Energy and spectroscopic parameters of neutral and cations isomers of the CnH2 (n = 2-6) families using high-level ab-initio approaches.

Cationic species, previously detected from ion-induced desorption of solid methane by plasma desorption mass spectrometry (PDMS), and neutral species, are investigated using high-level ab-initio approaches. From a set of 25 cationic and 26 neutral structures belonging to CnH2 (n = 2-6) families, it was obtained the energy, rotational constants, harmonic vibrational frequency, charge distribution and excitation energies. The ZPVE-corrected energies, at CCSD(T)-F12; CCSD(T)-F12/RI/(cc-pVTZ-F12, cc-pVTZ-F12-CABS, cc-pVQZ/C) (n = 2-5) and CCSD(T)/cc-pVTZ (n = 6) levels, reveal that the topology of the most stable isomer vary with n and the charge. Out of 674 harmonic frequencies, those with maximum intensity are generally in the 3000-3500 cm-1 range. Analysis of 169 vertical transition energies calculated with the EOM-CCSD approach, suggest three C6H2 species as potential carriers of the diffuse interstellar bands (DIB). Systematic comparison of properties between neutral and cationic species can assist in the structural description of complex matrices.

Unexpected discovery: "A new 3,3'-bipyrazolo[3,4-b]pyridine scaffold and its comprehensive analysis".

In this study, a novel 3,3'-bipyrazolo [3,4-b]pyridine-type structure was synthesized from 5-acetylamino-3-methyl-1-phenylpyrazole using the Vilsmeier-Haack reaction as a key step. The spectroscopic properties and structural elucidation of the compound were determined with the use of FT-IR, HRMS, 1H NMR, and 13C NMR. Likewise, the theoretical analysis of the IR and NMR spectra allowed peaks to be assigned and a solid correlation was demonstrated between the experimental and theoretical results. Finally, ab initio calculations based on the density functional theory method at the B3LYP/6-311G (d,p) level of theory were used to determine the conformational energy barrier, facilitating the identification of the most probable conformers of the synthesized compound. Overall, our findings contribute to the understanding of bipyrazolo [3,4-b]pyridine derivatives.

Absorption spectra of p-nitroaniline derivatives: charge transfer effects and the role of substituents.

CONTEXT: Push-pull compounds are model systems and have numerous applications. By changing their substituents, properties are modified and new molecules for different applications can be designed. The work investigates the gas-phase electronic absorption spectra of 15 derivatives of push-pull para-nitroaniline (pNA). This molecule has applications in pharmaceuticals, azo dyes, corrosion inhibitors, and optoelectronics. Both electron-donor and electron-withdrawing groups were investigated. Employing machine learning-derived Hammett's constants σm, σm0, σR, and σI, correlations between substituents and electronic properties were obtained. Overall, the σm0 constants presented the best correlation with HOMO and LUMO energies, whereas the σR constants best agreed with the transition energy of the first band and HOMO-LUMO energy gap. Electron-donors, which have lower σR values, redshift the absorption spectrum and reduce the HOMO-LUMO energy gap. Conversely, electron-withdrawing groups (higher σR's) blueshift the spectrum and increase the energy gap. The second band maximum energies, studied here for the first time, showed no correlation with σ but tended to increase with σ. A comprehensive charge transfer (CT) analysis of the main transition of all systems was also carried out. We found that donors (lower σ's) slightly enhance the CT character of the unsubstituted pNA, whereas acceptors (higher σ's) decrease it, leading to increased local excitations within the aromatic ring. The overall CT variation is not large, except for pNA-SO2H, which considerably decreases the total CT value. We found that the strong electron donors pNA-OH, pNA-OCH3, and pNA-NH2, which have the smallest HOMO-LUMO energy gaps and lowest σ's, have potential for optoelectronic applications. The results show that none of the studied molecules is fluorescent in the gas phase. However, pNA-NH2 and pNA-COOH in cyclohexane and water reveal fluorescence upon solvation. METHODS: We investigated theoretically employing the second-order algebraic diagrammatic construction (ADC(2)) ab initio wave function and time-dependent density functional theory (TDDFT) the gas-phase electronic absorption spectra of 15 derivatives of p-nitroaniline (pNA). The investigated substituents include both electron-donor (C6H5, CCH, CH3, NH2, OCH3, and OH,) and electron-withdrawing (Br, CCl3, CF3, Cl, CN, COOH, F, NO2, and SO2H) substituents.

Disentangling the Effects of Laser and Electron Irradiation on AgX (X = Cl, Br, and I): Insights from Quantum Chemical Calculations.

The effects on the lattice structure and electronic properties of different polymorphs of silver halide, AgX (X = Cl, Br, and I), induced by laser irradiation (LI) and electron irradiation (EI) are investigated using a first-principles approach, based on the electronic temperature (Te) within a two-temperature model (TTM) and by increasing the total number of electrons (Ne), respectively. Ab initio molecular dynamics (AIMD) simulations provide a clear visualization of how Te and Ne induce a structural and electronic transformation process during LI/EI. Our results reveal the diffusion processes of Ag and X ions, the amorphization of the AgX lattices, and a straightforward interpretation of the time evolution for the formation of Ag and X nanoclusters under high values of Te and Ne. Overall, the present work provides fine details of the underlying mechanism of LI/EI and promises to be a powerful toolbox for further cross-scale modeling of other semiconductors.

13 C NMR as an analytical tool for the detection of carbonic acid and pKa determination.

NMR spectroscopy has become a standard technique in studies both on carbon capture and storage. 13 C NMR allows the detection of two peaks for carbonated aqueous samples: one for CO2(aq) and another one for the species H2 CO3 , HCO3 - , and CO3 2- -herein collectively named Hx CO3 x-2 . The chemical shift of this second peak depends on the molar fraction of the three species in equilibrium and has been used to assess the equilibrium between HCO3 - and CO3 2- . The detection of H2 CO3 at low pH solutions is hindered, because of the concurrent liberation of CO2 when the medium is acidified. Herein, a valved NMR tube facilitates the detection of the Hx CO3 x-2 peak across a wide pH range, even at pH 1.8 where the dominant species is H2 CO3 . The method employed the formation of frozen layers of NaH13 CO3 and acid solutions within the tube, which are mixed as the tube reaches room temperature. At this point, the tube is already securely sealed, preventing any loss of CO2 to the atmosphere. A spectrophotometry approach allowed the measurement of the actual pH inside the pressurized NMR tube. The chemical shift for H2 CO3 was determined as 160.33 ± 0.03 ppm, which is in good agreement with value obtained by DFT calculations combined with Car-Parrinello molecular dynamics. The H2 CO3 pKa value determined by the present method was 3.41 ± 0.03, for 15% D2 O aqueous medium and 0.8 mol/L ionic strength. The proposed method can be extended to studies about analogs such as alkyl carbonic and carbamic acids.

Molecular Oxygen Trimer: Multiplet Structures and Stability.

We present a detailed theoretical study of the molecular oxygen trimer where the potential energy surfaces of the seven multiplet states have been calculated by means of a pair approximation with very accurate dimer ab initio potentials. In order to obtain all the states a matrix representation of the potential using the uncoupled spin representation has been applied. The S = 0 ${S = 0}$ and S = 1 ${S = 1}$ states are nearly degenerate and low-lying isomers appear for most multiplicities. A crucial point in deciding the relative stabilities is the zero-point energy which represents a sizable fraction of the electronic well-depth. Therefore, we have performed accurate diffusion Monte Carlo studies of the lowest state in each multiplicity. Analysis of the wavefunction allows a deeper interpretation of the cluster structures, finding that they are significantly floppy in most cases.

Water Self-Dissociation is Insensitive to Nanoscale Environments.

Nanoconfinement effects on water dissociation and reactivity remain controversial, despite their importance to understand the aqueous chemistry at interfaces, pores, or aerosols. The pKw in confined environments has been assessed from experiments and simulations in a few specific cases, leading to dissimilar conclusions. Here, with the use of carefully designed ab initio simulations, we demonstrate that the energetics of bulk water dissociation is conserved intact to unexpectedly small length-scales, down to aggregates of only a dozen molecules or pores of widths below 2 nm. The reason is that most of the free-energy involved in water autoionization comes from breaking the O-H covalent bond, which has a comparable barrier in the bulk liquid, in a small droplet of nanometer size, or in a nanopore in the absence of strong interfacial interactions. Thus, dissociation free-energy profiles in nanoscopic aggregates or in 2D slabs of 1 nm width reproduce the behavior corresponding to the bulk liquid, regardless of whether the corresponding nanophase is delimited by a solid or a gas interface. The present work provides a definite and fundamental description of the mechanism and thermodynamics of water dissociation at different scales with broader implications on reactivity and self-ionization at the air-liquid interface.

An approach based on genetic algorithms and machine learning coupled for studying alloy and molecular clusters by optimizing quantum energy surfaces.

A new genetic algorithm has been proposed focusing on direct ab initio potential energy surface (PES) global minima search. Besides the commonly used operators, this new approach uses an operator to: improve the initial cluster generation, classify and compare all generated clusters, and use machine learning to model the quantum PES used in parallel optimization. Part of the validation process for this methodology was done with C u n A u m ( n + m ≤ X for X = 14 , 19 , 38 , 55 ) and A u n A g n ( n = 10 , 20 , 30 , 40 , 50 , 60 , 70 , and 75). The results are in fair agreement with the literature and led to a new global minimum for C u 12 A u 7 . A search has been done for the lowest energies of L i n nanoclusters with 2-8 atoms using the DFT approach and for L i 3 , L i 4 , L i 2 H , L i 3 H using DLPNO-CCSD(T) approach. NQGA successfully performed the MP2 optimizations for ( H 2 O ) 11 cluster. In all cases, the proposed genetic algorithm located the previously reported global minima with very efficient performance. The new proposed methodology makes it possible to optimize cluster geometries directly using high-level ab initio methods relinquishing any bias introduced by a classical approach. Our results show that this proposed method has great potential applications due to its flexibility and efficiency in identifying global minima in the tested atomic systems.

Structure and size-dependent vibrational and thermal properties of Ni clusters: A systematic ab initio approach.

There is scarce information on the vibrational and thermal properties of small Ni clusters. Here, the outcomes of ab initio spin-polarized density functional theory calculations on the size and geometry effects upon the vibrational and thermal properties of Nin (n = 13 and 55) clusters, are discussed. For theses clusters a comparison is presented between the closed shell symmetric octahedral (Oh) and the icosahedral (Ih) geometries. The results indicate that the Ih isomers are lower in energy. Besides, ab initio molecular dynamics runs at T = 300K show that Ni13 and Ni55 clusters transform from their initial Oh geometries towards the corresponding Ih ones. For Ni13, we also consider the lowest energy less symmetric layered 1-3-6-3 structure, and the cuboid, recently observed experimentally for Pt13, which is competitive in energy but is unstable, as phonon analysis reveals. We calculate their vibrational density of states (νDOS) and heat capacity, and compare with the Ni FCC bulk counterpart. The characteristic features of the νDOS curves of these clusters are interpreted in terms of the clusters' sizes, the interatomic distance contractions, the bond order values as well as the internal pressure and strains of the clusters. We find that the softest possible frequency of the clusters is size and structure-dependent, being the smallest for the Oh ones. We identify mostly shear, tangential type displacements involving mainly surface atoms for the lowest frequency of the spectra of both Ih and Oh isomers. For the maximum frequencies of these clusters the central atom shows anti-phase movements against groups of nearest neighbor atoms. An excess of heat capacity at low temperatures with respect to the bulk is found, while at high temperatures a constant limiting value, close but lower to the Dulong and Petit value, is determined.

Effect of Pt Decoration on the Optical Properties of Pristine and Defective MoS2: An Ab-Initio Study.

Using structural relaxation calculations and first-principles molecular dynamics (FPMD), we performed numerical simulations to explore the interaction of a 2D MoS2 surface and a platinum atom, calculating the optical properties of the resulting material. We explored three initial positions for the interaction of the Pt atom and the pristine MoS2 surface, plus another position between Pt and the MoS2 surface with a sulfur vacancy VS. The surface absorbed the Pt atom in all cases considered, with absorption energies ranging from -2.77 eV to -5.83 eV. We calculated the optical properties and band structure of the two cases with the largest absorption energies (-3.45 eV and -5.83 eV). The pristine MoS2 is a semiconductor with a gap of around 1.80 eV. With the adsorption of the Pt atom (the -3.45 eV case), the material reduces its band gap to 0.95 eV. Additionally, the optical absorption in the visible range is greatly increased. The energy band structure of the 2D MoS2 with a sulfur vacancy VS shows a band gap of 0.74 eV, with consequent changes in its optical properties. After the adsorption of Pt atoms in the VS vacancy, the material has a band gap of 1.06 eV. In this case, the optical absorption in the visible range increases by about eight times. The reflectivity in the infrared range gets roughly doubled for both situations of the Pt-absorbed atom considered. Finally, we performed two FPMD runs at 300 K to test the stability of the cases with the lowest and highest absorption energies observed, confirming the qualitative results obtained with the structural relaxations.

CO Oxidation Catalytic Effects of Intrinsic Surface Defects in Rhombohedral LaMnO3.

There is an ongoing effort to replace rare and expensive noble-element catalysts with more abundant and less expensive transition metal oxides. With this goal in mind, the intrinsic defects of a rhombohedral perovskite-like structure of LaMnO3 and their implications on CO catalytic properties were studied. Surface thermodynamic stability as a function of pressure (P) and temperature (T) were calculated to find the most stable surface under reaction conditions (P=0.2 atm, T=323 K to 673 K). Crystallographic planes (100), (111), (110), and (211) were evaluated and it was found that (110) with MnO2 termination was the most stable under reaction conditions. Adsorption energies of O2 and CO on (110) as well as the effect of intrinsic defects such as Mn and O vacancies were also calculated. It was found that O vacancies favor the interaction of CO on the surface, whereas Mn vacancies can favor the formation of carbonate species.

Ab initioscreening of two-dimensional CuQxand AgQxchalcogenides.

Two-dimensional (2D) chalcogenides have attracted great interest from the scientific community due to their intrinsic physical-chemical properties, which are suitable for several technological applications. However, most of the reported studies focused on particular compounds and composition, e.g., MoS2, MoSe2, WS2, and WSe2. Thus, there is an increased interest to extend our knowledge on 2D chalcogenides. Here, we report a density functional theory (DFT) screening of 2D coinage-metal chalcogenides (MQx), whereM= Cu, Ag,Q= S, Se, Te,x= 0.5, 1.0, 1.5, 2.0, with the aim to improve our atomistic understanding of the physical-chemical properties as a function of cation (M), anion (Q), and composition (x). Based on 258 DFT calculations, we selected a set of 22 stableMQxmonolayers based on phonons analyses, where we identified 9 semiconductors (7 AgQxand 2 CuQx), with band gaps from 0.07 eV up to 1.67 eV, while the remaining systems have a metallic character. Using all 258 systems, we found a logarithmic correlation between the average weighted bond lengths and effective coordination number of cations and anions. As expected, the monolayer cohesive energies increase with the radius of theQspecies (i.e., from S to Te). Furthermore, an increase in the anion size diminishes the work function for nearly allMQxmonolayers, which can be explained by the nature of the electronic states at the valence band maximum.

Copper isotope composition of hemocyanin.

BACKGROUND: Copper is a metal that plays a central role in biology, for example, as co-factor in various redox enzymes. Its stable isotopic composition is being used as tracer of its transport in living organisms and as a biomarker for diseases affecting its homeostasis. While the application of copper stable isotopes to biological studies is a growing field, there are presently no biological standards that are systematically analyzed in the different laboratories, as it is the case for geological samples (e.g., by using widely available basalt samples). It is therefore paramount for the community to establish such standard. Copper also binds oxygen in the respiratory protein, hemocyanin, in the hemolymph of mollusks and arthropods and is thus critical to respiration for these species. METHODS: Here, the Cu isotope composition of hemocyanin of different modern species of mollusks and arthropods (Megathura crenulate Keyhole limpet, Limulus polyphemus Horseshoe crab and Concholepas concholepas Chilean abalone), as well as theoretical constraints on the origin of these isotopic fractionations through ab initio calculations are reported. RESULTS: The isotopic fractionation factors for Cu(I) and Cu(II), both in hemocyanin and in seawater, predict an enrichment in the lighter isotope of Cu in the hemocyanin by over 1 permil compared to seawater. The hemocyanin of Chilean abalone and Horseshoe crab have Cu isotope compositions (δ65Cu = +0.63 ± 0.04‰ and +0.61 ± 0.04‰, respectively, with δ65Cu the permil deviation of the 65Cu/63Cu ratio from the NIST SRM 976 standard), similar to that of the octopus reported in literature (+0.62‰), that are undistinguishable from seawater, suggesting quantitative Cu absorption for these organisms. Conversely, the Keyhole limpet is enriched in the lighter isotope of Cu, which is in line with the ab initio calculation and therefore Cu isotopic fractionation during incorporation of Cu into the hemocyanin. CONCLUSIONS: Because these hemocyanin standard samples are widely available, they could serve in the future as inter-laboratory standards to verify the accuracy of the Cu isotopic measurements on biological matrices.

Planar Hypercoordinate Carbons in Alkali Metal Decorated CE3 2- and CE2 2- Dianions.

After exploring the potential energy surfaces of Mm CE2 p (E=S-Te, M=Li-Cs, m=2, 3 and p=m-2) and Mn CE3 q (E=S-Te, M=Li-Cs, n=1, 2, q=n-2) combinations, we introduce 38 new global minima containing a planar hypercoordinate carbon atom (24 with a planar tetracoordinate carbon and 14 with a planar pentacoordinate carbon). These exotic clusters result from the decoration of V-shaped CE2 2- and Y-shaped CE3 2- dianions, respectively, with alkali counterions. All these 38 systems fulfill the geometrical and electronic criteria to be considered as true planar hypercoordinate carbon systems. Chemical bonding analyses indicate that carbon is covalently bonded to chalcogens and ionically connected to alkali metals.

Phototribology: Control of Friction by Light.

In dry sliding, the coefficient of friction depends on the material pair and contact conditions. If the material and operating conditions remain unchanged, the coefficient of friction is constant. Obviously, we can tune friction by surface treatments, but it is a nonreversible process. Here, we report active control of friction forces on TiO2 thin films under UV light. It is reversible and stable and can be tuned/controlled with the light wavelength. The analysis of atomic force microscopy signals by wavelet spectrograms reveals different mechanisms acting in the darkness and under UV. Ab initio simulations on UV light-exposed TiO2 show a lower atomic orbital overlapping on the surface, which leads to a friction reduction of up to 60%. We suggest that photocontrol of friction is due to the modification of atomic orbital interactions from both surfaces at the sliding interface.

Taming the Antiferromagnetic Beast: Computational Design of Ultrashort Mn-Mn Bonds Stabilized by N-Heterocyclic Carbenes.

The development of complexes featuring low-valent, multiply bonded metal centers is an exciting field with several potential applications. In this work, we describe the design principles and extensive computational investigation of new organometallic platforms featuring the elusive manganese-manganese bond stabilized by experimentally realized N-heterocyclic carbenes (NHCs). By using DFT computations benchmarked against multireference calculations, as well as MO- and VB-based bonding analyses, we could disentangle the various electronic and structural effects contributing to the thermodynamic and kinetic stability, as well as the experimental feasibility, of the systems. In particular, we explored the nature of the metal-carbene interaction and the role of the ancillary η6 coordination to the generation of Mn2 systems featuring ultrashort metal-metal bonds, closed-shell singlet multiplicities, and positive adiabatic singlet-triplet gaps. Our analysis identifies two distinct classes of viable synthetic targets, whose electrostructural properties are thoroughly investigated.

Neither too Classic nor too Exotic: One-Electron Na⋠B Bond in NaBH3 - Cluster.

It is here reported that the NaBH3 - cluster exhibits a Na⋅B one-electron bond, a well-established type of electron-deficient bonding in the literature. The topological analysis of the electron localization function, at the correlated level, reveals that Na- , when approaching the bonding distance, fairly distributes its valence electron pair between two lobes. One of these electrons is used to bond with BH3 , which participates through its boron empty p-orbital. Furthermore, the bonding situation of LiBH3 - , KBH3 - , MgBH3 , and CaBH3 global minima structures are similar to that of NaBH3 - , extending the family of these new one-electron bond systems with biradicaloid character.

On the stability and chemical bond of noble gas halide cations NgX+ (Ng = He - Rn; X = F - I).

Despite the belief that noble gases (Ng) are completely inert and cannot form stable molecules, a variety of Ng compounds have been reported under laboratory conditions and others were recently detected in the interstellar media, raising interest in knowing and studying their bond nature and the physicochemical properties associated with their stability. In the present work, a systematic analysis of the thermodynamic stability of noble gas halide cations (NgX+ ) at the CCSD(T)/def2-QZVP level have been performed. In addition, chemical bond was characterized through Natural Bonding Theory (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Energy Decomposition Analysis (EDA) with relativistic corrections. All methods suggest that NgX+ compounds possess a strong covalent bond. However, results show that only compounds containing Ar-Rn atoms are thermodynamic stable with a highly energetic and endergonic dissociation process. For these reasons, it is possible to suggest that several compounds that have not yet been reported could be obtained at the laboratory level or observed in the interstellar medium.

Interaction and Reactivity of Cisplatin Physisorbed on Graphene Oxide Nano-Prototypes.

The physical adsorption of cisplatin (CP) on graphene oxide (GO) and reduced graphene oxide (rGO) is investigated at the DFT level of theory by exploiting suitable molecular prototypes representing the most probable adsorbing regions of GO and rGO nano-structures. The results show that the CP binding energy is enhanced with respect to that for the interaction with pristine graphene. This is due to the preferential adsorption of the drug in correspondence of the epoxy and hydroxy groups located on GO basal plane: an energy decomposition analysis of the corresponding binding energy reveals that the most attractive contribution comes from the electrostatic attraction between the -NH 3 ends of CP and the oxygen groups on (r)GO, which can be associated with hydrogen bonding effects. Moreover, it is found that the reactivity of the physically adsorbed CP is practically unaltered being the free energy variation of the first hydrolysis reaction almost matching that of its free (unadsorbed drug) counterpart. The reported results suggest that the CP physical adsorption on GO and rGO carriers is overall feasible being an exergonic process in aqueous solution. The CP adsorption could facilitate its solubility and transport in water solutions, exploiting the high hydrophilicity of the peripheral carboxylic groups located on the edge of the GO and rGO nano-structures. Moreover, the the higher affinity of CP with respect to the oxidized sites suggests a possible dependence of drug loading and release on pH conditions, which would highly facilitate its specific delivery.

IRC data for a mechanistic route starting with H2O adsorption and finishing with H2 desorption from graphene.

Intrinsic reaction coordinate (IRC) data regarding the interactions of water with a carbene-like active site located at the edge of a polyaromatic hydrocarbon [1-3] has been obtained using density functional theory (DFT) and the 6-31g(d) basis set as implemented in the Gaussian 16 software [4]. The data is presented as two videos (frontal and lateral mechanism views) combining four consecutive IRC calculations corresponding to the four different transition states presented on "https://doi.org/10.1016/j.carbon.2020.01.011" [3] (Figure 6, side approach). These videos provide powerful insights on two key aspects: a) the rotational process that occurs during water adsorption and b) the hydrogen gas desorption process during water gasification of carbons.