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.

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.

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.

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.

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.

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.

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.

Strategy for Modeling the Infrared Spectra of Ion-Containing Water Drops.

Hydrated ions are ubiquitous in environmental and biological media. Understanding the perturbation exerted by an ion on the water hydrogen bond network is possible in the nanodrop regime by recording vibrational spectra in the O-H bond stretching region. This has been achieved experimentally in recent years by forming gaseous ions containing tens to hundreds of water molecules and recording their infrared photodissociation spectra. In this paper, we demonstrate the capabilities of a modeling strategy based on an extension of the AMOEBA polarizable force field to implement water atomic charge fluctuations along with those of intramolecular structure along the dynamics. This supplementary flexibility of nonbonded interactions improves the description of the hydrogen bond network and, therefore, the spectroscopic response. Finite temperature IR spectra are obtained from molecular dynamics simulations by computing the Fourier transform of the dipole moment autocorrelation function. Simulations of 1-2 ns are required for extensive sampling in order to reproduce the experimental spectra. Furthermore, bands are assigned with the driven molecular dynamics approach. This method package is shown to compare successfully with experimental spectra for 11 ions in water drops containing 36-100 water molecules. In particular, band frequency shifts of the free O-H stretching modes at the cluster surface are well reproduced as a function of both ion charge and drop size.

Tuning the Stability of Pd(IV) Intermediates Using a Redox Non-innocent Ligand Combined with an Organolanthanide Fragment.

The unique combination of a divalent organolanthanide fragment, Cp*2Yb, with bipyrimidine (bipym) and a palladium bis-alkyl fragment, PdMe2, allows the rapid formation and stabilization of a PdIV tris-alkyl moiety after oxidative addition with MeI. The crucial role of the organolanthanide fragment is demonstrated by the substitution of bipym by the 4,5,9,10-tetraazaphenanthrene ligand, which drastically modifies the electronic structure and tunes the stability of the PdIV species.

Electronic Structures of Mono-Oxidized Copper and Nickel Phosphasalen Complexes.

Non-innocent ligands render the determination of the electronic structure in metal complexes difficult. As such, a combination of experimental techniques and quantum chemistry are required to correctly elucidate them. This paper deals with the one-electron oxidation of copper(II) and nickel(II) complexes featuring a phosphasalen ligand (Psalen), which differs from salen analogues by the presence of iminophosphorane groups (P=N) instead of imines. Various experimental techniques (X-ray diffraction, cyclic voltammetry, NMR, EPR, and UV/Vis spectroscopies, and magnetic measurements) as well as quantum chemical calculations were used to define the electronic structure of the oxidized complexes. These can be modified by a small change in the ligand structure, that is, the replacement of a tert-butyl group by a methoxy on the phenoxide ring. The different techniques have allowed quantifying the amount of spin density located on the metal center and on the Psalen ligands. All complexes were found to possess a multi-configurational ground state, in which the ratio of the +II versus +III oxidation state of the metal center, and therefore the phenolate versus phenoxyl radical ligand character, varies upon the substituents. The tert-butyl group favors a strong localization on the metal center whereas with the methoxy group the metallic configurations decrease and the ligand configurations increase. The importance of the geometrical considerations compared with the electronic substituent effect is highlighted by the differences observed between the solid-state (EPR, magnetic measurements) and solution characterizations (EPR and NMR data).

Assessment of Density Functionals for Computing Thermodynamic Properties of Lanthanide Complexes.

The equilibrium between the radical phenanthroline complex Cp*2 Sm(phen) and the coupling product (Cp*2 Sm(phen))2 has been investigated based on quantum chemistry calculations. Topological analyses pointed out that the C-C bond created has a partial covalent character, explaining why both the monomeric and the dimeric forms exist in equilibrium. A large variety of density functionals have been tested to reproduce experimental thermodynamic data for this equilibrium. Finally, the PBE0-D3 and M06-2X functionals lead to a good evaluation of the energies and enable a correct description of the ligand to metal charge transfer, both in the 4f and 5d metal orbitals.

Divalent Thulium Triflate: A Structural and Spectroscopic Study.

The first molecular TmII luminescence measurements are reported along with rare magnetic, X and Q bands EPR studies. Access to simple and soluble molecular divalent lanthanide complexes is highly sought for small-molecule activation studies and organic transformations using single-electron transfer processes. However, owing to their low stability and propensity to disproportionate, these complexes are hard to synthetize and their electronic properties are therefore almost unexplored. Herein we present the synthesis of [Tm(µ-OTf)2 (dme)2 ]n , a rare and simple coordination compound of divalent thulium that can be seen as a promising starting material for the synthesis of more elaborated complexes. This reactive complex was structurally characterized by X-ray diffraction analysis and its electronic structure has been compared with that of its halide cousin TmI2 (dme)3 .

Chirality-dependent structuration of protonated or sodiated polyphenylalanines: IRMPD and ion mobility studies.

Ion mobility experiments are combined with Infra-Red Multiple Photon Dissociation (IRMPD) spectroscopy and quantum chemical calculations for assessing the role of chirality in the structure of protonated and sodiated di- or tetra-peptides. Sodiated systems show a strong chirality dependence of the competition between Na(+)O and Na(+)π interactions. Chirality effects are more subtle in protonated systems and manifest themselves by differences in the secondary interactions such hydrogen bonds between neutral groups or those involving the aromatic rings.

Structure and thermodynamics of Mg:phosphate interactions in water: a simulation study.

The association of Mg(2+) and H2 PO4 (-) in water can give insights into Mg:phosphate interactions in general, which are very widespread, but for which experimental data is surprisingly sparse. It is studied through molecular dynamics simulations (>100 ns) by using the polarizable AMOEBA force field, and the association free energy is computed for the first time. Explicit consideration of outer-sphere and two types of inner-sphere association provides considerable insight into the dynamics and thermodynamics of ion pairing. After careful assessment of the computational approximations, the agreement with experimental values indicates that the methodology can be extended to other inorganic and biological Mg:phosphate interactions in solution.

Hydration of the sulfate dianion in cold nanodroplets: SO4(2-)(H2O)12 and SO4(2-)(H2O)13.

The structures, energetics and infrared spectra of SO4(2-)(H2O)12 and SO4(2-)(H2O)13 have been investigated by a combination of classical polarizable molecular dynamics and static quantum chemical calculations. Snapshots extracted from MD trajectories were used as inputs for local DFT optimization. Energies of the most stable structures were further refined at the ab initio level. A number of new low energy structures have thus been identified. The most stable structures of SO4(2-)(H2O)12 have the sulfate on the surface of the water cluster, while it may be slightly more burried in SO4(2-)(H2O)13, however still with an incomplete first hydration shell. Differences in the infrared spectra arise in part from mixing of sulfate stretching and water librational modes in the 900-1100 cm(-1) region, leading to some sensitivity of the IR spectrum to the structure. Second shell water molecules however do not generate signatures that are specific enough to relate spectra to structures straightforwardly, at least in this frequency range. Thus the emergence of a new band at 970 cm(-1) in the SO4(2-)(H2O)13 spectrum cannot be taken as a clue as to the number of water molecules which is necessary for a cluster to close the first hydration shell of sulfate. This number is at least 14 and possibly larger. However the density of low energy isomers is large enough that individual structures may loose meaning at all but the lowest temperatures.

Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field.

The calculation of infrared spectra by molecular dynamics simulations based on the AMOEBA polarizable force field has recently been demonstrated [Semrouni et al., J. Chem. Theory Comput., 2014, 10, 3190]. While this approach allows access to temperature and anharmonicity effects, band assignment requires additional tools, which we describe in this paper. The Driven Molecular Dynamics approach, originally developed by Bowman, Kaledin et al. [Bowman et al. J. Chem. Phys., 2003, 119, 646, Kaledin et al. J. Chem. Phys., 2004, 121, 5646] has been adapted and associated with AMOEBA. Its advantages and limitations are described. The IR spectrum of the Ac-Phe-Ala-NH2 model peptide is analyzed in detail. In addition to differentiation of conformations by reproducing frequency shifts due to non-covalent interactions, DMD allows visualizing the temperature-dependent vibrational modes.