Hydrogen-Bonded Bridges in Complexes of o-Cyanophenol: Laser-Induced Fluorescence and IR/UV Double-Resonance Studies

Homochiral vs. heterochiral preference in chiral self-recognition of cyclic diols

The structure and clustering propensity of a chiral derivative of cis-1,2-cyclohexanediol, namely, 1-phenyl-cis-1,2-cyclohexanediol (cis-PCD), has been studied under supersonic expansion conditions by combining laser spectroscopy with quantum chemistry calculations. The presence of the phenyl substituent induces conformational locking relative to cis-1,2-cyclohexanediol (cis-CD), and only one conformer of the bare molecule is observed by both Raman and IR-UV double resonance spectroscopy. The homochiral preference inferred for the dimer formation at low enough temperature is in line with the formation of a conglomerate in the solid state. The change in clustering propensity in cis-PCD relative to trans-1,2-cyclohexanediol (trans-CD), which shows heterochiral preference, is explained by the presence of the phenyl substituent rather than the effect of cis-trans isomerism. Indeed the transiently chiral cis-CD also forms preferentially heterodimers, whose structure is very close to that of the corresponding trans-CD dimer.

Setting up the HyDRA blind challenge for the microhydration of organic molecules

The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates...

IRMPD Spectra of Protonated Hydroxybenzaldehydes: Evidence of Torsional Barriers in Carboxonium Ions

Protonation at the formyl oxygen atom of benzaldehydes leading to the formation of carboxonium ions yields two distinct isomers, depending on the relative orientation of the proton either cis or trans with respect to the hydrogen atom on the adjacent carbon. In this context, the IR multiple photon dissociation (IRMPD) spectra of protonated ortho, meta, and para-hydroxybenzaldehydes (OH-BZH⁺ ), delivered into the gas phase by electrospray ionization of hydro-alcoholic solutions, are reported in the 3200-3700 cm^-1 spectral range. This range is characteristic of O-H stretching modes and thus able to differentiate cis and trans carboxonium isomers. Comparison between IRMPD spectra and DFT calculations at the B3LYP/6-311++G(2df2p) level suggests that for both p-OH-BZH⁺ and m-OH-BZH⁺ only cis conformers are present in the ion population analyzed. For o-OH-BZH⁺ , IRMPD spectroscopy points to a mixture comprising one trans and more than one cis conformers. The energy barrier for cis-trans isomerization calculated for each OH-BZH⁺ isomer is a measure of the degree of π-electron delocalization. Furthermore, IRMPD spectra of p-OH-BZH⁺ , m-OH-BZH⁺ and protonated phenol (this last used as reference) were recorded also in the fingerprint range. Both the observed C-O and O-H stretching vibrations appear to be a measure of π-electron delocalization in the ions.

Stereochemistry-dependent structure of hydrogen-bonded protonated dimers: the case of 1-amino-2-indanol

Stereochemistry effects on the structure of molecular aggregates are studied in the prototypical 1-amino-2-indanol. Conformer-selective IR-UV double resonance spectroscopy reveals how stereochemistry shapes its dimers.

Undervalued N3 Coordination Revealed in the Cisplatin Complex with 2'-Deoxyadenosine-5'-monophosphate by a Combined IRMPD and Theoretical Study

The complex obtained by the reaction of cisplatin and 2'-deoxyadenosine-5'-monophosphate (5'-dAMP) in water has been isolated and detected by electrospray ionization mass spectrometry. The so-formed cis-[PtCl(NH₃)₂(5'-dAMP)]⁺ complex has been studied in detail by infrared multiple photon dissociation (IRMPD) spectroscopy in two spectral ranges, namely, 700-1900 and 2800-3800 cm^-1, backed by quantum-chemical calculations at the B3LYP/LACV3P/6-311G** level of theory. In agreement with the computational results, the vibrational spectroscopic characterization of cis-[PtCl(NH₃)₂(5'-dAMP)]⁺ shows that the sampled ionic population comprises two major isomers, differentiated in the X-H stretching region by their distinct fragmentation patterns. One of these species presents coordination of the platinum moiety at the N3 position of adenine, whereas in the second one, platinum is bound at the N1 position of adenine. IRMPD kinetics have allowed an estimation of their relative proportions. Surprisingly, the most abundant component of cis-[PtCl(NH₃)₂(5'-dAMP)]⁺ is the N3 isomer, although it is slightly less stable than the other potential isomers in the gas phase. In contrast, the lowest-energy species, namely, the one showing cisplatin binding to the N7 position of adenine, seems to be the one less represented in the sampled ionic population. These findings suggest that the reaction of cisplatin with 5'-dAMP is governed by the kinetics of the process occurring in solution rather than by the thermodynamic factors.

Cisplatin and transplatin interaction with methionine: bonding motifs assayed by vibrational spectroscopy in the isolated ionic complexes

IRMPD spectroscopy discloses N- versus S-platination.

Cisplatin Primary Complex with l-Histidine Target Revealed by IR Multiple Photon Dissociation (IRMPD) Spectroscopy

The primary complex obtained from cisplatin and l-histidine in water has been detected and isolated by electrospray ionization. The so-obtained cis-[PtCl(NH₃ )₂ (histidine)]⁺ complex has been characterized in detail by high-resolution mass spectrometry (MS), tandem MS, IR multiple photon dissociation (IRMPD) spectroscopy, and by quantum chemical calculations. The structural features revealed by IRMPD spectroscopy indicate that platinum binds to the imidazole group, which presents tautomeric forms. Thus, depending on the position of the amino acid pendant on the imidazole ring, isomeric complexes are formed that are remarkably different with respect to the ease with which they undergo fragmentation when activated either by energetic collisions or by multiple IR photon absorption. It is shown here how IRMPD kinetics can allow their relative proportions to be estimated.

Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy

The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems.

Conformational flexibility of mephenesin

The mephenesin molecule (3-(2-methylphenoxy)propane-1,2-diol) serves as a test bank to explore several structural and dynamical issues, such as conformational flexibility, the orientation of the carbon linear chain relative to the benzene plane, or the effect of substituent position on the rotational barrier of a methyl group. The molecule has been studied by rotational spectroscopy in the 4-18 GHz frequency range by Fourier-transform methods in a supersonic expansion. The experiment has been backed by a previous conformational search plus optimization of the lowest energy structures by ab initio and density functional quantum calculations. The three lowest-lying conformers that can interconvert to each other by simple bond rotations have been detected in the jet. Rotational parameters for all structures have been obtained, and methyl torsional barriers have been determined for the two lowest-lying rotamers. The lowest-lying structure of mephenesin is highly planar, with all carbon atoms lying nearly in the benzene ring plane, and is stabilized by the formation of cooperative intramolecular hydrogen bonding. An estimation of the relative abundance of the detected conformers indicates that the energetically most stable conformer will have an abundance near 80% at temperatures relevant for biological activity.

Behind the reactivity of lactones: a computational and spectroscopic study of phenol·γ-butyrolactone

In this work, the intermolecular interaction between phenol and γ-butyrolactone (GBL) has been studied by a combination of spectroscopic and computational techniques. The electronic and vibrational transitions of phenol · GBL were measured in a supersonic jet expansion by resonant two-photon ionization (R2PI) and ion dip IR (IDIR) spectroscopy. The results obtained were compared with calculations carried out with both M06-2X and MP2 molecular orbital methods in order to characterize the intermolecular interactions. The singly detected conformer is stabilized by a relatively strong hydrogen bond in which phenol acts as a proton donor to the carbonyl group of GBL. The phenol · GBL2 cluster has also been studied, finding up to three populated conformers. Nevertheless, in the three species, the main interaction between the phenolic hydroxyl group and the GBL's carbonyl group remains similar to that of phenol · GBL. Furthermore, the C ═ O · · · H interaction is reinforced.

Vibrational quenching of excitonic splittings in H-bonded molecular dimers: the electronic Davydov splittings cannot match experiment

The S(1)/S(2) state exciton splittings of symmetric doubly hydrogen-bonded gas-phase dimers provide spectroscopic benchmarks for the excited-state electronic couplings between UV chromophores. These have important implications for electronic energy transfer in multichromophoric systems ranging from photosynthetic light-harvesting antennae to photosynthetic reaction centers, conjugated polymers, molecular crystals, and nucleic acids. We provide laser spectroscopic data on the S(1)/S(2) excitonic splitting Δ(exp) of the doubly H-bonded o-cyanophenol (oCP) dimer and compare to the splittings of the dimers of (2-aminopyridine)(2), [(2AP)(2)], (2-pyridone)(2), [(2PY)(2)], (benzoic acid)(2), [(BZA)(2)], and (benzonitrile)(2), [(BN)(2)]. The experimental S(1)/S(2) excitonic splittings are Δ(exp) = 16.4 cm(-1) for (oCP)(2), 11.5 cm(-1) for (2AP)(2), 43.5 cm(-1) for (2PY)(2), and <1 cm(-1) for (BZA)(2). In contrast, the vertical S(1)/S(2) energy gaps Δ(calc) calculated by the approximate second-order coupled cluster (CC2) method for the same dimers are 10-40 times larger than the Δ(exp) values. The qualitative failure of this and other ab initio methods to reproduce the exciton splitting Δ(exp) arises from the Born-Oppenheimer (BO) approximation, which implicitly assumes the strong-coupling case and cannot be employed to evaluate excitonic splittings of systems that are in the weak-coupling limit. Given typical H-bond distances and oscillator strengths, the majority of H-bonded dimers lie in the weak-coupling limit. In this case, the monomer electronic-vibrational coupling upon electronic excitation must be accounted for; the excitonic splittings arise between the vibronic (and not the electronic) transitions. The discrepancy between the BO-based splittings Δ(calc) and the much smaller experimental Δ(exp) values is resolved by taking into account the quenching of the BO splitting by the intramolecular vibronic coupling in the monomer S(1) ← S(0) excitation. The vibrational quenching factors Γ for the five dimers (oCP)(2), (2AP)(2), (2AP)(2), (BN)(2), and (BZA)(2) lie in the range Γ = 0.03-0.2. The quenched excitonic splittings Γ[middle dot]Δ(calc) are found to be in very good agreement with the observed splittings Δ(exp). The vibrational quenching approach predicts reliable Δ(exp) values for the investigated dimers, confirms the importance of vibrational quenching of the electronic Davydov splittings, and provides a sound basis for predicting realistic exciton splittings in multichromophoric systems.

Scales of oxidation potentials, pK(a), and BDE of various hydroquinones and catechols in DMSO

The one-electron oxidation potentials [E(ox)(NHE)(H(2)Q)], pK(a) (pK(a1) and pK(a2)) values, and bond dissociation energies (BDE(1) and BDE(2)) of 118 important p- and o-dihydroquinones in DMSO were systematically predicted for the first time by using DFT method and the PCM cluster continuum model. The calculated results agree well with the available experimental determinations. The study shows that all the five thermodynamic parameters correlate well with the Hammett substituent parameters σ(p) (for p-H(2)Q, E(ox)(NHE)(H(2)Q(·+)/H(2)Q) = 1.66Σσ(p) + 0.54, pK(a1) = -5.69Σσ(p) + 16.54, pK(a2) = -5.19Σσ(p) + 23.91, BDE(1) = 3.43Σσ(p) + 82.29, BDE(2) = 4.64Σσ(p) + 67.70 and for o-H(2)Q, E(ox)(NHE)(H(2)Q(·+)/H(2)Q) = 1.85Σσ(p) + 0.46, pK(a1) = -5.53Σσ(p) + 13.28, pK(a2) = -5.24Σσ(p) + 26.70, BDE(1) = 3.54Σσ(p) + 82.08, BDE(2) = 3.82Σσ(p) + 75.93), which hints that we can get these thermodynamic parameters as long as the structure of the hydroquinones were known. The comparisons of the calculated five thermodynamic parameters between p-hydroquinones and o-hydroquinones and the number of the phenyl ring effects on these thermodynamic parameters were also studied. At last, intramolecular hydrogen bond energies in hydroquinones at neutral, radical cation, radical, anion different state were systematically calculated and analyzed. Combined with the papers published in our group before, we will have a systematic thermodynamic picture of the transfer details between different kinds of quinones and corresponding hydroquinones, which strongly promote the fast development of the understanding and applications of quinones.

Chirality recognition between neutral molecules in the gas phase

Noncovalent interactions are particularly intriguing when they involve chiral molecules, because the interactions change in a subtle way upon replacing one of the partners by its mirror image. The resulting phenomena involving chirality recognition are relevant in the biosphere, in organic synthesis, and in polymer design. They may be classified according to the permanent or transient chirality of the interacting partners, leading to chirality discrimination, chirality induction, and chirality synchronization processes. For small molecules, high-level quantum chemical calculations for such processes are feasible. To provide reliable connections between theory and experiment, such phenomena are best studied in vacuum isolation at low temperature, using rotational, vibrational, electronic, and photoionization spectroscopy. We review these techniques and the results which have become available in recent years, with special emphasis on dimers of permanently chiral molecules and on the influence of conformational flexibility. Analogies between the microscopic mechanisms and macroscopic phenomena and between intra- and intermolecular cases are drawn.

Differing Adsorption Behavior of Environmentally Important Cyanophenol Isomers at the Air−Water Interface

Vibrational sum-frequency spectroscopy and surface tensiometry have been used to study the adsorption of m- and p-cyanophenol at the air-water interface. Spectra of the cyano (CN) group under different polarization schemes are utilized to determine its hydrogen bonding environment and orientation. For both isomers, it is found that the cyano group is hydrogen bonded at the interface but that the CN orientation is independent of surface density. The average CN tilt angle (theta(0)), however, is found to differ between the isomers, such that the CN group points down toward the aqueous phase for m-cyanophenol (theta(0) = 96-106 degrees ) but points up toward the vapor phase for the p-cyanophenol (theta(0) = 65-80 degrees ). In addition, this average tilt angle is distributed over a narrow range, sigma(0) < 10 degrees for the meta isomer and sigma(0) < 16 degrees for the para isomer.

Intra- vs. intermolecular hydrogen bonding: dimers of alpha-hydroxyesters with methanol

Intermolecular hydrogen bonding competes with an intramolecular hydrogen bond when methanol binds to an alpha-hydroxyester. Disruption of the intramolecular OH...O=C contact in favour of a cooperative OH...OH...O=C sequence is evidenced by FTIR spectroscopy for the addition of methanol to the esters methyl glycolate, methyl lactate and methyl alpha-hydroxyisobutyrate in seeded supersonic jet expansions. Comparison of the OH stretching modes with quantum-chemical harmonic frequency calculations and 18O labelling of methanol unambiguously prove the insertion of methanol into the intramolecular hydrogen bond. This is in marked contrast to UV/IR hole burning studies of the homologous system methyl lactate: (+/-)-2-naphthyl-1-ethanol, where only addition complexes were found and the intramolecular hydrogen bond was conserved. This switch in hydrogen bond pattern from aliphatic to aromatic heterodimers is thought to reflect not only a kinetic propensity but also a thermodynamic preference for addition complexes when dispersion forces become more important in aromatic systems.

Chiral recognition between lactic acid derivatives and an aromatic alcohol in a supersonic expansion: electronic and vibrational spectroscopy

Jet-cooled diastereoisomeric complexes formed between a chiral probe, (+/-)-2-naphthyl-1-ethanol, and chiral lactic acid derivatives have been characterised by laser-induced fluorescence and IR fluorescence-dip spectroscopy. Complexes with non chiral alpha-hydroxyesters and chiral beta-hydroxyesters have also been studied for the sake of comparison. DFT calculations have been performed to assist in the analysis of the vibrational spectra and the determination of the structures. The observed 1 : 1 complexes correspond to the addition of the hydroxy group of the chromophore on the oxygen atom of the hydroxy in alpha-position relative to the ester function. Moreover, (+/-)-methyl lactate and (+/-)-ethyl lactate complexes with (+/-)-2-naphthyl-1-ethanol show an enantioselectivity in the size of the formed adducts: while fluorescent 1 : 1 complexes are the most abundant species observed when mixing (S)-2-naphthyl-1-ethanol with (R)-methyl or ethyl lactate, they are absent in the case of the SS mixture, which only shows 1 : 2 adducts. This property has been related to steric hindrance brought by the methyl group on the hydroxy-bearing carbon atom.

PCM Study of the Solvent and Substituent Effects on the Conformers, Intramolecular Hydrogen Bonds and Bond Dissociation Enthalpies of 2-Substituted Phenols

A PCM continuum model, at the DFT/B3LYP level, is used to study the solvent and substituent effects on the conformers, intramolecular hydrogen bond (HB) enthalpies, (Delta H(intra)s), and O-H bond dissociation enthalpies, (BDEs), in 2-substituted phenols, 2-X-ArOH, in the liquid phase. Two electron-donating (edg) and three electron-withdrawing (ewg) substituents are chosen, involved in a variety of biochemical transformations. Seven solvents, differing in their H-bonding ability and polarity, are selected to model different environmental situations. Very good correlations are found between the computed R(O-H) and nu(O-H) values in solution for all non-HB 2-X-ArOH, showing that the former can be used as an universal molecular descriptor for the latter and vice-versa. In all 2-X-ArOH, the HB parent conformer is the most stable in all media, closely matching frequency experimental data in CCl4. However, for all 2-X-ArO*, the most stable conformer either forms a "reverse"-HB or a HB is not formed, due to the long distance or steric effects. Changes in the stability, in solution, are observed for some of the 2-X-ArO* conformers. The intramolecular HB-strength in solution, Delta H(S,intra), varies significantly with the size of the HB ring formed and the nature of the substituents. Reasonable correlations, derived between the two energetic parameters (BDE(aw,sol) and Delta H(S,intra)) and the solvent ( and a), and/or molecular, [R(O-H) and nu(O-H)] ones, allow for an approximate estimation of the two former from the four latter. 2-X(edg) decrease BDEs (hence, increase the antioxidant efficiency of the solute, too) in all media; 2-X(ewg) present an opposite result. Moreover, an isodesmic reactions study affords total stabilization effect (TSE) values (identical to the Delta[BDE(aw)]s), which are mainly governed by the stabilization of the phenolic radical (SPR) than that of the parent molecule (SPP). Quantitative correlations between the two effects in the TSE in both the gas and the liquid phases are also given. Unlike in the protic solvents, the better stabilization of the radical than the parent species, derived for the 2-X(edg)-ArOH in the aprotic, apolar, and/or low polar solvents, could account well for their smaller BDE(sol)s. An effective antioxidant in solution should involve either one of the two edg in any one of the two latter solvents.

Spectrochemical, ab initio and density functional studies on the conversion of 2-hydroxybenzonitrile (o-cyanophenol) into the oxyanion

The spectral and structural changes caused by the conversion of 2-hydroxybenzonitrile (o-cyanophenol) into the corresponding oxyanion have been followed by IR spectra, ab initio and density functional force field calculations. In agreement between theory and experiment, the conversion is accompanied by a 29 cm(-1) frequency decrease of the cyano stretching band, 2.7-fold increase in its integrated intensity, 5.8-fold (total value) intensification of the aromatic skeletal bands of Wilson's 8 and 19 types, and other essential spectral changes. According to the calculations, the strongest structural changes are the shortening of the Ph-O bond with 0.10 A, lengthenings of the adjacent CC bonds in the phenylene ring with 0.06 A and bond angle variations near the oxyanionic center. All these changes are connected with the formation of a quasi-ortho-quinonoidal structure of the o-phenylene ring in the oxyanion. According to the electronic density analysis, 0.41 e(-) (Mulliken) or 0.56 e(-) (natural bond orbital, NBO) of the anionic charge remain localized at the oxyanionic center. Conformations and hydrogen bonds have also been discussed on the basis of experimental and theoretical data.

Chiral Recognition in Jet-Cooled Complexes

Jet-cooled complexes formed between a chiral probe [(±)-2-naphthyl-1-ethanol] and chiral bifunctional partners that show an intramolecular hydrogen bond have been studied by laser-induced fluorescence and IR fluorescence-dip spectroscopy as well as with DFT calculations. Chiral discrimination results in a chirality-dependent competition between the intramolecular and the intermolecular hydrogen bonds. In the case of (±)-methyl lactate, this competition manifests itself in the size of the formed adducts. In particular, while 1 : 1 complexes are the most abundant species observed when (R)-2-naphthyl-1-ethanol is mixed with (S)-methyl lactate, they are absent in the case of the SS mixture, which only forms 1 : 2 adducts.