Ab Initio Molecular Quantum Research Articles

The Reaction Mechanism and Rates at Ru Single-Atom Catalysts for Hydrogenation of Biomass BHMF to Produce BHMTHF for Renewable Polymers.

Realizing high selectivity for producing biodegradable 2,5-bis(hydroxymethyl)tetrahydrofuran (BHMTHF) for renewable polymers from 5-hydroxymethylfurfural (HMF) biomass through ring hydrogenation on single-atom catalysts poses a considerable challenge due to the complexity of HMF functional groups and the difficulty of H2 dissociation. We developed a detailed reaction mechanism based on ab initio molecular dynamics (AIMD) and quantum mechanics (QM) to find that Ru single-atom catalysts can simultaneously dissociate H2 and perform the ring hydrogenation of biomass-derived 2,5-bis(hydroxymethyl)furan (BHMF) to produce biodegradable BHMTHF, with a free energy barrier of 0.82 eV. The unique property of Ru single-atom sites enables H2 to dissociate easily on a single active site of Ru to participate directly in the reaction without diffusion. Furthermore, our predicted reaction rate from microkinetic analysis indicates that ring hydrogenation and side-chain hydrogenolysis are much faster than ring-opening hydrogenation over the range of 300-550 K. The product BHMTHF dominates with a selectivity of 98.9% at 300 and 78.4% at 550 K (the second product is 5-methylfurfural (5-MFA)). This study underscores the unique effectiveness of Ru single atoms in ring hydrogenation reactions using H2 as the hydrogen source, offering insights for the design of single-atom catalysts for other biomass reactions.

Theoretical insights into the diverse stabilizing effects of fenchyl alcohol/thymol eutectic solvent on carotenoids

Carotenoids, a class of vital natural pigments, are known for their antioxidant properties and are integral to various industrial applications. However, their instability during processing and storage has limited their broader utilization. This study investigated the stabilizing effects of a fenchyl alcohol/thymol-based deep eutectic solvent (DES) on a spectrum of carotenoids, including lutein, zeaxanthin, astaxanthin, and β-carotene. Through a combination of ab initio molecular dynamics (AIMD) simulations and quantum chemical calculations, we elucidated the molecular interactions and stabilization mechanisms within the DES environment (methanol as the benchmark). Our findings reveal that the DES could exert varying degrees of influence on the stability of different types of carotenoids. The temperature-dependent behavior of carotenoids in the DES suggested a complex interplay between hydrogen bonding, dispersion forces, and the inherent structural properties of carotenoids. AIMD simulations provided a detailed picture of the structural organization and hydrogen bond network topology within the DES, highlighting the role of temperature on the stability and orientation of solvent molecules around carotenoids. Energy decomposition analysis (EDA), Hirshfeld surface analysis, and visual study of interactions further dissected the non-covalent interactions, emphasizing the significance of electrostatic and dispersion forces-driven non-covalent interactions (van der Waals dispersion interactions) in stabilizing carotenoids within the DES matrix. In comparison to methanol, the interactions between components of the eutectic system and the target molecules demonstrate enhanced dynamism, increased complementarity, and a greater variety of interaction patterns. This research presented a novel perspective on the use of DESs for the stabilization of carotenoids, offering potential solutions to enhance their industrial applicability and performance. The insights gained from this study are crucial for the development of sustainable and eco-friendly solvent systems, aligning with the growing demand for green chemistry in the pharmaceutical, cosmetic, and food industries.

Theoretical Investigation on the Initial Reaction Mechanism of Hexaethynylbenzene on Au(111) Surface.

Graphyne has attracted considerable interest and attention since its successful synthesis, due to its enormous potential for applications in the fields of electronics, energy, catalysis, information technology, etc. Although various methods for synthesizing graphyne have been explored, single-layer graphynes have not been successfully developed. Hexaethynylbenzene (HEB) is considered an ideal precursor molecule because it can undergo Glaser coupling reactions between molecules to synthesize single layer graphdiyne on single crystal metal surfaces via on-surface reactions. Unfortunately, this method fails to achieve the expected results, and the underlying mechanism is not clear. In this work, we employed a combination of ab initio molecular dynamics (AIMD) and quantum mechanics (QM) methods to investigate the initial reaction mechanism of HEB molecules on a Au(111) surface. We revealed that HEB molecules undergo both intermolecular coupling and intramolecular cyclization on the Au(111) surface. The favorable pathways of these two types of reactions were then distinguished, confirming that the distance between the terminal carbon atoms of the ethynyl groups plays an important role in C-C coupling. The insights revealed from this work could facilitate the rational design of precursor molecules and deepen the understanding of the reaction processes.

Rare Events Sampling Methods for Quantum and Classical Ab Initio Molecular Dynamics.

We provide an approach to sample rare events during classical ab initio molecular dynamics and quantum wavepacket dynamics. For classical AIMD, a set of fictitious degrees of freedom are introduced that may harmonically interact with the electronic and nuclear degrees of freedom to steer the dynamics in a conservative fashion toward energetically forbidden regions. A similar approach when introduced for quantum wavepacket dynamics has the effect of biasing the trajectory of the wavepacket centroid toward the regions of the potential surface that are difficult to sample. The approach is demonstrated for a phenol-amine system, which is a prototypical problem for condensed phase-proton transfer, and for model potentials undergoing wavepacket dynamics. In all cases, the approach yields trajectories that conserve energy while sampling rare events.

Deep eutectic solvent-functionalized amorphous UiO-66 for efficient extraction and ultrasensitive analysis of perfluoroalkyl substances in infant milk powder

In this study, a convenient and effective method for determination of perfluoroalkyl substances (PFASs) in infant formula was developed based on a novel dispersive solid-phase extraction using deep eutectic solvent-functionalized amorphous UiO-66 (DES/aUiO-66) as sorbent. The synthesis of materials could be achieved without the use of complex and environmentally unfriendly procedures. Parameters were systematically investigated to establish a simple, fast, and efficient green pretreatment method. The method demonstrated high sensitivity, good precision, a detection limit of 0.330–0.529 ng·kg−1, and low matrix effects (< 12.8%). The mechanism for this material was elucidated by ab initio molecular dynamics (AIMD) simulations and quantum chemistry calculations. The presence of massive pore structures and collectively synergistic binding sites facilitated affinity adsorption toward PFASs. Finally, this method was applied to the monitoring of PFASs in 10 actual milk powder samples. This groundbreaking approach opens new possibilities for the advancement of analytical techniques and food safety monitoring.

Selective Synthesis of Functionalized 3(2H)‐Furanones via Tandem Michael Addition/Rearrangement/Cyclization Reaction of Aliphatic Alkynones: A Combined Experimental and Theoretical Study

AbstractA novel catalyst‐ and solvent‐controlled dimerization of aliphatic alkynones through tandem Michael addition/rearrangement/cyclization sequence has been developed. The elaborated protocol provides a convenient chemo‐, regio‐ and stereoselective access to rare 3(2H)‐furanones decorated with 2‐exo‐methylene and 4‐ethenyl functionalities. A comprehensive density functional theory (DFT) study of possible reaction mechanism including ab initio molecular dynamics (AIMD) simulations and quantum theory of atoms in molecules (QTAIM) analysis of various substrate/catalyst/solvent complexes has revealed the Janus‐like behavior of the employed sodium tert‐butoxide/toluene system that is responsible both for the chemoselectivity of the initial addition step and the inhibition of the final cyclization step.

Investigation of the effects of solvent on oxygen evolution reactions on the surface of magnesium oxide

In this research, due to the importance of oxygen evolution reactions (OER) in the production of hydrogen gas, the effects of the solvent on the OER steps on the magnesium oxide surface have been studied. For this purpose, the difference in free energy value in OER steps on the Magnesium oxide surface for two systems (in the presence and the absence of solvent) have been investigated using molecular dynamics (MD) simulation and thermodynamic integration (TI). These results are in perfect agreement with the results obtained from ab initio molecular dynamics simulations and quantum mechanics calculations. Our findings show that the presence of water solvent around the surface of magnesium oxide has a crucial role on OER and leads to an increase more than twofold in the free energy of all steps. Also, the presence of the solvent has the most effect on the third step of OER, and its ΔG increases by about 1.9 eV. This fact can be attributed to the approach of the water molecules to the substrate spontaneously, which increases the probability of forming hydrogen bonds and the number of contacts, leading to more favorable thermodynamic reactions. Close inspection of the calculated binding energies between the substrate and the intermediates confirms that the binding energy of OER's second step is significantly higher than the other steps and is the velocity determining step.

Can the presence of a fluorine-containing functional group in eutectic mixtures indeed bring fluorous affinity for fluorotelomer alcohol?

We focus on deep eutectic solvents (DESs) and investigate their potential for perfluoroalkyl substance (PFAS) remediation through ab initio molecular dynamics (AIMD) simulations and quantum chemistry calculations.

Numerically Exact Solution for a Real Polaritonic System under Vibrational Strong Coupling in Thermodynamic Equilibrium: Loss of Light-Matter Entanglement and Enhanced Fluctuations.

The first numerically exact simulation of a full ab initio molecular quantum system (HD+) under strong ro-vibrational coupling to a quantized optical cavity mode in thermal equilibrium is presented. Theoretical challenges in describing strongly coupled systems of mixed quantum statistics (bosons and Fermions) are discussed and circumvented by the specific choice of our molecular system. Our numerically exact simulations highlight the absence of zero temperature for the strongly coupled matter and light subsystems, due to cavity-induced noncanonical conditions. Furthermore, we explore the temperature dependency of light-matter quantum entanglement, which emerges for the ground state but is quickly lost already in the deep cryogenic regime. This is in contrast to predictions from the Jaynes-Cummings model, which is the standard starting point to model collective strong-coupling chemistry phenomenologically. Moreover, we find that the fluctuations of matter remain modified by the quantum nature of the thermal and vacuum-field fluctuations for significant temperatures, e.g., at ambient conditions. These observations (loss of entanglement and coupling to quantum fluctuations) have implications for the understanding and control of polaritonic chemistry and materials science, since a semiclassical theoretical description of light-matter interaction becomes reasonable, but the typical (classical) canonical equilibrium assumption for the nuclear subsystem remains violated. This opens the door for quantum fluctuation-induced stochastic resonance phenomena under vibrational strong coupling, which have been suggested as a plausible theoretical mechanism to explain the experimentally observed resonance phenomena in the absence of periodic driving that has not yet been fully understood.

Mechanisms of Reactions between HOI and HY (Y = Cl, Br, I) on a Water Nanodroplet Surface.

Iodine chemistry has a broad range of implications for atmospheric processes including new particle formation. Hypoiodous acid (HOI) is a major iodine reservoir species. Its heterogeneous recycling in marine aerosols influences the lifetime of ozone in the troposphere. One important step of such recycling is the reaction between HOI and HY (Y = Cl, Br, I). In this article, we employ ab initio molecular dynamics (AIMD) and quantum chemistry to investigate these reactions at the surface of atmospheric aerosols. Di-halogen (XY) can be formed in a picosecond time scale, with the formation of a loop structure connected by hydrogen and halogen bonds. The photolysis of XY at the surface of an aerosol is faster than in the gas phase. In addition to the formation of di-halogen, a new pathway to forming a [H2O···I···OH2]+ complex by the direct or indirect proton transition is identified. Results presented in this study deepen our understanding of the faster iodine-heterogeneous recycling at the surface of aerosols.

Chemistry without the Born-Oppenheimer approximation.

Chemistry without the Born-Oppenheimer approximation.

Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface.

Ab initio molecular dynamics (AIMD) and quantum mechanics/molecular mechanics (QM/MM) methods are powerful tools for studying proton solvation, transfer, and transport processes in various environments. However, due to the high computational cost of such methods, achieving sufficient sampling of rare events involving excess proton motion—especially when Grotthuss proton shuttling is involved—usually requires enhanced free energy sampling methods to obtain informative results. Moreover, an appropriate collective variable (CV) that describes the effective position of the net positive charge defect associated with an excess proton is essential both for tracking the trajectory of the defect and for the free energy sampling of the processes associated with the resulting proton transfer and transport. In this work, such a CV is derived from first principles using constrained density functional theory (CDFT). This CV is applicable to a broad array of proton transport and transfer processes as studied via AIMD and QM/MM simulations.

The Beginning of HCN Polymerization: Iminoacetonitrile Formation and Its Implications in Astrochemical Environments.

Hydrogen cyanide (HCN) is known to react with complex organic materials and is a key reagent in the formation of various prebiotic building blocks, including amino acids and nucleobases. Here, we explore the possible first step in several such processes, the dimerization of HCN into iminoacetonitrile. Our study combines steered ab initio molecular dynamics and quantum chemistry to evaluate the kinetics and thermodynamics of base-catalyzed dimerization of HCN in the liquid state. Simulations predict a formation mechanism of iminoacetonitrile that is consistent with experimentally observed time scales for HCN polymerization, suggesting that HCN dimerization may be the rate-determining step in the assembly of more complex reaction products. The predicted kinetics permits for iminoacetonitrile formation in a host of astrochemical environments, including on the early Earth, on periodically heated subsurfaces of comets, and following heating events on colder bodies, such as Saturn’s moon Titan.

On the role of water in the hydrogen bond network in DESs: an ab initio molecular dynamics and quantum mechanical study on the urea-betaine system.

We herein report an ab initio molecular dynamics study on a natural DES composed of urea and betaine in a 3 : 2 ratio, as a test case for evaluating the water effect. The article deals with a theoretical study using both ab initio molecular dynamics and quantum chemistry computations in order to unravel the role of water in the nanostructure of a urea-betaine mixture. Preliminary molecular dynamics outcomes (both radial and spatial distribution functions) suggest that water promotes the association between urea and betaine by increasing the hydrogen bond network and precluding the aggregation of urea molecules. In other words, the presence of water allows a less restrictive hydrogen bond network, presenting a regimen where the strong hydrogen bond interactions are replaced by a wide variety of weaker hydrogen bond interactions. On the other hand, in a water free DES there is a regimen where strong urea-betaine interactions are dominant. It is shown that second order perturbation theory energy analysis provides cogent insights into charge spreading and hydrogen bond patterns. A vibrational analysis (both IR and power spectrum) over the ab initio molecular dynamics trajectories in the water free DES as well as in the urea-betaine-water systems reveals that our results are consistent with the second order perturbation theory analysis and with the hydrogen bond network pattern.

Hydration of NH_{4}^{+} in Water: Bifurcated Hydrogen Bonding Structures and Fast Rotational Dynamics.

Understanding the hydration and diffusion of ions in water at the molecular level is a topic of widespread importance. The ammonium ion (NH_{4}^{+}) is an exemplar system that has received attention for decades because of its complex hydration structure and relevance in industry. Here we report a study of the hydration and the rotational diffusion of NH_{4}^{+} in water using abinitio molecular dynamics simulations and quantum MonteCarlo calculations. We find that the hydration structure of NH_{4}^{+} features bifurcated hydrogen bonds, which leads to a rotational mechanism involving the simultaneous switching of a pair of bifurcated hydrogen bonds. The proposed hydration structure and rotational mechanism are supported by existing experimental measurements, and they also help to rationalize the measured fast rotation of NH_{4}^{+} in water. This study highlights how subtle changes in the electronic structure of hydrogen bonds impacts the hydration structure, which consequently affects the dynamics of ions and molecules in hydrogen bonded systems.

Ultrafast interfacial charge transfer from the LUMO+1 in ruthenium(ii) polypyridyl quinoxaline-sensitized solar cells.

This paper describes the implementation of robust and modular sensitizers containing aromatic-amphiphilic ligands to provide new insights into the relationship between the molecular structure and electron injection process governing the efficiency of dye-sensitized solar cells (DSSCs). The significance of this work lies in the combination of favorable experimental and theoretical results in a new class of Ru(ii) polypyridyl complexes with the molecular formula of [Ru(E101)(Dicnq)x(Y)] which is named M101-M104 when X = 1 and Y = bpy, X = 1 and Y = phen, X = 2, and X = 1 and Y = 2 NCS, respectively. E101 and Dicnq ligands are 1,10-phenanthroline-5,6 heptan ammin and 6,7-dicyanodipyrido[2,2-d:2',3'-f]quinoxaline, respectively. The good agreement between the experimental and the time-dependent density functional theory (TDDFT)-calculated absorption spectra of the M101-104 sensitizers allowed us to provide a detailed assignment of the main spectral features of the investigated dyes. M102 which contained phen as an ancillary ligand had the best photovoltaic performance which can be attributed to the higher light harvesting of M102 in the visible light region. A DSSC based on complex M102 without the E101 ligand did not show any observable power conversion efficiency (PCE), indicating the importance of the amphiphilic ligand, E101. Transient absorption studies indicated that the ratio of kreg/krec (krec = the rate constant of the recombination of the dye and kreg = the rate constant of regeneration in the presence of the electrolyte) for M101-104 is 1.1, 2.9, 1.3, and 1.2, clearly confirming a weak competition between dye regeneration and recombination. Therefore, because this ratio for M101, 103, and 104 is small, kreg ≈ krec, the operation of the device has been limited by back electron transports, subsequently enhancing the recombination process. However, the rate of recombination is relatively normal for an efficient DSSC, while the rate of regeneration is very low. Subsequently, the PCE will be poor, confirming the role of aliphatic chains in reducing the recombination process. To obtain a deeper insight into the charge transfer process in the investigated devices, ab initio DFT molecular dynamics simulations and quantum dynamics of electronic relaxation were carried out, clearly showing that the interfacial electron transfer (IET) time scale particularly depends on the type of ancillary ligand. The IET results substantially proved that M102 has the fast lifetime of 2.3 ps and 90 fs for the LUMO and LUMO+1, respectively, indicating the experimentally higher PCE of M102 compared to the other three investigated sensitizers.

Ab Initio Chemical Kinetics for the Thermal Decomposition of SiH4 + Ion and Related Reverse Ion–Molecule Reactions of Interest to PECVD of a-Si:H Films

The thermal unimolecular decomposition of SiH4 + ion and its related reverse reactions, SiH3 + + H and SiH2 + + H2, have been investigated by ab initio molecular orbital and quantum statistical variational RRKM theory calculations. The potential energy surface has been calculated at different levels of theory; the results at the highest level, CCSD(T)/CBS//CCSD(T)/6-311++G(3df,2p), show that the decomposition of SiH4 + can mainly occur via a barrierless channel giving SiH2 + + H2 lying 11.8 kcal/mol above the reactant, or via a transition state forming SiH3 +···H complex to be followed by a barrierless decomposition yielding SiH3 + + H lying 23.5 kcal/mol above the reactant. Barrierless processes were calculated using the CASPT2 and CASSCF methods with the 6-311++G(3df,2p) basis set and fitted with Morse potentials. The rate constants were predicted by solving master equations based on the RRKM theory at the E,J-resolved level; the results show that the channel SiH4 + → SiH2 + + H2 is predominate under PEVCD conditions. For H- and H2-capturing by SiH3 + and SiH2 + ions, respectively, the rate constants were found to be weakly dependent on temperature at the high-pressure limit and decrease rapidly with pressure. The calculated heats of formation of the SiH x + (x = 2–4) ions are in close agreement with available thermochemical data.

Identification of Di(oxymethylene)glycol in the Raman Spectrum of Formaldehyde Aqueous Solutions by ab Initio Molecular Dynamics Simulations and Quantum Chemistry Calculations.

Di(oxymethylene)glycol forms in formaldehyde aqueous solutions by polymerization of methanediol. The structure and hydrogen bond interactions of di(oxymethylene)glycol with water were characterized by performing Car-Parrinello molecular dynamics simulations. The anharmonic vibrational frequencies of di(oxymethylene)glycol in solution were determined with ab initio calculations considering explicitly the hydrogen-bonded water molecules, while other interactions with solvent were described within a polarizable continuum model approach. The calculations allow for a detailed interpretation of the experimental Raman spectrum of formaldehyde aqueous solutions, leading to the assignment of the band at 920 cm(-1) to the symmetric CO stretching mode of di(oxymethylene)glycol.

Saddle-shaped porphyrins for dye-sensitized solar cells: new insight into the relationship between nonplanarity and photovoltaic properties.

We report on the theoretical and experimental studies of the new dye-sensitized solar cells functionalized with 5,10,15,20-tetrakis(4-carboxyphenyl)porphyrin zinc(II) complexes bearing 2- and 8-bromo substituents at the β positions. In agreement with the results of TD-DFT calculations, the absorption maxima of di- and octa-brominated Zn(II) complexes, ZnTCPPBr2 and ZnTCPPBr8, exhibited large red-shift compared to that of the non-brominated free base porphyrin (H2TCPP). Furthermore, DFT calculations showed that the higher stabilization of the LUMO levels relative to the HOMO ones makes the HOMO-LUMO gap of the brominated Zn-porphyrins models smaller compared to that of the nonbrominated counterparts, which explains the red shifts of the Soret and Q bands of the brominated compounds. Solar cells containing the new saddle-shaped Zn(II) porphyrins were subjected to analysis in a photovoltaic calibration laboratory to determine their solar to electric energy conversion. In this regard, we found that the overall conversion efficiency of ZnTCPPBr8 adsorbed on TiO2 nanocrystalline films was 5 times as large as that of ZnTCPPBr2 adsorbed on the same films. The effect of the increasing number of Br groups on the photovoltaic performance of the complexes was compared to the results of computational methods using ab initio DFT molecular dynamics simulations and quantum dynamics calculations of electronic relaxation to investigate the interfacial electron transfer (IET) in TCPPBrx/TiO2-anatase nanostructures. Better IET in ZnTCPPBr8 compared to ZnTCPPBr2, and in H2TCPP was evaluated from interfacial electron transfer (IET) simulations. The IET results indicate that electron injection in ZnTCPPBr8-TiO2 (τ = 25 fs) can be up to 5 orders of magnitude faster than ZnTCPPBr2-TiO2 (τ = 125 fs). Both experimental and theoretical results demonstrate that the increase of the number of bromo-substituents at the β-pyrrole positions of the porphyrin macrocycle created a new class of porphyrin-based DSSC, which exhibits a remarkable increase in the photovoltaic performance compared to non-brominated porphyrins.

New photosensitizers containing the dipyridoquinoxaline moiety and their use in dye-sensitized solar cells

New Ru(II) polypyridyl complexes containing two N, N bidentate ligands, [Ru(phendione)2dpq(COOH)2](BF4)2 (L101), {Ru(phendione)[dpq(COOH)2]2}(BF4)2 (L102) and [Ru(phendione)dpq(COOH)2 (SCN)2](L103), (phendione=5,6 dione-1,10-phenanthroline and dpq(COOH)2=6,7-dicarboxylicdipyrido[2,2-d:2′,3′f]quinoxaline) have been synthesized and characterized, and attached to a TiO2 substrate to be tested as solar cell sensitizers. We found that the solar to electricity conversion efficiency of cell is strongly affected by the type of ancillary ligand, the efficiency of L102 (with one phendione moiety) adsorbed on TiO2 nanocrystalline films being 2.5 times as large as that of L101 (with two phendione moieties) adsorbed on the same films. The effect of ancillary ligand on the photovoltaic performance of the complexes was compared to results of computational methods by ab initio DFT molecular dynamics simulations and quantum dynamics calculations of electronic relaxation to investigate the interfacial electron transfer in L101–103/TiO2-anatase nanostructures. It is found that the primary process in the interfacial electron-transfer dynamics involves an ultrafast (τ1=6fs) electron-injection. The concepts of attribute ancillary ligand substitution and HOMO–LUMO alignment of dye with conduction band of semiconductor and electrolyte redox state are shown very helpful for tuning the photovoltaic properties and the rational architecture of polypyridyl photosensitizer with anticipated good properties.