. However, the same is not true for their BCC counterparts. Very few studies exist concerning the deformation behaviour of twinned BCC nanowires. In view of this, molecular dynamics (MD) simulations have been performed to understand the deformation mechanisms in twinned BCC Fe nanowires. The twin boundaries (TBs) were oriented parallel to the loading direction [110] and the number of TBs is varied from one to three. MD simulation results indicate that deformation under the compressive loading of twinned BCC Fe nanowires is dominated by a unique de-twinning mechanism involving the migration of a special twin–twin junction. This de-twinning mechanism results in the complete annihilation of pre-existing TBs along with reorientation of the nanowire. Further, it has been observed that the annihilation of pre-existing TBs has occurred through two different mechanisms, one without any resolved shear stress and other with finite and small resolved shear stress. The present study enhances our understanding of de-twinning in BCC nanowires.

Molecular Dynamics Simulation Applied to the Study of Optical Absorption Spectra of Nd2O3

1991 ◽  
Vol 02 (01) ◽  
pp. 348-352
Author(s):  
SVERKER EDVARDSSON ◽  
MATS WOLF ◽  
JOSH THOMAS ◽  
ANTONIO FLORES
Keyword(s):  
Molecular Dynamics ◽  
Optical Absorption ◽  
Absorption Spectra ◽  
Md Simulation ◽  
Rare Earth Ions ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Optical Absorption Spectra ◽  
Mechanical Formalism ◽  
Quantum Mechanical Formalism

An analysis is made of the optical absorption spectra for rare-earth ions in the presence of different local crystal environments. A molecular dynamics (MD) simulation is performed to provide a large ensemble of configurations for which the quantum-mechanical formalism of Judd and Ofelt for electric dipole transitions has been applied. Preliminary calculations for Nd2O3 are presented from which a dynamical picture of the spectrum emerges in which the intensity of some lines are seen to undergo substantial changes during the simulation. This suggests the existence of special arrangements of atoms for which transitions are particularly favorable.

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