Arrangement Of Protons Research Articles

Networks of Hydrogen Bond Networks in Water Clusters.

Water clusters play a prominent role in atmospheric and solution chemistry. Numerous arrangements of protons, H-bond configurations or networks, shape the cluster properties. Studies of small water clusters by cryogenic scanning tunneling microscopy and high-resolution rovibrational spectroscopy have established proton rearrangement mechanisms forming pathways between H-bond networks. The mechanisms, concerted tunneling in particular, describe the local processes connecting pairs of configurations. Here, proton rearrangement networks mapping these transformations are defined and explored to provide a global view of the H-bond configurations in clusters. The networks are constructed for clusters of different sizes and structures. Their analysis reveals an odd-even effect with respect to the number of water molecules, exponential growth of the small-world character, bimodality of the degree distributions, and gapped assortativity of the networks. The last two properties signify the unexpected division of H-bond configurations into two classes according to their network connectivity. The results demonstrate qualitative differences between proton rearrangement mechanisms, suggest a strong influence of the cluster structure. The generated networks are of interest as real-world models for network rewiring; they establish an alternative platform for studies of proton rearrangements in H-bonded systems.

Electron Orbiting Patterns

This article presents electron orbiting patterns based on a symmetrical orthogonal arrangement of protons and neutrons in the nucleus of an atom as outlined in a published article titled An Orthogonal Mechanical Model of Stable Nuclei (Dana George Cottrell, 2021). In that article, an electron orbiting arrangement about the orthogonal axes was developed which adapted the mechanical models to the Periodic Table. This article will show how electron orbiting patterns on two axes group elements in accordance to the Periodic Table. In the interest of simplicity, binding energies and energy levels using quantum and wave mechanics are not described in this article.

Quantifying charge state heterogeneity for proteins with multiple ionizable residues

Ionizable residues can release and take up protons and this has an influence on protein structure and function. The extent of protonation is linked to the overall pH of the solution and the local environments of ionizable residues. Binding or unbinding of a single proton generates a distinct charge microstate defined by a specific pattern of charges. Accordingly, the overall partition function is a sum over all charge microstates and Boltzmann weights of all conformations associated with each of the charge microstates. This ensemble-of-ensembles description recast as a q-canonical ensemble allows us to analyze and interpret potentiometric titrations that provide information regarding net charge as a function of pH. In the q-canonical ensemble, charge microstates are grouped into mesostates where each mesostate is a collection of microstates of the same net charge. Here, we show that leveraging the structure of the q-canonical ensemble allows us to decouple contributions of net proton binding and release from proton arrangement and conformational considerations. Through application of the q-canonical formalism to analyze potentiometric measurements of net charge in proteins with repetitive patterns of Lys and Glu residues, we determine the underlying mesostate pKa values and, more importantly, we estimate relative mesostate populations as a function of pH. This is a strength of using the q-canonical approach that cannot be replicated using purely site-specific analyses. Overall, our work shows how measurements of charge equilibria, decoupled from measurements of conformational equilibria, and analyzed using the framework of the q-canonical ensemble, provide protein-specific quantitative descriptions of pH-dependent populations of mesostates. This method is of direct relevance for measuring and understanding how different charge states contribute to conformational, binding, and phase equilibria of proteins.

An Orthogonal Mechanical Model of Stable Nuclei

The following article presents a mechanical model approach for stable atomic nuclei based on a symmetrical orthogonal arrangement of protons and neutrons. This rigid approach lends support to nuclear pairing, shell modeling (without gaps), and symmetry concepts of nuclear structure and does not support independent particle models where nucleons move in mean free paths within the nucleus. The disparity between the number of stable nuclides with an even number of protons and those with an odd number of protons is examined and then used to postulate possible orthogonal mechanical models of nuclei. The ability to predict subsequent abundant nuclei based on the pattern developed for the first twenty or so nuclides gives credence to the proposed model. To further validate this pattern, an electron orbiting arrangement about the orthogonal axes is developed which adapts the pattern to the periodic table. Each vertical column in the periodic table makes up a related group of elements based on their chemical behavior. This article will show how electron orbiting patterns on two axes group elements in accordance to the Periodic Table and opens the door for pushing physics beyond the standard mode (BSM). In the interest of simplicity, binding energies and energy levels using quantum and wave mechanics are not described in this article.

Solution of spherical equation in 3 dimensions for hydrogen atom with quantum numbers 4≤ n≤ 5

The lightest and simplest arrangement of protons and electrons is a hydrogen atom. One of the wave characteristics of an atom can be known using the Schrodinger equation. Schrodinger’s equations of spherical coordinates consist of radial equations and angular equations. Quantum numbers 4≤ n ≤ 5from the Schrodinger equation sphere coordinates produce different angular wave functions. To find out the angular wave equation using normalization conditions . Based on the normalization conditions for n = 4 a wave function is produced , while for n = 5 a wave function is .

Island of Heavyweights.

The article focuses on the scientists' efforts in the past decade to find the world's heaviest element. It refers to the discovery of oganesson in 2006 by a Russian-American research team using a particle accelerator in Dubna, Russia. It also explores the island of stability describing special arrangements of protons and neutrons that makes an element stable.

High precision determination of the melting points of water TIP4P/2005 and water TIP4P/Ice models by the direct coexistence technique.

An exhaustive study by molecular dynamics has been performed to analyze the factors that enhance the precision of the technique of direct coexistence for a system of ice and liquid water. The factors analyzed are the stochastic nature of the method, the finite size effects, and the influence of the initial ice configuration used. The results obtained show that the precision of estimates obtained through the technique of direct coexistence is markedly affected by the effects of finite size, requiring systems with a large number of molecules to reduce the error bar of the melting point. This increase in size causes an increase in the simulation time, but the estimate of the melting point with a great accuracy is important, for example, in studies on the ice surface. We also verified that the choice of the initial ice Ih configuration with different proton arrangements does not significantly affect the estimate of the melting point. Importantly this study leads us to estimate the melting point at ambient pressure of two of the most popular models of water, TIP4P/2005 and TIP4P/Ice, with the greatest precision to date.

Alternating current breakdown voltage of ice electret

Ice has low environmental impact. Our research objectives are to study the availability of ice as a dielectric insulating material at cryogenic temperatures. We focus on ferroelectric ice (iceXI) at cryogenic temperatures. The properties of iceXI, including its formation, are not clear. We attempted to obtain the polarized ice that was similar to iceXI under the applied voltage and cooling to 77 K. The polarized ice have a wide range of engineering applications as electronic materials at cryogenic temperatures. This polarized ice is called ice electret. The structural difference between ice electret and normal ice is only the positions of protons. The effects of the proton arrangement on the breakdown voltage of ice electret were shown because electrical properties are influenced by the structure of ice. We observed an alternating current (ac) breakdown voltage of ice electret and normal ice at 77 K. The mean and minimum ac breakdown voltage values of ice electret were higher than those of normal ice. We considered that the electrically weak part of the normal ice was improved by applied a direct electric field.

The impact of modular substitution on crystal packing: the tale of two ureas

A small library of 13 (3a–m) compounds with modular positioning of iodide and urea/thiourea groups was synthesized in excellent yields in a single step synthetic protocol. The existence of the anticipated (thio)urea derivatives was unambiguously established using a combination of 1–2D NMR spectroscopy, ESI-MS and single crystal X-ray diffraction studies. These (thio)urea compounds were classified into four classes as follows: a) mono-substituted urea, b) di-substituted urea, c) di-substituted thiourea and d) electronically tailored di-substituted thiourea. The changes in molecular conformation and crystal packing due to the change in the relative positioning of the iodo group at the phenyl ring attached to one of the N atoms and different substituents at other N atoms in urea and thiourea derivatives have been discussed. The urea derivatives, in general, display the chain association through one-dimensional three-centered N–H⋯O hydrogen bonding interactions due to the trans–trans orientation of both NH protons with respect to the carbonyl group, whereas the thiourea compounds exhibit a centrosymmetric dimeric assembly via the complementary N–H⋯S interactions because of the trans–cis arrangement of the NH protons leading to either a helical or a sheet pattern. The presence of a nitro group at the para position of the thiourea derivative leads to trans–trans arrangement of both NH protons with respect to the thiocarbonyl groups, thus yielding a chain assembly through one-dimensional three-centered N–H⋯S interactions similar to urea derivatives. Associations of these chains or sheets in urea/thiourea derivatives through halogen bonding interactions (hal⋯hal, hal⋯π, hal⋯S etc.) generate a 2D assembly.

Proton Matrix ENDOR Studies on Ca2+-depleted and Sr2+-substituted Manganese Cluster in Photosystem II

Proton matrix ENDOR spectra were measured for Ca(2+)-depleted and Sr(2+)-substituted photosystem II (PSII) membrane samples from spinach and core complexes from Thermosynechococcus vulcanus in the S2 state. The ENDOR spectra obtained were similar for untreated PSII from T. vulcanus and spinach, as well as for Ca(2+)-containing and Sr(2+)-substituted PSII, indicating that the proton arrangements around the manganese cluster in cyanobacterial and higher plant PSII and Ca(2+)-containing and Sr(2+)-substituted PSII are similar in the S2 state, in agreement with the similarity of the crystal structure of both Ca(2+)-containing and Sr(2+)-substituted PSII in the S1 state. Nevertheless, slightly different hyperfine separations were found between Ca(2+)-containing and Sr(2+)-substituted PSII because of modifications of the water protons ligating to the Sr(2+) ion. Importantly, Ca(2+) depletion caused the loss of ENDOR signals with a 1.36-MHz separation because of the loss of the water proton W4 connecting Ca(2+) and YZ directly. With respect to the crystal structure and the functions of Ca(2+) in oxygen evolution, it was concluded that the roles of Ca(2+) and Sr(2+) involve the maintenance of the hydrogen bond network near the Ca(2+) site and electron transfer pathway to the manganese cluster.

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics.

A structural characterization of the hydrated form of the brownmillerite-type phase Ba2In2O5, Ba2In2O4(OH)2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25−32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba2In2O4(OH)2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H–17O double resonance experiments.

Synthesis, Structures and Properties of Two New Coordination Polymers with Unprecedented Water Cluster

Two new complexes, [Eu2(NIPH)2(H2O)14](HNIPH)2(H2O)7 (1) [Co2(abtc)(phen)4(H2O)]·12(H2O) (2) (H2NIPH = 5-nitroisophthalic acid, H4abtc = 3,3′,5,5′-azobenzenetetracarboxylic acid, phen = 1,10-phenanthroline, DMF = N,N′-dimethylformamide) have been synthesized and characterized by infrared spectrum, thermal gravimetric analysis, X-ray single crystal diffraction and photoluminescence properties. Complex 1 upon slow evaporation at room temperature gave a 0-D structure, and seven independent water molecules and their equivalent held together by hydrogen bonds with an ordered proton arrangement form a 1-D hydrogen-bonded water tape. An unusual water tape notated T10(0)A0 is observed in 2. A 1-D water tape by connecting five-ten-five membered water rings through hydrogen bonds. Multiple hydrogen bonds and π–π stacking interactions play important roles in the formation of the 3-D networks. Fascinatingly, these lattice water molecules display unprecedented water cluster and play important roles in the stabilizing the whole network.

Thermodynamic properties and phase transitions of Tutton salt (NH4)2Fe(SO4)2·6H2O from MAS NMR and single-crystal NMR

The thermodynamic properties and phase transitions of Tutton salt (NH4)2Fe(SO4)2·6H2O were investigated using thermogravimetric analysis, differential scanning calorimetry, and nuclear magnetic resonance. The first mass loss occurs around 330 K (Td), which is interpreted as the onset of partial thermal decomposition. Phase transitions were found at 387 K (=TC1) and 500 K (=TC2). The temperature dependences of the spin–lattice relaxation time in the rotating frame, T1ρ, and that in the laboratory frame, T1, for the H nuclei change abruptly near TC1. These changes are associated with changes in the geometry of the arrangement of octahedral water molecules and ammonium protons.

First-Principles Study of the Infrared Spectra of the Ice Ih (0001) Surface

We present a study of the infrared (IR) spectra of the (0001) deuterated ice surface based on first-principles molecular dynamics simulations. The computed spectra show a good agreement with available experimental IR measurements. We identified the bonding configurations associated with specific features in the spectra, allowing us to provide a detailed interpretation of IR signals. We computed the spectra of several proton ordered and disordered models of the (0001) surface of ice, and we found that IR spectra do not appear to be a sensitive probe of the microscopic arrangement of protons at ice surfaces.

Investigation of the hydrogen bonding in ice Ih by first-principles density function methods

It is a well recognized difficult task to simulate the vibrational dynamics of ices using the density functional theory (DFT), and there has thus been rather limited success in modelling the inelastic neutron scattering (INS) spectra for even the simplest structure of ice, ice Ih, particularly in the translational region below 400 cm(-1). The reason is partly due to the complex nature of hydrogen bonding (H-bond) among water-water molecules which require considerable improvement of the quantum mechanical simulation methods, and partly owing to the randomness of protons in ice structures which often requires simulation of large super-lattices. In this report, we present the first series of successful simulation results for ice Ih using DFT methods. On the basis of the recent advancement in the DFT programs, we have achieved for the first time theoretical outcomes that not only reproduce the rotational frequencies between 500 to 1200 cm(-1) for ice Ih, but also the two optic peaks at ∼240 and 320 cm(-1) in the translational region of the INS spectra [J. C. Li, J. Chem. Phys 105, 6733 (1996)]. Besides, we have also investigated the impact of pairwise configurations of H(2)O molecules on the H-bond and found that different proton arrangements of pairwise H(2)O in the ice Ih crystal lattice could not alter the nature of H-bond as significantly as suggested in an early paper [J. C. Li and D. K. Ross, Nature (London) 365, 327 (1993)], i.e., reproducing the two experimental optic peaks do not need to invoke the two H-bonds as proposed in the previous model which led to considerable debates. The results of this work suggest that the observed optic peaks may be attributed to the coupling between the two bands of H-O stretching modes in H(2)O. The current computational work is expected to shed new light on the nature of the H-bonds in water, and in addition to offer a new approach towards probing the interaction between water and biomaterials for which H-bond is essential.

Charge-order driven proton arrangement in a hydrogen-bonded charge-transfer complex based on a pyridyl-substituted TTF derivative

A unique N(+)-H···N hydrogen-bonded (H-bonded) dimer motif based on partially oxidized pyridyl-substituted TTF was constructed in the charge-transfer complex. The charge ordering in the TTF column by the charge disproportionation in the dimer regulates the arrangement of the H-bonded proton, evidencing the proton-electron coupled state.

Self-Assembled Thermally Highly Stable 1-Dimensional Proton Arrays

From a red proton complex of aldehyde derivatives of polyaromatic hydrocarbon with strong intermolecular hydrogen bonding, which are novel examples of intermolecular proton-bonded aldehydes of polyaromatic hydrocarbons, we find one-dimensional proton arrangement. The complex formed as 9-antraldehyde (Ant-CHO) reacts with HAuCl(4) to form [(Ant-CHO)(2)H](+)[AuCl(4)](-) under dry condition, which are confirmed by single-crystal structure determination and infrared spectra analysis at varying temperatures. Since the compounds of distinctively hydrophobic nature are soluble only in limited organic polar solvents, the strong hydrogen bonds are clearly observed from both the electron density of X-ray analysis and the characteristic signature of the IR frequency. The proton complex units have the typical O-H(+)-O distance of the strong hydrogen bond similar to the Zundel-like cationic hydrogen bond (where two O atoms share a proton in the midpoint of the short O-O distance of approximately 2.4 A). The chemical shift of 20.18 ppm originated from the protons of the O-H(+)-O hydrogen bonds would be the largest downfield shifted value among those of protons in O-H...O bonds reported in various solid materials, indicating very short strong hydrogen bonds for the O-H(+)-O. The complexes are stabilized with the pi-pi intermolecular interactions of the polyaromatic hydrocarbon ligands, resulting in layered structures. The spectral signatures around approximately 900, approximately 1200, and approximately 1700 cm(-1) for the Zundel-like proton bond are clearly characterized.

Effects of “excessive” exciton interactions in polarized IR spectra of the hydrogen bond in 2-butynoic acid crystals: Proton transfer induced by dynamical co-operative interactions involving hydrogen bonds

In this article, we present the results of our study of polarized IR spectra of the hydrogen bond in crystals of 2-butynoic acid (CH 3C CCOOH) as well as in crystals of its deuterium derivative (CH 3C CCOOD). 2-Butynoic acid can exist in two polymorphous crystalline forms: in the “α” form, based on a classic dimer motif and in the “β” form, based on the catamer pattern of the hydrogen bond arrangement. By cooling the melted substance crystals of the “β” phase were obtained selectively. The polarized IR spectra of the hydrogen bond in the “β” form of 2-butynoic acid crystals were measured at room temperature and at the temperature of liquid nitrogen in the ν O–H and ν O–D band frequency ranges. In terms of the “strong-coupling” theory the fine structure patterns of the ν O–H and ν O–D polarized bands were quantitatively explained along with the dichroic and the H/D isotopic effects in the spectra. To interpret the main properties of the spectra the existence of a non-conventional effect concerning a self-stimulated concerted proton position rearrangements in the neighboring cells in the lattice had to be assumed. On the basis of the spectra of isotopically diluted crystalline samples of 2-butynoic acid it was suggested that a random distribution of protons and deuterons occurred in the open chains of the hydrogen bonded molecules. However, coordination in the mutual arrangement of protons and deuterons in the neighboring hydrogen bonds from the closely spaced molecular chains was found to be non-random. This fact was ascribed to dynamical co-operative interactions, most strongly involving hydrogen bonds from different chains in the modified lattice. These non-conventional interactions were responsible for appearance of the so-called H/D “self-organization” isotopic effects in the spectra.

Ba 2In 2O 4(OH) 2: Proton sites, disorder and vibrational properties

The structure of Ba 2In 2O 4(OH) 2 is analysed by the explicit full optimization of a large number of possible proton arrangements using periodic density functional theory. It is shown that the experimental assignments in which protons appear to be located at high symmetry positions with unphysical bond lengths do not correspond to minima on the potential energy hypersurface. The apparent sites are averages of a number of possible proton locations involving a set of possible local structural environments in which the internuclear separations are more realistic. Such problems with structural refinements are common where profile refinement programs place the atoms at the average position due to dynamic and/or static disorder. Thus while the calculations support a previous neutron diffraction analysis of the structure in that the average structure contains two different proton sites, they also reveal substantial information about the local environments of the protons. In all optimizations, the protons moved from the average positions suggested in the neutron diffraction study with calculated O–H and OH⋯O distances consistent with those observed in other oxides. The energies of different proton distributions vary significantly so the protons are not randomly distributed. We also present an analysis of the vibrational properties of the O–H bonds. Since the strength of the hydrogen bonds is closely related to the local structural environments of the protons, a range of vibrational frequencies is obtained providing a prediction of the vibrational spectra. In O–H⋯O linkages, O–H stretching modes soften with increasing H⋯O hydrogen bond strength, while the in-plane and out-of-plane bending or libration modes stiffen. Together, our results show how modern theoretical methods can provide a clearer understanding of the structure and dynamics of a complex inorganic material.

A reexamination of the ice III/IX hydrogen bond ordering phase transition

Ice III is a hydrogen bond disordered crystal which when cooled 1 K / min or faster transforms to an antiferroelectric hydrogen bond ordered structure, ice IX. Throughout its region of stability, experiments indicate that the H bonds in ice III are, in fact, partially ordered, i.e., some proton arrangements are preferred. In addition, there has been evidence that the structure of ice IX retains some residual disorder after the transition. Diffraction experiments and calorimetry apparently conflict with regard to the degree of ordering at the ice III/IX transition. Mean field statistical mechanical theories have been used to link partial occupations from diffraction data with thermodynamics. In this work, we investigate the ice III/IX proton ordering phase transition using electronic density functional theory calculations for small unit cells, extended to simulate the phase transition in a large unit cell using graph invariants. In agreement with experiment, we observe partial ordering over a wide range of temperatures as ice III transforms to partially disordered ice IX, near 126 K, which becomes fully ordered at lower temperatures. We compare our results from full statistical mechanical simulations with mean field models, finding small errors for the low-temperature ice IX phase and much larger errors for the high-temperature ice III phase. The failure of mean field theories may explain the apparent conflict between diffraction experiments and calorimetry.