Low-frequency Intermolecular Vibrations Research Articles

Hydration structure and dynamics, ultraviolet–visible and fluorescence spectra of caffeine in ambient liquid water. A combined classical molecular dynamics and quantum chemical study

The hydration structure and related dynamics of caffeine diluted in ambient liquid water have been extensively studied by performing classical molecular dynamics simulations, using our previously developed potential model of caffeine and the TIP4P/2005 water model. The results obtained have revealed that the first hydration shell of caffeine contains on average 56 water molecules. Hydrated caffeine forms in total 3 hydrogen bonds with its neighbor water molecules, with the Ocaffeine … Hwater hydrogen bonds exhibiting similar lifetimes with the ones corresponding to Owater … Hwater hydrogen bonds in liquid water. The self-diffusion coefficient of caffeine has been found to be four times lower than the corresponding value for water, being also in agreement with recent experimental measurements. The presence of water molecules inside the solvation shell of caffeine changes significantly their low-frequency intermolecular vibrations, as reflected on the calculated atomic velocity time correlation functions and corresponding spectral densities. Using the estimated average intermolecular structure of the first hydration shell of caffeine, the molecular cluster caffeine@W56 was optimized via quantum chemical calculations and subsequently the time-dependent density functional theory was used in order to predict the ultraviolet–visible and fluorescence spectra of hydrated caffeine. The results obtained are in agreement with recent experimental studies, which have proposed that such spectroscopic measurements can be used for the direct determination of alkaloids in aqueous extracts of natural products. In this framework, multi-scale molecular modelling providing accurate predictions of experimental data could also be a very useful tool, linking theoretical physical chemistry with analytical chemistry applications.

Broadband infrared absorption spectroscopy of low-frequency inter-molecular vibrations in crystalline poly(L-lactide)

The broadband vibrations of poly l-lactide (PLLA) were investigated by terahertz (THz) spectroscopy in the range of 2–16 THz, infrared (IR) spectroscopy, density functional theory (DFT), and classical molecular dynamics (MD) simulations. Characteristic functional group peaks were observed in the IR spectra, which were independent of the crystallinity. A simple model analysis utilizing DFT calculations with an isolated l-lactide monomer and MD simulations for nine polymer chains in a unit cell were performed to investigate the origin of intra-molecular vibrations between molecular chains. Experimentally observed peaks in the THz region were assigned to the inter- and intra-molecular vibration modes. Results showed that classical MD calculations are a particularly powerful tool for the vibrational-mode analysis of inter-molecular interactions.

Beyond single crystals: Imaging rubrene polymorphism across crystalline batches through lattice phonon Raman microscopy.

Polymorphism is an issue troubling numerous scientific fields. A phenomenon where molecules can arrange in different orientations in a crystal lattice, polymorphism in the field of organic photovoltaic materials can dramatically change electronic properties of these materials. Rubrene is a benchmark photovoltaic material showing high carrier mobility in only one of its three polymorphs. To use rubrene in devices, it is important to quantify the polymorph distribution arising from a particular crystal growth method. However, current methods for characterizing polymorphism are either destructive or inefficient for batch scale characterization. Lattice phonon Raman spectroscopy has the ability to distinguish between polymorphs based on low frequency intermolecular vibrations. We present here the addition of microscopy to lattice phonon Raman spectroscopy, which allows us to not only characterize polymorphs efficiently and nondestructively through Raman spectroscopy but also concurrently gain information on the size and morphology of the polymorphs. We provide examples for how this technique can be used to perform large, batch scale polymorph characterization for crystals grown from solution and physical vapor transport. We end with a case study showing how Raman microscopy can be used to efficiently optimize a green crystal growth method, selecting for large orthorhombic crystals desired for rubrene electronic device applications.

Supercritical Water is not Hydrogen Bonded.

Thinking about water is inextricably linked to hydrogen bonds, which are highly directional in character and determine the unique structure of water, in particular its tetrahedral H‐bond network. Here, we assess if this common connotation also holds for supercritical water. We employ extensive ab initio molecular dynamics simulations to systematically monitor the evolution of the H‐bond network mode of water from room temperature, where it is the hallmark of its fluctuating three‐dimensional network structure, to supercritical conditions. Our simulations reveal that the oscillation period required for H‐bond vibrations to occur exceeds the lifetime of H‐bonds in supercritical water by far. Instead, the corresponding low‐frequency intermolecular vibrations of water pairs as seen in supercritical water are found to be well represented by isotropic van‐der‐Waals interactions only. Based on these findings, we conclude that water in its supercritical phase is not a H‐bonded fluid.

One-Dimensional Adiabatic Model Approach for Calculating Progressions in Vibrational Spectra of Ion-Water Complexes.

Many water-anion complexes of the form X-·(H2O), where X- is a polyatomic anion, display a peak progression in the OH stretch region of the vibrational spectra with spacings of 65-85 cm-1. These progressions result from strong anharmonic coupling between the OH stretch and a low-frequency intermolecular rock vibration. In this study, we calculate these progressions in HCO2-·(H2O), NO3-·(H2O), and CS2-·(H2O) by use of a one-dimensional adiabatic model with rock potentials generated from ab initio energies and frequencies. The importance of using a geometry-dependent reduced mass in calculating the peak spacings is demonstrated. We find that the one-dimensional adiabatic model is more successful in predicting peak spacings in the spectrum of HCO2-·(H2O) than for NO3-·(H2O), for which the rock vibration is highly anharmonic.

Lennard–Jones Lecture 2017*

ABSTRACTSome examples of the use of molecular dynamics simulation to study solutions of small molecules in ionic liquids are discussed. It is shown that electrostatic forces, while not the dominant solute–solvent interaction, determine the local solute environment. The solubility of aromatics and the changes in the spectra of low-frequency intermolecular vibrations in two related ionic liquids (one dicationic and one monocationic) are compared with experimental results and related to the local environment.

Pronounced low-frequency vibrational thermal transport in C60 fullerite realized through pressure-dependent molecular dynamics simulations

Fullerene condensed-matter solids can possess thermal conductivities below their minimum glassy limit while theorized to be stiffer than diamond when crystallized under pressure. These seemingly disparate extremes in thermal and mechanical properties raise questions into the pressure dependence on the thermal conductivity of ${\mathrm{C}}_{60}$ fullerite crystals, and how the spectral contributions to vibrational thermal conductivity changes under applied pressure. To answer these questions, we investigate the effect of strain on the thermal conductivity of ${\mathrm{C}}_{60}$ fullerite crystals via pressure-dependent molecular dynamics simulations under the Green-Kubo formalism. We show that the thermal conductivity increases rapidly with compressive strain, which demonstrates a power-law relationship similar to their stress-strain relationship for the ${\mathrm{C}}_{60}$ crystals. Calculations of the density of states for the crystals under compressive strains reveal that the librational modes characteristic in the unstrained case are diminished due to densification of the molecular crystal. Over a large compression range (0--20 GPa), the Leibfried-Schl\omann equation is shown to adequately describe the pressure dependence of thermal conductivity, suggesting that low-frequency intermolecular vibrations dictate heat flow in the ${\mathrm{C}}_{60}$ crystals. A spectral decomposition of the thermal conductivity supports this hypothesis.

Energy Transfer to the Hydrogen Bond in the (H2O)2 + H2O Collision.

Trajectory procedures are used to study the collision between the vibrationally excited H2O and the ground-state (H2O)2 with particular reference to energy transfer to the hydrogen bond through the inter- and intramolecular pathways. In nearly 98% of the trajectories, energy transfer processes occur on a subpicosecond scale (≤0.7 ps). The H2O transfers approximately three-quarters of its excitation energy to the OH stretches of the dimer. The first step of the intramolecular pathway in the dimer involves a near-resonant first overtone transition from the OH stretch to the bending mode. The energy transfer probability in the presence of the 1:2 resonance is 0.61 at 300 K. The bending mode then redistributes its energy to low-frequency intermolecular vibrations in a series of small excitation steps, with the pathway which results in the hydrogen-bonding modes gaining most of the available energy. The hydrogen bonding in ∼50% of the trajectories ruptures on vibrational excitation, leaving one quantum in the bend of the monomer fragment. In a small fraction of trajectories, the duration of collision is longer than 1 ps, during which the dimer and H2O form a short-lived complex through a secondary hydrogen bond, which undergoes large amplitude oscillations.

Vibrational Coupling at the Topmost Surface of Water Revealed by Heterodyne-Detected Sum Frequency Generation Spectroscopy.

Unraveling vibrational coupling is the key to consistently interpret vibrational spectra of complex molecular systems. The vibrational spectrum of the water surface heavily suffers from vibrational coupling, which hinders complete understanding of the molecular structure and dynamics of the water surface. Here we apply heterodyne-detected sum frequency generation spectroscopy to the water surface and accomplish the assignment of a weak vibrational band located at the lower energy side of the free OH stretch. We find that this band is due to a combination mode of the hydrogen-bonded OH stretch and a low-frequency intermolecular vibration, and this combination band appears in the surface vibrational spectrum through anharmonic vibrational coupling that takes place exclusively at the topmost surface.

Intermolecular vibrations and vibrational dynamics of a phenol⋯methanol binary complex studied by LIF spectroscopy

Low-frequency intermolecular vibrations in S0 and S1 states of p-fluorophenol (pFP) methanol binary complex have been studied using laser induced fluorescence (LIF) spectroscopy in a supersonic jet expansion. Vibrational fundamentals of five such modes show up in fluorescence excitation (FE) spectrum, and corresponding ground state frequencies are obtained measuring disperse fluorescence (DF) spectra. Signatures of strong coupling between the hydrogen bond stretching fundamental (σ01) and a ring mode of pFP moiety in S1 state are revealed. In comparison with the analogous pFP-water complex, the present system displays very low threshold (∼170cm−1) for vibrational energy relaxation in S1 state.

Five intermolecular vibrations of the CO2 dimer observed via infrared combination bands.

The weakly bound van der Waals dimer (CO2)2 has long been of considerable theoretical and experimental interest. Here, we study its low frequency intermolecular vibrations by means of combination bands in the region of the CO2 monomer ν3 fundamental (≈2350 cm-1), which are observed using a tunable infrared laser to probe a pulsed supersonic slit jet expansion. With the help of a recent high level ab initio calculation by Wang, Carrington, and Dawes, four intermolecular frequencies are assigned: the in-plane disrotatory bend (22.26 cm-1); the out-of-plane torsion (23.24 cm-1); twice the disrotatory bend (31.51 cm-1); and the in-plane conrotatory bend (92.25 cm-1). The disrotatory bend and torsion, separated by only 0.98 cm-1, are strongly mixed by Coriolis interactions. The disrotatory bend overtone is well behaved, but the conrotatory bend is highly perturbed and could not be well fitted. The latter perturbations could be due to tunneling effects, which have not previously been observed experimentally for CO2 dimer. A fifth combination band, located 1.3 cm-1 below the conrotatory bend, remains unassigned.

Charge-Transfer Mobility Parameters in Photoelectronic Devices: The Advanced Miller-Abrahams Computation.

The local hopping step of the electron transfer (ET) reaction is investigated for a real organic material composed of molecules M (N,N'-di(1-naphthyl)-N,N'-diphenyl-(1,1'-biphenyl)-4,4'-diamine). This material is implemented in light-emitting photoelectronic devices. The conductivity effect is simulated and calculated at a molecular level. We have studied the ET mechanism alternative to that suggested by the usually employed Marcus-like polaron model. The ion-molecular binary complex M(+)M (for hole transfer) is considered as a reaction center. The reaction dynamics is carried through the low-frequency intermolecular vibration coordinate connecting its fragments (the promotion mode). Its coupling to the acoustic phonon bath serves for a dissipation of the reaction energy misfit. The high-frequency intramolecular vibrations (the reorganization modes) modulate the reaction kinetics via Franck-Condon factors induced by their polarization. The ET rate constants are evaluated in terms of the computational algorithm described earlier (Basilevsky, M. V.; et al. J. Chem. Phys. 2013 139, 234102). Standard quantum-chemical and molecular dynamical techniques are used for a calculation of all necessary parameters of this model. The macroscopic charge-carrier mobility of the material is estimated by properly averaging the rate constants over the total simulation cell.

The nature of the transition mismatches with Watson–Crick architecture: the G*·T or G·T* DNA base mispair or both? A QM/QTAIM perspective for the biological problem

This study provides the first accurate investigation of the tautomerization of the biologically important guanine*·thymine (G*·T) DNA base mispair with Watson–Crick geometry, involving the enol mutagenic tautomer of the G and the keto tautomer of the T, into the G·T* mispair (∆G = .99 kcal mol−1, population = 15.8% obtained at the MP2 level of quantum-mechanical theory in the continuum with ε = 4), formed by the keto tautomer of the G and the enol mutagenic tautomer of the T base, using DFT and MP2 methods in vacuum and in the weakly polar medium (ε = 4), characteristic for the hydrophobic interfaces of specific protein–nucleic acid interactions. We were first able to show that the G*·T↔G·T* tautomerization occurs through the asynchronous concerted double proton transfer along two antiparallel O6H···O4 and N1···HN3 H-bonds and is assisted by the third N2H···O2 H-bond, that exists along the entire reaction pathway. The obtained results indicate that the G·T* base mispair is stable from the thermodynamic point of view complex, while it is dynamically unstable structure in vacuum and dynamically stable structure in the continuum with ε = 4 with lifetime of 6.4·10−12 s, that, on the one side, makes it possible to develop all six low-frequency intermolecular vibrations, but, on the other side, it is by three orders less than the time (several ns) required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication. One of the more significant findings to emerge from this study is that the short-lived G·T* base mispair, which electronic interaction energy between the bases (−23.76 kcal mol−1) exceeds the analogical value for the G·C Watson–Crick nucleobase pair (−20.38 kcal mol−1), “escapes from the hands” of the DNA replication machinery by fast transforming into the G*·T mismatch playing an indirect role of its supplier during the DNA replication. So, exactly the G*·T mismatch was established to play the crucial role in the spontaneous point mutagenesis.

A QM/QTAIM microstructural analysis of the tautomerisation via the DPT of the hypoxanthine·adenine nucleobase pair

We provide a pathway for the tautomerisation of the biologically important hypoxanthine·adenine (Hyp·Ade) nucleobase pair (Cs) formed by the keto tautomer of the Hyp and the amino tautomer of the Ade into the Hyp*·Ade* base pair (Cs) formed by the enol tautomer of the Hyp and the imino tautomer of the Ade by applying quantum-mechanical calculations and Bader's Quantum Theory of Atoms in Molecules analysis. It was found out that the dipole active Hyp·Ade↔Hyp*·Ade* tautomerisation occurs via the asynchronous concerted double proton transfer (DPT) through the TSHyp·Ade↔Hyp*·Ade* (Cs). Based on the sweeps of the energies of the intermolecular H-bonds along the intrinsic reaction coordinate, it was established that the N6H···O6 H-bond (5.40) is cooperative with the N1H···N1 H-bond (6.99) in the Hyp·Ade base pair, as well as the O6H···N6 H-bond (11.50) is cooperative with the N1H···N1 H-bond (7.28 kcal·mol−1) in the Hyp*·Ade* base pair, mutually strengthening each other. The Hyp*·Ade* base pair possesses an extremely short lifetime 2.68·10−14 s, which is predetermined by the negative value of the Gibbs free energy of the reverse barrier of its tautomerisation, and all of the six low-frequency intermolecular vibrations cannot develop during this period of time. Consequently, the Hyp·Ade→Hyp*·Ade* DPT tautomerisation cannot serve as a source of the rare tautomers of the bases.

How does the long G·G* Watson-Crick DNA base mispair comprising keto and enol tautomers of the guanine tautomerise? The results of a QM/QTAIM investigation.

The double proton transfer (DPT) in the long G·G* Watson-Crick base mispair (|C6N1(G*)N1C6(G)| = 36.4°; C1 symmetry), involving keto and enol tautomers of the guanine (G) nucleobase, along two intermolecular neighboring O6H···O6 (8.39) and N1···HN1 (6.14 kcal mol(-1)) H-bonds that were established to be slightly anti-cooperative, leads to its transformation into the G*·G base mispair through a single transition state (|C6N1N1C6| = 37.1°; C1), namely to the interconversion into itself. It was shown that the G·G* ↔ G*·G tautomerisation via the DPT is assisted by the third specific contact, that sequentially switches along the intrinsic reaction coordinate (IRC) in an original way: (G)N2H···N2(G*) H-bond (-25.13 to -10.37) → N2···N2 van der Waals contact (-10.37 to -9.23) → (G)N2···HN2(G*) H-bond (-9.23 to 0.79) → (G*)N2···HN2(G) H-bond (0.79 to 7.35 Bohr). The DPT tautomerisation was found to proceed through the asynchronous concerted mechanism by employing the QM/QTAIM approach and the methodology of the scans of the geometric, electron-topological, energetic, polar and NBO properties along the IRC. Nine key points, that can be considered as part of the tautomerisation repertoire, have been established and analyzed in detail. Furthermore, it was shown that the G·G* or G*·G base mispair is a thermodynamically and dynamically stable structure with a lifetime of 8.22 × 10(-10) s and all 6 low-frequency intermolecular vibrations are able to develop during this time span. Lastly, our results highlight the importance of the G·G* ↔ G*·G DPT tautomerisation, which can have implications for biological and chemical sensing applications.

Is the DPT tautomerization of the long A·G Watson–Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question

Herein, we first address the question posed in the title by establishing the tautomerization trajectory via the double proton transfer of the adenine·guanine (A·G) DNA base mispair formed by the canonical tautomers of the A and G bases into the A*·G* DNA base mispair, involving mutagenic tautomers, with the use of the quantum-mechanical calculations and quantum theory of atoms in molecules (QTAIM). It was detected that the A·G ↔ A*·G* tautomerization proceeds through the asynchronous concerted mechanism. It was revealed that the A·G base mispair is stabilized by the N6H···O6 (5.68) and N1H···N1 (6.51) hydrogen bonds (H-bonds) and the N2H···HC2 dihydrogen bond (DH-bond) (0.68 kcal·mol(-1) ), whereas the A*·G* base mispair-by the O6H···N6 (10.88), N1H···N1 (7.01) and C2H···N2 H-bonds (0.42 kcal·mol(-1) ). The N2H···HC2 DH-bond smoothly and without bifurcation transforms into the C2H···N2 H-bond at the IRC = -10.07 Bohr in the course of the A·G ↔ A*·G* tautomerization. Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···O6 H-bond is anticooperative to the two others-N1H···N1 and N2H···HC2 in the A·G base mispair, while the latters are significantly cooperative, mutually strengthening each other. In opposite, all three O6H···N6, N1H···N1, and C2H···N2 H-bonds are cooperative in the A*·G* base mispair. All in all, we established the dynamical instability of the А*·G* base mispair with a short lifetime (4.83·10(-14) s), enabling it not to be deemed feasible source of the A* and G* mutagenic tautomers of the DNA bases. The small lifetime of the А*·G* base mispair is predetermined by the negative value of the Gibbs free energy for the A*·G* → A·G transition. Moreover, all of the six low-frequency intermolecular vibrations cannot develop during this lifetime that additionally confirms the aforementioned results. Thus, the A*·G* base mispair cannot be considered as a source of the mutagenic tautomers of the DNA bases, as the A·G base mispair dissociates during DNA replication exceptionally into the A and G monomers in the canonical tautomeric form.

Does the tautomeric status of the adenine bases change upon the dissociation of the A*·Asyn Topal–Fresco DNA mismatch? A combined QM and QTAIM atomistic insight

We have scrupulously explored the tautomerisation mechanism via the double proton transfer of the A*·A(syn) Topal-Fresco base mispair (C(s) symmetry), formed by the imino and amino tautomers of the adenine DNA base in the anti- and syn-conformations, respectively, bridging quantum-mechanical calculations with Bader's quantum theory of atoms in molecules. It was found that the A*·A(syn) ↔ A·A*(syn) tautomerisation is the asynchronous concerted process. It was established that the A*·A(syn) DNA mismatch is stabilized by the N6H···N6 (6.35) and N1H···N7 (6.17) hydrogen (H) bonds, whereas the A·A*(syn) base mispair (Cs) by the N6H···N6 (8.82) and N7H···N1 (9.78) H-bonds and the C8H···HC2 HH-bond (0.30 kcal mol(-1)). Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···N6 and N1H···N7/N7H···N1 H-bonds are anti-cooperative and mutually weaken each other in the A*·A(syn) and A·A*(syn) mispairs. It was revealed that the A·A*(syn) DNA mismatch is a dynamically unstable structure with a short lifetime of 1.12 × 10(-13) s and any of its 6 low-frequency intermolecular vibrations can develop during this period of time. This observation makes it impossible to change the tautomeric status of the A bases upon the dissociation of the A*·A(syn) base mispair into the monomers during DNA replication.

The physicochemical essence of the purine·pyrimidine transition mismatches with Watson-Crick geometry in DNA: A·C* versa A*·C. A QM and QTAIM atomistic understanding

It was established for the first time by DFT and MP2 quantum-mechanical (QM) methods either in vacuum, so in the continuum with a low dielectric constant (ε = 4), typical for hydrophobic interfaces of specific protein-nucleic acid interactions, that the repertoire for the tautomerisation of the biologically important adenine·cytosine* (A·C*) mismatched DNA base pair, formed by the amino tautomer of the A and the imino mutagenic tautomer of the C, into the A*·C base mispair (∆G = 2.72 kcal mol−1 obtained at the MP2 level of QM theory in the continuum with ε = 4), formed by the imino mutagenic tautomer of the A and the amino tautomer of the C, proceeds via the asynchronous concerted double proton transfer along two antiparallel H-bonds through the transition state (TSA·C*↔A*·C). The limiting stage of the A·C*→A*·C tautomerisation is the final proton transfer along the intermolecular N6H···N4 H-bond. It was found that the A·C*/A*·C DNA base mispairs with Watson–Crick geometry are associated by the N6H⋯N4/N4H⋯N6, N3H⋯N1/N1H⋯N3 and C2H⋯O2 H-bonds, respectively, while the TSA·C*↔A*·C is joined by the N6–H–N4 covalent bridge and the N1H⋯N3 and C2H⋯O2 H-bonds. It was revealed that the A·C*↔A*·C tautomerisation is assisted by the true C2H⋯O2 H-bond, that in contrast to the two others conventional H-bonds exists along the entire intrinsic reaction coordinate (IRC) range herewith becoming stronger at the transition from vacuum to the continuum with ε = 4. To better understand the behavior of the intermolecular H-bonds and base mispairs along the IRC of the A·C*↔A*·C tautomerisation, the profiles of their electron-topological, energetical, geometrical, polar and charge characteristics are reported in this study. It was established based on the profiles of the H-bond energies that all three H-bonds are cooperative, mutually strengthening each other. The nine key points, providing a detailed physicochemical picture of the A·C*↔A*·C tautomerisation, were revealed and thoroughly examined along the IRC. It was shown that the A*·C base mispair with the population ~1 % obtained at the MP2 level of QM theory in the continuum with ε = 4 is thermodynamically and dynamically stable structure. Its lifetime was calculated to be 5.76·10−10 s at the MP2 level of QM theory in the continuum with ε = 4. This lifetime, from the one side, enables all six low-frequency intermolecular vibrations to develop, but, from the other side, it is by order less than the time (several ns) required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication. This means that the A*·C base mispair “slips away from the hands” of the replication machinery into the A·C* mismatched base pair. Consequently, the authors came to the conclusion that exactly the A·C* base mispair is an active player of the point mutational events and is effectively dissociated by the replication machinery into the A and C* monomers in contrast to the A*·C base mispair, playing the mediated role of a provider of the A·C* base mispair in DNA that is synthesised.

The physico-chemical mechanism of the tautomerisation via the DPT of the long Hyp∗·Hyp Watson–Crick base pair containing rare tautomer: A QM and QTAIM detailed look

We showed that biologically important planar Hyp∗·Hyp base pair (Cs) formed by the enol and keto tautomers of the hypoxanthine tautomerises via the synchronous concerted mechanism through the TS (C2v). The five key points were detected and completely investigated along the IRC of the Hyp∗·Hyp↔Hyp·Hyp∗ tautomerisation via the DPT. It was found that intermolecular antiparallel О6Н…О6 and N1H…N1 H-bonds are cooperative and mutually reinforce each other. It was proved that the Hyp∗·Hyp/Hyp·Hyp∗ base pair is dynamically stable structure with a lifetime 8.2×10−12 s and all its six low-frequency intermolecular vibrations are able to develop during this period of time.

Atomistic nature of the DPT tautomerisation of the biologically important C·C* DNA base mispair containing amino and imino tautomers of cytosine: a QM and QTAIM approach

A theoretical study of tautomerisation of the biologically important cytosine·cytosine* (C·C*) DNA mismatch with a propeller-like structure (|C4N3N3C4| = 32.4°; C1 symmetry) and cis-oriented N1H glycosidic bonds, formed by the amino and imino tautomers of the C nucleobase, via the asynchronous concerted double proton transfer (DPT) along two H-bonds through the transition state (TSC·C*↔C*·C) (|C4N3N3C4| = 48.5°; C1 symmetry) into the C*·C mispair was carried out for the first time. It was established that the C·C*/C*·C DNA base mispair is associated by the antiparallel N4H···N4 (6.66 kcal mol(-1)), N3H···N3 (6.47 kcal mol(-1)) H-bonds and the O2···O2 van der Waals (vdW) contact (0.33 kcal mol(-1)), while the zwitterionic TSC·C*↔C*·C is stabilized by the parallel N4(+)H···N4(-) (13.55 kcal mol(-1)), N3(+)H···N3(-) (13.20 kcal mol(-1)) H-bonds and the O2(+)···O2(-) vdW contact (0.60 kcal mol(-1)). It was shown that the C·C* ↔ C*·C tautomerisation via the DPT is assisted by the O2···O2 vdW contact, that in contrast to the two others N4H···N4 and N3H···N3 H-bonds exists along the entire intrinsic reaction coordinate (IRC) range. The positive values of the Grunenberg's compliance constants (30.919 and 21.384 Å mdyn(-1) for C·C*/C*·C and TSC·C*↔C*·C, respectively) indicate that the O2···O2 vdW contact is a stabilizing closed-shell interaction. It was found that the middle N3H···N3 H-bond is anti-cooperative with the upper N4H···N4 H-bond and cooperative with the lower O2···O2 vdW contact. The 9 key points, which can be considered as electron-topological "fingerprints" of the asynchronous concerted C·C* ↔ C*·C tautomerisation process via the DPT were revealed along the IRC and examined in detail. It was shown that the C·C*/C*·C base mispair is a thermodynamically and dynamically stable structure. Its lifetime is equal to 1.53 × 10(-7) s at the MP2/cc-pVQZ//B3LYP/6-311++G(d,p) level of theory in vacuum. All 6 low-frequency intermolecular vibrations are able to develop during this time span.