Dimers of formic acid: Structures, stability, and double proton transfer

Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization

An excitonic coupling model is developed based on an equation-of-motion coupled cluster combined with the fragment molecular orbital method. The effects of polarization and excitonic coupling on the splitting of quasi-degenerate levels in systems containing multiple chromophores are elucidated on dimers of formaldehyde, water, formic acid, hydrogen fluoride, and carbon monoxide. It is shown that the level structure is mainly determined by the mutual polarization of chromophores and to a lesser extent by the excitonic coupling. The role of symmetry in excitonic coupling in dimers is discussed. The excitonic coupling between all residues in the photoactive yellow protein (PDB: 2PHY) is analyzed.

Enabling Carbonized Polymer Dots with Color-tunable Time-dependent Room Temperature Phosphorescence through Confining Carboxyl Dimer Association

Developing a facile strategy to realize fine-tuning of phosphorescence color in time-dependent room temperature phosphorescence (RTP) materials is essential but both theoretically and practically rarely exploited. Through simultaneously confining carboxyl dimer association and isolated carboxyl into the particle via a simple hydrothermal treatment of polyacrylic acid, a dual-peak emission of red phosphorescence (645 nm) and green phosphorescence (550 nm) was observed from carbonized polymer dots (CPDs). The ratio of the two luminescent species can be well regulated by hydrochloric acid inhibiting the dissociation of carboxyl to promote hydrogen bond. Due to comparable but different lifetimes, color-tunable time-dependent RTP with color changing from yellow to green or orange to green were obtained. Based on the crosslinking enhanced emission effect, the phosphorescence visible time was even extended to 7 s through introducing polyethylenimide. This study not only proposes a novel and facile method for developing CPDs with color-tunable time-dependent RTP, but also provides a bran-new non-conjugated red phosphorescence unit and its definite structure.

Ultrafast Proton Transfer and Contact Ion-Pair Formation in Formic Acid Clusters

The ultrafast proton transfer dynamics of homogeneous formic acid clusters (FA)n, n < 10, are investigated with femtosecond time-resolved mass spectrometry. We monitor the proton transfer pathway following Rydberg state electronic relaxation and find that successful ion pair formation increases logarithmically with cluster size. Ab initio calculations demonstrate similar excitation/relaxation behavior for each cluster, revealing a contact ion pair forms between two molecules composing the cluster before finally a formate anion (HCOO-) is dissociated by the probe pulse. The sub-ps time scale for rearrangement and proton transfer increases almost linearly with cluster size, requiring ∼67 fs per additional formic acid molecule and ranging from 213 ± 51 fs for the trimer to 667 ± 116 fs for FA9. The near-linear trends measured for both rearrangement lifetime and ion pair formation suggest that proton transfer is unlikely in the formic acid dimer but becomes prominent in small clusters.

Formic and acetic acid pKa values increase under nanoconfinement

Organic acids are prevalent in the environment and their acidity and the corresponding dissociation constants can change under varying environmental conditions. The impact of nanoconfinement (when acids are confined within nanometer-scale domains) on physicochemical properties of chemical species is poorly understood and is an emerging field of study. By combining infrared and Raman spectroscopies with molecular dynamics (MD) simulations, we quantified the effect of nanoconfinement in silica nanopores on one of the fundamental chemical reactions-the dissociation of organic acids. The pKa of formic and acetic acids confined within cylindrical silica nanopores with 4 nm diameters were measured. MD models were constructed to calculate the shifts in the pKa values of acetic acid nanoconfined within 1, 2, 3, and 4 nm silica slit pores. Both experiments and MD models indicate a decrease in the apparent acid dissociation constants (i.e., increase in the pKa values) when organic acids are nanoconfined. Therefore, nanoconfinement stabilizes the protonated species. We attribute this observation to (1) a decrease in the average dielectric response of nanoconfined aqueous solutions where charge screening may be decreased; or (2) an increase in proton concentration inside nanopores, which would shift the equilibrium towards the protonated form. Overall, the results of this study provide the first quantification of the pKa values for nanoconfined formic and acetic acids and pave the way for a unifying theory predicting the impact of nanoconfinement on acid-base chemistry.

Intermolecular Charge Transfer Induced Fragmentation of Formic Acid Dimers

We investigate the intermolecular nonradiative charge transfer process in a double hydrogen-bonded formic acid (FA) dimer, initiated by electron-collision induced double ionization of one FA molecule. Through fragment ions and electron coincident momentum measurements and ab initio calculations, we obtain direct evidence that electron transfer from the neighboring FA molecule to fill one of the two vacancies occurs by a potential energy curve crossing of FA^{++}+FA with FA^{+}+FA^{+*} curves, forming an electronic excited state of dicationic dimers. This process causes the breaking of two hydrogen bonds and subsequently the cleavage of C─H and C─O covalent bonds in the dimers, which is expected to be a general phenomenon occurring in molecular complexes and can have important implications for radiation damage to biological matter.

The transition state region in nonsynchronous concerted reactions

The critical and vanishing points of the reaction force F(ξ) = -dV(ξ)/dξ yield five important coordinates (ξ_R, ξ_R^* , ξ_TS, ξ_P^* , ξ_P) along the intrinsic reaction coordinate (IRC) for a given concerted reaction or reaction step. These points partition the IRC into three well-defined regions, reactants (ξ_R→ξ_R^* ), transition state (ξ_R^* →ξ_P^* ), and products (ξ_P^* →ξ_P), with traditional roles of mostly structural changes associated with the reactants and products regions and mostly electronic activity associated with the transition state (TS) region. Following the evolution of chemical bonding along the IRC using formal descriptors of synchronicity, reaction electron flux, Wiberg bond orders, and their derivatives (or, more precisely, the intensity of the electron activity) unambiguously indicates that for nonsynchronous reactions, electron activity transcends the TS region and takes place well into the reactants and products regions. Under these circumstances, an extension of the TS region toward the reactants and products regions may occur.

Dissecting Bonding Interactions in Cysteine Dimers

Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions.

Microsolvation of electrons by a handful of ammonia molecules

Microsolvation of electrons in ammonia is studied here via anionic NH_{3 n} ^- clusters with n = 2-6. Intensive samplings of the corresponding configurational spaces using second-order perturbation theory with extended basis sets uncover rich and complex energy landscapes, heavily populated by many local minima in tight energy windows as calculated from highly correlated coupled cluster methods. There is a marked energetical preference for structures that place the excess electron external to the molecular frame, effectively coordinating it with the three protons from a single ammonia molecule. Overall, as the clusters grow in size, the lowest energy dimer serves as the basic motif over which additional ammonia molecules are attached via unusually strong charge-assisted hydrogen bonds. This is a priori quite unexpected because, on electrostatic grounds, the excess electron would be expected to be in contact with as many protons as possible. Accordingly, a full quantum mechanical treatment of the bonding interactions under the tools provided by the quantum theory of atoms in molecules is carried out in order to dissect and understand the nature of intermolecular contacts. Vertical detachment energies reveal bound electrons even for n = 2.

Formation and evolution of C-C, C-O, C[double bond, length as m-dash]O and C-N bonds in chemical reactions of prebiotic interest

A series of prebiotic chemical reactions yielding the precursor building blocks of amino acids, proteins and carbohydrates, starting solely from HCN and water is studied here. We closely follow the formation and evolution of the pivotal C-C, C-O, C[double bond, length as m-dash]O, and C-N bonds, which dictate the chemistry of the molecules of life. In many cases, formation of these bonds is set in motion by proton transfers in which individual water molecules act as catalysts so that water atoms end up in the products. Our results indicate that the prebiotic formation of carbon dioxide, formaldehyde, formic acid, formaldimine, glycolaldehyde, glycine, glycolonitrile, and oxazole derivatives, among others, are best described as highly nonsynchronous concerted single step processes. Nonetheless, for all reactions involving double proton transfer, the formation and breaking of O-H bonds around a particular O atom occur in a synchronous fashion, apparently independently from other primitive processes. For the most part, the first process to initiate seems to be the double proton transfer in the reactions where they are present, then bond breaking/formation around the reactive carbon in the carbonyl group and finally rupture of the C-N bonds in the appropriate cases, which are the most reluctant to break. Remarkably, within the limitations of our non-dynamical computational model, the wide ranges of temperature and pressure in which these reactions occur, downplay the problematic determination of the exact constraints on the early Earth.

Concerted Double Hydrogen-Bond Breaking by Intermolecular Coulombic Decay in the Formic Acid Dimer

Hydrogen bonds are ubiquitous in nature and of fundamental importance to the chemical and physical properties of molecular systems in the condensed phase. Nevertheless, our understanding of the structural and dynamical properties of hydrogen-bonded complexes in particular in electronic excited states remains very incomplete. Here, by using formic acid (FA) dimer as a prototype of DNA base pair, we investigate the ultrafast decay process initiated by removal of an electron from the inner-valence shell of the molecule upon electron-beam irradiation. Through fragment-ion and electron coincident momentum measurements and ab initio calculations, we find that de-excitation of an outer-valence electron at the same site can initiate ultrafast energy transfer to the neighboring molecule, which is in turn ionized through the emission of low-energy electrons. Our study reveals a concerted breaking of double hydrogen-bond in the dimer initiated by the ultrafast molecular rotations of two FA⁺ cations following this nonlocal decay mechanism.

Analysis of Conformational Preferences in Caffeine

High level DLPNO−CCSD(T) electronic structure calculations with extended basis sets over B3LYP−D3 optimized geometries indicate that the three methyl groups in caffeine overcome steric hindrance to adopt uncommon conformations, each one placing a C−H bond on the same plane of the aromatic system, leading to the C−H bonds eclipsing one carbonyl group, one heavily delocalized C−N bond constituent of the fused double ring aromatic system, and one C−H bond from the imidazole ring. Deletion of indiscriminate and selective non-Lewis orbitals unequivocally show that hyperconjugation in the form of a bidirectional −CH3 ⇆ aromatic system charge transfer is responsible for these puzzling conformations. The structural preferences in caffeine are exclusively determined by orbital interactions, ruling out electrostatics, induction, bond critical points, and density redistribution because the steric effect, the allylic effect, the Quantum Theory of Atoms in Molecules (QTAIM), and the non-covalent interactions (NCI), all predict wrong energetic orderings. Tiny rotational barriers, not exceeding 1.3 kcal/mol suggest that at room conditions, each methyl group either acts as a free rotor or adopts fluxional behavior, thus preventing accurate determination of their conformations. In this context, our results supersede current experimental ambiguity in the assignation of methyl conformation in caffeine and, more generally, in methylated xanthines and their derivatives.

A Comprehensive Picture of the Structures, Energies, and Bonding in the Alanine Dimers

High level quantum mechanical computations and extensive stochastic searches of the potential energy surfaces of the Alanine dimers uncover rich and complex structural and interaction landscapes. A total of 416 strongly bound (up 13.4 kcal mol^-1 binding energies at the DLPNO-CCSD(T)/6-311++G(d,p) level corrected by the basis set superposition error and by the zero point vibrational energies over B3LYP-D3 geometries), close energy equilibrium structures were located, bonded via 32 specific types of intermolecular contacts including Y⋅⋅⋅H-X primary and Y⋅⋅⋅H-C secondary hydrogen bonds, H⋅⋅⋅H dihydrogen contacts, and non conventional anti-electrostatic Y δ - ⋯ X δ - interactions. The putative global minimum is triply degenerate, corresponding to the structure of the common dimer of a carboxylic acid. All quantum descriptors of chemical bonding point to a multitude of weak individual interactions within each dimer, whose cumulative effect results in large binding energies and in an attractive fluxional wall of non-covalent interactions in the interstitial region between the monomers.

Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes

The insertion process of Naproxen into model dimyristoylphosphatidylcholine (DMPC) membranes is studied by resorting to state-of-the-art classical and quantum mechanical atomistic computational approaches. Molecular dynamics simulations indicate that anionic Naproxen finds an equilibrium position right at the polar/nonpolar interphase when the process takes place in aqueous environments. With respect to the reference aqueous phase, the insertion process faces a small energy barrier of ≈5 kJ mol^-1 and yields a net stabilization of also ≈5 kJ mol^-1. Entropy changes along the insertion path, mainly due to a growing number of realizable microstates because of structural reorganization, are the main factors driving the insertion. An attractive fluxional wall of noncovalent interactions is characterized by all-quantum descriptors of chemical bonding (natural bond orbitals, quantum theory of atoms in molecules, noncovalent interaction, density differences, and natural charges). This attractive wall originates in the accumulation of tiny transfers of electron densities to the interstitial region between the fragments from a multitude of individual intermolecular contacts stabilizing the tertiary drug/water/membrane system.

A molecular twist on hydrophobicity

A thorough exploration of the molecular basis for hydrophobicity with a comprehensive set of theoretical tools and an extensive set of organic solvent S/water binary systems is discussed in this work. Without a single exception, regardless of the nature or structure of S, all quantum descriptors of bonding yield stabilizing S⋯water interactions, therefore, there is no evidence of repulsion and thus no reason for etymological hydrophobicity at the molecular level. Our results provide molecular insight behind the exclusion of S molecules by water, customarily invoked to explain phase separation and the formation of interfaces, in favor of a complex interplay between entropic, enthalpic, and dynamic factors. S⋯water interfaces are not just thin films separating the two phases; instead, they are non-isotropic regions with density gradients for each component whose macroscopic stability is provided by a large number of very weak dihydrogen contacts. We offer a definition of interface as the region in which the density of the components in the A/B binary system is not constant. At a fundamental level, our results contribute to better current understanding of hydrophobicity.

Notwithstanding the very weak nature of individual contacts, it is the cumulative effect of a large number of interactions (green NCI surfaces) which provides macroscopic stability to the interfaces.

A new instrument for kinetics and branching ratio studies of gas phase collisional processes at very low temperatures

A new instrument dedicated to the kinetic study of low-temperature gas phase neutral-neutral reactions, including clustering processes, is presented. It combines a supersonic flow reactor with vacuum ultra-violet synchrotron photoionization time-of-flight mass spectrometry. A photoion-photoelectron coincidence detection scheme has been adopted to optimize the particle counting efficiency. The characteristics of the instrument are detailed along with its capabilities illustrated through a few results obtained at low temperatures (<100 K) including a photoionization spectrum of n-butane, the detection of formic acid dimer formation, and the observation of diacetylene molecules formed by the reaction between the C₂H radical and C₂H₂.

Double-Ring Epimerization in the Biosynthesis of Clavulanic Acid

All reaction steps during the biosynthesis of suicidal clavulanic acid (coformulated with β-lactam antibiotics and used to fight bacterial infections) are known, except for the crucial 3S,5S → 3R,5R double epimerization needed to produce a biologically active stereoisomer, for which mechanistic hypothesis is subject to debate. In this work, we provide evidence for a reaction channel for the double inversion of configuration that involves a total of six reaction steps. When mediated by an enzyme with a terminal S-H bond, this highly complex reaction is spontaneous in the absence of solvents. Polarizable continuum models introduce reaction barriers in aqueous environments because of the strong destabilization of the first transition state. Molecular geometries and electronic structures in both cases indicate that solvent-free spontaneity and aqueous medium barriers are both firmly rooted in a substantial reorganization of the electron density right at the onset of the reaction, mostly involving a cyclic evolution/involution of large regions of π delocalization used to stabilize the excess charge left after the initial proton abstraction.

A detailed look at the bonding interactions in the microsolvation of monoatomic cations

Global and local descriptors of the properties of intermolecular bonding, formally derived from independent methodologies (QTAIM, NCI, NBO, density differences) afford a highly complex picture of the bonding interactions responsible for microsolvation of monoatomic cations. In all cases, the dominant factor dictating geometries and interaction strengths is the electrophilic power of the metal cation. The formal charge disrupts the hydrogen bonding network otherwise present in pristine water clusters, making the hydrogen bonds considerably stronger, even inducing some degree of covalency. All MO interactions are highly ionic, with strengths than in some cases approach that of the reference LiCl bond. Accumulation of electron density in the region connecting MO is observed, thus, ionic bonding in the microsolvation of monoatomic cations is not as simple as an electrostatic interaction between opposing charges.

Concerted Pair Motion Due to Double Hydrogen Bonding: The Formic Acid Dimer Case

Formic acid dimer as the prototypical doubly hydrogen-bonded gas-phase species is discussed from the perspective of the three translational and the three rotational degrees of freedom which are lost when two formic acid molecules form a stable complex. The experimental characterisation of these strongly hindered translations and rotations is reviewed, as are attempts to describe the associated fundamental vibrations, their combinations, and their thermal shifts by different electronic structure calculations and vibrational models. A remarkable match is confirmed for the combination of a CCSD(T)-level harmonic treatment and an MP2-level anharmonic VPT2 correction. Qualitatively correct thermal shifts of the vibrational spectra can be obtained from classical molecular dynamics in CCSD(T)-quality force fields. A detailed analysis suggests that this agreement between experiment and composite theoretical treatment is not strongly affected by fortuitous error cancellation but fully converged variational treatments of the six pair or intermolecular modes and their overtones and combinations in this model system would be welcome.

Dissection of the Mechanism of the Wittig Reaction

A wide variety of descriptors of the evolution of bonding, rooted in the formalism of quantum mechanics, but otherwise conceptually and methodologically independent of each other (based on the quantum theory of atoms in molecules and natural bond orbitals), consistently indicate that in the mechanism of the salt-free Wittig reaction, regardless of the nature of the ylide, regardless of the nature of the transition state, and regardless of the positioning of the substituents around the reactive center, the degree of advance in the formation of the emerging C-C bond as early as at the transition state for the oxaphosphetane formation step is firmly tied to the stereochemistry of the final alkene. In addition to the fast evolution of the emerging C-C bond, very early in the reaction, a long range, weak interaction between a lone pair in the oxygen atom of the carbonyl group and an empty p orbital in the phosphorous atom, resulting from the polarization of the P═C bond in the ylide (n_O → π_P═C^*), clamps the P═C and C═O bonds to the positions required for the subsequent formation of oxaphosphetanes, thus explaining the formation of cyclic intermediates rather than betaines. Each step of the Wittig reaction is a highly asynchronous process.

Antioxidant activity of curcuminoids

An exploration of the antioxidant power of curcumin, demethoxycurcumin, and bisdemethoxycurcumin, three natural antioxidants found in Curcuma longa, is reported in this work. We exhaust all structural possibilities leading to intramolecular hydrogen bonding and evaluate 15 isomers in total. Calculations were carried out in the gas phase and in the presence of solvents (water, to mimic biological media, and ethanol, to reproduce experimental assays) following the hydrogen atom transfer (HAT) and single electron transfer (SET) mechanisms. CH3OH-O hydrogen bonds are directly related to the antioxidant power via both mechanisms. We provide evidence to explain the experimental observations and to understand the fundamental factors driving antioxidant activity from a molecular perspective. Noticeably, the solvent enhances the antioxidant power in every case. All structures considered here are predicted to have better antioxidant abilities than phenol, and come very close to or surpass vitamin E.

Understanding the nature of bonding interactions in the carbonic acid dimers

Carbonic acid dimer, (CA)₂, (H₂CO₃)₂, helps to explain the existence of this acid as a stable species, different to a simple sum between carbon dioxide and water. Five distinct, well characterized types of intermolecular interactions contribute to the stabilization of the dimers, namely, C=O⋯H-O, H-O⋯H-O, C=O⋯C=O, C=O⋯O-H, and C-O⋯O-H. In many cases, the stabilizing hydrogen bonds are of at least the same strength as in the water dimer. We dissect the nature of intermolecular interactions and assess their influence on stability. For a set of 40 (H₂CO₃)₂ isomers, C=O⋯H-O hydrogen bonds between the carbonyl oxygen in one CA molecule and the acidic hydrogen in the hydroxyl group at a second CA molecule are the major stabilizing factors because they exhibit the shortest interaction distances, the largest orbital interaction energies, and the largest accumulation of electron densities around the corresponding bond critical points. In most cases, these are closed-shell hydrogen bonds, however, in a few instances, some covalent character is induced. Bifurcated hydrogen bonds are a common occurrence in the dimers of carbonic acid, resulting in a complex picture with multiple orbital interactions of various strengths. Two anti-anti monomers interacting via the strongest C=O⋯H-O hydrogen bonds are the ingredients for the formation of the lowest energy dimers. Graphical Abstract Carbonic acid dimer, (CA)₂, (H₂CO₃)₂, helps explaining the existence of this acid as a stable species, different to a simple sum between carbon dioxide and water. Five distinct, well-characterized types of intermolecular interactions contribute to the stabilization of the dimers, namely, C=O⋯H-O, H-O⋯O-H, C=O⋯C=O, C=O⋯O-C, and C-O⋯O-C. In many cases, the stabilizing hydrogen bonds are of at least the same strength as in the water dimer.

Formic acid dimers in a nitrogen matrix

Formic acid (HCOOH) dimers are studied by infrared spectroscopy in a nitrogen matrix and by ab initio calculations. We benefit from the use of a nitrogen matrix where the lifetime of the higher-energy (cis) conformer is very long (∼11 h vs. 7 min in an argon matrix). As a result, in a nitrogen matrix, a large proportion of the cis conformer can be produced by vibrational excitation of the lower-energy (trans) conformer. Three trans-trans, four trans-cis, and three cis-cis dimers are found in the experiments. The spectroscopic information on most of these dimers is enriched compared to the previous studies in an argon matrix. The cis-cis dimers of ordinary formic acid (without deuteration) are reported here for the first time. Several conformational processes are obtained using selective excitation by infrared light, some of them also for the first time. In particular, we report on the formation of cis-cis dimers upon vibrational excitation of trans-cis dimers. Tunneling decays of several dimers have been detected in the dark. The tunneling decay of cis-cis dimers of formic acid as well as the stabilization of cis units in cis-cis dimers is also observed for the first time.

Entropy drives the insertion of ibuprofen into model membranes

Entropy drives the insertion of ibuprofen into cell membranes.

Fe3+chelating quinoline–hydrazone hybrids with proven cytotoxicity, leishmanicidal, and trypanocidal activities

Neglected tropical diseases cause great concern in developing countries where there are millions of reported infected humans. Our calculations support a direct relationship between biological activity and the Fe³⁺chelating ability of the shown set of quinoline–hydrazone hybrids.