Reparameterization of GFN1-xTB for atmospheric molecular clusters: applications to multi-acid-multi-base systems

Atmospheric molecular clusters, the onset of secondary aerosol formation, are a major part of the current uncertainty in modern climate models. Quantum chemical (QC) methods are usually employed in a funneling approach to identify the lowest free energy cluster structures. However, the funneling approach highly depends on the accuracy of low-cost methods to ensure that important low-lying minima are not missed. Here we present a reparameterized GFN1-xTB model based on the clusteromics I-V datasets for studying atmospheric molecular clusters (AMC), denoted AMC-xTB. The AMC-xTB model reduces the mean of electronic binding energy errors from 7-11.8 kcal mol-1 to roughly 0 kcal mol-1 and the root mean square deviation from 7.6-12.3 kcal mol-1 to 0.81-1.45 kcal mol-1. In addition, the minimum structures obtained with AMC-xTB are closer to the ωB97X-D/6-31++G(d,p) level of theory compared to GFN1-xTB. We employ the new parameterization in two new configurational sampling workflows that include an additional meta-dynamics sampling step using CREST with the AMC-xTB model. The first workflow, denoted the "independent workflow", is a commonly used funneling approach with an additional CREST step, and the second, the "improvement workflow", is where the best configuration currently known in the literature is improved with a CREST + AMC-xTB step. Testing the new workflow we find configurations lower in free energy for all the literature clusters with the largest improvement being up to 21 kcal mol-1. Lastly, by employing the improvement workflow we massively screened 288 new multi-acid-multi-base clusters containing up to 8 different species. For these new multi-acid-multi-base cluster systems we observe that the improvement workflow finds configurations lower in free energy for 245 out of 288 (85.1%) cluster structures. Most of the improvements are within 2 kcal mol-1, but we see improvements up to 8.3 kcal mol-1. Hence, we can recommend this new workflow based on the AMC-xTB model for future studies on atmospheric molecular clusters.

Hydrated cation-π interactions of π-electrons with hydrated Mg2+ and Ca2+ cations

Hydrated cation-π interactions at liquid-solid interfaces between hydrated cations and aromatic ring structures of carbon-based materials are pivotal in many material, biological, and chemical processes, and water serves as a crucial mediator in these interactions. However, a full understanding of the hydrated cation-π interactions between hydrated alkaline earth cations and aromatic ring structures, such as graphene remains elusive. Here, we present a molecular picture of hydrated cation-π interactions for Mg2+ and Ca2+ by using the density functional theory methods. Theoretical results show that the graphene sheet can distort the hydration shell of the hydrated Ca2+ to interact with Ca2+ directly, which is water-cation-π interactions. In contrast, the hydration shell of the hydrated Mg2+ is quite stable and the graphene sheet interacts with Mg2+ indirectly, mediated by water molecules, which is the cation-water-π interactions. These results lead to the anomalous order of adsorption energies for these alkaline earth cations, with hydrated Mg2+-π < hydrated Ca2+-π when the number of water molecules is large (n ≥ 6), contrary to the order observed for cation-π interactions in the absence of water molecules (n = 0). The behavior of hydrated alkaline earth cations adsorbed on a graphene surface is mainly attributed to the competition between the cation-π interactions and hydration effects. These findings provide valuable details of the structures and the adsorption energy of hydrated alkaline earth cations adsorbed onto the graphene surface.

Enhancing antibacterial properties by regulating valence configurations of copper: a focus on Cu-carboxyl chelates

Optimizing the antibacterial effectiveness of copper ions while reducing environmental and cellular toxicity is essential for public health. A copper chelate, named PAI-Cu, is skillfully created using a specially designed carboxyl copolymer (a combination of acrylic and itaconic acids) with copper ions. PAI-Cu demonstrates a broad-spectrum antibacterial capability both in vitro and in vivo, without causing obvious cytotoxic effects. When compared to free copper ions, PAI-Cu displays markedly enhanced antibacterial potency, being about 35 times more effective against Escherichia coli and 16 times more effective against Staphylococcus aureus. Moreover, Gaussian and ab initio molecular dynamics (AIMD) analyses reveal that Cu+ ions can remain stable in the carboxyl compound's aqueous environment. Thus, the superior antibacterial performance of PAI-Cu largely stems from its modulation of copper ions between mono- and divalent states within the Cu-carboxyl chelates, especially via the carboxyl ligand. This modulation leads to the generation of reactive oxygen species (˙OH), which is pivotal in bacterial eradication. This research offers a cost-effective strategy for amplifying the antibacterial properties of Cu ions, paving new paths for utilizing copper ions in advanced antibacterial applications.

Interaction of Glutamic Acid/Protonated Glutamic Acid with Amide and Water Molecules: A Theoretical Study

Amino acids are important nitrogen-containing compounds and organic carbon components that exist widely in the atmosphere. The formation of atmospheric aerosols is affected by their interactions with amides. The dimers formed by glutamic acid (Glu) or protonated glutamic acid (Glu⁺) with three kinds of amide molecules (formamide FA, acetamide AA, urea U) and the hydrated clusters formed by Glu or Glu⁺, U molecules along with one to six water molecules were systematically studied at the M06-2X/6-311++G(3df,3pd) level. U is predicted to form a more stable structure with Glu/Glu⁺ than FA and AA by thermodynamics. If the concentration ratio of FA to U is less than 10⁴, U will play a critical role in NPF. The degree of hydration in Glu⁺-mU-nW is higher than that of Glu-mU-nW (m = 0, 1; n = 0-6) clusters. Notably, Glu contributes more to the Rayleigh scattering properties than glutaric acid and sulfuric acid, and thus may lead to the destruction of atmospheric visibility. This study is helpful to better understand the properties of organic aerosols containing amino acids or amides.

Photochemistry of the pyruvate anion produces CO2, CO, CH3-, CH3, and a low energy electron

The photochemistry of pyruvic acid has attracted much scientific interest because it is believed to play critical roles in atmospheric chemistry. However, under most atmospherically relevant conditions, pyruvic acid deprotonates to form its conjugate base, the photochemistry of which is essentially unknown. Here, we present a detailed study of the photochemistry of the isolated pyruvate anion and uncover that it is extremely rich. Using photoelectron imaging and computational chemistry, we show that photoexcitation by UVA light leads to the formation of CO₂, CO, and CH₃⁻. The observation of the unusual methide anion formation and its subsequent decomposition into methyl radical and a free electron may hold important consequences for atmospheric chemistry. From a mechanistic perspective, the initial decarboxylation of pyruvate necessarily differs from that in pyruvic acid, due to the missing proton in the anion.

Pyruvic acid and its conjugate base, the pyruvate anion, are largely present in the atmosphere. Here the authors, using photoelectron imaging and quantum chemistry calculations, investigate the photochemistry of isolated pyruvate anions initiated by UVA radiation and report the formation of CO₂, CO, and CH₃⁻ further decomposing into CH₃ and a free electron.

Stabilizing the Exotic Carbonic Acid by Bisulfate Ion

Carbonic acid is an important species in a variety of fields and has long been regarded to be non-existing in isolated state, as it is thermodynamically favorable to decompose into water and carbon dioxide. In this work, we systematically studied a novel ionic complex [H₂CO₃·HSO₄]^- using density functional theory calculations, molecular dynamics simulations, and topological analysis to investigate if the exotic H₂CO₃ molecule could be stabilized by bisulfate ion, which is a ubiquitous ion in various environments. We found that bisulfate ion could efficiently stabilize all the three conformers of H₂CO₃ and reduce the energy differences of isomers with H₂CO₃ in three different conformations compared to the isolated H₂CO₃ molecule. Calculated isomerization pathways and ab initio molecular dynamics simulations suggest that all the optimized isomers of the complex have good thermal stability and could exist at finite temperatures. We also explored the hydrogen bonding properties in this interesting complex and simulated their harmonic infrared spectra to aid future infrared spectroscopic experiments. This work could be potentially important to understand the fate of carbonic acid in certain complex environments, such as in environments where both sulfuric acid (or rather bisulfate ion) and carbonic acid (or rather carbonic dioxide and water) exist.

Hydrated cation-π interactions of π-electrons with hydrated Li+, Na+, and K+ cations

Cation-π interactions are essential for many chemical, biological, and material processes, and these processes usually involve an aqueous salt solution. However, there is still a lack of a full understanding of the hydrated cation-π interactions between the hydrated cations and the aromatic ring structures on the molecular level. Here, we report a molecular picture of hydrated cation-π interactions, by using the calculations of density functional theory (DFT). Specifically, the graphene sheet can distort the hydration shell of the hydrated K+ to interact with K+ directly, which is hereafter called water-cation-π interactions. In contrast, the hydration shell of the hydrated Li+ is quite stable and the graphene sheet interacts with Li+ indirectly, mediated by water molecules, which we hereafter call the cation-water-π interactions. The behavior of hydrated cations adsorbed on a graphene surface is mainly attributed to the competition between the cation-π interactions and hydration effects. These findings provide valuable details of the structures and the adsorption energy of hydrated cations adsorbed onto the graphene surface.

Hydration motifs of ammonium bisulfate clusters show complex temperature dependence

The role of water in the formation of particles from atmospheric trace gases is not well understood, in large part due to difficulties in detecting its presence under atmospheric conditions and the variety of possible structures that must be screened computationally. Here, we use infrared spectroscopy and variable-temperature ion trap mass spectrometry to investigate the structural motifs adopted by water bound to ammonium bisulfate clusters and their temperature dependence. For clusters featuring only acid-base linkages, water adopts a bridging arrangement spanning an adjacent ammonium and bisulfate. For larger clusters, water can also insert into a bisulfate-bisulfate hydrogen bond, yielding hydration isomers with very similar binding energies. The population of these isomers shows a complex temperature evolution, as an apparent third isomer appears with a temperature dependence that is difficult to explain using simple thermodynamic arguments. These observations suggest that the thermodynamics of water binding to atmospheric clusters such as these may not be straightforward.

Molecular Specificity and Proton Transfer Mechanisms in Aerosol Prenucleation Clusters Relevant to New Particle Formation

Atmospheric aerosol particles influence the Earth's radiative energy balance and cloud properties, thus impacting the air quality, human health, and Earth's climate change. Because of the important scientific and overarching practical implications of aerosols, the past two decades have seen extensive research efforts, with emphasis on the chemical compositions and underlying mechanisms of aerosol formation. It has been recognized that new particle formation (NPF) contributes up to 50% of atmospheric aerosols. Nowadays, the general consensus is that NPF proceeds via two distinct stages: the nucleation from gaseous precursors to form critical nuclei of sub-1-2 nm size, and the subsequent growth into large particles. However, a fundamental understanding of both the NPF process and molecular-level characterization of the critical size aerosol clusters is still largely missing, hampering the efforts in developing reliable and predictive aerosol nucleation and climate models.Both field measurements and laboratory experiments have gathered convincing evidence about the importance of volatile organic compounds (VOCs) in enhancing the nucleation and growth of aerosol particles. Numerous and abundant small clusters composed of sulfuric acid or bisulfate ion and organic molecules have been shown to exist in ∼2 nm sized aerosol particles. In particular, kinetic studies indicated the formation of clusters with one H₂SO₄ and one or two organics being the rate-limiting step.This Account discusses our effort in developing an integrated approach, which involves the laboratory cluster synthesis via electrospray ionization, size and composition analysis via mass spectrometry, photoelectron spectroscopic characterization, and quantum mechanics based theoretical modeling, to investigate the structures, energetics, and thermodynamics of the aerosol prenucleation clusters relevant to NPF. We have been focusing on the clusters formed between H₂SO₄ or HSO₄^- and the organics from oxidation of both biogenic and anthropogenic emissions. We illustrated the significant thermodynamic advantage by involving organic acids in the formation and growth of aerosol clusters. We revealed that the functional groups in the organics play critical roles in promoting NPF process. The enhanced roles were quantified explicitly for specific functional groups, establishing a Molecular Scale that ranks highly hierarchic intermolecular interactions critical to aerosol formation. The different cluster formation pathways, probably mimicking the various polluted industrial environments, that involve cis-pinonic and cis-pinic acids were unveiled as well. Furthermore, one intriguing fundamental phenomenon on the unusual protonation pattern, which violates the gas-phase acidity (proton affinity) prediction, was discovered to be common in sulfuric acid-organic clusters. The mechanism underlying the phenomenon has been rationalized by employing the temperature-dependent experiments of sulfuric acid-formate/halide model clusters, which could explain the high stability of the sulfuric acid containing aerosol clusters. Our work provides critical molecular-level information to shed light on the initial steps of nucleation of common atmospheric precursors and benchmarks critical data for large-scale theoretical modeling to further address problems of environmental interest.

NWPEsSe: An Adaptive-Learning Global Optimization Algorithm for Nanosized Cluster Systems

Global optimization constitutes an important and fundamental problem in theoretical studies in many chemical fields, such as catalysis, materials, or separations problems. In this paper, a novel algorithm has been developed for the global optimization of large systems including neat and ligated clusters in the gas phase and supported clusters in periodic boundary conditions. The method is based on an updated artificial bee colony (ABC) algorithm method, that allows for adaptive-learning during the search process. The new algorithm is tested against four classes of systems of diverse chemical nature: gas phase Au₅₅, ligated Au₈²⁺, Au₈ supported on graphene oxide and defected rutile, and a large cluster assembly [Co₆Te₈(PEt₃)₆][C₆₀]_n, with sizes ranging between 1 and 3 nm and containing up to 1300 atoms. Reliable global minima (GMs) are obtained for all cases, either confirming published data or reporting new lower energy structures. The algorithm and interface to other codes in the form of an independent program, Northwest Potential Energy Search Engine (NWPEsSe), is freely available, and it provides a powerful and efficient approach for global optimization of nanosized cluster systems.

Probing Orientation-Specific Charge-Dipole Interactions between Hexafluoroisopropanol and Halides: A Joint Photoelectron Spectroscopy and Theoretical Study

The interactions between hexafluoroisopropanol (HFIP) and halogen anions X^- (F^-, Cl^-, Br^-, and I^-) have been investigated using negative ion photoelectron (NIPE) spectroscopy and ab initio calculations. The measured NIPE spectrum of each [HFIP·X]^- (X = Cl, Br, and I) complex shows a pattern identical to the corresponding X^- by shifting to the high electron binding energy side, indicative of the formation of the [HFIP···X^-] structure in which X^- interacts with HFIP via charge-dipole interactions. However, the spectrum of [HFIP·F]^- appears completely different from that of F^- and is more similar to the spectrum of the deprotonated HFIP anion (HFIP_-H^-). The geometry and electron density calculations indicate that a neutral HF molecule is formed upon HFIP interacting with F^- via proton transfer, rendering a stable structure of [HFIP_-H···HF]^-. Two conformers of [HFIP_-H·HF]^- with HFIP being in synperiplanar and antiperiplanar configurations, respectively, are observed, providing direct experimental evidences to show the distinctly different and orientation-specific interactions between HFIP and halide anions.

Spectroscopic evidence for intact carbonic acid stabilized by halide anions in the gas phase

The whole series of halide anions can stabilize elusive carbonic acid in the gas phase through dual hydrogen bonds.

A density functional theory study of the molecular interactions between a series of amides and sulfuric acid

Amides, a class of nitrogen-containing organic pollutants in the atmosphere, may affect the formation of atmospheric aerosols by the interactions with sulfuric acid. Here, the molecular interactions of sulfuric acid with formamide, methylformamide, dimethylformamide, acetamide, methylacetamide and dimethylacetamide was investigated by density functional theory. Geometry optimization and Gibbs free energy calculation were carried out at M06-2X/6-311++G(3df,3pd) level. The results indicate that the addition of amides to H₂SO₄ might have a promoting effect on atmospheric new particle formation at 298.15 K and 1 atm. In the initial stage of new particle formation, the binding capacity of amides and sulfuric acid is stronger than ammonia, but weaker than methylamine. It is worth noting that the trans-methylacetamide could have similar capabilities of stabilizing sulfuric acid as dimethylamine. In the presence of water, amides are found to only have a weak enhancement capability on new particle formation. In addition, we can infer from evaporation rate that the small molecule clusters of formamide and sulfuric acid may be more energetically favorable than macromolecule clusters.

Hydration motifs of ammonium bisulfate clusters of relevance to atmospheric new particle formation

We have analyzed the binding motifs of water bound to a prototypical cluster containing three ammonium cations and two bisulfate anions using mass-selective vibrational spectroscopy and quantum chemical calculations.