Molecular Dynamics Simulations of Hydrogen Bond Dynamics and Far-Infrared Spectra of Hydration Water Molecules around the Mixed Monolayer-Protected Au Nanoparticle

2015 ◽  
Vol 119 (4) ◽  
pp. 1768-1781 ◽  
Author(s):  
Zhen Yang ◽  
Yunzhi Li ◽  
Guobing Zhou ◽  
Xiangshu Chen ◽  
Duanjian Tao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Infrared Spectra ◽  
Far Infrared ◽  
Au Nanoparticle ◽  
Water Molecules ◽  
Hydration Water ◽  
Dynamics Simulations ◽  
Hydrogen Bond Dynamics ◽  
Far Infrared Spectra

What Far-Infrared Spectra Can Contribute to the Development of Force Fields for Ionic Liquids Used in Molecular Dynamics Simulations

ChemPhysChem ◽  
2009 ◽  
Vol 10 (8) ◽  
pp. 1181-1186 ◽  
Author(s):  
Thorsten Köddermann ◽  
Koichi Fumino ◽  
Ralf Ludwig ◽  
José N. Canongia Lopes ◽  
Agílio A. H. Pádua
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Infrared Spectra ◽  
Force Fields ◽  
Far Infrared ◽  
Dynamics Simulations ◽  
Far Infrared Spectra

scholarly journals Far Infrared Spectra by Molecular Dynamics Method.

1991 ◽  
Vol 57 (541) ◽  
pp. 3306-3309
Author(s):  
Souhei MATSUMOTO ◽  
Masahiro SHOJI ◽  
Susumu KOTAKE
Keyword(s):  
Molecular Dynamics ◽  
Infrared Spectra ◽  
Far Infrared ◽  
Molecular Dynamics Method ◽  
Dynamics Method ◽  
Far Infrared Spectra

The Far Infrared Spectra of Partially Orientationally Ordered Water Molecules: Hexamethylenetetramine Hexahydrate at 95 K

1975 ◽  
Vol 53 (17) ◽  
pp. 2642-2645 ◽  
Author(s):  
John E. Bertie ◽  
Marco Solinas
Keyword(s):  
Infrared Spectrum ◽  
Infrared Spectra ◽  
Far Infrared ◽  
Clathrate Hydrate ◽  
Factor Group ◽  
Water Molecules ◽  
Disordered Solids ◽  
Ordered Water ◽  
Far Infrared Spectra ◽  
Three Phases

The far infrared spectra of four isotopic modifications of the partially orientationally ordered clathrate hydrate hexamethylenetetramine hexahydrate at 95 K are reported. The spectra are assigned to absorption allowed under the diffraction factor group, and to disorder-allowed absorption, following the theory for absorption by translational vibrations in orientationally disordered solids. Three phases formed primarily by hydrogen-bonded water molecules are known to be significantly, but only partially, orientationally ordered, hexamethylenetetramine hexahydrate, ice V, and ice VI. Of these phases, only ice VI fails to show sharp absorption in its far infrared spectrum in addition to the broad, disorder-allowed absorption.

Molecular Dynamics Study of Interfacial Thermal Resistance of Mercapto-Alkanol Self-Assembled Monolayer and Water

2009 ◽  
Author(s):  
Touru Kawaguchi ◽  
Gota Kikugawa ◽  
Ikuya Kinefuchi ◽  
Taku Ohara ◽  
Shinichi Yatuzuka ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Thermal Resistance ◽  
Chem Phys ◽  
Nonequilibrium Molecular Dynamics ◽  
Interfacial Thermal Resistance ◽  
Water Molecules ◽  
Self Assembled Monolayer ◽  
Self Assembled ◽  
Dynamics Simulations

The interfacial thermal resistance of 11-mercaptoundecanol (-S(CH2)11OH) self-assembled monolayer (SAM) adsorbed on Au(111) substrate and water was investigated using nonequilibrium molecular dynamics simulations. The interfacial thermal resistance was found to be a half of that in the system which consists of 1-dodecanthiol (-S(CH2)11CH3) SAM adsorbed on Au(111) and toluene [Kikugawa G. et al., J. Chem. Phys. (2009)]. The effective thermal energy transfer originates from hydrogen-bond structure between the SAM and water molecules in spite of weak structurization of water molecules near the SAM surface.

scholarly journals Dynamic Properties of Water Confined in Graphene-Based Membrane: A Classical Molecular Dynamics Simulation Study

Membranes ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 165 ◽  
Author(s):  
One-Sun Lee
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Graphene Sheets ◽  
Water Molecules ◽  
Energy Profile ◽  
Confined Water ◽  
Graphene Surface ◽  
Dynamics Simulations ◽  
Density Of Water

We performed molecular dynamics simulations of water molecules inside a hydrophobic membrane composed of stacked graphene sheets. By decreasing the density of water molecules inside the membrane, we observed that water molecules form a droplet through a hydrogen bond with each other in the hydrophobic environment that stacked graphene sheets create. We found that the water droplet translates as a whole body rather than a dissipate. The translational diffusion coefficient along the graphene surface increases as the number of water molecules in the droplet decreases, because the bigger water droplet has a stronger van der Waals interaction with the graphene surface that hampers the translational motion. We also observed a longer hydrogen bond lifetime as the density of water decreased, because the hydrophobic environment limits the libration motion of the water molecules. We also calculated the reorientational correlation time of the water molecules, and we found that the rotational motion of confined water inside the membrane is anisotropic and the reorientational correlation time of confined water is slower than that of bulk water. In addition, we employed steered molecular dynamics simulations for guiding the target molecule, and measured the free energy profile of water and ion penetration through the interstice between graphene sheets. The free energy profile of penetration revealed that the optimum interlayer distance for desalination is ~10 Å, where the minimum distance for water penetration is 7 Å. With a 7 Å interlayer distance between the graphene sheets, water molecules are stabilized inside the interlayer space because of the van der Waals interaction with the graphene sheets where sodium and chloride ions suffer from a 3–8 kcal/mol energy barrier for penetration. We believe that our simulation results would be a significant contribution for designing a new graphene-based membrane for desalination.

Hydrogen bond-induced responses in mid- and far-infrared spectra of interfacial water at phospholipid bilayers

2020 ◽  
Vol 518 ◽  
pp. 112626
Author(s):  
Yi Luo ◽  
Guobing Zhou ◽  
Li Li ◽  
Shiyue Xiong ◽  
Zhen Yang ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Infrared Spectra ◽  
Far Infrared ◽  
Phospholipid Bilayers ◽  
Interfacial Water ◽  
Induced Responses ◽  
Far Infrared Spectra

Far‐Infrared Spectra and Hydrogen‐Bond Frequencies of Imidazole

1968 ◽  
Vol 48 (7) ◽  
pp. 3079-3084 ◽  
Author(s):  
C. Perchard ◽  
A. Novak
Keyword(s):  
Hydrogen Bond ◽  
Infrared Spectra ◽  
Far Infrared ◽  
Far Infrared Spectra

scholarly journals Infrared Spectra of the Clathrate Hydrates

1978 ◽  
Vol 21 (85) ◽  
pp. 694-696
Author(s):  
D. A. Othen ◽  
P. G. Wright ◽  
F. E. Bates ◽  
D. K. Hendricksen ◽  
S. M. Jacobs ◽  
...  
Keyword(s):  
Ethylene Oxide ◽  
Infrared Spectra ◽  
Guest Molecule ◽  
Far Infrared ◽  
Water Molecules ◽  
Guest Molecules ◽  
Oxide Structure ◽  
Trimethylene Oxide ◽  
Ray Methods ◽  
Far Infrared Spectra

AbstractDetailed mid- and far-infrared spectra have been recorded for authenticated samples of several clathrate hydrates with the two main structures, I and II, at temperatures between 150 and 4 K. The systems are complicated, yet a detailed analysis of the many interesting spectral features is required before reliable, detailed information can be obtained. Consequently only rather general conclusions can be drawn at present.The mid-infrared spectra have been recorded for the structure I hydrates and deuterates of ethylene oxide, trimethylene oxide, and cyclopropane, and the structure II hydrate and deuterate of trimethylene oxide, all at 100 K. The OD stretching vibrations of isolated HDO molecules, vOD (HDO), and of the fully deuterated forms, vOD(D2O), have also been recorded for cyclopropane and trimethylene oxide structure I hydrates at 40 K, and the absorption by the guest molecules has been studied for all of the structure I hydrates at temperatures down to 40 K.The absorption by the water molecules at 100 K is similar to that in ice, with frequencies that vary in the expected way with the lattice parameter and, hence, the hydrogen bond lengths. The shapes of the vOH(H2O)vOD(D2O), and vR(D2O) bands are essentially the same for structures I and II, while the vOD(D2O) band varies only slightly and depends more on the guest molecule than on the structure. The water absorption changed only slightly when the samples were cooled from 100 to 40 K.The vOD(HDO) bands provide clear evidence that the distribution of hydrogen bond lengths in cyclopropane hydrate differs from those in ethylene oxide and trimethylene oxide structure I hydrates, even though powder X-ray methods indicate that the three hydrates are isostructural. The difference is attributed to an interaction between the hydrogen bonds and the dipole moment of the guest which is too irregular to be sensed by powder X-ray methods.Some absorption bands of the guest molecules are visible in the spectra of structure I hydrates and, as expected, fewer are visible in the spectra of structure II hydrates, which have a higher water-to-guest ratio. For both structures more guest bands are visible in the spectra of deuterates since the D2O absorption is weaker than that of H2O. The guest bands are single in most cases, with half-widths of 1 to 5 cm-1 for ethylene oxide and cyclopropane and 5 to 15 cm-1 for trimethylene oxide in its deuterates of both structures. One band of ethylene oxide at 100 K and below is a doublet, and one degenerate and one non-degenerate vibration of cyclopropane yields a doublet at 40 K. This must mean that there are two non-equivalent positions for the guest molecule in the tetrakaidecahedral cage of the structure I hydrate at these temperatures.Far infrared spectra have been recorded of the structure I hydrates of ethylene oxide, cyclopropane, trimethylene oxide, and xenon, and of the structure II hydrates of trimethylene oxide, cyclopropane, tetrahydrofuran, cyclobutanone, and 1,3-dioxolane, all at 4.3 K. The spectra of the hydrates and corresponding deuterates have enabled the absorption by the rotational vibrations of the guest molecules in the cage to be identified. The absorption above 100 cm-1 by the translational vibrations of the water molecules is significantly different for the two structures, but is rather insensitive to the guest molecule within one structure.A careful search was made for evidence of the transition in trimethylene oxide structure I hydrate at which the guest molecules partly order, that was detected by Davidson from dielectric studies. No spectral changes due to the transition were detected.Papers describing this work have been published in Canadian. Journal of Chemistry, Vol. 51, No. 8, 1973, p. 1159-68; Vol. 53, No. 1, 1975, p. 71-75; Vol. 55, No. 10, 1977, p. 1777-85. A further paper is accepted for publication in Journal of Chemical Physics and others arc in preparation.

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