Cooperative Strengthening of an Intramolecular O—H···O Hydrogen Bond by a Weak C—H···O Counterpart: Matrix-Isolation Infrared Spectroscopy and Quantum Chemical Studies on 3-Methyl-1,2-cyclohexanedione

CH⋯O H-bond mediated tautomerization of 2-methyl-1,3-cyclohexanedione: A combined IR spectroscopic and theoretical study

Molecular association and its impact on the keto-enol tautomerization of 2-methyl-1,3-cyclohexanedione (MCHD) have been investigated in low temperature argon matrix and thin solid film. The system exists exclusively in diketo tautomeric form in argon matrix. The CH⋯O H-bonded homodimers of the diketo tautomer are produced by annealing the matrix at 28 K. No trace of the keto-enol tautomer is observed in matrix isolated homodimers in the temperature range of 8-28 K. However, tautomeric conversion initiates in a thin film of pure diketo tautomer when the temperature of the film is raised to ~170 K. Transition state calculations on the monomeric and dimeric MCHD demonstrate that CH⋯O H-bond formations between diketo tautomers play a vital role in lowering the tautomerization barrier. However, the extent of CH⋯O H-bonded dimer formation in matrix isolation, as well as extent of tautomerization in the neat sample are found to be smaller than that for the previously reported 1,3-cyclohexanedione (CHD) under similar experimental conditions (J. Phys. Chem. A 2012, 116, 3836-3845). Electronic structure calculations suggest that formation of the CH⋯O H-bonded dimer is less feasible in presence of the bulky 2-methyl groups of MCHD, as compared to CHD. Additionally, the transition state geometry of the dimeric keto-enol product of MCHD, as compared to the same for CHD, is more strained and offers a weaker CH---O H-bond that contributes to lesser tautomeric conversion in the former.

Impact of donor acidity and acceptor anharmonicity on vc=o spectral shifts in O-H···O=C H-bonded ketone-alcohol complexes: An IR spectroscopic investigation

O-H···O=C Hydrogen bonding (H-bonding) results in spectral shifts in both ν_O-H and ν_C=O modes. A large number of investigations exist in literature that focuses on how the spectral shifts vary with certain properties of the donors and acceptors. However information on how the magnitude of spectral shift is dictated individually by the donor and acceptor is not yet clear to us. Here, IR spectroscopy in room temperature CCl₄ solution has been used to investigate how ν_C=O spectral shifts of ketones in H-bonded complexes with alcohols are influenced by change in donor and acceptor properties. For this purpose 25 number of O-H···O=C H-bonded complexes formed by 5 different ketones and 5 alcohols have been studied. The magnitude of red-shifts shown by the ν_C=O bands were found to show systematic trends with changing donor and acceptor species. It was found that for a particular ketone, the magnitude of shift increases monotonically with acidity of the alcohols. Spectral shifts were found to increase in a linear fashion with decreasing p^K_a of the donor alcohols. On the other hand, when the alcohol were kept fixed, the spectral shift was found to be dependent on the CO bond strength of the ketones. We found spectral shifts to linearly increase with increasing anharmonicity constant and decreasing dissociation energy of CO bond. Finally, it has been shown that there exist concomitant correlations of the spectral shifts with donor p^K_a and acceptor ν_C=O anharmonicity constant/bond dissociation energy. The relations have been validated for H-bonded complexes of 1,4-cyclohexanedione with the above mentioned five alcohols.

Cooperative nature of the sulfur centered hydrogen bond: investigation of (H2S)n (n = 2-4) clusters using an affordable yet accurate level of theory

Existing studies have shown that appreciably high level quantum chemical calculations are required to reproduce experimental energetic and geometric features of a H₂S dimer. This condition severely restricts any practical possibility of obtaining reliable results for higher order H₂S clusters. We have shown here that the binding energies calculated at the CCSD(T)/CBS level with counterpoise corrected geometries calculated at the MP2/aug-cc-pV(Q+d)Z level of theory excellently match with the experimental results for the H₂S dimer. Subsequently, the above mentioned levels of theory were used for trimers and tetramers. (H₂S)_n (n = 2-4) clusters were found to show cooperative strengthening of S-HS hydrogen bonds, which is clearly evident from the evolution of binding energies and hydrogen bond lengths, with increasing cluster size. Localized molecular orbital energy decomposition analyses have been carried out to understand how the contributions of various energy components modulate with the size of the clusters and what are their relative contributions towards the overall stabilization of the clusters. Natural bond orbital and atoms in molecules analyses were also carried out in order to look into the evolution of the electronic charge transfer and electron density topology with cluster size.

Modulations of νO-H and νC═O Stretching Frequencies of Difluoroacetic Acid with Internal Rotation of CHF2 Rotor: A Combined Vapor Phase and Matrix Isolation Infrared Spectroscopy Study

Mid-infrared spectra of difluoroacetic acid (DFAA) have been measured by isolating the molecule in argon and nitrogen matrices at 8 K and also in the vapor phase at room temperature. In argon matrix, the O-H stretching fundamental (ν_O-H) of -COOH group appears as a doublet with band maxima at 3554 and 3558 cm^-1, and a similar doublet for C═O stretching fundamental appears at 1800 and 1810 cm^-1. In the vapor phase, the ν_O-H transition is featured with multiple peaks, and the observed band shape has been deconvoluted as superposition of two transitions both having A-type rotational band contours. We have attributed these transitions to the two internal rotational isomers corresponding to the two distinct minima along -CHF₂ torsional coordinate of the molecule. Natural bond orbital (NBO) analysis reveals that these torsional minima are the manifestations of different second order interactions involving bonding and antibonding orbitals corresponding to the rotor -CHF₂ and COOH groups of the molecule. By use of the theoretically predicted rotational constants of the rotamers, the band profile for ν_O-H has been simulated satisfactorily by means of the PGOPHER method, and this has allowed estimating accurately the energy difference between the two rotamers as 0.54 kcal/mol. The predicted energy barrier for interconversion between the rotamers is very small, ∼0.5 kcal/mol from rotamer II to rotamer I, which implies that the molecule could hop almost freely between the two rotameric forms at room temperature. As a result, the frequencies of the key stretching vibrational modes, like ν_O-H, ν_C═O, and ν_C-H, undergo modulation with internal rotation of the rotor -CHF₂ group. Such modulation of high frequency modes could be an efficient mechanism for acceleration of rotor-induced IVR (intramolecular vibrational redistribution) well documented in the literature. Furthermore, the spectra measured in matrix isolated environment show signatures for an energetically higher third rotamer, where -OH and -C═O groups are in anti orientation. It has also been shown that DFAA can easily form weak hydrogen bonded dimeric complexes with molecular nitrogen (N₂), which causes ν_O-H to undergo a red shift of ∼30 cm^-1 in argon matrix for all three DFAA monomers.

Stereo-preference of camphor for H-bonding with phenol, methanol and chloroform: A combined matrix isolation IR spectroscopic and quantum chemical investigation

Camphor is known to be held in the substrate pocket of cytochrome P450cam enzyme via H-bond with a tyrosine residue of the enzyme in a unique orientation. This structural exclusivity results in regio- and stereo-specific hydroxylation of camphor by the enzyme. We have carried out a combined IR spectroscopic and quantum chemical investigation to shed light on the factors influencing the conformational exclusivity of 1R-(+)-camphor in the substrate pocket of Cytochrome P450cam, and to determine whether the selectivity is an inherent property of the substrate itself, or is imposed by the enzyme. For this purpose, complexes of camphor have been studied with three H-bond donors namely phenol, methanol and chloroform. Each of the three donors was found to form stable complexes with two distinct conformers; the one mimicking the conformation in enzyme substrate pocket was found to be more stable of the two, for all three donors. Experimentally, both conformers of the H-bonded complexes were identified separately for phenol and methanol in an argon matrix at 8 K, but not for chloroform due to very small energy barrier for interconversion of the two conformers. In room temperature solution phase spectra of camphor with all three donors, the differences in spectral attributes between the two isomeric H-bonded complexes were lost due to thermal motions.

Antagonistic Interplay Between an Intermolecular CH···O and an Intramolecular OH···O Hydrogen Bond in a 1:1 Complex Between 1,2-Cyclohexanedione and Chloroform: A Combined Matrix Isolation Infrared and Quantum Chemistry Study

Matrix isolation infrared spectra of a weak C-H···O hydrogen-bonded complex between the keto-enol form of 1,2-cyclohexanedione (HCHD) and chloroform have been measured. The spectra reveal that the intramolecular O-H···O H-bond of HCHD is weakened as a result of complex formation, manifesting in prominent blue shift (∼23 cm^-1) of the ν_O-H band and red shifts (∼7 cm^-1) of ν_C═O bands of the acceptor (HCHD). The ν_C-H band of donor CHCl₃ undergoes a large red shift of ∼33 cm^-1. Very similar spectral effects are also observed for formation of the complex in CCl₄ solution at room temperature. Our analysis reveals that out of several possible iso-energetic conformational forms of the complex, the one involving antagonistic interplay between the two hydrogen bonds (intermolecular C-H···O and intramolecular O-H···O) is preferred. The combined experimental and calculated data presented here suggest that in condensed media, conformational preferences are guided by directional hyperconjugative charge transfer interactions at the C-H···O hydrogen bonding site of the complex.

Cooperative effect on phenolic νO-H frequencies in 1:1 hydrogen bonded complexes of o-fluorophenols with water: A matrix isolation infrared spectroscopic study

Matrix isolation infrared spectra of 1:1 complexes of two ortho-fluorophenols, 2-fluorophenol (2-FPh) and 2,6-difluorophenol (2,6-DFPh), with water and benzene have been analyzed in combination with electronic structure calculations to investigate cooperative effect in O-H···O-H···F hydrogen bonded linkage, which manifests as large spectral shifts of the phenolic O-H stretching fundamental. Calculation predicts that a nearly planar cyclic geometry is preferred by the binary water complexes of the syn conformer of 2-FPh as well as 2,6-DFPh, and the observed spectral shifts are in good agreement with the predicted shifts for such conformers. On the other hand, for other possible isomeric structures, the molecular plane of water moiety is oriented perpendicular to that of the fluorophenols, and the observed as well as predicted shifts are smaller than those of the ortho substituted fluorophenols, although the total binding energies are predicted to be larger for the former. The observed spectral shifts are however consistent with local interaction energy parameters, like hyperconjugative charge transfer and accumulation of electron density (ρ) along the O-H···O hydrogen bond path. For the binary O-H···π hydrogen bonded benzene complexes of the fluorophenols, where cooperative interaction is not possible, the observed shifts are consistent with the conformers preferred according to total binding energies as well as local charge transfer effects of the complexes.

First steps in growth of a polypeptide toward β-sheet structure

The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. However, the stability of this structure is highly dependent upon interpeptide H-bonds with the second chain. The latter forces include not only the usual NH···O interaction, but also a pair of CH···O H-bonds. The secondary minimum is also of C7 type and likewise depends in part upon CH···O H-bonds for its stability. The latter interactions also play a part in the tertiary minimum. A two-strand β-sheet structure is not yet in evidence for this small model system, requiring additional peptide units to be added to each chain.

Photodissociation dynamics of enolic 1,2-cyclohexanedione at 266, 248, and 193 nm: mechanism and nascent state product distribution of OH

The photodissociation dynamics of 1,2-cyclohexanedione (CHD), which exists in enolic form in gas phase, is studied using pulsed laser photolysis (LP)-laser induced fluorescence (LIF) "pump-and-probe" technique at room temperature. The nascent state distribution of the OH radical, formed after initial photoexcitation of the molecule to it is (π, π*) and Rydberg states, is determined. The initial (π, π*) and Rydberg states are prepared by excitation with the fourth harmonic output of Nd:YAG (266 nm)/KrF (248 nm) and ArF (193 nm) lasers, respectively. The ro-vibrational distribution of the nascent OH photofragment is measured in collision-free conditions using LIF. The OH fragments are formed in the vibrationally cold state at all the above wavelengths of excitation but differ in rotational state distributions. At 266 nm photolysis, the rotational population of OH shows a curvature in Boltzmann plot, which is fairly described by two types of Boltzmann-like distributions characterized by rotational temperatures of 3100 ± 100 and 900 ± 80 K. However, at 248 nm photolysis, the rotational distribution is described by a single rotational temperature of 950 ± 80 K. The spin-orbit and Λ-doublets ratios of OH fragments formed in the dissociation process are also measured. The average translational energy in the center-of-mass coordinate, partitioned into the photofragment pairs of the OH formation channels, is determined to be 12.5 ± 3.0, 12.7 ± 3.0, and 12.0 ± 3.0 kcal/mol at 266, 248, and 193 nm excitation, respectively. The energy partitioning into various degrees of freedom of products is interpreted with the help of different models, namely, statistical, impulsive, and hybrid models. To understand the nature of the dissociative potential energy surface involved in the OH formation channel, detailed ab initio calculations are performed using configuration interaction-singles (CIS) method. It is proposed that at 266 nm photolysis, the OH fragment is formed from two different excited state structures, one with a strong H bonding, similar to that in the ground state, and another without effective H bonding, whereas, at 248 nm photodissociation, it seems that the OH formation occurs mainly from the excited state, which lacks effective H-bonding. At 193 nm excitation, the initially prepared population in the Rydberg state crosses over to a nearby σ* repulsive state along the C-O bond, from where the dissociation takes place. The exit barrier for the OH dissociation channel is estimated to be 14 kcal/mol. The existence of dynamical constraint due to strong hydrogen bond in the ground state is effectively present in the dissociation process at 266 and somewhat deficient at 248 nm photolysis.

Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNA(Phe)

Conformational preferences of hypermodified nucleic acid base hydroxywybutine (OHyW) have been studied using quantum chemical single point semi-empirical PM3 method. Automated geometry optimization using semi-empirical RM1, molecular mechanics force field (MMFF) along with ab-initio HF-SCF (6-31G** basis set) and DFT (B3LYP/6-31G** basis set) calculations have also been made to compare the salient features. Molecular electrostatic potentials (MEPs) depict the polarities of hydroxywybutine (OHyW) side chain. Another conformational study showed that hydroxywybutosine side chain interacts with adjacent bases within the anticodon loop of tRNA(Phe). The solvent accessible surface area (SASA) calculations revealed the structural role of hydroxywybutine in anticodon loop. Explicit molecular dynamics (MD) simulation has been done over the PM3 most stable structure of OHyW. The hydroxywybutine side chain prefers 'distal' conformation i.e. spreads away from the cyclic five membered imidazole moiety of modified tricyclic guanine base. The predicted preferred conformation of hydroxywybutine may prevent extended Watson-Crick base pairing during protein biosynthesis process. This conformation of OHyW stabilized by intramolecular interactions between O(6)⋯HO(16), O(6)⋯HC(15) and O(20)⋯HC(17). Further stabilization is also expected from interactions between O(22)⋯HC(16) and O(23)⋯HC(15). Explicit molecular dynamics (MD) simulation over the PM3 most stable structure of OHyW support the preferred geometry by preserving the 'distal' orientation of hydroxywybutine side chain and intramolecular hydrogen bonding interactions. MD simulation study revealed the role of hydroxyl group of OHyW to avoid fluctuations and prevent multiple iso-energetic conformations of hydroxywybutine side chain as compared to wybutine (yW).

"Additive" cooperativity of hydrogen bonds in complexes of catechol with proton acceptors in the gas phase: FTIR spectroscopy and quantum chemical calculations

Experimental study of hydrogen bond cooperativity in hetero-complexes in the gas phase was carried out by IR-spectroscopy method. Stretching vibration frequencies of O-H groups in phenol and catechol molecules as well as of their complexes with nitriles and ethers were determined in the gas phase using a specially designed cell. O-H groups experimental frequency shifts in the complexes of catechol induced by the formation of intermolecular hydrogen bonds are significantly higher than in the complexes of phenol due to the hydrogen bond cooperativity. It was shown that the cooperativity factors of hydrogen bonds in the complexes of catechol with nitriles and ethers in the gas phase are approximately the same. Quantum chemical calculations of the studied systems have been performed using density functional theory (DFT) methods. It was shown, that theoretically obtained cooperativity factors of hydrogen bonds in the complexes of catechol with proton acceptors are in good agreement with experimental values. Cooperative effects lead to a strengthening of intermolecular hydrogen bonds in the complexes of catechol on about 30%, despite the significant difference in the proton acceptor ability of the bases. The analysis within quantum theory of atoms in molecules was carried out for the explanation of this fact.