Condensed-phase Chemistry Research Articles

Dissoziative Elektronenanlagerungsdynamik eines vielversprechenden Krebsmedikaments zeigt sein Potential als Radiosensitizer

Abstract2‐Bromo‐1‐(3,3‐dinitroazetidin‐1‐yl)ethan‐1‐on (RRx‐001) ist ein Chemotherapeutikum für sauerstoffarme Tumore und zeigte bereits Synergieeffekte in Kombination mit Strahlentherapie. Die Wechselwirkung des Moleküls mit niederenergetischen Sekundärelektronen, die in großer Zahl in der physikalisch‐chemischen Phase der Bestrahlung gebildet werden, könnten für diesen Synergieeffekt verantwortlich sein. Die vorliegende Studie konzentriert sich auf die ersten Schritte in der Wechselwirkung von RRx‐001 mit niederenergetischen Elektronen, in denen das temporäre negative Ion gebildet wird und rasch fragmentiert. Die Kombination von Resultaten zweier Versuchsaufbauten erlaubt es uns, den Zerfall des RRx‐001 Anions auf verschiedenen Zeitskalen zu entflechten. Die alleinige Anwesenheit des eingefangenen Elektrons führt zu einer raschen Abspaltung von NO2 und HNO2, während NO2− und Br− Anionen direkt beziehungsweise über andere Zwischenprodukte gebildet werden. Auf Basis quantenchemischer Rechnungen schlagen wir einen bidirektionalen Wechsel zwischen π*(NO2) und σ*(C−Br) Zuständen vor, welcher die experimentellen Spektren erklärt. Die beobachtete schnelle Dynamik lässt auch Schlussfolgerungen für die Chemie des Anions in der kondensierten Phase zu.

A comprehensive evaluation of enhanced temperature influence on gas and aerosol chemistry in the lamp-enclosed oxidation flow reactor (OFR) system

Abstract. Oxidation flow reactors (OFRs) have been extensively utilized to examine the formation of secondary organic aerosol (SOA). However, the UV lamps typically employed to initiate the photochemistry in OFRs can result in an elevated reactor temperature when their implications are not thoroughly evaluated. In this study, we conducted a comprehensive investigation into the temperature distribution within an Aerodyne potential aerosol mass OFR (PAM-OFR) and then examined the subsequent effects on flow and chemistry due to lamp heating. A lamp-induced temperature increase was observed, which was a function of lamp-driving voltage, number of lamps, lamp types, OFR residence time, and positions within the PAM-OFR. Under typical PAM-OFR operational conditions (e.g., < 5 d of equivalent atmospheric OH exposure under low-NOx conditions), the temperature increase typically ranged from 1–5 °C. Under extreme (but less frequently encountered) conditions, the heating could reach up to 15 °C. The influences of the increased temperature over ambient conditions on the flow distribution, gas, and condensed-phase chemistry within PAM-OFR were evaluated. Our findings indicate that the increase in temperature altered the flow field, resulting in a diminished tail on the residence time distribution and corresponding oxidant exposure due to faster recirculation. According to simulation results from a radical chemistry box model, the variation in absolute oxidant concentration within PAM-OFR due to temperature increase was minimal (< 5 %). The temperature influences on seed organic aerosol (OA) and newly formed secondary OA were also investigated, suggesting that an increase in temperature can impact the yield, size, and oxidation levels of representative biogenic and anthropogenic SOA types. Recommendations for temperature-dependent SOA yield corrections and PAM-OFR operating protocols that mitigate lamp-induced temperature enhancement and fluctuations are presented. We recommend blowing air around the reactor's exterior with fans during PAM-OFR experiments to minimize the temperature increase within PAM-OFR. Temperature increases are substantially lower for OFRs utilizing less powerful lamps compared to the Aerodyne version.

Enhanced Organic Nitrate Formation from Peroxy Radicals in the Condensed Phase.

Organic alkoxy (RO) and peroxy (RO2) radicals are key intermediates in multiphase atmospheric oxidation chemistry, though most of the study of their chemistry has focused on the gas phase. To better understand how radical chemistry may vary across different phases, we examine the chemistry of a model system, the 1-pentoxy radical, in three phases: the aqueous phase, the condensed organic phase, and the gas phase. In each phase, we generate the 1-pentoxy radical from the photolysis of n-pentyl nitrite, run the chemistry under conditions in which RO2 radicals react with NO, and detect the products in real time using an ammonium chemical ionization mass spectrometer (NH4 + CIMS). The condensed-phase chemistry shows an increase in formation of organic nitrate (RONO2) from the downstream RO2+NO reaction, which is attributed to potential collisional and solvent-cage stabilization of the RO2-NO complex. We further observe an enhancement in the yield of carbonyl relative to hydroxy carbonyl products in the condensed phase, indicating changes to RO radical kinetics. The different branching ratios in the condensed phase impact the product volatility distribution as well as HO x -NO x chemistry, and may have implications for nitrate formation, aqueous aerosol formation, and radical cycling within atmospheric particles and droplets.

Dissociative Electron Attachment Dynamics of a Promising Cancer Drug Indicates Its Radiosensitizing Potential.

2-Bromo-1-(3,3-dinitroazetidin-1-yl)ethan-1-one (RRx-001) is a hypoxic cell chemotherapeutics with already demonstrated synergism in combined chemo-radiation therapy. The interaction of the compound with secondary low-energy electrons formed in large amounts during the physico-chemical phase of the irradiation may lead to these synergistic effects. The present study focuses on the first step of RRx-001 interaction with low-energy electrons in which a transient anion is formed and fragmented. Combination of two experiments allows us to disentangle the decay of the RRx-001 anion on different timescales. Sole presence of the electron initiates rapid dissociation of NO2 and HNO2 neutrals while NO2 - and Br- anions are produced both directly and via intermediate complexes. Based on our quantum chemical calculations, we propose that bidirectional state switching between π*(NO2) and σ*(C-Br) states explains the experimental spectra. The fast dynamics monitored will impact the condensed phase chemistry of the anion as well.

Exploring the frontiers of condensed-phase chemistry with a general reactive machine learning potential.

Atomistic simulation has a broad range of applications from drug design to materials discovery. Machine learning interatomic potentials (MLIPs) have become an efficient alternative to computationally expensive ab initio simulations. For this reason, chemistry and materials science would greatly benefit from a general reactive MLIP, that is, an MLIP that is applicable to a broad range of reactive chemistry without the need for refitting. Here we develop a general reactive MLIP (ANI-1xnr) through automated sampling of condensed-phase reactions. ANI-1xnr is then applied to study five distinct systems: carbon solid-phase nucleation, graphene ring formation from acetylene, biofuel additives, combustion of methane and the spontaneous formation of glycine from early earth small molecules. In all studies, ANI-1xnr closely matches experiment (when available) and/or previous studies using traditional model chemistry methods. As such, ANI-1xnr proves to be a highly general reactive MLIP for C, H, N and O elements in the condensed phase, enabling high-throughput in silico reactive chemistry experimentation.

Condensed-phase isomerization through tunnelling gateways

Quantum mechanical tunnelling describes transmission of matter waves through a barrier with height larger than the energy of the wave1. Tunnelling becomes important when the de Broglie wavelength of the particle exceeds the barrier thickness; because wavelength increases with decreasing mass, lighter particles tunnel more efficiently than heavier ones. However, there exist examples in condensed-phase chemistry where increasing mass leads to increased tunnelling rates2. In contrast to the textbook approach, which considers transitions between continuum states, condensed-phase reactions involve transitions between bound states of reactants and products. Here this conceptual distinction is highlighted by experimental measurements of isotopologue-specific tunnelling rates for CO rotational isomerization at an NaCl surface3,4, showing nonmonotonic mass dependence. A quantum rate theory of isomerization is developed wherein transitions between sub-barrier reactant and product states occur through interaction with the environment. Tunnelling is fastest for specific pairs of states (gateways), the quantum mechanical details of which lead to enhanced cross-barrier coupling; the energies of these gateways arise nonsystematically, giving an erratic mass dependence. Gateways also accelerate ground-state isomerization, acting as leaky holes through the reaction barrier. This simple model provides a way to account for tunnelling in condensed-phase chemistry, and indicates that heavy-atom tunnelling may be more important than typically assumed.

Machine‐Learning a Solution for Reactive Atomistic Simulations of Energetic Materials

AbstractMany of the safety and performance‐related properties of energetic materials (EM) are related to complex condensed phase chemistry at extreme P,T conditions eluding direct experimental investigation. Atomistic simulations can play a vital role in generating insight into EM chemistry, but they rely critically on the availability of suitable interatomic potentials (“force fields”). The ChIMES machine learning approach enables generation of interatomic potentials for condensed phase reacting systems, with accuracy similar to Kohn‐Sham density functional theory through its unique, highly flexible orthogonal basis set of interaction functions and systematically improvable many‐body expansion of interatomic interactions. ChIMES has been successfully applied to a variety of systems including simple model energetic materials, both as a correction for simpler quantum theory and as a stand‐alone interatomic potential. In this perspective, the successes and challenges of applying the ChIMES approach to the reactive molecular dynamics of energetic materials are outlined. Our machine‐learned approach is general and can be applied to a variety of different application areas where atomic‐level calculations can be used to help guide and elucidate experiments.

Macrocyclic tetra(azo-) and tetra(azoxyfurazan)s: Comparative study of decomposition and combustion with linear analogs

Thermal decomposition and combustion of macrocyclic tetra(azofurazan), TATF, and tetra(azoxyfurazan), TOATF, were studied using a number of complementary experimental techniques, namely thermogravimetry, differential scanning calorimetry, manometry, microthermocouple measurements in a combustion wave. Kinetic studies of polyazo- and azoxyfurazans have demonstrated that macrocycles, TATF and TOATF, have a different mechanism of thermal decomposition than their linear counterparts. While linear azo- and azoxyfurazans have relatively low activation energy (130–143 ​kJ·mol−1) of thermal decomposition, the activation energies for macrocyclic TATF and TOATF are 202–210 ​kJ·mol−1, which is close to the calculated breaking energy of the C-NN bond. The initial stage of decomposition of these macrocycles is the monomolecular cleavage of the C-NN bond, while linear azofurazan decomposes according to a concerted mechanism, loss N2 or N2O molecules. It was found that the condensed-phase chemistry determines the combustion mechanism of TOATF. Combustion instability is observed for TATF in the pressure range below 3 ​MPa. Both macrocyclic TATF and TOATF are relatively fast-burning energetic compounds, with burning rates exceeding the burning rates of the CL-20.

Transporting and concentrating vibrational energy to promote isomerization.

Visible-light absorption and transport of the resultant electronic excitations to a reaction centre through Förster resonance energy transfer1-3 (FRET) are critical to the operation of biological light-harvesting systems4, and are used in various artificial systems made of synthetic dyes5, polymers6 or nanodots7,8. The fundamental equations describing FRET are similar to those describing vibration-to-vibration (V-V) energy transfer9, and suggest that transport and localization of vibrational energy should, in principle, also be possible. Although it is known that vibrational excitation can promote reactions10-16, transporting and concentrating vibrational energy has not yet been reported. We have recently demonstrated orientational isomerization enabled by vibrational energy pooling in a CO adsorbate layer on a NaCl(100) surface17. Here we build on that work to show that the isomerization reaction proceeds more efficiently with a thick 12C16O overlayer that absorbs more mid-infrared photons and transports the resultant vibrational excitations by V-V energy transfer to a 13C18O-NaCl interface. The vibrational energy density achieved at the interface is 30 times higher than that obtained with direct excitation of the interfacial CO. We anticipate that with careful system design, these concepts could be used to drive other chemical transformations, providing new approaches to condensed phase chemistry.

Infrared Multiple Photon Dissociation Spectroscopy of Protonated Cyameluric Acid.

The present study reports the first structural characterization of protonated cyameluric acid ([CA + H]+) in the gas phase, which paves the way for prospective bottom-up research on the condensed-phase chemistry of CA in the protonated form. A number of [CA + H]+ keto-enol isomers can a priori be produced as a result of protonation at available N and O positions of precursor neutral CA tautomers, yet ab initio computations predict different reduced [CA + H]+ isomer populations dominating the solution and gas phases that are involved in the ion generation process (i.e., electrospray ionization). Infrared multiple photon dissociation spectra were recorded in the 990-1900 and 3300-3650 cm-1 regions and compared with theoretical [B3LYP/6-311++G(d,p)] IR absorption spectra of several [CA + H]+ isomers, providing a satisfactory agreement for the most stable monohydroxy form in the gas phase, [1358a]+, yet the contribution of its nearly isoenergetic OH rotamer, [1358b]+, cannot be neglected. This is indicative of the occurrence of [CA + H]+ isomer interconversion reactions, assisted by protic solvent molecules, during their transfer into the gas phase. The results suggest that available O positions on neutral CA are energetically favored protonation sites in the gas phase.

Ab-Initio Molecular Dynamics Simulation of Condensed-Phase Reactivity: The Electrolysis of Amino Acids and Peptides

Electrolysis is a potential candidate for a quick method of wastewater cleansing. However, it is necessary to know what compounds might be formed from bioorganic matter. We want to know if there are toxic intermediates and if it is possible to influence the product formation by the variation in initial conditions. In the present study, we use Car–Parrinello molecular dynamics to simulate the fastest reaction steps under such circumstances. We investigate the behavior of amino acids and peptides under anodic conditions. Such highly reactive situations lead to chemical reactions within picoseconds, and we can model the reaction mechanisms in full detail. The role of the electric current is to discharge charged species and, hence, to produce radicals from ions. This leads to ultra-fast radical reactions in a bulk environment, which can also be seen as redox reactions as the oxidation states change. In the case of amino acids, the educts can be zwitterionic, so we also observe complex acid–base chemistry. Hence, we obtain the full spectrum of condensed-phase chemistry.

Many-body reactive force field development for carbon condensation in C/O systems under extreme conditions.

We describe the development of a reactive force field for C/O systems under extreme temperatures and pressures, based on the many-body Chebyshev Interaction Model for Efficient Simulation (ChIMES). The resulting model, which targets carbon condensation under thermodynamic conditions of 6500 K and 2.5 g cm-3, affords a balance between model accuracy, complexity, and training set generation expense. We show that the model recovers much of the accuracy of density functional theory for the prediction of structure, dynamics, and chemistry when applied to dissociative condensed phase systems at 1:1 and 1:2 C:O ratios, as well as molten carbon. Our C/O modeling approach exhibits a 104 increase in efficiency for the same system size (i.e., 128 atoms) and a linear system size scalability over standard quantum molecular dynamics methods, allowing the simulation of significantly larger systems than previously possible. We find that the model captures the condensed-phase reaction-coupled formation of carbon clusters implied by recent experiments, and that this process is susceptible to strong finite size effects. Overall, we find the present ChIMES model to be well suited for studying chemical processes and cluster formation at pressures and temperatures typical of shock waves. We expect that the present C/O modeling paradigm can serve as a template for the development of a broader high pressure-high temperature force-field for condensed phase chemistry in organic materials.

Local Acid Strength of Solutions and Its Quantitative Evaluation Using Excess Infrared Nitrile Probes.

We propose the concept of local acidity in condensed-phase chemistry in this work. The feature is demonstrated in trifluoroethanol (TFE) by employing two Fourier-transform infrared spectroscopy (FTIR) nitrile probes, acetonitrile (CH3CN) and benzonitrile (PhCN). Specifically, three positive excess peaks were found in the binary systems composed of TFE and a probe using excess spectroscopy. To characterize the local acidity quantitatively, we have tried to correlate the wavenumbers of the positive excess peaks of the probes and the pKa values in water of a series of XH-containing compounds (X = O, N, and C). Good linear relationships were discovered. Accordingly, three different pKa values of TFE were determined based on the three positive excess infrared peaks, which are attributed to the monomer, dimer, and trimer of TFE with the help of quantum-chemical calculations. The concept of local acidity and its quantitative evaluation enrich our knowledge of acid-base chemistry and will shed light on a better understanding of microstructures of solutions.

Outer-sphere effects on ligand-field excited-state dynamics: solvent dependence of high-spin to low-spin conversion in [Fe(bpy)3]2.

In condensed phase chemistry, the solvent can have a significant impact on everything from yield to product distribution to mechanism. With regard to photo-induced processes, solvent effects have been well-documented for charge-transfer states wherein the redistribution of charge subsequent to light absorption couples intramolecular dynamics to the local environment of the chromophore. Ligand-field excited states are expected to be largely insensitive to such perturbations given that their electronic rearrangements are localized on the metal center and are therefore insulated from so-called outer-sphere effects by the ligands themselves. In contrast to this expectation, we document herein a nearly two-fold variation in the time constant associated with the 5T2 → 1A1 high-spin to low-spin relaxation process of tris(2,2′-bipyridine)iron(ii) ([Fe(bpy)3]2+) across a range of different solvents. Likely origins for this solvent dependence, including relevant solvent properties, ion pairing, and changes in solvation energy, were considered and assessed by studying [Fe(bpy)3]2+ and related derivatives via ultrafast time-resolved absorption spectroscopy and computational analyses. It was concluded that the effect is most likely associated with the volume change of the chromophore arising from the interconfigurational nature of the 5T2 → 1A1 relaxation process, resulting in changes to the solvent–solvent and/or solvent–solute interactions of the primary solvation shell sufficient to alter the overall reorganization energy of the system and influencing the kinetics of ground-state recovery.

Identifying reactive intermediates by mass spectrometry.

Development of new reactions requires finding and understanding of novel reaction pathways. In challenging reactions such as C–H activations, these pathways often involve highly reactive intermediates which are the key to our understanding, but difficult to study. Mass spectrometry has a unique sensitivity for detecting low abundant charged species; therefore it is increasingly used for detection of such intermediates in metal catalysed- and organometallic reactions. This perspective shows recent developments in the field of mass spectrometric research of reaction mechanisms with a special focus on going beyond mass-detection. Chapters discuss the advantages of collision-induced dissociation, ion mobility and ion spectroscopy for characterization of structures of the detected intermediates. In addition, we discuss the relationship between the condensed phase chemistry and mass spectrometric detection of species from solution.

Competing Molecular and Radical Pathways in the Dissociation of Halons via Direct Chemical Dynamics Simulations.

A great deal of attention has been given to the decomposition chemistry of halons (halomethanes) due to their role in stratospheric ozone depletion. Knowledge of certain aspects of dissociation of halons such as the competition between radical and molecular pathways and their mechanistic details is limited. Halon molecules can isomerize to an iso form containing a halogen-halogen bond and such iso-halon forms have been identified as intermediates in condensed phase chemistry. Recently, a quantum chemistry study of role of iso-halons in the gas phase decomposition of halomethanes has been reported. In the present work, we have investigated the ground state dissociation chemistry of select halon molecules - CF2Cl2, CF2Br2, CHBr3, and CH2BrCl using electronic structure theory calculations and direct chemical dynamics simulations. Classical trajectories were generated on-the-fly using density functional PBE0/6-31G* level of theory at a fixed total energy. Simulation results showed that molecular products, in general, were dominant for all the four molecules at the chosen energy. A variety of mechanisms such as direct dissociation via multicenter transition states, decomposition via isomerization, radical recombinations, and roaming pathways contributed to the formation of molecular products. Atomic level mechanisms are presented, and the role of iso-halons in the gas phase chemistry of halomethanes is clearly established.

Carbon Dioxide Diffusivity in Single, Levitated Organic Aerosol Particles.

The diffusivity of molecules relevant to condensed-phase chemistry within viscous secondary organic aerosol (SOA) remains highly uncertain. Whereas there has been an effort to characterize water diffusivity as well as the diffusivity of larger compounds, data are lacking almost entirely for small molecules, such as carbon dioxide (CO2). Here we use photochemically generated CO2 in single particles of aqueous citric acid as a SOA proxy, levitated in an electrodynamic balance, to deduce CO2 diffusivity in the particle with unprecedented accuracy. For medium viscosities at intermediate relative humidities (∼25-40% RH), we find CO2 diffusivities DCO2 ≈ 10-14 m2 s-1, agreeing with the Stokes-Einstein relationship based on current viscosity data but 10 times lower than that for water. Conversely, under dry high-viscosity conditions, we find that DCO2 ≈ 10-16 m2 s-1, which is 10 times higher than for water. We infer that the chemical degradation of atmospheric SOA particles will likely not be limited by CO2 diffusivity.

Apparent contradiction between calculated kinetic and potential energy fractions of phonons in molecular solids with implications on condensed-phase chemistry

ABSTRACTMany computational and experimental analyses of molecular excitation rely on relative atomic velocities to identify the excitation of chemical bonds. These are often interpreted through the aid of normal mode calculations. We address two potential gaps in this approach: 1. Relative velocities may not reflect the total potential energy absorbed by the bond. 2. Normal mode calculations omit interactions between neighboring molecules, effectively assuming a similarity between condensed- and gas-phase chemistry. Phonon calculations implicitly include interactions between neighboring molecules and allow analyses of both relative velocities and potential energies in solids.In the present work, we compare kinetic and potential energy fractions of the phonon modes of the molecular solids nitromethane and β-HMX. We show that velocity-based methods are likely sufficient to analyze nitromethane. However, they cannot detect the majority of excitation ofthe N-N bonds in β-HMX, the scission of which appears to begin major decomposition pathways in the molecules.In the broader context of condensed-phase chemistry, this implies that important interactions may not all be identifiable through analyses that rely solely on relative atomic velocities.

Reactivity of Metal Clusters.

We summarize here the research advances on the reactivity of metal clusters. After a simple introduction of apparatuses used for gas-phase cluster reactions, we focus on the reactivity of metal clusters with various polar and nonpolar molecules in the gas phase and illustrate how elementary reactions of metal clusters proceed one-step at a time under a combination of geometric and electronic reorganization. The topics discussed in this study include chemical adsorption, addition reaction, cleavage of chemical bonds, etching effect, spin effect, the harpoon mechanism, and the complementary active sites (CAS) mechanism, among others. Insights into the reactivity of metal clusters not only facilitate a better understanding of the fundamentals in condensed-phase chemistry but also provide a way to dissect the stability and reactivity of monolayer-protected clusters synthesized via wet chemistry.

Reactive simulation of the chemistry behind the condensed-phase ignition of RDX from hot spots.

Chemical events that lead to thermal initiation and spontaneous ignition of the high-pressure phase of RDX are presented using reactive molecular dynamics simulations. In order to initiate the chemistry behind thermal ignition, approximately 5% of RDX crystal is subjected to a constant temperature thermal pulse for various time durations to create a hot spot. After application of the thermal pulse, the ensuing chemical evolution of the system is monitored using reactive molecular dynamics under adiabatic conditions. Thermal pulses lasting longer than certain time durations lead to the spontaneous ignition of RDX after an incubation period. For cases where the ignition is observed, the incubation period is dominated by intermolecular and intramolecular hydrogen transfer reactions. Contrary to the widely accepted unimolecular models of initiation chemistry, N-N bond dissociations that produce NO2 species are suppressed in the condensed phase. The gradual temperature and pressure increase in the incubation period is accompanied by the accumulation of short-lived, heavier polyradicals. The polyradicals contain intact triazine rings from the RDX molecules. At certain temperatures and pressures, the polyradicals undergo ring-opening reactions, which fuel a series of rapid exothermic chemical reactions leading to a thermal runaway regime with stable gas-products such as N2, H2O and CO2. The evolution of the RDX crystal throughout the thermal initiation, incubation and thermal runaway phases observed in the reactive simulations contains a rich diversity of condensed-phase chemistry of nitramines under high-temperature/pressure conditions.