Evidence for coherent proton tunneling in a hydrogen bond network

Multidimensional insights into the repeated electromagnetic field stimulation and biosystems interaction in aging and age-related diseases

We provide a multidimensional sequence of events that describe the electromagnetic field (EMF) stimulation and biological system interaction. We describe this process from the quantum to the molecular, cellular, and organismal levels. We hypothesized that the sequence of events of these interactions starts with the oscillatory effect of the repeated electromagnetic stimulation (REMFS). These oscillations affect the interfacial water of an RNA causing changes at the quantum and molecular levels that release protons by quantum tunneling. Then protonation of RNA produces conformational changes that allow it to bind and activate Heat Shock Transcription Factor 1 (HSF1). Activated HSF1 binds to the DNA expressing chaperones that help regulate autophagy and degradation of abnormal proteins. This action helps to prevent and treat diseases such as Alzheimer’s and Parkinson’s disease (PD) by increasing clearance of pathologic proteins. This framework is based on multiple mathematical models, computer simulations, biophysical experiments, and cellular and animal studies. Results of the literature review and our research point towards the capacity of REMFS to manipulate various networks altered in aging (Reale et al. PloS one 9, e104973, 2014), including delay of cellular senescence (Perez et al. 2008, Exp Gerontol 43, 307-316) and reduction in levels of amyloid-β peptides (Aβ) (Perez et al. 2021, Sci Rep 11, 621). Results of these experiments using REMFS at low frequencies can be applied to the treatment of patients with age-related diseases. The use of EMF as a non-invasive therapeutic modality for Alzheimer’s disease, specifically, holds promise. It is also necessary to consider the complicated and interconnected genetic and epigenetic effects of the REMFS-biological system’s interaction while avoiding any possible adverse effects.

Crystalline hydrogen bonding of water molecules confined in a metal-organic framework

Hydrogen bonding (H-bonding) of water molecules confined in nanopores is of particular interest because it is expected to exhibit chemical features different from bulk water molecules due to their interaction with the wall lining the pores. Herein, we show a crystalline behavior of H-bonded water molecules residing in the nanocages of a paddlewheel metal-organic framework, providing in situ and ex situ synchrotron single-crystal X-ray diffraction and Raman spectroscopy studies. The crystalline H-bond is demonstrated by proving the vibrational chain connectivity arising between hydrogen bond and paddlewheel Cu-Cu bond in sequentially connected Cu-Cu·····coordinating H₂O·····H-bonded H₂O and by proving the spatial ordering of H-bonded water molecules at room temperature, where they are anticipated to be disordered. Additionally, we show a substantial distortion of the paddlewheel Cu²⁺-centers that arises with water coordination simultaneously. Also, we suggest the dynamic coordination bond character of the H-bond of the confined water, by which an H-bond transitions to a coordination-bond at the Cu²⁺-center instantaneously after dissociating a previously coordinated H₂O.

Quantum dynamics of a hole migration through DNA: A single strand DNA model

A model predicting the behavior of a hole acting on the DNA strand was investigated. The hole-DNA interaction on the basis of a quantum-classical, non-linear DNA single strand model was described. The fact that a DNA molecule is formed by a furanose ring as its sugar, phosphate group and bases was taken into consideration. Based on the model, results were obtained for the probability of a hole location on the DNA base sequences, such as GTTGGG, GATGTGGG, GTTGTTGGG as well as on the sugar-phosphate groups mated with them.

Complexation of solvents and conformational equilibria in solutions of the simplest calix[4]arenes

Structure optimization and calculation of electronic adsorption spectra of 25,26,27,28-tetrahydroxycalix[4]arene and 25,27-dimethoxy-26,28-dihydroxycalix[4]arene conformers have been performed by density-functional theory using hybrid B3LYP functional in cc-p VTZ and cc-p VDZ basis sets in Gaussian 09 package. Analysis of experimental UV-Vis spectra of solutions of 25,26,27,28-tetrahydroxycalix[4]arene, 4-tert-butylcalix[4]arene and 25,27-dimethoxy-26,28-dihydroxycalix[4]arene in various solvents has been carried out. It was shown that the ratio of absorption maxima at characteristic wavelengths at ca. 274 and 283 nm may be used to assess the extent of calix[4]arene/solvent interactions. The conclusion is drawn that spectral characteristics of calix[4]arenes are strongly affected by acid-base interactions.

Quantum simulation of collective proton tunneling in hexagonal ice crystals

The effect of proton tunneling on many-body correlated proton transfer in hexagonal ice is investigated by quantum simulation. Classical single-particle hopping along individual hydrogen bonds leads to charge defects at high temperature, whereas six protons in ringlike topologies can move concertedly as a delocalized quasiparticle via collective tunneling at low temperature, thus preventing the creation of high-energy topological defects. Our findings rationalize many-body quantum tunneling in hydrogen-bonded networks and suggest that this phenomenon might be more widespread than previously thought.

Quantum combinatorial model of gene expression

We propose that the DNA within the chromatin behaves as a dynamic combinatorial library capable of forming novel structures by reversible processes. We also hypothesize that states within the library may be linked via quantum tunneling. RNA polymerase then could scan these states and the system decoheres to the “appropriate” state. Two ways of sustaining quantum coherence at relevant time scales could be possible, first, screening: the quantum system can be kept isolated from its decohering environment, second, the existence of decoherence free subspaces .We discuss the role of superconductivity in context of avoiding decoherence in context of our hypothesis.

Anomalous proton dynamics in ice at low temperatures

We present incoherent quasielastic neutron scattering measurements on ice Ih (ordinary ice) and Ic (cubic ice) which show the existence of nonharmonic motion of hydrogen at low temperatures, down to 5 K. We show that this dynamics is localized, nonvibrational, and related to the hydrogen disorder since it is absent in ordered ice VIII. A main jump distance of 0.75 A is identified, hence close to the distance between the two possible proton sites along the oxygen-oxygen bond. The dynamics is non-Arrhenius, has a large time rate of 2.7x10(11) s-1, and affects only a few percent of the total number of hydrogen atoms in the crystal. These results give evidence for the existence of concerted proton tunneling in these ice phases.

Mechanism of hydrogen-bond array isomerization in tetrahydroxycalix[4]arene and tetrahydroxythiacalix[4]arene

Possible rearrangement mechanisms of hydrogen-bond arrays formed at the lower rim of tetrahydroxycalix[4]arene and tetrahydroxythiacalix[4]arene were studied by means of density functional theory and the resolution identity approximation modification of Møller-Plesset perturbation theory (RI-MP2). Influence of solvent to height of energy barriers was quantified by use of the conductorlike screening model (COSMO) of implicit solvent (chloroform). Generally, two types of mechanisms were investigated. The first is represented by a synchronous single-step jump of all four hydroxyl protons. Pathways of the second mechanism include the rotation of one or more hydroxyl groups around the CAr-O bond. Theoretical results, in agreement with recently published experimental data (Lang et al. J. Chem. Phys. 2005, 122, 044056), prefer a jump mechanism for the methylene-bridged calix[4]arene. Concerning the thiacalix[4]arene, results obtained by COSMO as well as RI-MP2 calculations show that the rotational mechanism is very competitive and it could even be more favorable.

Secondary alpha isotope effects on deuterium tunneling in triplet o-methylanthrones: extraordinary sensitivity to barrier width

The rates of deuterium transfer in the photoenolization of triplet 1,4-dimethyl-10H-anthracen-9-one (1) with varying degrees of deuterium label in their methyl groups (1-d3, 1-d2, and 1-d) have been investigated as a function of temperature between 5 and 77 K. Measurable rate constants in the case of 1-d3 and 1-d2 were used to construct Arrhenius plots which illustrate the expected curvature and leveling off of rate constant versus temperature. The difference in tunneling rate constants of 1-d3 and 1-d2 yields a tunneling isotope effect, TIE = 2.4, which is attributed to the secondary alpha isotopic substitution. Density functional theory (DFT, B3LYP/6-31G*) calculations were carried out to obtain structural and energetic information for the H(D) transfer along the triplet state zero-point energy levels. The temperature dependence of the rate constants for each isotopologue was simulated with a model that considers the frequency of the C-D stretching mode and the quantum mechanical permeability determined from calculated energy parameters. The model suggests that a difference in barrier width of only 0.015 A between 1-d3 and 1-d2 leads to the observed 2-fold difference between tunneling rates.

Syntheses, conformations, and basicities of bicyclic triamines

The multistep syntheses of several bicyclic triamines are described, all of which have an imbedded 1,5,9-triazacyclododecane ring. In 1,5,9-triazabicyclo[7.3.3]pentadecanes 12, 13, 15, and 16, two nitrogens are bridged by three carbons. The monoprotonated forms of these triamines are highly stabilized by a hydrogen-bonded network involving the bridge and both bridgehead nitrogens, producing a difference of more than 8 pK(a) units in acidities of their monoprotonated and diprotonated forms. The one- and zero-carbon bridges in 1,5,9-triazabicyclo[9.1.1]tridecane (23) and 7-methyl-1,5,9-triazabicyclo[5.5.0]dodecane (39) do not enhance the stabilities of their monoprotonated forms. X-ray crystal structures and computational studies of 12.HI and 16.HI reveal similar, but somewhat weaker, hydrogen-bonded networks, relative to 15.HI. The activation free energies for conformational inversion of 13.HI (14.4 +/- 0.2 kcal/mol), 16.HI (15.0 +/- 0.1 kcal/mol) and 16 (8.8 +/- 0.3 kcal/mol) were measured by variable-temperature (1)H and (13)C NMR spectroscopy. These experimental barriers give an estimate of 6.2 kcal/mol for the strength of the bifurcated hydrogen bond between the bridge nitrogen and cavity proton in 16.HI. Computational studies support the hypothesis that N-inversion occurs in an open conformation, leading to an estimate of 10.32 kcal/mol for the enthalpy of the bifurcated hydrogen bond in 16.HI in the gas phase.

The ground-state tunneling splitting of various carboxylic acid dimers

Carboxylic acid dimers in gas phase reveal ground-state tunneling splittings due to a double proton transfer between the two subunits. In this study we apply a recently developed accurate semiclassical method to determine the ground-state tunneling splittings of eight different carboxylic acid derivative dimers (formic acid, benzoic acid, carbamic acid, fluoro formic acid, carbonic acid, glyoxylic acid, acrylic acid, and N,N-dimethyl carbamic acid) and their fully deuterated analogs. The calculated splittings range from 5.3e-4 to 0.13 cm(-1) (for the deuterated species from 2.8e-7 to 3.3e-4 cm(-1)), thus indicating a strong substituent dependence of the splitting, which varies by more than two orders of magnitude. One reason for differences in the splittings could be addressed to different barriers heights, which vary from 6.3 to 8.8 kcal/mol, due to different mesomeric stabilization of the various transition states. The calculated splittings were compared to available experimental data and good agreement was found. A correlation could be found between the tunneling splitting and the energy barrier of the double proton transfer, as the splitting increases with increased strength of the hydrogen bonds. From this correlation an empirical formula was derived, which allows the prediction of the ground-state tunneling splitting of carboxylic acid dimers at a very low cost and the tunneling splittings for parahalogen substituted benzoic acid dimers is predicted.

Voltage-gated proton channels and other proton transfer pathways

Proton channels exist in a wide variety of membrane proteins where they transport protons rapidly and efficiently. Usually the proton pathway is formed mainly by water molecules present in the protein, but its function is regulated by titratable groups on critical amino acid residues in the pathway. All proton channels conduct protons by a hydrogen-bonded chain mechanism in which the proton hops from one water or titratable group to the next. Voltage-gated proton channels represent a specific subset of proton channels that have voltage- and time-dependent gating like other ion channels. However, they differ from most ion channels in their extraordinarily high selectivity, tiny conductance, strong temperature and deuterium isotope effects on conductance and gating kinetics, and insensitivity to block by steric occlusion. Gating of H(+) channels is regulated tightly by pH and voltage, ensuring that they open only when the electrochemical gradient is outward. Thus they function to extrude acid from cells. H(+) channels are expressed in many cells. During the respiratory burst in phagocytes, H(+) current compensates for electron extrusion by NADPH oxidase. Most evidence indicates that the H(+) channel is not part of the NADPH oxidase complex, but rather is a distinct and as yet unidentified molecule.

Assembling phenomena of calix[4]hydroquinone nanotube bundles by one-dimensional short hydrogen bonding and displaced pi-pi stacking

Using the computer-aided molecular design approach, we recently reported the synthesis of calix[4]hydroquinone (CHQ) nanotube arrays self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (H-bonds) and aromatic-aromatic interactions. Here, we assess various calculation methods employed for both the design of the CHQ nanotubes and the study of their assembly process. Our calculations include ab initio and density functional theories and first principles calculations using ultrasoft pseudopotential plane wave methods. The assembly phenomena predicted prior to the synthesis of the nanotubes and details of the refined structure and electronic properties obtained after the experimental characterization of the nanotube crystal are reported. For better characterization of intriguing 1-D short H-bonds and exemplary displaced pi-pi stacks, the X-ray structures have been further refined with samples grown in different solvent conditions. Since X-ray structures do not contain the positions of H atoms, it is necessary to analyze the system using quantum theoretical calculations. The competition between H-bonding and displaced pi-pi stacking in the assembling process has been clarified. The IR spectroscopic features and NMR chemical shifts of 1-D short H-bonds have been investigated both experimentally and theoretically. The dissection of the two most important interaction components leading to self-assembly processes would help design new functional materials and nanomaterials.

A new conceptual framework for enzyme catalysis. Hydrogen tunnelling coupled to enzyme dynamics in flavoprotein and quinoprotein enzymes

Recent years have witnessed high levels of activity in identifying enzyme systems that catalyse H-transfer by quantum tunneling. Rather than being restricted to a small number of specific enzymes as perceived initially, it has now become an accepted mechanism for H-transfer in a growing number of enzymes. Furthermore, H-tunneling is driven by the thermally induced dynamics of the enzyme. In some of those enzymes that break stable C-H bonds the reaction proceeds purely by quantum tunneling, without the need to partially ascend the barrier. Enzymes studied that fall into this category include the flavoprotein and quinoprotein amine dehydrogenases, which have proved to be excellent model systems. These enzymes have enabled us to study the relationship between barrier shape and reaction kinetics. This has involved studies with "slow" and "fast" substrates and enzymes impaired by mutagenesis. A number of key questions now remain, including the nature of the coupling between protein dynamics and quantum tunneling. The wide-ranging implications of quantum tunneling introduce a paradigm shift in the conceptual framework for enzyme catalysis, inhibition and design.