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Hydrogen bonds (H-bonds) are ubiquitous in peptides and proteins and are central to the stabilization of their structures. Inter-residue H-bonds between non-adjacent backbone amide NH and C=O motifs lead to the well-known secondary structures of helices, turns and sheets, but it is recognized that other H-bonding modes may be significant, including the weak intra-residue H-bond (called a C5 H-bond) that implicates the NH and C=O motifs of the same amino acid residue. Peptide model compounds that adopt stable C5 H-bonds are not readily available and the so-called 2.05-helix, formed by successive C5 H-bonds, is an elusive secondary structure. Using a combination of theoretical chemistry and spectroscopic studies in both the gas phase and solution phase, we have demonstrated that derivatives of 3-amino-1-methylazetidine-3-carboxylic acid, Aatc(Me) can form sidechain–backbone N–H···N C6γ H-bonds that accompany—and thereby stabilize—C5 H-bonds. In the capped trimer of Aatc(Me), extended C5/C6γ motifs are sufficiently robust to challenge classical 310-helix formation in solution and the fully-extended 2.05-helix conformer has been characterized in the gas phase. Concurrent H-bonding support for successive C5 motifs is a new axiom for stabilizing the extended backbone secondary structure in short peptides.

International audience; S-containing amino acids can lead to two types of local NH•••S interactions which bridge backbone NH sites to the side chain to form either intra-or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-L-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C-and N-capped model compound for one Cys(Me) residue adopts a preferred C5-C6γ conformation which combines an intra-residue N−H•••O=C backbone interaction (C5) and an inter-residue N−H•••S interaction implicating the side-chain sulfur atom (C6γ ). In contrast, the dominant conformation of the C-and N-capped model compound featuring two consecutive Cys(Me) residues is a regular type I β-turn. This structure is incompatible with concomitant C6 interactions, which are no longer in evidence. Instead, C5γ interactions occur, that are fully consistent with the turn geometry and additionally stabilize the structure. Comparison with the thietane amino acid Attc, which exhibits a rigid cyclic side chain, pinpoints the significance of side chain flexibility for the specific conformational behavior of Cys(Me).

The first steps of ion dissociation in microhydrated H2-tagged ion pairs (Ca2+, AcO−)(H2O)n=0–8 and (Ba2+, AcO−)(H2O)n=0–5 are revealed by IR photodissociation laser spectroscopy and DFT-D frequency calculations.

International audience; Models of asparagine-containing dipeptides, specifically designed to favor intrinsic folding into an Asx-turn, were characterized both theoretically, using quantum chemistry, and experimentally, using laser spectroscopy in the gas phase. Both approaches provided evidence for the spontaneous folding of both the Asn-Ala and Asn-Gly dipeptide models into the most stable Asx-turn, a conformation stabilized by a C10 H-bond which was very similar to a type II’ $\beta$-turn. In parallel, analysis of the Asx-turns implicating asparagine in crystallized protein structures in the Protein Data Bank revealed a sequence-dependent behavior. In Asn-Ala sequences, the Asx-turn was found in conjunction with a type I $\beta$-turn whose position immediately preceeding the central residues of the turn (position i) was occupied by the Asn residue. The observation that the Asx turn in these structures is mostly of type II’ (i.e. its most stable innate structure) suggests that this motif may foster the formation and/or enhance the stability of the backbone $\beta$-turn. In contrast, the Asx turns observed in Asn-Gly sequences extensively adopted a type II Asx-turn structure, suggesting that their formation should be ascribed to other factors, such as hydration. The fact that the Asx-turn in a Asn-Gly sequence is also often found in combination with a hydrated $\beta$-bulge supports the premise that a Asn-Gly sequence might efficiently promote the formation of the $\beta$-bulge secondary structure.

The present benchmark calculations testify to the validity of time-dependent density functional theory (TD-DFT) when exploring the low-lying excited states potential energy surfaces of models of phenylalanine protein chains. Among three functionals suitable for systems exhibiting charge-transfer excited states, LC-ωPBE, CAM-B3LYP, and ωB97X-D, which were tested on a reference peptide system, we selected the ωB97X-D functional, which gave the best results compared to the approximate coupled-cluster singles and doubles (CC2) method. A quantitative agreement for both the geometrical parameters and the vibrational frequencies was obtained for the lowest singlet excited state (a ππ* state) of the series of capped peptides. In contrast, only a qualitative agreement was met for the corresponding adiabatic zero-point vibrational energy (ZPVE)-corrected excitation energies. Two composite protocols combining CC2 and DFT/TD-DFT methods were then developed to improve these calculations. Both protocols substantially reduced the error compared to CC2 and experiment, and the best of both even led to results of CC2 quality at a lower cost, thus providing a reliable alternative to this method for very large systems.

The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6δ and inter-residue 7δ H-bonds. The aim of the present article is to document how the substitution of sulfur with a selenium atom affects the H-bonding of the Met system. This was investigated both experimentally and theoretically by conformation-resolved optical spectroscopy, following an isolated molecule approach. The present work emphasizes the similarities of the Met and Sem residues in terms of conformational structures, energetics, NH⋯Se/S H-bond strength and NH stretch spectral shifts, but also reveals subtle behavior differences between them. It provides evidence for the sensitivity of the H-bonding network with the folding type of the Sem/Met side-chains, where a simple flip of the terminal part of the side-chain can induce an extra 50 cm−1 spectral shift of the NH stretch engaged in a 7δ NH⋯S/Se bond.

International audience; The present work uses ATR-FTIR spectroscopy assisted by simulations in explicit solvent and frequency calculations to investigate the supramolecular structure of carboxylate alkali-metal ion pairs in aqueous solutions. ATR-FTIR spectra in the 0.25-4.0 M concentration range displayed cation-specific behaviors, which enabled the measurement of the appearance concentration thresholds of contact ion pairs between 1.9 and 2.6 M depending on the cation. Conformational explorations performed using a non-local optimization method associated to a polarizable forcefield (AMOEBA), followed by high quantum chemistry level (RI-B97-D3/dhf-TZVPP) optimizations, mode-dependent scaled harmonic frequency calculations and electron density analyses, were used to identify the main supramolecular structures contributing to the experimental spectra. A thorough analysis enables us to reveal the mechanisms responsible for the spectroscopic sensitivity of the carboxylate group and the respective role played by the cation and the water molecules, highlighting the necessity of combining advanced experimental and theoretical techniques to provide a fair and accurate description of ion pairing.

Nature makes extensive and elaborate use of hydrogen bonding to assemble and stabilize biomolecular structures. The shapes of peptides and proteins rely significantly on N–H⋯O Created by potrace 1.16, written by Peter Selinger 2001-2019 C interactions, which are the linchpins of turns, sheets and helices. The C5 H-bond, in which a single residue provides both donor and acceptor, is generally considered too weak to force the backbone to adopt extended structures. Exploiting the synergy between gas phase (experimental and quantum chemistry) and solution spectroscopies to decipher IR spectroscopic data, this work demonstrates that the extended C5-based conformation in 4-membered ring heterocyclic α-amino acid derivatives is significantly stabilized by the formation of an N–H⋯X H-bond. In this synergic system the strength of the C5 interaction remains constant while the N–H⋯X H-bond strength, and thereby the support provided by it, varies with the heteroatom., In 4-membered ring heterocyclic α-amino acid derivatives, extended conformations based on intraresidue C5 H-bonds can be stabilized by N–H⋯X H-bonds, making the combined C5–C6γ structures prominent in both gas phase and in weakly polar solutions.

In addition to the classical N–H⋯OC non-covalent interaction, less conventional types of hydrogen bonding, such as N–H⋯S, may play a key role in determining the molecular structure. In this work, using theoretical calculations in combination with spectroscopic analysis in both gas phase and solution phase, we demonstrate that both these H-bonding modes exist simultaneously in low-energy conformers of capped derivatives of Attc, a thietane α-amino acid. 6-Membered ring inter-residue N–H⋯S interactions (C6γ), assisted by hyperconjugation between the thietane ring and the backbone, combine with 5-membered ring intra-residue backbone N–H⋯OC interactions (C5) to provide a C5–C6γ feature that stabilizes a planar geometry in the monomer unit. Two contiguous C5–C6γ features in the planar dimer implicate an unprecedented three-centre H-bond of the type CO⋯H(N)⋯SR2, while the trimer adopts two C5–C6γ features separated by a Ramachandran α-type backbone configuration. These low-energy conformers are fully characterized in the gas phase and support is presented for their existence in solution state., In addition to N–H⋯OC bonds, less conventional N–H⋯S hydrogen bonds are found to stabilize extended backbone geometries in derivatives of a thietane α-amino acid, providing a promising tool for the design of new peptidomimetic architectures.

International audience; Benchmarking calculations on excited states of models of phenylalanine protein chains are presented to assess the ability of alternative methods to the standard and most commonly used multiconfigurational wave function-based method, the complete active space self-consistent field (CASSCF), in recovering the non-dynamical correlation for systems that become not affordable by the CASSCF. The exploration of larger active spaces beyond the CASSCF limit is benchmarked through three strategies based on the reduction in the number of determinants: the restricted active space self-consistent field, the generalized active space self-consistent field (GASSCF), and the occupation-restricted multiple active space (ORMAS) schemes. The remaining dynamic correlation effects are then added by the complete active space second-order perturbation theory and by the multireference difference dedicated configuration interaction methods. In parallel, the approximate second-order coupled cluster (CC2), already proven to be successful for small building blocks of model proteins in one of our previous works [Ben Amor et al., J. Chem. Phys. 148, 184105 (2018)], is investigated to assess its performances for larger systems. Among the different alternative strategies to CASSCF, our results highlight the greatest efficiency of the GASSCF and ORMAS schemes in the systematic reduction of the configuration interaction expansion without loss of accuracy in both nature and excitation energies of both singlet ππ* and nπ*CO excited states with respect to the equivalent CASSCF calculations. Guidelines for an optimum applicability of this scheme to systems requiring active spaces beyond the complete active space limit are then proposed. Finally, the extension of the CC2 method to such large systems without loss of accuracy is demonstrated, highlighting the great potential of this method to treat accurately excited states, mainly single reference, of very large systems.I. INTRODU

UV chromophores are frequently used as probes of the molecular structure. In particular, they are sensitive to the electric field generated by the molecular environment, resulting in the observation of Stark effects on UV spectra. While these environment-induced electronic Stark effects (EI-ESE) are already used for conformational analysis in the condensed phase, this work explores the potential of such an approach when performed at much higher conformational resolution in the gas phase. By investigating model alkali benzylacetate and 4-phenylbutyrate ion pairs, where the electric field applied to the phenyl ring is chemically tuned by changing the nature of the alkali cation, this work demonstrates that precise conformational assignments can be proposed based on the correlation between the conformation-dependent calculated electric fields and the frequency of the electronic transitions observed in the experimental UV spectra. Remarkably, the sole analysis of Stark effects and fragmentation patterns in mass-selected UV spectra provided an accurate and complete conformational analysis, where spectral differences as small as a few cm−1 between electronic transitions were rationalized. This case study illustrates that the identification of EI-ESE together with their interpretation at the modest cost of a ground state electric field calculation qualify UV spectroscopy as a powerful tool for conformational analysis., The correlation between experimental electronic transitions and calculated electric fields leads to precise conformational assignments and opens up the possibility of interpreting electronic spectra in a quantitative manner at the wavenumber scale.

S-containing amino acids can lead to two types of local NH···S interactions which bridge backbone NH sites to the side chain to form either intra- or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-L-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas-phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C- and N-capped model compound for one Cys(Me) residue adopts a preferred C5-C6γ conformation which combines an intra-residue N-H···O=C backbone interaction (C5) and an inter-residue N-H···S interaction implicating the side-chain sulfur atom (C6γ). In contrast, the dominant conformation of the C- and N-capped model compound featuring two consecutive Cys(Me) residues is a regular type I β-turn. This structure is incompatible with concomitant C6γ interactions, which are no longer in evidence. Instead, C5γ interactions occur, that are fully consistent with the turn geometry and additionally stabilize the structure. Comparison with the thietane amino acid Attc, which exhibits a rigid cyclic side chain, pinpoints the significance of side chain flexibility for the specific conformational behavior of Cys(Me).

International audience; Models of protein chains containing a seleno-cysteine (Sec) residue have been investigated by gas phase laser spectroscopy in order to document the effect of the H-bonding properties of the SeH group in the folding of the Sec side chain, by comparison with recent data on Ser- and Cys-containing sequences. Experimental data, complemented by quantum chemistry calculations and natural bonding orbital (NBO) analyses, are interpreted in terms of the formation of a so-called 5g intra-residue motif, which bridges the acceptor chalcogen atom of the side chain to the NH bond of the same residue. This local structure, in which the O/S/Se atom is close to the plane of the N-terminal side amide, is constrained by local backbone-side chain hyperconjugation effects involving the S and Se atoms. Theoretical investigations of the Cys/Sec side chain show that (i) this 5g motif is an intrinsic feature of these residues, (ii) the corresponding H-bond is strongly non-linear and intrinsically weak, (iii) but enhanced byg- and b-turn secondary structures, which promote a more favorable 5g H-bonding approach and distance. The resulting H-bonds are slightly stronger in selenocysteine than in cysteine, but nearly inexistent in serine, whose side chain in contrast behaves as a H-bonding donor. The modest spectral shifts of the Cys/Sec NH stretches measured experimentally reflect the moderate strength of the 5g H-bonding, in agreement with the correlation obtained with a NBO-based H-bond strength indicator.The evolution along the Ser, Cys and Sec series emphasizes the compromise between the several factors that control the H-bonding in a hyperconjugation-constrained geometry, among them the chalcogen van der Waals and covalent radii. It also illustrates the 5g H-bond enhancements with the Sec and Cys residues favoured by the constraints imposed by the g- and b-turn structures of the peptide chain

11 pags., 5 figs., 3 tabs., A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field. These structural and spectroscopic results, complemented by a theoretical Natural Bond Orbital analysis, enabled us to document the capacity of the weakly polar-CH2-SH side chain of Cys to adapt itself to the intrinsic local preferences of the peptide backbone, i.e., a γ-turn or a β-sheet extended secondary structure. The corresponding local H-bonding bridges the side chain acceptor S atom to the backbone NH donor site of the same or the next residue along the chain, through a 5-or a 6-membered ring respectively., Support from the French National Research Agency (ANR; Grant ANR-17-CE29-0008 ‘‘TUNIFOLD-S’’) and from the ‘‘Investissements d’Avenir’’ Funding program (LabEx PALM; grant ANR-10-LABX-0039-PALM; DIRCOS) are acknowledged. This work was granted access to the HPC facility of [TGCC/CINES/ IDRIS] under the Grant 2019-A0050807540 awarded by GENCI (Grand Equipement National de Calcul Intensif) and to the CCRT High Performance Computing (HPC) facility at CEA under the Grant CCRT2019-p606bren. We also acknowledge the use of the computing facility cluster Me´soLUM of the LUMAT federation (FR LUMAT 2764). The financial fundings from Ministerio de Ciencia e Innovacion (CTQ2016-76393-P), Junta de Castilla y Leon (Grant VA077U16) and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC-2013-SyG, Grant Agreement no. 610256 NANOCOSMOS, are gratefully acknowledged.

International audience; In addition to the classical N-H/O]C non-covalent interaction, less conventional types of hydrogen bonding, such as N-H/S, may play a key role in determining the molecular structure. In this work, using theoretical calculations in combination with spectroscopic analysis in both gas phase and solution phase, we demonstrate that both these H-bonding modes exist simultaneously in low-energy conformers of capped derivatives of Attc, a thietane a-amino acid. 6-Membered ring inter-residue N-H/S interactions (C6 g), assisted by hyperconjugation between the thietane ring and the backbone, combine with 5-membered ring intra-residue backbone N-H/O]C interactions (C5) to provide a C5-C6 g feature that stabilizes a planar geometry in the monomer unit. Two contiguous C5-C6 g features in the planar dimer implicate an unprecedented three-centre H-bond of the type C]O/H(N)/SR 2 , while the trimer adopts two C5-C6 g features separated by a Ramachandran a-type backbone configuration. These low-energy conformers are fully characterized in the gas phase and support is presented for their existence in solution state.

International audience; Extensive benchmarking calculations are presented to assess the accuracy of the standard approximate coupled cluster singles and doubles method (CC2) in studying ππ* excited states properties of model protein chains containing a phenylalanine residue, namely capped peptides, whose ground state conformers adopt the prototypical secondary structural features of proteins. First, the dependence with the basis set of the CC2 excitation energies, CC2 geometry optimizations, and amide A region frequencies of the lowest ππ* excited state in a reference system, the N-acetylphenylalaninylamide, are investigated, and the results are compared with experimental data. Second, at the best level of theory determined, the CC2/aug(N,O,π)-cc-pVDZ//CC2/cc-pVDZ level, a series of capped peptides of increasing size and containing residues of different nature are investigated. Along the series, compared to the experimental values, a mean absolute error of 0.10 eV is achieved for the 0–0 transition energies with a systematic overestimation. In addition, mode-dependent linear scaling functions for the calculated frequencies of the amide A region have been determined from the set of 95 experimental frequencies available; they lead to a quantitative simulation of the observed shifts of the amide A region frequencies upon ππ* excitation (root-mean-square deviation of 5 cm–1). These results confirm the reliability of the CC2 method to characterize the lowest ππ* excited state of such medium-sized systems, emphasizing this class of theoretical approaches as a relevant spectroscopic tool, including for tasks as difficult as conformational assignment.

International audience; Asparagine (Asn) is a powerful turn-inducer residue, with a large propensity to occupy the second position in the central region of β-turns of proteins. The present work aims at investigating the role of a local anchoring between the Asn side chain and the main chain in this remarkable property. For this purpose, the H-bonding patterns of an asparagine residue in an isolated protein chain fragment forming a γ- or a β-turn have been determined using IR/UV double resonance gas phase spectroscopy on laser-desorbed, jet-cooled short models in conjunction with relevant quantum chemistry calculations. These gas phase data provide evidence for an original double anchoring linking the Asn primary amide side chain (SC), which adopts a gauche+ rotameric form, to its main chain (MC) local environment. From both IR spectroscopic evidence (H-bond induced red shifts) and quantum chemistry, Asn SC is found to behave as a stronger H-bond acceptor than donor, resulting in stronger MC→SC H-bonds than SC→MC ones. These gas phase structural data, relevant to a hydrophobic environment, have been used as a reference to assess the anchoring taking place in high resolution crystallized proteins of the Protein Data Bank. This approach reveals that, when the SC adopts a gauche+ orientation, the stronger MC→SC bonds are preserved in many cases whereas the SC→MC bonds are always disrupted, in qualitative agreement with the gas phase ranking of these interactions. Most interestingly, when Asn occupies the second position of central part of a β-turn (i.e., the very turn-inducer position), the MC→SC H-bonds are also disrupted and replaced by a water-mediated SC to MC anchoring. Owing to the specific features of the hydrated Asn side chain, we propose that it could be a turn precursor structure, able to facilitate turn formation in the early events of the folding process.

International audience; Stark spectral shifts of a molecular probe are commonly used to estimate the local electric field in condensed media. The very large fields reported, typically in the 0.1–10 GV m–1 range, are, however, difficult to reproduce in a controlled manner, limiting the calibration of these molecular probes to ranges below 0.1 GV m–1. In this context, we investigated gas-phase, isolated, molecular ion pairs, where a phenyl ring is immersed in the electric field produced by the nearby ionic groups. The intensity of the electric field is chemically tuned in the 1 GV m–1 range by changing the nature of the cations, and the phenyl ring response is monitored by UV spectroscopy. A quadratic Stark effect is observed, demonstrating the possibility to characterize molecular probes in a solvent-free environment and in the very large field range they typically meet in condensed media such as biological environments.

International audience; Natural bond orbital (NBO) analysis of electron delocalization in a series of capped isolated peptides is used to diagnose amide–amide H-bonding and backbone-induced hyperconjugative interactions, and to rationalize their spectral effects. The sum of the stabilization energies corresponding to the interactions between NBOs that are involved in the H-bonding is demonstrated as an insightful indicator for the H-bond strength. It is then used to decouple the effect of the H-bond distance from that, intrinsic, ofthe donor/acceptor relative orientation, i.e., the geometrical approach. The diversity of the approaches given by the series of peptides studied enables us to illustrate the crucial importance of the approach when the acceptor is a carbonyl group, and emphasizes that efficient approaches can be achieved despite not matching the usual picture of a proton donor directly facing a lone pair of the proton acceptor, i.e., that encountered in intermolecular H-bonds. The study also illustrates the role ofbackbone flexibility, partly controlled by backbone–amide hyperconjugative interactions, in influencing the equilibrium structures, in particular by frustrating or enhancing the HB for a given geometrical approach. Finally, the presently used NBO-based HB strength indicator enables a fair prediction of the frequency of the proton donor amide NH stretching mode, but this simple picture is blurred by ubiquitous hyperconjugative effects between the backbone and amide groups, whose magnitude can becomparable to that of the weakest H-bonds.

The effect of complexation with sulfuric acid on the photo-dissociation of protonated Cinchona alkaloids, namely cinchonidine (Cd), quinine (Qn) and quinidine (Qd), is studied by combining laser spectroscopy with quantum chemical calculations. The protonated complexes are structurally characterized in a room-temperature ion trap by means of infra-red multiple photon dissociation (IRMPD) spectroscopy in the fingerprint and the ν(XH) (X = C, N, O) stretch regions. Comparison with density functional theory calculations including dispersion (DFT-D) unambiguously shows that the complex consists of a doubly protonated Cinchona alkaloid strongly bound to a bisulfate HSO4- anion, which bridges the two protonated sites of the Cinchona alkaloid. UV excitation of the complex does not induce loss of specific photo fragments, in contrast to the protonated monomer or dimer, for which photo-specific fragments were observed. Indeed the UV-induced fragmentation pattern is identical to that observed in collision-induced dissociation experiments. Analysis of the nature of the first electronic transitions at the second order approximate coupled-cluster level (CC2) explains the difference in the behavior of the complex relative to the monomer or dimer towards UV excitation.

International audience; In solution, an ion pair consists of a positive ion (cation, z+) and a negative ion (anion, z-) bonded together by the attractive electrostatic forces between them, forming a supramolecular neutral complex. Several types of ion pairs coexist: contact (CIP), solvent-shared (SIP) and solvent-separated (SSIP), in equilibrium with free ions (FI); their distribution depends on many parameters, and especially the ion concentration. Ion pairing occurs frequently in environments that are naturally rich in ions like seawater, inorganic atmospheric aerosol particles, or living organisms, and thus is of central importance in understanding chemical and biological processes in solution. Ion pairing is suspected to be involved in many ion specific effects, but their characterization as well as their properties still remain mostly to be understood despite the numerous experiments carried out in solution during the past decades. In addition, theoretical chemistry approaches often struggle to establish a quantitative picture of ion pairing. A striking example of the difficulties encountered is illustrated by a recent set of studies on carboxylate anions paired with alkali metal cations which have led to inconsistent conclusions.[1,2] Relying on IR spectroscopic experiments recently developed in our group on isolated neutral ion pairs,[3] we investigated carboxylate anions paired to alkali metal cations by using an original approach where gas phase results were used as an input to refine high level quantum chemistry calculations in solution, leading to an unprecedented level of accuracy in vibrational frequency prediction. First, gas phase experiments focused on a series of isolated contact ion pairs ([M+, Ph-CH2-COO-] with M= Li, Na, K, Rb, Cs) for which UV and conformer-selective IR spectra were recorded. These experiments provided vibrational frequencies of the carboxylate stretch enabling us to assess the accuracy of mode-dependent scaled harmonic frequency calculations at the RI-B97-D3/dhf-TZVPP level. This level of calculation was then employed on large water clusters embedding a free acetate ion or its CIPs or SIPs with a sodium cation to obtain the individual vibrational spectra of these species in solution. These theoretical results show that the stretching modes of carboxylate are sensitive to both SIP and CIP formation. FT-IR spectroscopy confirms this finding since solutions of increasing concentrations exhibit spectral evolutions consistent with the presence of specific types of solvent-shared and contact ion pairs. By providing relevant guidelines for the interpretation of solution phase IR spectra, this work illustrates the potential of the approach for the elucidation of supramolecular structures in electrolyte solutions.[4]

International audience; High resolution infrared spectroscopy combining an external cavity quantum cascade laser with a pulsed pin hole supersonic jet is used to investigate small van der Waals (vdW) heteroclusters containing SF6 and rare gas (Rg) atoms in the ν3 region of SF6. In the first step of the analysis, the rovibrational band contours of parallel and perpendicular transitions of 1 : 1 SF6–Rg heterodimers (Rg = Ar, Kr, Xe) are simulated to derive ground and excited state parameters and hence ground state and equilibrium S–Rg distances with a precision better than 0.5 pm. These values are used to assess quantum chemistry calculations (DFT-D method) as well as semi-empirical predictions (combination rules). In the second step, the spectral signatures of the 1 : 1 heterodimers and of larger heteroclusters containing up to three Rg atoms have been identified by considering reduced vibrational red shifts, i.e., shifts normalized to the average 1 : 1 red shift. The reduced vibrational red shifts within the series of bands observed and assigned to 1 : 1 and 1 : 2 complexes are found to be independent of the Rg atom, which suggests similar 1 : 1 and 1 : 2 structures along the Rg series. In addition, the increasing number of bands when going from monomer to 1 : 2 complexes illustrates the increased lifting of vibrational degeneracy induced by Rg solvation. Finally, the vibrational shifts of the 1 : 1 SF6–Rg heterodimers are found to fit an intermolecular interaction model in which long-range attractive and short-range repulsive contributions to the vibrational shift are found to partially cancel out, the former being dominant. From the same model, well depths are obtained and are found to compare well with quantum chemistry calculations and semi-empirical combination rules.

International audience; A benchmark set of relevant geometries of a model protein, the N-acetylphenylalanylamide, is presented to assess the validity of the approximate second-order coupled cluster (CC2) method in studying low-lying excited states of such bio-relevant systems. The studies comprise investigations of basis-set dependence as well as comparison with two multireference methods, the multistate complete active space 2nd order perturbation theory (MS-CASPT2) and the multireference difference dedicated configuration interaction (DDCI) methods. First of all, the applicability and the accuracy of the quasi-linear multireference difference dedicated configuration interaction method have been demonstrated on bio-relevant systems by comparison with the results obtained by the standard MS-CASPT2. Second, both the nature and excitation energy of the first low-lying excited state obtained at the CC2 level are very close to the Davidson corrected CAS+DDCI ones, the mean absolute deviation on the excitation energy being equal to 0.1 eV with a maximum of less than 0.2 eV. Finally, for the following low-lying excited states, if the nature is always well reproduced at the CC2 level, the differences on excitation energies become more important and can depend on the geometry.

This work describes the use of conformer-selective laser spectroscopy following supersonic expansion to probe the local folding proclivities of four-membered ring cyclic β-amino acid building blocks. Emphasis is placed on stereochemical effects as well as on the structural changes induced by the replacement of a carbon atom of the cycle by a nitrogen atom. The amide A IR spectra are obtained and interpreted with the help of quantum chemistry structure calculations. Results provide evidence that the building block with a trans-substituted cyclobutane ring has a predilection to form strong C8 hydrogen bonds. Nitrogen-atom substitution in the ring induces the formation of the hydrazino turn, with a related but distinct hydrogen-bonding network: the structure is best viewed as a bifurcated C8/C5 bond with the N heteroatom lone electron pair playing a significant acceptor role, which supports recent observations on the hydrazino turn structure in solution. Surprisingly, this study shows that the cis-substituted cyclobutane ring derivative also gives rise predominantly to a C8 hydrogen bond, although weaker than in the two former cases, a feature that is not often encountered for this building block.

International audience; The stereochemistry of hydrazides makes them especially interesting as building blocks for molecular design. An exhaustive conformational analysis of three model hydrazides was conducted in a conformer-selective approach by using a combination of high-level quantum chemistry calculations and vibrational spectroscopy in the gas phase and in solution. The NH stretch frequency was found to be highly sensitive to hyperconjugation, thus making it an efficient probe of the conformation of the neighboring nitrogen atom. This property greatly assisted the identification of the isomers observed experimentally in the conformer pool. A rationalization of the hydrazide conformational landscape is proposed, therefore paving the way for a better characterization of secondary structures in larger systems.

International audience; Conformer-selective IR gas phase spectroscopy and high level quantum chemistry methods have been used to characterise the diversity of local NH–π interactions between the π ring of a phenylalanine aromatic residue and the nearby main chain amide groups. The study of model systems shows how the amide NH stretch vibrational features, in the 3410–3460 cm−1 frequency range, can be used to monitor the strength of these local π H-bonds, which is found to depend on both the backbone conformation and the aromatic side chain orientation. This is rationalized in terms of partial electron transfer between the π cloud and the main chain NH bonds, with the help of analysis tools based on Natural Bonding Orbitals and Non-Covalent Interactions plots. The experimental study, extended to the NH–π interactions when the Phe residue is excited in its first ππ* electronic state, also demonstrates the principle of the ππ* labelling technique, i.e. a selective labelling of those NH bonds in a peptide molecule that are in close contact with an aromatic ring, as an elegant tool for IR spectroscopic assignments. The validation of theoretical predictions against experimental data (frequency change upon excitation) eventually qualifies the use of the CC2 method for the description of the ππ* excited states of systems having a phenyl ring, both in terms of structure, vibrational modes and nature of excited states.

International audience; The coexistence of several types of ion pairs in solution together with their elusive nature hampers their experimental characterization, which relies in practice on theoretical models resorting to numerous approximations. In this context, a series of isolated contact ion pairs between a lithium cation and phenyl-tagged carboxylate anions of various lengths (Ph-(CH2)n-COO−, n = 1−3) has been investigated in a conformer-selective manner by IR and UV laser spectroscopy, in conjunction with quantum chemistry calculations. The typical gas-phase IR signature of the bidentate structure formed between the carboxylate moiety and Li+ has thus been obtained in the CO2 − stretch region. In addition to the cation− anion interaction, a cation−π interaction occurs simultaneously in the largest system investigated (n = 3). The resulting distorted ion pair structure has been evidenced from both the IR signature of the CO2 − stretches and the unique vibrationally resolved UV spectroscopy of a phenyl ring interacting with a cation. Such specific spectroscopic signatures of contact ion pairs provide experimental benchmarks, alternative to theoretical predictions, that can assist the assignment of vibrational spectra in solution.

International audience; The validity of the description of the DFT approximations currently implemented in plane wave DFT codes (LDA, GGA, meta-GGA, hybrid, GGA + empirical dispersion correction) for interactions between rare gases and open-shell atoms which form materials is poorly known. We have performed a first assessment of the accuracy of these functionals for the description of the bonds formed by helium, argon, krypton and xenon with various open-shell atoms. This evaluation has been done on model molecular systems for which precise experimental data are available and reference post-Hartree-Fock calculations (CCSD(T) using large basis sets) are feasible. The results show that when the rare gas atom shares density with the neighbouring atoms, the GGA functionals yield good geometries and qualitatively correct binding energies, even if these are quite significantly overestimated. The use of hybrid functionals enables us to obtain good geometries and satisfactory binding energies. For compounds in which the rare gas atom forms weak dispersive-like bonding, the accuracy yielded by the various functionals is not as good. No functional gives satisfactory binding energies for all the compounds investigated. Several GGA and hybrid functionals yield correct geometries, even if some isomers are not obtained. One GGA functional (PBE) yields qualitatively correct results for the compounds of the three rare gases and several hybrid functionals give satisfactory energies for He compounds. The addition of an empirical dispersive correction improves the results on association compounds, but several isomers are not found.

(Dibenzoylmethanato)boron difluoride (DBMBF2) was found to form with benzene (B) and its methylated derivatives (MB) in cyclohexane (cHex) two types of ground state complexes. The first complexes with low stoichiometries 2 : 1, 1 : 1 and 1 : 2 do not fluoresce when they are excited. On the other hand, the ground state complexes with high stoichiometry, DBMBF2–(B)n or DBMBF2–(MB)n (with n ≫ 2), exhibit a strong fluorescence in their excited states. These findings differ from the previous results, where the strongly fluorescing complexes have been argued to be the 1 : 1 and 1 : 2 exciplexes, complexes of the singlet excited state of DBMBF2 with one or two B or MB molecules. These differences are discussed in terms of the solute–solute and solute–solvent interactions when DBMBF2 and MB are solutes in cyclohexane or when MB is a co-solvent of cyclohexane in binary mixtures of DBMBF2. We also argue that the use of well-suited analytical methods is important for the determination of the nature of the various complexes. Furthermore, to understand the nature of the interactions between benzene and DBMBF2 molecules, we attempt to predict the sites of interaction between DBMBF2 and benzene molecules by determining theoretically the structure of the 1 : 1 complex.

Recent experiments have investigated the dissociative ionization of NaI and CsI, each aggregated with a molecule of acetonitrile CH3CN, using two femtosecond laser pulses. The first, the pump pulse, excites the NaI or CsI diatom to a dissociative state. The second, the probe pulse, then ionizes the sodium or cesium atom after a variable delay time, and the resulting ion is detected. In the case of NaI, the ion signal is characterized by a single maximum. For CsI, however, an oscillatory signal is observed. By performing two-dimensional wave packet propagations, we are able to reproduce this behavior, which can be explained using simple physical arguments.

International audience; A conformation-selective photophysics study in phenylalanine model peptides, combining pump-probe gas phase experiments and excited state calculations, highlights for the first time the quenching properties of a primary amide group (through its nπ* excited state) along with the effect of vibrational energy that facilitates access to the conical intersection area.

International audience; The primary step of the near UV photophysics of a phenylalanine residue is investigated in one- and two-color pump–probe R2PI nanosecond experiments carried out on specific conformers of the Ac-Gly-Phe-NH2 molecule and related neutral compounds isolated in a supersonic expansion. Compared to toluene, whose ππ* state photophysics is dominated by intersystem crossing with a lifetime of [similar]80 ns at the origin, the first ππ* state of Phe in the peptide environment is systematically found to be shorter-lived. The lifetime at the origin of transition is found to be significantly shortened in the presence of a primary amide (–CONH2) group (20–60 ns, depending on the conformer considered), demonstrating the existence of an additional non-radiative relaxation channel related to this chemical group. The quenching effect induced by the peptide environment is still more remarkable beyond the origin of the ππ* state, since vibronic bands of one of the 4 conformers observed (the 27-ribbon conformation) become barely detectable in the ns R2PI experiment, suggesting a significant conformer-selective lifetime shortening (below 100 ps). These results on dipeptides, which extend previous investigations on shorter Phe-containing molecules (N-Ac-Phe-NH2 and N-Ac-Phe-NH-Me), confirm the existence of conformer-dependent non-radiative deactivation processes, whose characteristic timescales range from tens of ns down to hundreds of ps or below. This dynamics is assigned to two distinct mechanisms: a first one, consistent with an excitation energy transfer from the optically active ππ* state to low-lying amide nπ* excited states accessed through conical intersections, especially in the presence of a C-terminal primary amide group (–CONH2); a second one, responsible for the short lifetimes in 27 ribbon structures, would be more specifically triggered by phenyl ring vibrational excitations. Implications in terms of spectroscopic probing of Phe in a peptide environment, especially in the presence of a quenching amide group, are discussed.

International audience; The intrinsic conformational landscape of two phenylalanine-containing protein chain models (-Gly-Phe- and -Ala-Phe- sequences) has been investigated theoretically and experimentally in the gas phase. The near UV spectroscopy (first ππ* transition of the Phe ring) is obtained experimentally under jet conditions where the conformational features can be resolved. Single-conformation IR spectroscopy in the NH stretch region is then obtained by IR/UV double resonance in the ground state, leading to resolved vibrational spectra that are assigned in terms of conformation and H-bonding content from comparison with quantum chemistry calculations. For the main conformer, whose UV spectrum exhibits a significant Franck–Condon activity in low frequency modes involving peptide backbone motions relative to the Phe chromophore, excited state IR spectroscopy has also been recorded in a UV/IR/UV experiment. The NH stretch spectral changes observed in such a ππ* labeling experiment enable us to determine those NH bonds that are coupled to the phenyl ring; they are compared to CC2 excited state calculations to quantify the geometry change upon ππ* excitation. The complete and consistent series of data obtained enable us to propose an unambiguous assignment for the gallery of conformers observed and to demonstrate that, in these two sequences, three conceptually important local structural motifs of proteins (β-strands, 27 ribbons, and β-turns) are represented. The satisfactory agreement between the experimental conformational distribution and the predicted landscape anticipated from the DFT-D approach demonstrates the capabilities of a theoretical method that accounts for dispersive interactions. It also shows that the flaws, inherent to a resonant two-photon ionization detection scheme, often evoked for aromatic chromophores, do not seem to be significant in the case of Phe.

Infrared induced isomerization of methanol-acetonitrile mixed aggregates trapped in argon and nitrogen matrices has been studied using an optical parametric oscillator for monochromatic irradiations at the OH and CH stretching frequencies of complexed methanol. Several forms of the 1:1 complex have been characterized by most of their vibrational modes; two (Ar) or three (N2) hydrogen-bonded forms are observed after matrix deposition; upon irradiation they are converted into another H-bonded and one non-H-bonded species. This unbonded species is highly unstable, with a lifetime of the order of 24 min in argon at 7.2 K. In the presence of an excess of acetonitrile, larger aggregates are identified, with OH stretching frequencies weakly redshifted with respect to those of the 1:1 complex. They are also infrared photosensitive, giving rise to non-hydrogen- bonded structures. The possible structures of the heterodimer have been calculated theoretically. The deepest minimum of the potential energy surface is th...

An ab initio study of the Nan(OH)n, Nan(OH)n-1+, Agn(OH)n, and Agn(OH)n-1+ clusters with n up to four is presented. The results of this study show that, in accordance with experimental observations, the sodium hydroxide clusters are almost purely ionic, while the Ag-O bond exhibits a significant covalent character. The perturbation caused by the non-spherical OH- group relatively to an atomic anion, as well as the influence on structures and energies of the covalent character of the metal-oxygen bond are determined. The appearance of metal-metal bonds in the silver hydroxide clusters is also discussed. Finally, the theoretical results obtained on the Na-OH clusters are compared to experimental results available on the dissociation of the Nan(OH)n-1+ clusters.

Atomic charge models are known to be unsatisfactory for representing the ab initio electrostatic potential (ESP) of n, -alkanes. A new method for deriving atomic charges and dipoles is proposed and applied to n-alkanes ranging from C4 to C10. Electrostatic parameters found by this method reproduce accurately the ab initio ESP. The issues of transferability and conformational dependence are also addressed by introducing charges and dipoles taken from a truncated distributed multipole analysis, in the same spirit as the restrained electrostatic potential method. A transferable model is proposed for larger alkanes (>C10). We also estimate the error made when using a set of Boltzmann-weighted electrostatic parameters for all conformers. The reduced number of electrostatic sites considered in our model makes it suitable for computer simulation of liquid n-alkanes.

A microscopic approach to the in vacuo energetics of the binding of a water molecule to the side chain of tryptophan, modeled by an indole molecule, is presented. Two binding sites have been studied, the most bound one, which corresponds to the conventional NH−OH2 hydrogen bond and a slightly less bound, so-called π-type hydrogen bond in which the hydrogen atoms interact with the π aromatic ring of indole. The structure of these two complexation sites as well as the potential energy surface has been obtained by a semiempirical model coupled with efficient procedures for the exploration of the surface. The H-bonded complex was observed in the supersonic expansion, and its binding energy (4.84 ± 0.23 kcal/mol) was measured using a laser two-color photofragmentation technique. The nonstandard H-bonded complex, not observed with indole, was observed with 1-methylindole, a substituted indole, in which the formation of the conventional bond is hindered. Its binding energy, measured with a similar accuracy (4.10...

In this paper we report on the structure of van der Waals anthracene–argonn (n=1–6) clusters, which were interrogated by a complete set of experimental diagnoses based upon mass-selective, fragmentation-free, two-color, resonant two-photon ionization and laser induced fluorescence as well as a theoretical modeling of the ionization energy. We were able to provide a global assignment of the spectral features which rests on several independent sources of information: the spectral shifts δν and linewidths of the S1←S0 transition, the ionization energy shifts δI.E. and threshold widths and their comparison with the theoretical simulations, the hole-burning spectra, the structure-specific predissociation dynamics. The existence of two cluster ensembles, which present qualitatively different spectral features and significant relative intensity, has been evidenced for each cluster size. The first ensemble exhibits spectral features, typical of cold, rigid-like clusters. Only one prominent stable structure is found for each cluster size of this ensemble: (1|0) for n=1, (2|0) for n=2, (2|1) for n=3, (2|2) for n=4, (3|2) for n=5, (3|3) for n=6, where the notation (n-p|p) refers to the distribution of the argon atoms between the two molecular sides. The second ensemble has been assigned to more or less `hot' clusters having probably the same (n-p|p) arrangement as the first ones, but excited in high van der Waals vibrational levels through an intracluster vibrational relaxation of anthracene molecules. Results on similar heteroclusters reported in the literature are discussed on the light of our new assignment of the spectral features of small Ant–Arn clusters to structures differing by their internal energy content and not by their configuration.

The present study combines both experiment and molecular dynamics simulations in order to document the ionization behavior of the C6H6−H2O and C6H6−D2O complexes close to the ionization threshold, in particular its nonadiabatic character. Using the two-color two-photon resonant ionization laser technique, the ionization thresholds of these species have been measured together with the threshold for dissociative ionization. A binding energy has been deduced for the neutral species: D0(C6H6−H2O) = 106 ± 4 meV and D0(C6H6−D2O) = 116 ± 5 meV, which significantly increases the precision compared to literature. Using a semiempirical potential model, the minimum energy structures of the neutral and ionic species have been determined, and the potential energy surfaces have been analyzed using a two-dimensional approach. As a result, the formation of a stable C6H6+−H2O complex close to the threshold is found to be controlled by a pure quantum effect and is ascribed to the classically forbidden region of the neutra...

The present study combines both experiment and molecular modeling to describe the photoionization behavior of the gas-phase hydrogen-bonded complexes of phenol with water, methanol, and dimethyl ether, in particular the occurrence of fragmentation following ionization. Using the two-color two-photon resonant ionization laser technique, the threshold for dissociative ionization of these species has been measured. For the first time, precise binding energies have been deduced for the neutral species: D0(phenol−H2O) = 243 ± 5 meV and D0(phenol−CH3OH) = 265 ± 8 meV. Using a semiempirical potential model, the minimum energy structures of both neutral and ionic species have been determined. This theoretical study has emphasized the role of the dispersive interactions in the geometry of these neutral complexes, in particular the interactions between the alkyl group of the solvent molecule (CH3 in the case of methanol or dimethyl ether) and the π-cloud of the aromatic molecule. In addition, the comparison between...

The electron transfer (ET) rates induced by the electronic excitation of different isomers of anthracene complexes with aniline derivatives are deduced from their fluorescence and fluorescence exci...

The existence of isomeric forms of donor−acceptor complexes formed in the supersonic expansion was evidenced by their fluorescence, fluorescence excitation, and hole-burning spectra. For each complex, we observed two types of isomers: one E-isomer with broad structureless excitation spectra yielding diffuse, strongly red-shifted exciplex emission and a number of (one to five) R-isomers with narrow band excitation spectra yielding a resonant emission upon the excitation of the lowest vibrational levels of the excited electronic state and exciplex emission from higher levels. A detailed analysis of their excitation spectra (spectral shifts, vibrational structures, bandwidths) is given. The shape of the ground-state potential energy surface (depths and positions of the energy minima, heights of energy barriers, etc.) was determined by calculations involving the “exchange perturbation” treatment and simulated annealing method. The relation between the properties of observed species and calculated configurati...

A theoretical study of \(\) clusters with \(\) using density functional theory is presented. Tests of various functionals demonstrate that local spin density approximation (LSDA) is the most adequate functional for the study of these systems. Structures, vibrational frequencies, and IR intensities of the lowest energy isomer of the studied clusters obtained using LSDA are described, and the unusual properties of the Si-C clusters are discussed. A quantitative analysis of the obtained structures was carried out, and relations between the coordinations, interatomic distances, and angles observed in the Si-C clusters were obtained through introduction of the notion of coordination. This analysis also shows that the carbon atoms mainly exhibit sp and sp2 hybridizations, and that a majority of silicon atoms do not hybridize. This study is the fi rst step of the implementation of a semi-empirical potential, which would describe the moderately small Si-C clusters.

International audience; Isomer formation in dimeric complexes of a chiral naphthalene derivative (2-naphthyl-1-ethanol) with nonchiral or chiral primary and secondary alcohols (n-propanol, 2-methyl-1-butanol, 2-butanol, 2-pentanol) has been studied by hole-burning spectroscopy. Besides the spectroscopic discrimination between the homochiral and heterochiral complexes, previously observed in the fluorescence excitation spectra, ground-state depletion experiments have shown that each diastereoisomer is cooled in the jet in several isomeric forms. To get information on the structures of the complexes and on the influence of the solvent conformations of these structures, semiempirical calculations that rely on the exchange perturbation method have been performed. It has been shown that the most stable complexes involve a H-bond between the chromophore acting as the donor and the solvent and that they involve anti and gauche conformations of the solvent. The binding energy of the complexes results from a subtle balance between electrostatic and dispersive forces: the complexes involving the gauche and anti conformers of the solvent differ from each other by the amount of dispersion energy relative to the total interaction energy. The increase in the dispersive forces calculated for the complexes with the anti conformers has been related to a larger red shift of the absorption spectrum and is suggested to play a role in the observed chiral discrimination.