Spectroscopy and dynamics of double proton transfer in formic acid dimer

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

Formic acid-methanol complexation vs. esterification: elusive pre-reactive species identified by vibrational spectroscopy

Vibrational spectra of the mixed dimer and the two mixed trimers of methanol and formic acid as well as some of their isotopologues are presented. Out of the eight expected OH stretching fundamentals of these three pre-reactive hydrogen-bonded complexes, the three modes mainly involving an acid OH group bound to the alcohol appear to be missing in the jet-cooled spectra despite a combination of infrared and Raman probing. A possibility of spectral overlap is discussed in the mixed dimer case, but largely discarded. The missing modes correspond to (fractional) concerted elongation of all engaged OH bonds, promoting synchronous degenerate proton transfer between the molecules. One other trimer mode is very tentatively attributed to a broad spectral feature, whereas all OH bonds contacting carbonyl groups can be unambiguously identified by four relatively narrow infrared absorptions. The spectral features are confirmed by vibrational perturbation theory and deviate in a subtle but systematic way from scaled harmonic predictions which were previously validated for the formic acid complex with a more acidic alcohol. Despite being exothermic and exergonic, ester formation can only be detected in the rarefied gas expansions after extended pre-mixture of the gases, which somewhat contrasts the recent microwave spectroscopic evidence of in situ ester formation and in particular the lack of pre-reactive complex signals.

Gas-Phase Room-Temperature Detection of the tert-Butyl Hydroperoxide Dimer

We have detected the tert-butyl hydroperoxide dimer, (t-BuOOH)2, in the gas phase at room temperature using conventional FTIR techniques. The dimer is identified by an asymmetric absorbance band assigned to the fundamental hydrogen-bound OHb-stretch. The weighted band maximum of the dimer OHb-stretch is located at ∼3452 cm-1, red-shifted by ∼145 cm-1 from the monomer OH-stretching band. The gas-phase dimer assignment is supported by Ar matrix isolation FTIR experiments at 12 K and experiments with a partially deuterated sample. Computationally, we find the lowest energy structure of (t-BuOOH)2 to be a doubly hydrogen bound six-membered ring with non-optimal hydrogen bond angles. We estimate the gas-phase constant of dimer formation, K, to be 0.4 (standard pressure of 1 bar) using the experimental integrated absorbance and a theoretically determined oscillator strength of the OHb-stretching band.

Homogeneous Carbon Dot-Anchored Fe(III) Catalysts with Self-Regulated Proton Transfer for Recyclable Fenton Chemistry

Fenton chemistry has been widely studied in a broad range from geochemistry, chemical oxidation to tumor chemodynamic therapy. It was well established that Fe³⁺/H₂O₂ resulted in a sluggish initial rate or even inactivity. Herein, we report the homogeneous carbon dot-anchored Fe(III) catalysts (CD-COOFe^III) wherein CD-COOFe^III active center activates H₂O₂ to produce hydroxyl radicals (^•OH) reaching 105 times larger than that of the Fe³⁺/H₂O₂ system. The key is the ^•OH flux produced from the O-O bond reductive cleavage boosting by the high electron-transfer rate constants of CD defects and its self-regulated proton-transfer behavior probed by operando ATR-FTIR spectroscopy in D₂O and kinetic isotope effects, respectively. Organic molecules interact with CD-COOFe^III via hydrogen bonds, promoting the electron-transfer rate constants during the redox reaction of CD defects. The antibiotics removal efficiency in the CD-COOFe^III/H₂O₂ system is at least 51 times large than the Fe³⁺/H₂O₂ system under equivalent conditions. Our findings provide a new pathway for traditional Fenton chemistry.

Quantitative molecular simulations

All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular interactions. The present perspective provides an overview of the present status of quantitative atomistic simulations from colleagues' and our own efforts for gas- and solution-phase processes and for the dynamics on surfaces. Particular attention is paid to direct comparison with experiment. An outlook discusses present challenges and future extensions to bring such dynamics simulations even closer to reality.

Double proton transfer in hydrated formic acid dimer: Interplay of spatial symmetry and solvent-generated force on reactivity

The double proton transfer (DPT) reaction in the hydrated formic acid dimer (FAD) is investigated at molecular-level detail. For this, a global and reactive machine learned (ML) potential energy surface (PES) is developed to run extensive (more than 100 ns) mixed ML/MM molecular dynamics (MD) simulations in explicit molecular mechanics (MM) solvent at MP2-quality for the solute. Simulations with fixed – as in a conventional empirical force field – and conformationally fluctuating – as available from the ML-based PES – charge models for FAD show a significant impact on the competition between DPT and dissociation of FAD into two formic acid monomers. With increasing temperature the barrier height for DPT in solution changes by about 10% (∼1 kcal mol⁻¹) between 300 K and 600 K. The rate for DPT is largest, ∼1 ns⁻¹, at 350 K and decreases for higher temperatures due to destabilisation and increased probability for dissociation of FAD. The water solvent is found to promote the first proton transfer by exerting a favourable solvent-induced Coulomb force along the O–H⋯O hydrogen bond whereas the second proton transfer is significantly controlled by the O–O separation and other conformational degrees of freedom. Double proton transfer in hydrated FAD is found to involve a subtle interplay and balance between structural and electrostatic factors.

Simulation of double proton transfer in formic acid dimer by reactive ML potential in explicit molecular mechanics water solvent.

Infrared spectroscopy of 2-oxo-octanoic acid in multiple phases

Alpha-keto acids are environmentally and biologically relevant species whose chemistry has been shown to be influenced by their local environment. Vibrational spectroscopy provides useful ways to probe the potential inter- and intramolecular interactions available to them in several phases. We measure and compare the IR spectra of 2-oxo-octanoic acid (2OOA) in the gas phase, solid phase, and at the air-water interface. With theoretical support, we assign many of the vibrational modes in each of the spectra. In the gas phase, two types of conformers are identified and distinguished, with the intramolecularly H-bonded form being the dominant type, while the second conformer type identified does not have an intramolecular hydrogen bond. The van der Waals interactions between molecules in solid 2OOA manifest C-H and CO vibrations lower in energy than in the gas phase and we propose an intermolecular hydrogen bonding scheme for the solid phase. At the air-water interface the hydrocarbon tails of 2OOA do interact with each other while the carbonyls appear to interact with water in the subphase, but not with neighboring 2OOA as might be expected of a closely packed surfactant film.

Vibrational Stark fields in carboxylic acid dimers

Carboxylic acids form exceptionally stable dimers and have been used to model proton and double proton transfer processes. The stabilization energies of the carboxylic acid dimers are very weakly dependent on the nature of substitution. However, the electric field experienced by the OH group of a particular carboxylic acid is dependent more on the nature of the substitution on the dimer partner. In general, the electric field was higher when the partner was substituted with an electron-donating group and lower with an electron-withdrawing substituent on the partner. The Stark tuning rate (Δ) of the O-H stretching vibrations calculated at the MP2/aug-cc-pVDZ level was found to be weakly dependent on the nature of substitution on the carboxylic acid. The average Stark tuning rate of O-H stretching vibrations of a particular carboxylic acid when paired with other acids was 5.7 cm^-1 (MV cm^-1)^-1, while the corresponding average Stark tuning rate of the partner acids due to a particular carboxylic acid was 21.9 cm^-1 (MV cm^-1)^-1. The difference in the Stark tuning rate is attributed to the primary and secondary effects of substitution on the carboxylic acid. The average Stark tuning rate for the anharmonic O-D frequency shifts is about 40-50% higher than the corresponding harmonic O-D frequency shifts calculated at the B3LYP/aug-cc-pVDZ level, much greater than the typical scaling factors used, indicating the strong anharmonicity of O-H/O-D oscillators in carboxylic acid dimers. Finally, the linear correlation observed between pK_a and the electric field was used to estimate the pK_a of fluoroformic acid to be around 0.9.

Theoretical Aspects of Nonconventional Hydrogen Bonds in the Complexes of Aldehydes and Hydrogen Chalcogenides

Hydrogen bonds (H-bonds) in the complexes between aldehydes and hydrogen chalcogenides, XCHO...nH₂Z with X = H, F, Cl, Br, and CH₃, Z = O, S, Se, and Te, and n = 1,2, were investigated using high-level ab initio calculations. The C_sp2-H...O H-bonds are found to be about twice as strong as the C_sp2-H...S/Se/Te counterparts. Remarkably, the S/Se/Te-H...S/Se/Te H-bonds are 4.5 times as weak as the O-H...O ones. The addition of the second H₂Z molecule into binary systems induces stronger complexes and causes a positive cooperative effect in ternary complexes. The blue shift of C_sp2-H stretching frequency involving the C_sp2-H...Z H-bond sharply increases when replacing one H atom in HCHO by a CH₃ group. In contrast, when one H atom in HCHO is substituted with a halogen, the magnitude of blue-shifting of the C_sp2-H...Z H-bond becomes smaller. The largest blue shift up to 92 cm^-1 of C_sp2-H stretching frequency in C_sp2-H...O H-bond in CH₃CHO...2H₂O has rarely been observed and is much greater than that in the cases of the C_sp2-H...S/Se/Te ones. The C_sp2-H blue shift of C_sp2-H...Z bonds in the halogenated aldehydes is converted into a red shift when H₂O is replaced by a heavier analogue, such as H₂S, H₂Se, or H₂Te. The stability and classification of nonconventional H-bonds including C_sp2-H...Se/Te, Te-H...Te, and Se/Te-H...O have been established for the first time.

Transfer learned potential energy surfaces: accurate anharmonic vibrational dynamics and dissociation energies for the formic acid monomer and dimer

The vibrational dynamics of the formic acid monomer (FAM) and dimer (FAD) is investigated from machine-learned potential energy surfaces at the MP2 (PES_MP2) and transfer-learned (PES_TL) to the CCSD(T) levels of theory. The normal mode (MAEs of 17.6 and 25.1 cm⁻¹) and second order vibrational perturbation theory (VPT2, MAEs of 6.7 and 17.1 cm⁻¹) frequencies from PES_TL for all modes below 2000 cm⁻¹ for FAM and FAD agree favourably with experiment. For the OH stretch mode the experimental frequencies are overestimated by more than 150 cm⁻¹ for both FAM and FAD from normal mode calculations. Conversely, VPT2 calculations on PES_TL for FAM reproduce the experimental OH frequency to within 22 cm⁻¹. For FAD the VPT2 calculations find the high-frequency OH stretch at 3011 cm⁻¹, compared with an experimentally reported, broad (∼100 cm⁻¹) absorption band with center frequency estimated at ∼3050 cm⁻¹. In agreement with earlier reports, MD simulations at higher temperature shift the position of the OH-stretch in FAM to the red, consistent with improved sampling of the anharmonic regions of the PES. However, for FAD the OH-stretch shifts to the blue and for temperatures higher than 1000 K the dimer partly or fully dissociates using PES_TL. Including zero-point energy corrections from diffusion Monte Carlo simulations for FAM and FAD and corrections due to basis set superposition and completeness errors yields a dissociation energy of D₀ = −14.23 ± 0.08 kcal mol⁻¹ compared with an experimentally determined value of −14.22 ± 0.12 kcal mol⁻¹.

Neural network based PESs are constructed for formic acid monomer and dimer at the MP2 and transfer learned to the CCSD(T) level of theory. The PESs are used to study the vibrational dynamics and dissociation energy of the molecules.

Lactic Acid Spectroscopy: Intra- and Intermolecular Interactions

Lactic acid, a relevant molecule in biology and the environment, is an α-hydroxy acid with a high propensity to form hydrogen bonds, both internally and to other hydrogen-bond-accepting molecules. This work includes the novel recording of infrared spectra of gas-phase lactic acid using Fourier transform infrared spectroscopy, and the vibrational absorption features of lactic acid are assigned with the aid of computationally simulated vibrational spectra with anharmonic corrections. Theoretical chemistry methods are used to relate intramolecular hydrogen-bond strengths to the relative stability of lactic acid conformers. The formation of hydrogen-bonded lactic acid dimers and 1:1 water complexes is investigated by simulated vibrational spectra and calculated thermodynamic parameters for the lactic acid monomer and dimer and its water complex in the gas phase. The results of this study are discussed in the context of environmental chemistry with an emphasis on indoor environments.

Proton Transfer vs Complex Formation Channels in Ionized Formic Acid Dimer: A Direct Ab Initio Molecular Dynamics Study

Photoirradiation to a hydrogen-bonded system plays an important role in the initial DNA and enzyme damage processes. The formic acid (FA) dimer is a model compound of double proton transfer systems, such as DNA base pairs. In the present study, the reactions of the FA dimer cation, formed upon ionization of the neutral dimer, have been investigated by the direct ab initio molecular dynamics method. Two reaction channels were identified for the FA dimer cation: complex formation and proton transfer (PT). In the complex formation channel, the carbonyl oxygen atoms of the two FA monomers were bound symmetrically, and a face-to-face complex was formed. In the PT channel, the proton of FA⁺ was transferred to FA, forming the H⁺(HCOOH)--HCO₂ radical cation as product. At low temperature, the complex channel was dominant, whereas the PT channel increased with increasing temperature. The asymmetric spin distribution on the FA dimer cation exhibited a strong correlation with the PT channel.

Shifting formic acid dimers into perspective: vibrational scrutiny in helium nanodroplets

A metastable dimer of formic acid has been prepared inside superfluid helium nanodroplets and examined using IR spectroscopy and quantum chemical calculations.

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.

Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk

The molecular mechanics with proton transfer (MMPT) force field is combined with multistate adiabatic reactive molecular dynamics (MS-ARMD) to describe proton transport in the condensed phase. Parametrization for small protonated water clusters based on electronic structure calculations at the MP2/6-311+G(2d,2p) level of theory and refinement by comparing with infrared spectra for a protonated water tetramer yields a force field which faithfully describes the minimum energy structures of small protonated water clusters. In protonated water clusters up to (H₂O)₁₀₀H⁺, the proton hopping rate is around 100 hops/ns. This rate converges for 21 ≤ n ≤ 31, and no further speedup in bulk water is found. This indicates that bulklike behavior requires the solvation of a Zundel motif by ∼25 water molecules, which corresponds to the second solvation sphere. For smaller cluster sizes, the number of available states (i.e., the number of proton acceptors) is too small and slows down proton-transfer rates. The cluster simulations confirm that the excess proton is typically located on the surface. The free-energy surface as a function of the weights of the two lowest states and a configurational parameter suggests that the "special pair" plays a central role in rapid proton transport. The barriers between this minimum-energy structure and the Zundel and Eigen minima are sufficiently low (∼1 kcal/mol, consistent with recent experiments and commensurate with a hopping rate of ∼100/ns or 1 every 10 ps), leading to a highly dynamic environment. These findings are also consistent with recent experiments which find that Zundel-type hydration geometries are prevalent in bulk water.

IR Spectra of Hydrogen-Bonded Complexes of Trifluoroacetic Acid with Acetone and Diethyl Ether in the Gas Phase. Interaction between CH and OH Stretching Vibrations

The spectra of complexes of trifluoroacetic acid (TFA) with acetone and diethyl ether (DEE) and their perdeuterated isotopologues were extracted from the spectra of the mixture of the compounds recorded at room temperature. The ν(OH) bands of the complexes with protiated and deuterated acetone notably differ from each other, whereas these ν(OH) bands are practically not affected by the deuteration of DEE. An assumption about the interaction of CH and OH groups in the (CH₃)-C═O···HO fragment is made. According to density functional theory calculations, complexes of TFA with both acetone and DEE have a cyclic structure with one strong ═O···HO hydrogen bond and one weak CH···O═ bond. The structural, spectroscopic, and electronic properties indicate an essential role of weak bonds in the total complexation energy of the systems studied.

Quantum approaches to vibrational dynamics and spectroscopy: is ease of interpretation sacrificed as rigor increases?

The subject of this Perspective is quantum approaches, beyond the harmonic approximation, to vibrational dynamics and IR spectroscopy.

Teaching vibrational spectra to assign themselves

A new paradigm for assigning vibrational spectra is described. Instead of proceeding from potential to Hamiltonian to eigenvalues/eigenvectors/intensities to spectrum, the new method goes "backwards" directly from spectrum to eigenvectors. The eigenvectors then "assign" the spectrum, in that they identify the basis states that contribute to each eigenvalue. To start, we demonstrate an algorithm that can obtain useful estimates of the eigenvectors connecting a real, symmetric Hamiltonian to its eigenvalues even if the only available information about the Hamiltonian is its diagonal elements. When this algorithm is augmented with information about transition intensities, it can be used to assign a complex vibrational spectrum using only information about (1) eigenvalues (the peak centers of the spectrum) and (2) a harmonic basis set (taken to be the diagonal elements of the Hamiltonian). Examples will be discussed, including application to the vibrationally complex spectral region of the formic acid dimer.

Ab initio molecular dynamics studies of formic acid dimer colliding with liquid water

Ab initio molecular dynamics simulations of formic acid (FA) dimer colliding with liquid water at 300 K have been performed using density functional theory. The two energetically lowest FA dimer isomers were collided with a water slab at thermal and high kinetic energies up to 68kBT. Our simulations agree with recent experimental observations of nearly a complete uptake of gas-phase FA dimer: the calculated average kinetic energy of the dimers immediately after collision is 5 ± 4% of the incoming kinetic energy, which compares well with the experimental value of 10%. Simulations support the experimental observation of no delayed desorption of FA dimers following initial adsorption. Our analysis shows that the FA dimer forms hydrogen bonds with surface water molecules, where the hydrogen bond order depends on the dimer structure, such that the most stable isomer possesses fewer FA-water hydrogen bonds than the higher energy isomer. Nevertheless, even the most stable isomer can attach to the surface through one hydrogen bond despite its reduced hydrophilicity. Our simulations further show that the probability of FA dimer dissociation is increased by high collision energies, the dimer undergoes isomerization from the higher energy to the lowest energy isomer, and concerted double-proton transfer occurs between the FA monomers. Interestingly, proton transfer appears to be driven by the release of energy arising from such isomerization, which stimulates those internal vibrational degrees of freedom that overcome the barrier of a proton transfer.

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH)₂ and (DCOOH)₂, using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm^-1. Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm^-1. In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

Quantum and classical IR spectra of (HCOOH)2, (DCOOH)2 and (DCOOD)2 using ab initio potential energy and dipole moment surfaces

Full-dimensional (24 modes) quantum calculation of the IR spectrum of (DCOOD)₂, and comparison with classical MD one.

Kinetic isotope effects and how to describe them

We review several methods for computing kinetic isotope effects in chemical reactions including semiclassical and quantum instanton theory. These methods describe both the quantization of vibrational modes as well as tunneling and are applied to the ⋅H + H2 and ⋅H + CH4 reactions. The absolute rate constants computed with the semiclassical instanton method both using on-the-fly electronic structure calculations and fitted potential-energy surfaces are also compared directly with exact quantum dynamics results. The error inherent in the instanton approximation is found to be relatively small and similar in magnitude to that introduced by using fitted surfaces. The kinetic isotope effect computed by the quantum instanton is even more accurate, and although it is computationally more expensive, the efficiency can be improved by path-integral acceleration techniques. We also test a simple approach for designing potential-energy surfaces for the example of proton transfer in malonaldehyde. The tunneling splittings are computed, and although they are found to deviate from experimental results, the ratio of the splitting to that of an isotopically substituted form is in much better agreement. We discuss the strengths and limitations of the potential-energy surface and based on our findings suggest ways in which it can be improved.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

A synchrotron infrared absorption study of pressure induced polymerization of acrylamide

The hydrogen bonded dimeric structure of the model amide based molecular crystal acrylamide has been investigated under pressure using micro-spectroscopy, employing synchrotron infrared radiation up to 24GPa at room temperature. The high pressure spectra indicate systematic evolution of new features above 4GPa, which have been identified to be due to the emergence of a polymeric phase. The polymerization gets completed up to 16.8GPa and the observed changes are found to be irreversible upon the release of pressure. The behavior of NH stretching modes indicate that the uniform inter- and intra-dimeric interactions, rather than depicting a drastic reconstruction across the phase transition, show subtle modifications and become diverse in the high pressure polymeric phase.

The Influence of the Position of the Double Bond and Ring Size on the Stability of Hydrogen Bonded Complexes

To study the influence of the position of the double bond and ring size on the stability of hydrogen bonded complexes, the 1:1 complexes formed between 2,2,2-trifluoroethanol (TFE) and three heterocyclic compounds including 2,3-dihydrofuran (2,3-DHF), 2,5-dihydrofuran (2,5-DHF) and 3,4-dihydropyran (3,4-DHP) were investigated systematically. The formation of hydrogen bonded TFE−2,3-DHF, TFE−2,5-DHF and TFE−3,4-DHP complexes were identified by gas phase FTIR spectroscopy at room temperature, and the OH-stretching fundamental transition of TFE was red shifted upon complexation. The competition between the O atom and π-electrons bonding sites within the complexes was studied, and the O−H···π type hydrogen bond was found to be less stable than the O−H···O in all three cases. The observed red shifts of the OH-stretching fundamental transitions in the complexes were attributed to the formation of O−H···O hydrogen bond. Equilibrium constants of the complexation reactions were determined from measured and calculated OH-stretching fundamental intensities. Both theoretical calculations and experimental results reveal that the hydrogen bond strengths in the complexes follow the sequence: TFE−2,5-DHF > TFE−2,3-DHF ≈ TFE−3,4-DHP, thus the position of the double bond exerts significantly larger influence than ring size on the stability of the selected hydrogen bonded complexes.

Vibrational Spectroscopy and Proton Transfer Dynamics in Protonated Oxalate

The dynamics and infrared spectroscopic signatures of proton transfer in protonated oxalate (p-Oxa) are studied using classical and quantum dynamics. The intermolecular interactions are described by a force field suitable to follow proton transfer. This allows to carry out multiple extended classical molecular dynamics (MD) and ring polymer MD simulations from which the infrared spectrum is determined. Simulations at 600 K sample the quantum mechanical ground state probability distribution and best reproduce the experimentally observed maximum absorption wavelength and part of the line shape. Comparison with the experimentally measured spectrum provides an estimate for the barrier height for proton transfer which can not be determined directly from experiment. A barrier of 4.2 kcal/mol is found to best reproduce the position and width of the infrared absorption of the transferring proton in p-Oxa and also leads to an infrared (IR) spectrum in good agreement with experiment for the deuterated species d-Oxa. A novel means to capture the two resonance forms of oxalate depending on the localization of the excess proton on either CO moiety is found to yield improved results for the spectroscopy in the framework region between 1000 and 2000 cm^-1.

A QM/QTAIM research under the magnifying glass of the DPT tautomerisation of the wobble mispairs involving 2-aminopurine

In this study, a comprehensive survey of the changes of the physico-chemical parameters at each point of the IRC for the biologically important T·2AP*(w) ↔ T*·2AP(w) and G·2AP*(w) ↔ G*·2AP(w) DPT tautomerisation reactions involved in the point mutations (transitions and transversions) induced by 2-aminopurine (2AP) in DNA is provided.