Vibrational Circular Dichroism Spectroscopy with a Classical Polarizable Force Field: Alanine in the Gas and Condensed Phases.

Polarizable force fields are an essential component for the chemically accurate modeling of complex molecular systems with a significant degree of fluxionality, beyond harmonic or perturbative approximations. In this contribution we examine the performance of such an approach for the vibrational spectroscopy of the alanine amino acid, in the gas and condensed phases, from the Fourier transform of appropriate time correlation functions generated along molecular dynamics (MD) trajectories. While the infrared (IR) spectrum only requires the electric dipole moment, the vibrational circular dichroism (VCD) spectrum further requires knowledge of the magnetic dipole moment, for which we provide relevant expressions to be used with polarizable force fields. The AMOEBA force field was employed here to model alanine in the neutral and zwitterionic isolated forms, solvated by water or nitrogen, and as a crystal. Within this framework, comparison of the electric and magnetic dipole moments to those obtained with nuclear velocity perturbation theory based on density-functional theory for the same MD trajectories are found to agree well with one another. The statistical convergence of the IR and VCD spectra is examined and found to be more demanding in the latter case. Comparisons with experimental frequencies are also provided for the condensed phases.

Direct time-resolved observation of surface-bound carbon dioxide radical anions on metallic nanocatalysts.

Time-resolved identification of surface-bound intermediates on metallic nanocatalysts is imperative to develop an accurate understanding of the elementary steps of CO2 reduction. Direct observation on initial electron transfer to CO2 to form surface-bound CO2•- radicals is lacking due to the technical challenges. Here, we use picosecond pulse radiolysis to generate CO2•- via aqueous electron attachment and observe the stabilization processes toward well-defined nanoscale metallic sites. The time-resolved method combined with molecular simulations identifies surface-bound intermediates with characteristic transient absorption bands and distinct kinetics from nanosecond to the second timescale for three typical metallic nanocatalysts: Cu, Au, and Ni. The interfacial interactions are further investigated by varying the important factors, such as catalyst size and the presence of cation in the electrolyte. This work highlights fundamental ultrafast spectroscopy to clarify the critical initial step in the CO2 catalytic reduction mechanism.

Use of Gaussian-Type Functions for Describing Fast Ion-Matter Irradiation with Time-Dependent Density Functional Theory.

The electronic stopping power is an observable property that quantifies the ability of swift ions to penetrate matter to transfer energy to the electron cloud. The recent literature has proven the value of Real-Time Time-Dependent Density Functional Theory to accurately evaluate this property from first-principles, but questions remain regarding the capability of computer codes relying on atom-centered basis functions to capture the physics at play. In this Perspective, we draw attention to the fact that irradiation by swift ions triggers electron emission into the continuum, especially at the Bragg peak. We investigate the ability of Gaussian atomic orbitals (AOC), which were fitted to mimic continuum wave functions, to improve electronic stopping power predictions. AOC are added to standard correlation-consistent basis sets or STO minimal basis sets. Our benchmarks for water irradiation by fast protons clearly advocate for the use of AOC, especially near the Bragg peak. We show that AOC only need to be placed on the molecules struck by the ion. The number of AOC that are added to the usual basis set is relatively small compared to the total number of atomic orbitals, making the use of such a basis set an excellent choice from a computational cost point of view. The optimum basis set combination is applied for the calculation of the stopping power of a proton in water with encouraging agreement with experimental data.

OH Radical-Induced Oxidation in Nucleosides and Nucleotides Unraveled by Tandem Mass Spectrometry and Infrared Multiple Photon Dissociation Spectroscopy.

OH⋅-induced oxidation products of DNA nucleosides and nucleotides have been structurally characterized by collision-induced dissociation tandem mass spectrometry (CID-MS2 ) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. CID-MS2 results have shown that the addition of one oxygen atom occurs on the nucleobase moiety. The gas-phase geometries of +16 mass increment products of 2'-deoxyadenosine (dA(O)H+ ), 2'-deoxyadenosine 5'-monophosphate (dAMP(O)H+ ), 2'-deoxycytidine (dC(O)H+ ), and 2'-deoxycytidine 5'-monophosphate (dCMP(O)H+ ) are extensively investigated by IRMPD spectroscopy and quantum-chemical calculations. We show that a carbonyl group is formed at the C8 position after oxidation of 2'-deoxyadenosine and its monophosphate derivative. For 2'-deoxycytidine and its monophosphate derivative, the oxygen atom is added to the C5 position to form a C-OH group. IRMPD spectroscopy has been employed for the first time to provide direct structural information on oxidative lesions in DNA model systems.

Structure and bonding patterns in heterometallic organometallics with linear Ln-Pd-Ln motifs.

Complexes with short intermetallic distances between transition metal fragments and lanthanide (Ln) fragments are fascinating objects of study, owing to the ambiguity of the nature of the interaction. The addition of the divalent lanthanide fragments Cp*2Ln(OEt2) (Ln = Sm or Yb) to a Pd(ii) complex bearing the deprotonated form of the redox-active, non-symmetrical ligand, 2-pyrimidin-2-yl-1H-benzimidazole (Hbimpm), leads to two isostructural complexes, of the general formula (Cp*2Ln)2[µ-Pd(pyridyl)2] (Ln = Sm (4) and Yb (5)). These adducts have interesting features, such as unique linear Ln-Pd-Ln arrangements and short Ln-Pd distances, which deviate from the expected lanthanide contraction. A mixed computational and spectroscopic study into the formation of these adducts gathers important clues as to their formation. At the same time, thorough characterization of these complexes establishes the +3 oxidation state of all the involved Ln centers. Detailed theoretical computations demonstrate that the apparent deviation from lanthanide contraction is not due to any difference in the intermetallic interaction between the Pd and the Ln, but that the fragments are joined together by electrostatic interactions and dispersive forces. This conclusion contrasts with the findings about a third complex, Cp*2Yb(µ-Me)2PdCp* (6), formed during the reaction, which also possesses a short Yb-Pd distance. Studies at the CASSCF level of theory on this complex show several orbitals containing significant interactions between the 4f and 4d manifolds of the metals. This demonstrates the need for methodical and careful analyses in gauging the intermetallic interaction and the inadequacy of empirical metrics in describing such phenomena.

Influence of the environment on the infrared spectrum of alanine: An effective mode analysis.

The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000-2000 cm-1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.

Final Products of One-Electron Oxidation of Cyclic Dipeptides Containing Methionine Investigated by IRMPD Spectroscopy: Does the Free Radical Choose the Final Compound?

Reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) and the hydroxyl radical (•OH) have specific functions in biological processes, while their uncontrolled production and reactivity are known to be determining factors in pathophysiology. Methionine (Met) residues act as endogenous antioxidants, when they are oxidized into methionine sulfoxide (MetSO), thus depleting ROS and protecting the protein. We employed tandem mass spectrometry combined with IR multiple photon dissociation spectroscopy to study the oxidation induced by OH radicals produced by γ radiolysis on model cyclic dipeptides c(LMetLMet), c(LMetDMet), and c(GlyMet). Our aim was to characterize the geometries of the oxidized peptides in the gas phase and to understand the relationship between the structure of the 2-center 3-electron (2c-3e) free radical formed in the first step of the oxidation process and the final compound. Density functional theory calculations were performed to characterize the lowest energy structures of the final product of oxidation and to interpret the IR spectra. Collision-induced dissociation tandem mass spectrometry (CID-MS2) experiments of oxidized c(LMetLMet)H+ and c(LMetDMet)H+ led to the loss of one or two oxidized sulfenic acid molecules, indicating that the addition of one or two oxygen atoms occurs on the sulfur atom of both methionine side chains and no sulfone formation was observed. The CID-MS2 fragmentation mass spectrum of oxidized c(GlyMet)H+ showed only the loss of one oxidized sulfenic acid molecule. Thus, the final products of oxidation are the same regardless of the structure of the precursor sulfur-centered free radical.

In-depth theoretical understanding of the chemical interaction of aromatic compounds with a gold nanoparticle.

Gold Nanoparticles (GNPs), owing to their unique properties and versatile preparation strategy, have been demonstrated to exhibit promising applications in diverse fields, which include bio-sensors, catalysts, nanomedicines and radiotherapy. Yet, the nature of the interfacial interaction of GNPs with their chemical environment remains elusive. Experimental vibrational spectroscopy can reveal different interactions of aromatic biological molecules absorbed on GNPs, that may result from changes in the orientation of the molecule. However, the presence of multiple functional groups and the aqueous solvent introduces competition, and complexifies the spectral interpretations. Therefore, our objective is to theoretically investigate the adsorption of aromatic molecules containing various functional groups on the surface of GNPs to comparatively study their preferred adsorption modes. The interaction between Au32, as a model of GNPs, and a series of substituted aromatic compounds that includes benzene, aniline, phenol, toluene, benzoic acid, acetophenone, methyl benzoate, and thiophenol, is investigated. Our computed interaction energies highlight the preference of the aromatic ring to lie flat on the surface. The orientations of the molecules can be distinguished using infrared spectroscopy along with strong changes in intensity and significant shifts of some vibrational modes when the molecule interacts with the GNP. The interaction energy and the electron transfer between the nanoparticle and the aromatic molecule are not found to correlate, possibly because of significant back donation of electrons from GNPs to organic molecules as revealed by charge decomposition analysis. A thorough quantum topological analysis identifies multiple non-covalent interactions and assigns the nature of the interaction mostly to dative interactions between the aromatic ring and the GNP as well as dispersive interaction. Finally, energy decomposition analyses point out the role of the charge transfer energy contribution in the subtle balance of the different physical components.

Consistent Picture of Phosphate-Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization.

The binding of divalent cations to the ubiquitous phosphate group is essential for a number of key biological processes, such as DNA compaction, RNA folding, or interactions of some proteins with membranes. Yet, probing their binding sites, modes, and associated binding free energy is a challenge for both experiments and simulations. In simulations, standard force fields strongly overestimate the interaction between phosphate groups and divalent cations. Here, we examine how different strategies to include electronic polarization effects in force fields─implicitly, through the use of scaled charges or pair-specific Lennard-Jones parameters, or explicitly, with the polarizable force fields Drude and AMOEBA─capture the interactions of a model phosphate compound, dimethyl phosphate, with calcium and magnesium divalent cations. We show that both implicit and explicit approaches, when carefully parameterized, are successful in capturing the overall binding free energy and that common trends emerge from the comparison of different simulation approaches. Overall, the binding is very moderate, slightly weaker for Ca2+ than Mg2+, and the solvent-shared ion pair is slightly more stable than the contact monodentate ion pair. The bidentate ion pair is higher in energy (or even fully unstable for Mg2+). Our results thus suggest practical ways to capture the divalent cations with biomolecular phosphate groups in complex biochemical systems. In particular, the computational efficiency of implicit models makes them ideally suited for large-scale simulations of biological assemblies, with improved accuracy compared to state-of-the-art fixed-charge force fields.

Manifolds of low energy structures for a magic number of hydrated sulfate: SO42-(H2O)24.

Low energy structures of SO42-(H2O)24 have been obtained using a combination of classical molecular dynamics simulations and refinement of structures and energies by quantum chemical calculations. Extensive exploration of the potential energy surface led to a number of low-energy structures, confirmed by accurate calibration calculations. An overall analysis of this large set was made after devising appropriate structural descriptors such as the numbers of cycles and their combinations. Low energy structures bear common motifs, the most prominent being fused cycles involving alternatively four and six water molecules. The latter adopt specific conformations which ensure the appropriate surface curvature to form a closed cage without dangling O-H bonds and at the same time provide 12-coordination of the sulfate ion. A prominent feature to take into account is isomerism via inversion of hydrogen bond orientations along cycles. This generates large families of ca. 100 isomers for this cluster size, spanning energy windows of 10-30 kJ mol-1. This relatively ignored isomerism must be taken into account to identify reliably the lowest energy minima. The overall picture is that the magic number cluster SO42-(H2O)24 does not correspond to formation of a single, remarkable structure, but rather to a manifold of structural families with similar stabilities. Extensive calculations on isomerization mechanisms within a family indicate that large barriers are associated to direct inversion of hydrogen bond networks. Possible implications of these results for magic number clusters of other anions are discussed.

Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study.

While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water-gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNPs of varying sizes were compared to bulk water using classical molecular dynamics and quantum and semi-empirical methods. Classical molecular dynamics was used to understand the change in macroscopic properties of bulk water in the presence of different sizes of GNP, as well as by including salt ions. The analysis of these macroscopic properties has led to the conclusion that larger GNPs induce the rearrangement of water molecules to form a 2D hydrogen-bond network at the interface. Quantum methods were employed to understand the electronic nature of the interaction between water molecules and GNPs along with the change in the water orientation and the vibrational density of states. The stretching region of vibrational density of states was found to extend into the higher wavenumber region, as the size of the GNP increases. This extension represents the dangling water molecules at the interface, as a result of reorientation of the water molecules in the first solvation shell. This multi-level study suggests that in the presence of GNP of increasing sizes, the first water solvation shell undergoes a rearrangement to maximize the water-water interactions as well as the water-GNP interactions.

Bis-cyclooctatetraenyl Thulium(II): Highly Reducing Lanthanide Sandwich Single Molecule Magnets.

Divalent lanthanide organometallics are well-known highly reducing compounds usually used for single electron transfer reactivity and small molecule activation. Thus, their very reactive nature prevented for many years the study of their physical properties, such as magnetic studies on a reliable basis. In this article, the access to rare organometallic sandwich compounds of TmII with the cyclooctatetraenyl (Cot) ligand impacts on the use of divalent organolanthanide compounds as an additional strategy for the design of performing Single Molecule Magnets (SMM). Herein, the first divalent thulium sandwich complex with f13 configuration behaving as a Single Molecule Magnet in absence of DC field is highlighted.

Assessing cluster models of solvation for the description of vibrational circular dichroism spectra: synergy between static and dynamic approaches.

Solvation effects are essential for defining the shape of vibrational circular dichroism (VCD) spectra. Several approaches have been proposed to include them into computational models for calculating VCD signals, in particular those resting on the "cluster-in-a-liquid" model. Here we examine the capabilities of this ansatz on the example of flexible (1S,2S)-trans-1-amino-2-indanol solvated in dimethyl sulfoxide (DMSO). We compare cluster sets obtained from static calculations with results from explicit molecular dynamics (MD) trajectories based on either force field (FF) or first-principles (FP) methods. While the FFMD approach provides a broader sampling of configurational space, FPMD and time-correlation functions of dipole moments account for anharmonicity and entropy effects in the VCD calculation. They provide a means to evaluate the immediate effect of the solvent on the spectrum. This survey singles out several challenges associated with the use of clusters to describe solvation effects in systems showing shallow potential energy surfaces and non-covalent interactions. Static structures of clusters involving a limited number of solvent molecules satisfactorily capture the main effects of solvation in the bulk limit on the VCD spectra, if these structures are correctly weighted. The importance of taking into consideration their fluxionality, i.e. different solvent conformations sharing a same hydrogen bond pattern, and the limitations of small clusters for describing the solvent dynamics are discussed.

Atom economical coupling of benzophenone and N-heterocyclic aromatics with SmI2.

The use of stoechiometric SmI2 in combination with benzophenone and N-heterocyclic aromatics such as bipyridine, phenanthroline and pyridine allows the direct ortho-coupling of both partners in an atom economical reaction free of any other coupling additives. The transformation was investigated by 1H NMR, X-ray studies and theoretical calculations providing reaction intermediates and the reaction mechanism.

Reversible electron transfer in organolanthanide chemistry.

This article relates the synthesis and characterization of novel heterobimetallic complexes containing a low-valent lanthanide, a tetradentate redox non-innocent ligand, viz. the 4,5,9,10-tetraazaphenanthrene, taphen ligand and transition metal fragments of PdMe2 and PtMe2. The experimental results are supported by a theoretical study. Investigation of their reduction properties allowed the formation of isostructural original heterotrimetallic complexes containing two Cp*2Yb fragments and the (taphen)MMe2 (M = Pd and Pt) motifs. These complexes are stable in non-coordinating solvent such as toluene but decompose in coordinating solvents such as thf. Investigation of the internal electron transfer shows that the taphen ligand behaves as a two-electrons reservoir but is capable of transferring back only one electron in thf. This reversible electron(s) transfer is rare in organolanthanide chemistry and show the potential interest of these complexes in reductive chemistry. Additionally, the trinuclear complexes feature odd X-ray crystal structures in which a deviation of symmetry is observed. The latter observation was studied in depth using quantum chemistry calculations highlighting the role of non-covalent weak interactions.

Infrared Spectra of Deprotonated Dicarboxylic Acids: IRMPD Spectroscopy and Empirical Valence-Bond Modeling.

Experimental infrared multiple-photon dissociation (IRMPD) spectra recorded for a series of deprotonated dicarboxylic acids, HO2 (CH2 )n CO 2 - (n=2-4), are interpreted using a variety of computational methods. The broad bands centered near 1600 cm-1 can be reproduced neither by static vibrational calculations based on quantum chemistry nor by a dynamical description of individual structures using the many-body polarizable AMOEBA force field, strongly suggesting that these molecules experience dynamical proton sharing between the two carboxylic ends. To confirm this assumption, AMOEBA was combined with a two-state empirical valence-bond (EVB) model to allow for proton transfer in classical molecular dynamics simulations. Upon suitable parametrization based on ab initio reference data, the EVB-AMOEBA model satisfactorily reproduces the experimental infrared spectra, and the finite temperature dynamics reveals a significant amount of proton sharing in such systems.

Lanthanidocenes: Synthesis, Structure, and Bonding of Linear Sandwich Complexes of Lanthanides.

The Article presents the synthesis, structure, and bonding of a series of neutral and linear sandwich compounds with the cyclononatetraenyl (Cnt) ligand and divalent lanthanides. These compounds account for the emergence of the lanthanidocene series in reference to the ferrocene and uranocene. The synthetic strategy uses the solubility difference between two conformational isomers of the ligand, as well as the isomerization of the compounds induced by solvent coordination, yielding the isomorphous and isostructural neutral and rigorously linear sandwich complexes. The molecular structures feature a Cnt-Ln-Cnt angle of 180° and a ring size close to the Cnt-Cnt(centroid) distance. A qualitative molecular orbital diagram is provided, in D9 d symmetry, and DFT calculations enforce the bonding model.

Small molecule activation with divalent samarium triflate: a synergistic effort to cleave O2.

The divalent samarium triflate salt does not react with CO2 or water, but does react with traces of O2 or N2O to form a tetrameric bis-oxo samarium motif. The reaction with O2 is a 4e- reductive cleavage where the electrons are coming from four different samarium centers. This highlights a rare synergistic effect for cleaving O2, which has no precedent in divalent lanthanide complexes. Additionally, the addition of CO2 to the tetrameric bis-oxo intermediate leads to the formation of a tetrameric bis-carbonate samarium triflate. Thus, the concomitant reaction of CO2 with traces of O2 leads to the same bis-carbonate tetrameric assembly.

Preventing iron(ii) precipitation in aqueous systems using polyacrylic acid: some molecular insights.

We present molecular dynamics simulations of aqueous iron(ii) systems in the presence of polyacrylic acid (PAA) under the extreme conditions that take place in the secondary coolant circuit of a nuclear power plant. The aim of this work is to understand how the oligomer can prevent iron(ii) deposits, and to provide molecular interpretation. We show how, to this end, not only the complexant ability is necessary, but also the chain length compared to iron(ii) concentration. When the chain is long enough, a hyper-complexation phenomenon occurs that can explain the specific capacity of the polymer to prevent iron(ii) precipitation.