Mechanism of Phase Transition in dl-Methionine: Determining Cooperative and Molecule-by-Molecule Transformations.

The solid-state phase transition in dl-methionine has been extensively studied because of its atypical behavior. The transition occurs through changes in the molecular conformation and 3D packing of the molecules. Phase transitions in racemic aliphatic amino acid crystals are known to show different behaviors depending on whether conformational changes or packing changes are involved, where the former is thought to proceed through a nucleation-and-growth mechanism in a standard molecule-by-molecule picture, and the latter through a cooperative mechanism. The phase transition of dl-methionine resembles the thermodynamic, kinetic, and structural features of both categories: a conformational change and relative shifts between layers in two directions. The present paper presents molecular dynamics simulations of the phase transition to examine the underlying mechanism from two perspectives: (i) analysis of the scaling behavior of the free energy barriers involved in the phase transition and (ii) a structural inspection of the phase transition. Both methods can help to distinguish between a concerted phase change and a molecule-by-molecule or zip-like mechanism. The free energy predominantly scales with the system size, which suggests a cooperative mechanism. The structural changes draw, however, a slightly more complex picture. The conformational changes appear to occur in a molecule-by-molecule fashion, where the rotational movement is triggered by movement in the same layer. Conformational changes occur on a time scale nearly twice as long as the shifts between layers. Shifts in one direction appear to be less concerted than shifts in the perpendicular direction. We relate this to the edge-free energy involved in these shifts. We believe that the behavior observed in dl-methionine is likely applicable to phase transitions in other layered systems that interact through aliphatic chains as well.

Energy Transfer and Restructuring in Amorphous Solid Water upon Consecutive Irradiation.

Interstellar and cometary ices play an important role in the formation of planetary systems around young stars. Their main constituent is amorphous solid water (ASW). Although ASW is widely studied, vibrational energy dissipation and structural changes due to vibrational excitation are less well understood. The hydrogen-bonding network is likely a crucial component in this. Here, we present experimental results on hydrogen-bonding changes in ASW induced by the intense, nearly monochromatic mid-IR free-electron laser (FEL) radiation of the FELIX-2 beamline at the HFML-FELIX facility at the Radboud University in Nijmegen, The Netherlands. Structural changes in ASW are monitored by reflection-absorption infrared spectroscopy and depend on the irradiation history of the ice. The experiments show that FEL irradiation can induce changes in the local neighborhood of the excited molecules due to energy transfer. Molecular dynamics simulations confirm this picture: vibrationally excited molecules can reorient for a more optimal tetrahedral surrounding without breaking existing hydrogen bonds. The vibrational energy can transfer through the hydrogen-bonding network to water molecules that have the same vibrational frequency. We hence expect a reduced energy dissipation in amorphous material with respect to crystalline material due to the inhomogeneity in vibrational frequencies as well as the presence of specific hydrogen-bonding defect sites, which can also hamper the energy transfer.

IRFEL Selective Irradiation of Amorphous Solid Water: from Dangling to Bulk Modes.

Amorphous solid water (ASW) is one of the most widely studied solid phase systems. A better understanding of the nature of inter- and intramolecular forces in ASW is, however, still required to correctly interpret the catalytic role of ASW in the formation and preservation of molecular species in environments such as the icy surfaces of Solar System objects, on interstellar icy dust grains, and potentially even in the upper layers of the Earth's atmosphere. In this work, we have systematically exposed porous ASW (pASW) to mid-infrared radiation generated by a free-electron laser at the HFML-FELIX facility in The Netherlands to study the effect of vibrational energy injection into the surface and bulk modes of pASW. During multiple sequential irradiations on the same ice spot, we observed selective effects both at the surface and in the bulk of the ice. Although the density of states in pASW should allow for a fast vibrational relaxation through the H-bonded network, part of the injected energy is converted into structural ice changes as illustrated by the observation of spectral modifications when performing Fourier transform infrared spectroscopy in reflection-absorption mode. Future studies will include the quantification of such effects by systematically investigating ice thickness, ice morphology, and ice composition.

Molecular Dynamics Simulations of Energy Dissipation on Amorphous Solid Water: Testing the Validity of Equipartition.

Many different molecular species have been observed in the interstellar medium. These range from simple diatomic species to saturated organic molecules with several carbon atoms. The latter molecules are assumed to be formed predominantely on the surface of interstellar dust grains. All surface reactions that can proceed under the low interstellar temperatures are exothermic. Their exothermicity can be as high as a few electron volts, which is considerable compared to the thermal energy of the molecules at 10 K. It is postulated that this exothermicity can be used for the desorption of reaction products from the grain. In previous studies, we have shown that translational excitation can lead to desorption, whereas vibrational and rotational excitations are much less efficient in the desorption of surface products. Vibrational excitation is however much more likely upon bond formation than translational excitation. The present study follows energy dissipation upon translational, vibrational, or rotational excitation of admolecules on a surface and its conversion, or lack thereof, to different energy contributions. To this end, thousands of molecular dynamics simulations were performed with an admolecule on top of a surface that received a fixed amount of energy, vibrational, rotational, or translational. Three different surface species have been considered, CO2, H2O, and CH4, spanning a range in binding energies, the number of internal degrees of freedom, and molecular weights. A fast exchange of energy between vibrational stretches is observed, but only very limited exchange to rotational or translation excitation has been found. For the dissipation of energy to the surface, excitation of the surface-admolecule bond is critical. Astrochemical models often assume instantaneous equipartition of energy after a reaction process to estimate the amount of available energy for chemical desorption. Based on the present study, we conclude that this assumption is not justified.

Quantification of the Role of Chemical Desorption in Molecular Clouds.

ConspectusDark molecular clouds have low temperatures of approximately 10 K and experience very little UV irradiation. These clouds are the birthplace of new stars and consist of gas and dust particles. The latter can act as a meeting place to facilitate surface chemistry to form saturated molecules such as formaldehyde, methyl formate, and dimethyl ether. These complex organic molecules or COMs become encapsulated in the ice that forms on the dust grains, and these ices are the precursor for cometary ices and other icy bodies. They likely played a role in bringing material to the early earth.Although these COMs are likely formed on the surfaces of dust grains, several of them have been detected in the gas phase. This means that they have desorbed from the grain under these cold, dark conditions where thermal desorption and photodesorption are negligible. It has been speculated that reactive, or chemical, desorption is responsible for the high gas-phase abundance. After a surface reaction, its products might be vibrationally, translationally, and/or rotationally excited. Dissipation of the excess energy to translational energy can briefly increase the desorption rate, leading to chemical desorption. Astrochemical modellers have added terms to their rate equations to account for this effect. These terms, however, have had little experimental or theoretical verification.In this Account, we use classical molecular dynamics (MD) simulations to give adsorbed molecules a fixed amount of energy as a proxy for excess energy and to record whether this leads to desorption. The excitation energy can be varied freely while keeping all other variables constant. This allows for the study of trends rather than being limited to a single reaction and a single system. The focus is on the dependence of the chemical desorption on the excitation energy, excitation type, and binding energy. Rotational and vibrational excitation was explicitly taken into account. An analytical expression for the chemical desorption probability was obtained in this way. It depends on the binding energy and reaction enthalpy. This expression was then implemented in a gas-grain astrochemical code to simulate the chemical evolution of a dark molecular cloud, and the results were compared against observational abundances of COMs in three different molecular clouds. The results with our new expression based on the MD simulations show good agreement for all species except H2CO, which has both gas-phase and surface-formation routes. This is a significant improvement over models without chemical desorption or with other expressions for chemical desorption, as frequently used by other authors. It is encouraging to see that a general description with a firmer theoretical basis leads to a significant improvement. Understanding chemical desorption can help to explain the unexpectedly high gas-phase abundance of some COMs, and chemical desorption also provides a link between the gas phase and the ice mantle, and its understanding might help in creating a diagnostic tool to learn more about the ice composition.

The Rich Solid-State Phase Behavior of l-Phenylalanine: Disappearing Polymorphs and High Temperature Forms.

After years of controversy over the solid state structure of the essential amino acid l-phenylalanine, four different polymorphic forms were published recently. The common form I has symmetry P21 with four molecules in the asymmetric unit (Z' = 4), similar to form III, but with a different arrangement of molecular bilayers. Form II, obtained from the hydrate at very low humidity, is unrelated to forms I and III, as is the high-density form IV. The present investigation demonstrates that this prototype aromatic amino acid has two additional high-temperature phases Ih and IIIh obtained from form I and form III above 458 and 440 K, respectively, when flipping between two alternative side-chain conformations becomes dynamic and causes pairs of molecules, initially crystallographically independent, to become equivalent above a sharp transition temperature. These abrupt and reversible phase changes occur with a reduction of Z' from 4 (low T) to 2 (high T) and modified crystal symmetry. We furthermore experienced an example of disappearing polymorph for form I which after growing form III in one of our laboratories could no longer be crystallized at room temperature. In contrast, form III crystals may be irreversibly converted to form I crystals as a result of sliding of molecular bilayers in the crystal at elevated temperature. No conversions between the high-temperature forms Ih and IIIh were found. The remarkable crystallographic results are here corroborated by Molecular Dynamics and metadynamics simulations of the form I - form III system.

The Rich Solid-State Phase Behavior of dl-Aminoheptanoic Acid: Five Polymorphic Forms and Their Phase Transitions.

The rich landscape of enantiotropically related polymorphic forms and their solid-state phase transitions of dl-2-aminoheptanoic acid (dl-AHE) has been explored using a range of complementary characterization techniques, and is largely exemplary of the polymorphic behavior of linear aliphatic amino acids. As many as five new polymorphic forms were found, connected by four fully reversible solid-state phase transitions. Two low temperature forms were refined in a high Z' crystal structure, which is a new phenomenon for linear aliphatic amino acids. All five structures consist of two-dimensional hydrogen-bonded bilayers interconnected by weak van der Waals interactions. The single-crystal-to-single-crystal phase transitions involve shifts of bilayers and/or conformational changes in the aliphatic chain. Compared to two similar phase transitions of the related amino acid dl-norleucine, the enthalpies of transition and NMR chemical shift differences are notably smaller in dl-aminoheptanoic acid. This is explained to be a result of both the nature of the conformational changes and the increased chain length, weakening the interactions between the bilayers.

Report on the sixth blind test of organic crystal structure prediction methods.

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.

Do solid-to-solid polymorphic transitions in DL-norleucine proceed through nucleation?

DL-Norleucine is a molecular crystal exhibiting two enantiotropic phase transitions. The high temperature α ↔ γ transition has been shown to proceed through nucleation and growth [Mnyukh et al., J. Phys. Chem. Solids, 1975, 36, 127]. We focus on the low temperature ß â†” α transition in a combined computational and experimental study. The temperature dependence of the structural and energetic properties of both polymorphic forms is nearly identical. Molecular dynamics simulations and nudged elastic band calculations of the transition process itself, suggest that the transition is governed by cooperative movements of bilayers over relatively large energy barriers.

Water formation at low temperatures by surface O2 hydrogenation III: Monte Carlo simulation.

Water is the most abundant molecule found in interstellar icy mantles. In space it is thought to be efficiently formed on the surfaces of dust grains through successive hydrogenation of O, O2 and O3. The underlying physico-chemical mechanisms have been studied experimentally in the past decade and in this paper we extend this work theoretically, using Continuous-Time Random-Walk Monte Carlo simulations to disentangle the different processes at play during hydrogenation of molecular oxygen. CTRW-MC offers a kinetic approach to compare simulated surface abundances of different species to the experimental values. For this purpose, the results of four key experiments-sequential hydrogenation as well as co-deposition experiments at 15 and 25 K-are selected that serve as a reference throughout the modeling stage. The aim is to reproduce all four experiments with a single set of parameters. Input for the simulations consists of binding energies as well as reaction barriers (activation energies). In order to understand the influence of the parameters separately, we vary a single process rate at a time. Our main findings are: (i) The key reactions for the hydrogenation route starting from O2 are H + O2, H + HO2, OH + OH, H + H2O2, H + OH. (ii) The relatively high experimental abundance of H2O2 is due to its slow destruction. (iii) The large consumption of O2 at a temperature of 25 K is due to a high hydrogen diffusion rate. (iv) The diffusion of radicals plays an important role in the full reaction network. The resulting set of 'best fit' parameters is presented and discussed for use in future astrochemical modeling.

Monte Carlo calculations of the free energy of binary sII hydrogen clathrate hydrates for identifying efficient promoter molecules.

The thermodynamics of binary sII hydrogen clathrates with secondary guest molecules is studied with Monte Carlo simulations. The small cages of the sII unit cell are occupied by one H(2) guest molecule. Different promoter molecules entrapped in the large cages are considered. Simulations are conducted at a pressure of 1000 atm in a temperature range of 233-293 K. To determine the stabilizing effect of different promoter molecules on the clathrate, the Gibbs free energy of fully and partially occupied sII hydrogen clathrates are calculated. Our aim is to predict what would be an efficient promoter molecule using properties such as size, dipole moment, and hydrogen bonding capability. The gas clathrate configurational and free energies are compared. The entropy makes a considerable contribution to the free energy and should be taken into account in determining stability conditions of binary sII hydrogen clathrates.

Monte Carlo studies of surface chemistry and nonthermal desorption involving interstellar grains.

Although still poorly understood, the chemistry that occurs on the surfaces of interstellar dust particles profoundly affects the growth of molecules in the interstellar medium. The most important surface reaction is the conversion of atomic to molecular hydrogen, which is a precursor for all subsequent molecular development and which occurs both in diffuse and dense interstellar clouds. Another set of surface reactions produces icy mantles of many monolayers in cold and dense regions of the interstellar medium. The monolayers are dominated by water ice but also contain CO, CO(2), and occasionally methanol. In this work, we first review both our stochastic approach to the surface chemistry that can occur on small dust particles and how it has been applied to the problem of the formation of molecular hydrogen. This latter problem is strongly affected by the pulsed heating of smaller grains by photons. Photons are not the only source of pulsed heating; cosmic rays also can heat interstellar grains in a pulsed manner. Here, we calculate the heating by cosmic rays for different grain sizes and cosmic ray components. It is then shown that this mechanism is an important one for desorption of ice mantles.