Interaction of methanol with amorphous solid water

High sensitivity temperature-programmed desorption mass spectrometry (TPDMS) was employed in order to investigate the desorption kinetics of CCl4 from thin (∼500 ML (ML: monolayer)) amorphous D2O ice films. TPDMS experiments demonstrate that at low coverages CCl4 is trapped in the pores near the surface of microscopically rough ice. Three distinct desorption features, μ-, δ-, and ε-CCl4, consistent with the release of trapped CCl4 were observed. The μ-, δ-, and ε-CCl4 desorption yields demonstrate high sensitivity to the temperature and rate of ice film deposition. We interpret these results as evidence of the existence of three metastable forms of microporous amorphous ice, Iμ, Iδ, and Iε. Measurements of the relative desorption yields from CCl4 species trapped at the surface of ice films prepared at different temperatures and deposition rates were used in order to estimate the barriers to the diffusion of D2O on the surface of Iδ (EDδ) and Iε (EDε). The values obtained were EDδ = 5 ± 1 kcal mol-1 and EDε = 9 ± 2 kcal mol-1. We suggest that Iμ, Iδ, and Iε can be characterized respectively by the relative abundances of two-, three-, and four-coordinated D2O molecules at the ice surface. A proposed phase diagram for thin D2O ice films is presented.

Electronic structures of hexagonal ice (ice Ih), high-density amorphous ice (HDA), and very high-density amorphous ice (VHDA) are investigated using ab initio density functional theory (DFT) at 77 K under a pressure of 0.1 MPa, focusing on band structure, density of states (DOS), partial density of states (PDOS), and electron density. It is found that the integration intensity of the O-2p bonding band in HDA is 1.53 eV wider than that in the VHDA. Because more 2p electrons in HDA participate the 2p-1s hybridization of O-H. The classical molecular dynamics (MD) method has further been carried out to analyze the hydrogen bond network of HDA and VHDA with larger numbers of water molecules under the same temperature, pressure, and boundary conditions used as those during the DFT calculation. MD results show that there exists some water molecules with five hydrogen bonds in both HDA (4.1 +/- 0.1%) and VHDA (2.8 +/- 0.1%), as compared with the LDA, being consistent with the integration intensity results of PDOS. This result can be used to interpret the physical nature of the similar transition temperature of HDA and VHDA to LDA with different heating rates.

view Abstract Citations (157) References (75) Co-Reads Similar Papers Volume Content Graphics Metrics Export Citation NASA/ADS High-Density Amorphous Ice, the Frost on Interstellar Grains Jenniskens, P. ; Blake, D. F. ; Wilson, M. A. ; Pohorille, A. Abstract Most water ice in the universe is in a form which does not occur naturally on Earth and of which only minimal amounts have been made in the laboratory. We have encountered this "high-density amorphous ice" in electron diffraction experiments of low-temperature (T < 30 K) vapor-deposited water and have subsequently modeled its structure using molecular dynamics simulations. The characteristic feature of high-density amorphous ice is the presence of "interstitial" oxygen pair distances between 3 and 4 A. However, we find that the structure is best described as a collapsed lattice of the more familiar low-density amorphous form. These distortions are frozen in at temperatures below 38 K because, we propose, it requires the breaking of one hydrogen bond, on average, per molecule to relieve the strain and to restructure the lattice to that of low-density amorphous ice. Several features of astrophysical ice analogs studied in laboratory experiments are readily explained by the structural transition from high-density amorphous ice into low-density amorphous ice. Changes in the shape of the 3.07 microns water band, trapping efficiency of CO, CO loss, changes in the CO band structure, and the recombination of radicals induced by low-temperature UV photolysis all covary with structural changes that occur in the ice during this amorphous to amorphous transition. While the 3.07 microns ice band in various astronomical environments can be modeled with spectra of simple mixtures of amorphous and crystalline forms, the contribution of the high-density amorphous form nearly always dominates. Publication: The Astrophysical Journal Pub Date: January 1995 DOI: 10.1086/176585 Bibcode: 1995ApJ...455..389J Keywords: INFRARED: ISM: LINES AND BANDS; ISM: DUST; EXTINCTION; ISM: MOLECULES; LINE: PROFILES; MOLECULAR DATA; METHODS: LABORATORY; Density (Mass/Volume); Amorphous Materials; Ice; Frost; Interstellar Matter; Astronomy; Astrophysics; Cosmic Dust; Crystallinity; Electron Diffraction; Hydrogen Bonds; Molecular Dynamics; Radicals; Shapes; Trapping; Universe; Vapor Deposition; Water; Astrophysics full text sources ADS |

Chirality transfer, induction, and circularly polarized luminescence (CPL) using supramolecular hosts, such as macrocycles and cages, have been explored for wide-ranging applications in chiral reco...

Advances in nanotechnology lead to the development of nano-electro-mechanical systems (NEMS) such as nanomechanical resonators with ultra-high resonant frequencies. The ultra-high-frequency resonators have recently received significant attention for wide-ranging applications such as molecular separation, molecular transportation, ultra-high sensitive sensing, high-frequency signal processing, and biological imaging. It is well known that for micrometer length scale, first-principles technique, the most accurate approach, poses serious limitations for comparisons with experimental studies. For such larger size, classical molecular dynamics (MD) simulations are desirable, which require interatomic potentials. Additionally, a mesoscale method such as the coarse-grained (CG) method is another useful method to support simulations for even larger system sizes. Furthermore, quasi-two-dimensional (Q2D) materials have attracted intensive research interest due to their many novel properties over the past decades. However, the energy dissipation mechanisms of nanomechanical resonators based on several Q2D materials are still unknown. In this work, the addressed main issues include the development of the CG models for molybdenum disulphide (MoS2), investigation of the mechanism effects on black phosphorus (BP) nanoresonators and the application of graphene nanoresonators. The primary coverage and results of the dissertation are as follows: Method development. Firstly, a two-dimensional (2D) CG model for single layer MoS2 (SLMoS2) is analytically developed. The Stillinger-Weber (SW) potential for this 2D CG model is further parametrized, in which all SW geometrical parameters are determined analytically according to the equilibrium condition for each individual potential term, while the SW energy parameters are derived analytically based on the valence force field model. Next, the 2D CG model is further simplified to one-dimensional (1D) CG model, which describes the 2D SLMoS2 structure using a 1D chain model. This 1D CG model is applied to investigate the relaxed configuration and the resonant oscillation of the folded SLMoS2. Owning to the simplicity nature of the 1D CG model, the relaxed configuration of the folded SLMoS2 is determined analytically, and the resonant oscillation frequency is derived analytically. Considering the increasing interest in studying the properties of other 2D layered materials, and in particular those in the semiconducting transition metal dichalcogenide class like MoS2, the CG models proposed in current work provide valuable simulation approaches. Mechanism understanding. Two energy dissipation mechanisms of BP nanoresonators are focused exclusively, i.e. mechanical strain effects and defect effects (including vacancy and oxidation). Vacancy defect is intrinsic damping factor for the quality (Q)-factor, while mechanical strain and oxidation are extrinsic damping factors. Intrinsic dissipation (induced by thermal vibrations) in BP resonators (BPRs) is firstly investigated. Specifically, classical MD simulations are performed to examine the temperature dependence for the Q-factor of the single layer BPR (SLBPR) along the armchair and zigzag directions, where two-step fitting procedure is used to extract the frequency and Q-factor from the kinetic energy time history. The Q-factors of BPRs are evaluated through comparison with those of graphene and MoS2 nanoresonators. Next, effects of mechanical strain, vacancy and oxidation on BP nanoresonators are investigated in turn. Considering the increasing interest in studying the properties of BP, and in particular the lack of theoretical study for the BPRs, the results in current work provide a useful reference. Application. A novel application for graphene nanoresonators, using them to self-assemble small nanostructures such as water chains, is proposed. All of the underlying physics enabling this phenomenon is elucidated. In particular, by drawing inspiration from macroscale self-assembly using the higher order resonant modes of Chladni plates, classical MD simulations are used to investigate the self-assembly of water molecules using graphene nanoresonators. An analytic formula for the critical resonant frequency based on the interaction between water molecules and graphene is provided. Furthermore, the properties of the water chains assembled by the graphene nanoresonators are studied.

Many germ line antibodies have asparagine residues at specific sites to achieve specific antigen recognition. To study the role of asparagine residues in the stabilization of antigen-antibody complexes, we examined the interaction between hen egg white lysozyme (HEL) and the corresponding HyHEL-10 variable domain fragment (Fv). We introduced Ala and Asp substitutions into the Fv side chains of L-Asn-31, L-Asn-32, and L-Asn-92, which interact directly with residues in HEL via hydrogen bonding in the wild-type Fv-HEL complex, and we investigated the interactions between these mutant antibodies and HEL. Isothermal titration calorimetric analysis showed that all the mutations decreased the negative enthalpy change and decreased the association constants of the interaction. Structural analyses showed that the effects of the mutations on the structure of the complex could be compensated for by conformational changes and/or by gains in other interactions. Consequently, the contribution of two hydrogen bonds was minor, and their abolition by mutation resulted in only a slight decrease in the affinity of the antibody for its antigen. By comparison, the other two hydrogen bonds buried at the interfacial area had large enthalpic advantage, despite entropic loss that was perhaps due to stiffening of the interface by the bonds, and were crucial to the strength of the interaction. Deletion of these strong hydrogen bonds could not be compensated for by other structural changes. Our results suggest that asparagine can provide the two functional groups for strong hydrogen bond formation, and their contribution to the antigen-antibody interaction can be attributed to their limited flexibility and accessibility at the complex interface.

Molecular dynamics (MD) simulations together with accurate physics-based force fields are employed to determine the mobility of atomic oxygen in amorphous ice at low temperatures, characteristic for conditions in interstellar ices. From the simulations it is found that the mobility of atomic oxygen ranges from 60 to 480 angstroms2 ns(-1) in amorphous ice at temperatures between 50 and 200 K. Hence, the simulations establish that atomic oxygen is mobile to a certain degree and a chemical mechanism for water formation involving oxygen mobility is a realistic scenario. This is also confirmed by the computed migration barriers for oxygen diffusion by multiple umbrella sampling simulations, which yield barriers for diffusion in the range of 0.7-1.9 kcal mol(-1). The physics-based force field--based on a multipolar expansion of the electrostatic interactions--yields more pronounced energetics for oxygen migration pathways compared to the conventional point-charge models employed in typical simulations. Once formed, the computed solvation free energy suggests that atomic oxygen thermodynamically prefers to be localized inside amorphous ice and is available for chemical reaction, which may be relevant to water formation in and on grains.

Metal ions such as those of copper and zinc are considered to accelerate initial formation of amyloid fibril of amyloid-β (Aβ) peptides. In this study, the role of a zinc ion for Aβ peptide aggregation was investigated by the classical molecular dynamics (MD) simulations. The MD results indicated that the negatively-charged residues gained large stabilization in the existence of a zinc ion. On the other hand, histidine and tyrosine which were reported as making a bond with a metal ion were slightly stabled. Therefore, a zinc ion is thought of as combining with histidine or tyrosine after being attracted by negatively-charged residues, because these residues exist near negatively-charged residues. These results indicate that the metal-containing system needs to be treated by quantum-mechanical techniques.

HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential

Photodissociation of a HCl molecule adsorbed on ice at T = 210 K

The interactions between condensed molecules at cryogenic temperatures (15–200 K) have been investigated on the basis of secondary ion mass spectrometry. It is demonstrated that the protonated molecular ions, emitted via the proton transfer reactions, provide us unique information about the reorganization of hydrogen-bonded molecules. From the CH3OH molecules adsorbed on the D2O–ice surface, the D+(CH3OH) ions are sputtered predominantly in the temperature range between 100 and 150 K since most of the CH3OH molecules are bound to the D2O layer via hydrogen bonds. A rapid and almost complete H/D exchange, yielding the D+(CH3OD) species, occurs above 150 K due to the enhanced mobility of the surface D2O molecules. Up to the desorption temperature of 180 K, a considerable amount of methanol exists on the surface without mixing with the heavy-water layer due to hydrophobicity of the methyl group. On the methanol–ice surface, the adsorbed D2O molecules form hydrogen bonds preferentially with the CH3OH molecules and tend to be incorporated in the thin-layer bulk of methanol above 120 K.

A synergic approach combining molecular dynamics (MD) simulations and X-ray absorption spectroscopy (XAS) has been used to investigate diluted (0.1 M) aqueous solutions of two lanthanide ions (Ln3+), namely, La3+ and Dy3+, with triflate, nitrate, and bis(trifluoromethylsulfonyl)imide (Tf2N-) as counterions. The different complexing ability of the three anions has been highlighted by the analysis of the MD simulations: Tf2N- does not form inner-sphere complexes, while a small amount of triflate coordinates both the La3+ and Dy3+ cations in their first solvation shell. On the other hand, the nitrate ion is almost absent in the La3+ first coordination sphere, while forming contact ion pairs with Dy3+. Both lanthanide ions are found to preferentially interact with the water molecules, and the total number of oxygen atoms coordinating the Ln3+ cations in their first solvation sphere is the same in all of the solutions, regardless of whether they belong to water molecules or to the counterion. The presence of counterions in the cation first or second shell changes neither the first shell distance nor the symmetry of the hydration complex formed in solution. The MD results have been confirmed by comparison with the Ln K-edge XAS experimental data, and the quantitative analysis of the extended X-ray absorption fine structure (EXAFS) spectra of the three salt solutions has provided a definite proof of the accuracy of the force field employed in the simulations and of the MD structural result. The anion-water and water-water hydrogen bond lifetimes have been analyzed highlighting the slow down effect of the triflate, nitrate, and Tf2N- anions on the hydrogen bond dynamics in the Ln3+ first solvation shell, with the effect being stronger in the Dy3+ solutions, due to the higher charge density of the Dy3+ ion as compared to La3+.

The interactions of several compounds with the surfaces of amorphous and crystalline ice-h2 and ice-d2 in ultrahigh vacuum were studied using temperature-programmed desorption (TPD) and Fourier transform infrared reflection absorption spectroscopy (FTIRAS). The following compounds were studied: acetone, acetonitrile, carbon tetrachloride, chloroform, diethyl ether, 1-hexene, and 2-propanol. Without exception, compounds possessing a functional group capable of accepting a hydrogen bond from the OH group of water show one or more thermal desorption states from amorphous ice that are absent from the crystalline surface. Conversely, for compounds with no such functional group, the desorption spectra from amorphous and crystalline ice are essentially identical. The unique states exhibit kinetic isotope effects for desorption from ice-d2, whereas states that are common to both amorphous and crystalline surfaces exhibit no isotope effect. FTIRAS measurements show that adsorption of good hydrogen bond donors on the amorphous ice surface is accompanied by the disappearance of the vibrational mode associated with the free surface OH group of ice. When poor hydrogen bond donors are adsorbed on ice, the free OH group persists. FTIRAS measurements indicate that the free OH coverage on the surface of crystalline ice is approximately one-sixth of that on amorphous ice. Four possible explanations are considered for the observed differences between amorphous and crystalline ice, based on differences in surface area, porosity, permeability, and surface chemistry. It is concluded that the surface chemical properties of amorphous ice are different from those of crystalline ice, probably because the hydrogen bond donor ability of the crystalline surface is less than that of the amorphous surface.

Effects of temperature and isotopic substitution on electron attachment dynamics of guanine–cytosine base pair: Ring-polymer and classical molecular dynamics simulations

In recent years there has been growing interest in using electrochemical methods for hydrogenation of biomass-derived molecules for the formation of biofuels. Conventional hydrogenation processes require moderate temperatures between 433 and 678 K, pressures of 14,000 kPa, and external sources of dihydrogen for the stabilization and formation of biofuels. However, the same reaction can be performed using electrochemical reactors and much lower temperatures and pressures (293 K and 101 kPa) and with no supplied molecular hydrogen. In this work, we use a combined experimental–theoretical approach to identify atomistic features and parameters that affect the electrochemical hydrogenation (ECH) rates of different biomass organic compounds (such as aldehydes, ketones, and carboxylic acids) under ambient reaction conditions. In particular, we evaluated platinum group metals (PGM) and base-group metals (BGM) for the benzaldehyde ECH and correlated the activity with computationally-derived parameters. We then used these parameters to explain the dependence of molecule functionality on the ECH rates. The experiments were conducted using a continuous flow fixed bed reactor at room temperature and atmospheric pressure in the aqueous phase. We tested 7 metal catalysts with 12 substrates. Classical molecular dynamics simulations were performed on the metal’s most stable surfaces. The GROMACS package(83) was used for all classical molecular dynamics (MD) simulations. The results, summarized in Figure 1, indicate that the computationally-derived binding energy strongly correlates with the experimentally-derived ECH rates and hydrogen evolution reaction (HER) rates. The results suggest that Pd is the most active material for benzaldehyde ECH because it has an optimal organic reduction potential and binding energy compared to the other metals tested. However, Rh, which has a similar organic reduction potential, it is not active for benzaldehyde ECH due to the strong binding energy and high HER rates. These metrics were also used to evaluate the ECH activity of other biomass-derived molecules and we observed that the experimentally-derived parameters can be used to explain the differences in ECH activity with respect to benzaldehyde. For example, ketones such as acetophenone are not as active for ECH as benzaldehyde because of their binding energy. Figure 1