Hydrogen Positions Research Articles

Crystal chemistry and hydrogen bonding of rustumite Ca10(Si2O7)2(SiO4)(OH)2Cl2 with variable OH, Cl, F

Three samples of the skarn mineral rustumite Ca10(Si2O7)2(SiO4)(OH)2Cl2, space group C 2/ c , a ≈7.6, b ≈ 18.5, c ≈ 15.5 A, β ≈ 104°, with variable OH, Cl, F content were investigated by electron microprobe, single-crystal X-ray structure refinements, and Raman spectroscopy. “Rust1_LCl” is a low chlorine rustumite Ca10(Si2O7)2(SiO4)(OH1.88F0.12)(Cl1.28,OH0.72) from skarns associated with the Rize batholith near Ikizedere, Turkey. “Rust2_F” is a F-bearing rustumite Ca10(Si2O7)2(SiO4)(OH1.13F0.87) (Cl1 96OH0.04) from xenoliths in ignimbrites of the Upper Chegem Caldera, Northern Caucasus, Russia. “Rust3\_LCl\_F” represents a low-Cl, F-bearing rustumite Ca10(Si2O7)2[(SiO4)0.87(H4O4)0.13](OH1.01F0.99) (Cl1.00 OH1.00) from altered merwinite skarns of the Birkhin massif, Baikal Lake area, Eastern Siberia, Russia. Rustumite from Birkhin massif is characterized by a significant hydrogarnet-like or fluorine substitution at the apices of the orthosilicate group, leading to specific atomic displacements. The crystal structures including hydrogen positions have been refined from single-crystal X-ray data to R1 = 0.0205 (Rust1\_LCl), R1 = 0.0295 (Rust2\_F), and R1 = 0.0243 (Rust3\_LCl\_F), respectively. Depletion in Cl and replacement by OH is associated with smaller unit-cell dimensions. The substitution of OH by F leads to shorter hydrogen bonds O-H⋯F instead of O-H⋯OH. Raman spectra for all samples have been measured and confirm slight strengthening of the hydrogen bonds with uptake of F. This study discusses the complex crystal chemistry of the skarn mineral rustumite and may provide a wider understanding of the chemical reactions related to contact metamorphism of limestones.

Quantum mechanical calculation of diffusion of hydrogen isotopes in vanadium

Abstract Diffusion of hydrogen isotopes in vanadium was investigated by a quantum mechanical calculation. Wave functions and the corresponding eigen energies (E) for hydrogen isotopes were obtained as a function of hydrogen position along the diffusion path (ξ) by solving the three dimensional Schrodinger equation. Hydrogen potential was calculated by using a first principles method with a nudged elastic band technique. By analyzing the E–ξ curves, the tunneling matrix elements were obtained for the coincidence states between two neighboring tetrahedral sites. It was clarified that the tunneling between ground states was dominant at low temperatures, whereas the contribution of that between the first exited states becomes larger at higher temperatures. The transition temperature of the dominant tunneling decreases with the isotope mass. The calculated temperature dependence of the diffusion for the V–H system quantitatively agreed with the experimental data in the literature, although those for the V–D and –T systems were somewhat underestimated.

Crystal structure determination by combined synchrotronpowder X-ray diffraction and crystal structure prediction: 1 : 1 l-ephedrined-tartrate

The crystal structure of the diastereomeric salt 1 : 1 L-ephedrine D-tartrate (1 : 1 LD, C10H16NO+·C4H5O6−) was determined from high-resolution synchrotron powder X-ray diffraction (PXRD) data using global optimization in direct space (parallel tempering) together with computational modelling to locate hydrogen positions and refined by the Rietveld method. The structure is monoclinic, space group P21, with a = 18.82810(3) A, b = 7.19429(2) A, c = 5.73035(1) A, β = 95.9613(1)°, V = 772.006(3) A3, and Z = 2. Computational prediction of organic salt structures, especially hydrogen positions, is a valuable complementary technique to PXRD for the final stages of structure determination.

Proposal of Actual Positions of Hydrogen (H) and Helium (He) in Modern Periodic Table

The actual positions of H and He in modern periodic table can be determined according to their dual characteristics (electro-positive and electro-negative) and final electronic configuration respectively. It is seen that a new group for H and two sub-groups of 0-group (zero group) for He in periodic table are needed in this respect.

Diaminotriazine substituted diphenyl ether: reversible structural transformation and solvent dependent solid state fluorescence

The effect of molecular shape and position of hydrogen bonding functionality in the solid state structural self-assembly was investigated using diaminotriazine substituted diphenyl ether based positional isomers (1–5). The molecular shape was modulated by changing diaminotriazine position that produced channel supramolecular structures in 1, 3 and 5. There exists a direct correlation between the molecular shape and three dimensional structures; more linear molecules resulted in close-packing whereas molecules with a labyrinthine topology formed a channel structure. Supramolecular aspects pertaining to the influence of solvent of crystallization in structure formation and reversible structural transformation in solid state were also explored. 1–5 exhibited tunable solid state fluorescence (λmax = 437–496 nm) depending on the diaminotriazine substitutional position and 3 showed solvent-dependent solid state fluorescence. The present study describes the generation of a supramolecular channel structure with functional properties such as tunable fluorescence by varying the position of hydrogen bond functionality and solvent of crystallization.

酵素阻害剤複合体の中性子結晶構造解析による反応機構の解明

Neutron crystallography enables us to identify the accurate hydrogen positions in proteins, which play important roles in many chemical reactions in living system. Here we show our results of neutron structure determination of enzymes in complex with its inhibitors which corresponds to transition state analogues. Neutron structure analysis elucidated the detail catalytic reaction of each enzyme by direct observation of hydrogen atoms. Furthermore we would like to introduce a new neutron beam line for neutron structural biology planned at MLF in J-PARC.

Surprising Electronic Structure of the BeH– Dimer: a Full-Configuration-Interaction Study

The electronic structure of the beryllium hydride anion, BeH(-), was investigated at valence full-configuration-interaction (FCI) level, using large cc-pV6Z basis sets. It appears that there is a deep change of the wave function nature as a function of the internuclear distance: the ion structure goes from a weakly bonded Be···H(-) complex, at long distance, to a rather strongly bonded system (more than 2 eV) at short distance, having a (:Be-H)(-) Lewis structure. In this case, it is the beryllium atom that formally bears the negative charge, a surprising result in view of the fact that it is the hydrogen atom that has a larger electronegativity. Even more surprisingly, at very short distances the average position of the total electronic charge is close to the beryllium atom but on the opposite side with respect to the hydrogen position.

New Syntheses and Structural Characterization of NH3BH2Cl and (BH2NH2)3 and Thermal Decomposition Behavior of NH3BH2Cl

New convenient procedures for the preparation of ammonia monochloroborane (NH(3)BH(2)Cl) and cyclotriborazane [(BH(2)NH(2))(3)] are described. Crystal structures have been determined by single-crystal X-ray diffraction. Strong H···Cl···H bifurcated hydrogen bonding and weak N-H···H dihydrogen bonding are observed in the crystal structure of ammonia monochloroborane. When heated at 50 °C or under vacuum, ammonia monochloroborane decomposes to (NH(2)BHCl)(x), which was characterized by NMR, elemental analysis, and powder X-ray diffraction. Redetermination of the crystal structure of cyclotriborazane at low temperature by single-crystal X-ray diffraction analysis provides accurate hydrogen positions. Similar to ammonia borane, cyclotriborazane shows extensive dihydrogen bonding of N-H···H and B-H···H bonds with H(δ+)···H(δ-) interactions in the range of 2.00-2.34 Å.

Symmetrical Hydrogen Bonds in Iridium(III) Alkoxides with Relevance to Outer Sphere Hydrogen Transfer

A chelating ligand formed by deprotonation of 2-(2'-pyridyl)-2-propanol stabilizes a distorted trigonal bipyramidal geometry in a 16e(-) d(6) 5-coordinate iridium complex with the alkoxide acting as a π donor. Ambiphilic species such as AcOH bearing both nucleophilic and electrophilic functionality form adducts with the unsaturated iridium complex which contain strong intramolecular O···H···O hydrogen bonds that involve the basic alkoxide oxygen. Density functional theory (DFT) calculations on the isolated cations reproduce with high accuracy the geometrical features obtained via X-ray diffraction and corroborate the presence of very short hydrogen bonds with O···O distances of about 2.4 Å. Calculations further confirm the known trend that the hydrogen position in these bonds is sensitive to the O···O distance, with the shortest distances giving rise to symmetrical O···H···O interactions. Dihydrogen is shown to add across the Ir-O π bond in a presumed proton transfer reaction, demonstrating bifunctional behavior by the iridium alkoxide.

Crystal structure refinements of borate dimorphs inderite and kurnakovite using 11B and 25Mg nuclear magnetic resonance and DFT calculations

Borate minerals composed of [Bφ 3 ] triangles and/or [Bφ 4 ] tetrahedra (φ = O or OH) commonly exhibit complex polymerizations to form diverse polyanion groups. High-resolution solid-state magic angle spinning (MAS) 11 B and 25 Mg NMR spectroscopy at moderate to ultrahigh magnetic fields (9.4, 14.1, and 21.1 T) allows for very accurate NMR parameters to be obtained for the borate dimorphs, inderite, and kurnakovite, [MgB 3 O 3 (OH) 5 ·5H 2 O]. Improved agreement between experimental results and ab initio density functional theory (DFT) calculations using Full Potential Linear Augmented Plane Wave (FP LAPW) with WIEN2k validates the geometry optimization procedures for these minerals and permits refinements of the hydrogen positions relative to previous X-ray diffraction crystal structures. In particular, the optimized structures lead to significant improvements in the positions of the H atoms, suggesting that H atoms have significant effects on the 11 B and 25 Mg NMR parameters in inderite and kurnakovite. This study shows that combined high-resolution NMR spectroscopy and ab initio theoretical modeling provides an alternative method for the refinement of crystal structures, especially H positions.

Pressure-induced hydrogen bond symmetrisation in guyanaite, β-CrOOH: evidence from spectroscopy and ab initio simulations

Guyanaite, β-CrOOH, is a structural analogue of the high-pressure oxyhydroxide phases δ-AlOOH and ɛ-FeOOH. Here, it was synthesized in piston-cylinder and multi-anvil press experiments at 4–13.5 GPa and 900–1100 °C. The deuterated phase β-CrOOD was synthesized at 4 GPa and 600 °C. The samples were characterized at ambient conditions by X-ray diffraction, diffuse optical reflectance spectroscopy and infrared absorption (IR) spectroscopy. In addition, the structural evolution of β-CrOOH and β-CrOOD with increasing pressure up to about 20 GPa was studied by in situ IR spectroscopy in a diamond anvil cell (DAC). This investigation was complemented by first-principles calculations in the framework of the density-functional theory (DFT). A pronounced geometric isotope effect and very short O-H. . .O bond lengths of 2.497(3) A for β-CrOOH and 2.541(3) A for β-CrOOD are observed at ambient pressure. In the IR spectra, no bands show up above 2000 cm−1, which indicates strong hydrogen bonding. The evolution of OH- and OD-related vibrational bands with pressure studied by IR spectroscopy shows a discontinuity at about 5 GPa. The DFT calculations suggest that this change in compression mechanism is related to a second-order phase transition from the low-pressure phase with asymmetric hydrogen positions (space group P 21 nm or Pnnm ) to a high-pressure phase with space group Pnnm that is characterized by symmetric hydrogen bonds with two identical OH bond lengths of 1.20(1) A. Using density functional perturbation theory, the most prominent high-frequency modes observed in the IR spectra are assigned to O-H-O bending vibrations. The transition pressure for hydrogen bond symmetrisation in β-CrOOH is considerably lower than in other hydrous phases of recent interest, such as δ-AlOOH or phase D.

The Interaction of Flavonoid-Lysozyme and the Relationship Between Molecular Structure of Flavonoids and Their Binding Activity to Lysozyme

In this work, the interactions of twelve structurally different flavonoids with Lysozyme (Lys) were studied by fluorescence quenching method. The interaction mechanism and binding properties were investigated. It was found that the binding capacities of flavonoids to Lys were highly depend on the number and position of hydrogen, the kind and position of glycosyl. To explore the selectivity of the bindings of flavonoids with Lys, the structure descriptors of the flavonoids were calculated under QSAR software package of Cerius2, the quantitative relationship between the structures of flavonoids and their binding activities to Lys (QSAR) was performed through genetic function approximation (GFA) regression analysis. The QSAR regression equation was K(A) = 37850.460 + 1630.01Dipole +3038.330HD-171.795MR. (r = 0.858, r(CV)(2) = 0.444, F((11,3)) = 7.48), where K(A) is binding constants, Dipole, HD and MR was dipole moment, number of hydrogen-bond donor and molecular refractivity, respectively. The obtained results make us understand better how the molecular structures influencing their binding to protein which may open up new avenues for the design of the most suitable flavonoids derivatives with structure variants.

Translational and rotational mobility of methanol-d4 molecules in NaX and NaY zeolite cages: A deuteron NMR investigation

Nuclear magnetic resonance (NMR) provides means to investigate molecular dynamics at every state of matter. Features characteristic for the gas phase, liquid-like layers and immobilized methanol-d4 molecules in NaX and NaY zeolites were observed in the temperature range from 300K down to 20K. The NMR spectra at low temperature are consistent with the model in which molecules are bonded at two positions: horizontal (methanol oxygen bonded to sodium cation) and vertical (hydrogen bonding of hydroxyl deuteron to zeolite framework oxygen). Narrow lines were observed at high temperature indicating an isotropic reorientation of a fraction of molecules. Deuteron spin–lattice relaxation gives evidence for the formation of trimers, based on observation of different relaxation rates for methyl and hydroxyl deuterons undergoing isotropic reorientation. Internal rotation of methyl groups and fixed positions of hydrogen bonded hydroxyl deuterons in methyl trimers provide relaxation rates observed experimentally. A change in the slope of the temperature dependence of both relaxation rates indicates a transition from the relaxation dominated by translational motion to prevailing contribution of reorientation. Trimers undergoing isotropic reorientation disintegrate and separate molecules become localized on adsorption centers at 166.7K and 153.8K for NaX and NaY, respectively, as indicated by extreme broadening of deuteron NMR spectra. Molecules at vertical position remain localized up to high temperatures. That indicates the dominating role of the hydrogen bonding. Mobility of single molecules was observed for lower loading (86molecules/uc) in NaX. A direct transition from translation to localization was observed at 190K.

Minerals in cement chemistry: A single-crystal neutron diffraction and Raman spectroscopic study of thaumasite, Ca3Si(OH)6(CO3)(SO4){middle dot}12H2O

Thaumasite, Ca3Si(OH)6(CO3)(SO4)·12H2O, is recognized as a secondary-alteration mineral and indicator of sulfate attack in Portland cement in contact with sulfate-rich groundwater, especially in cold regions. The hydrogen positions in thaumasite have been determined from single-crystal neutron diffraction structure refinements at 300 and 22 K. No phase transitions occur within the temperature range investigated. The structure of thaumasite is largely held together by hydrogen bonding. The major structural units [CO3 groups, SO4 tetrahedra, Si(OH)6 octahedra, and Ca(OH)4(H2O)4 polyhedra] are interconnected via 10 distinct hydrogen bonds. Analysis of the difference-Fourier maps of the nuclear density reveals the positions of all 10 hydrogen atoms in the structure, and the hydrogen bonding becomes shorter (stronger) upon decreasing temperature to 22 K. The SO4 tetrahedron expands upon decreasing temperature (i.e., negative thermal expansion at the molecular level), driven by shortening of the hydrogen bonding between [Ca3Si(OH)6(H2O)12]4+ columns. Polarized Raman spectra of thaumasite show that the ν1 symmetric stretching modes of Si(OH)6, SO4, and CO3 occur at 658, 983, and 1066 cm−1, respectively. In addition, the out-of-plane bending mode (ν2) and asymmetric stretching mode (ν3) of the carbonate group are tentatively assigned to bands at 887 and 1400 cm−1, respectively. Bands at 418 and 455 cm−1 (and possibly at 477 cm−1) are attributed to the symmetric bending modes (ν2) of the sulfate group, and we observe a possible asymmetric stretching mode (ν3) of SO4 at 1090–1100 cm−1. Splitting of some sulfate and carbonate vibrational modes may occur due to hydrogen bonding on all the oxygen sites. At 1685–1710 cm−1 we observe the H2O bending modes (H-O-H), and from 2900–3600 cm−1 there are 13 distinct bands associated with bending overtones and the O-H stretching vibrations corresponding to H-positions determined in the neutron diffraction study. The effect of the low-temperature stability of thaumasite on the pronounced “thaumasite sulfate attack” of Portland cements observed in cold regions is discussed.

Crystal Structure of High-Pressure Phases V and VI of Potassium Dihydrogen Phosphate

Potassium dihydrogen phosphate KH 2 PO 4 is the most typical hydrogen-bonded ferroelectric. The P – T phase diagram and the existence of high-pressure phases V and VI have already been reported. However, their crystal structures remain unknown. We performed a powder x-ray diffraction experiment under high pressure using synchrotron radiation and analyzed the structures from the obtained data. The structures of phases V and VI were determined to be orthorhombic C 222 1 and triclinic P \bar1. Their hydrogen positions were predicted by a density functional theory calculation.

Order-parameter coupling in the improper ferroelectric lawsonite

Low-temperature specific heat and thermal expansion measurements are used to study the hydrogen-based ferroelectric lawsonite over the temperature range 1.8 K ≤ T ≤ 300 K. The second-order phase transition near 125 K is detected in the experiments, and the low-temperature phase is determined to be improper ferroelectric and co-elastic. In the ferroelectric phase T ≤ 125 K, the spontaneous polarization Ps is proportional to (1) the volume strain es, and (2) the excess entropy ΔSe. These proportionalities confirm the improper character of the ferroelectric phase transition. We develop a structural model that allows the off-centering of hydrogen positions to generate the spontaneous polarization. In the low-temperature limit we detect a Schottky anomaly (two-level system) with an energy gap of Δ ∼ 0.5 meV.

A flexible-hydrogen interaction model for protein-ligand docking

Although some docking methods accounting for protein flexibility exist, most large scale virtual screening approaches work with rigid protein models. A first step towards flexibility integration is the consideration of degrees of freedom resulting from hydrogens, especially, if involved in hydrogen bonding. To account for this type of flexibility, we present a flexible-hydrogen interaction model as part of a descriptor-based docking technique. The model discretizes interaction spheres of rigid and flexible hydrogen-bond donors and acceptors as interaction spots. A spot has an associated interaction direction which indicates hydrogen or lone pair orientation, and thus, the potential location of a hydrogen-bond counterpart. This new flexible-hydrogen interaction model is combined with a novel approach to describe hydrophobic contacts. Both are introduced in our descriptor-based docking approach named TrixX [1]. TrixX handles ligand flexibility by applying a conformer ensemble approach [2]. The latter allows for the use of efficient indexing techniques upon virtual screening. The discretized, flexible-hydrogen model proposes potential hydrogen and lone pair positions. However, these proposals may still slightly differ from their actual location which can be only determined in presence of pose and active site, i. e., after the docking stage. In order to grant a thorough assessment of hydrogen bonds, thereby, the predicted poses are forwarded to an efficient post-optimization of the hydrogen-bond network. It optimally aligns hydrogens, identifies favorable tautomeric and protonation states, and evaluates the predicted pose [3]. Redocking of the Astex Diverse Set [4] shows that the described docking method produces results in good agreement with co-crystalized ligand structures. Several case studies using different levels of discretization and post-optimization, illustrate the influence of our presented procedures in ligand placement and scoring. The studies highlight the impact of flexible hydrogens and lone pairs during docking and confirm the introduction of our flexible hydrogen model.

Imino hydrogen positions in nucleic acids from density functional theory validated by NMR residual dipolar couplings.

Hydrogen atom positions of nucleotide bases in RNA structures solved by X-ray crystallography are commonly derived from heavy-atom coordinates by assuming idealized geometries. In particular, N1–H1 vectors in G and N3–H3 vectors in U are commonly positioned to coincide with the bisectors of their respective heavy-atom angles. We demonstrate that quantum-mechanical optimization of the hydrogen positions relative to their heavy-atom frames considerably improves the fit of experimental residual dipolar couplings to structural coordinates. The calculations indicate that deviations of the imino N–H vectors in RNA U and G bases result from H-bonding within the base pair and are dominated by the attractive interaction between the H atom and the electron density surrounding the H-bond-acceptor atom. DFT optimization of H atom positions is impractical in structural biology studies. We therefore have developed an empirical relation that predicts imino N–H vector orientations from the heavy-atom coordinates of the base pair. This relation agrees very closely with the DFT results, permitting its routine application in structural studies.

Sarcosine sarcosinium chloride and sarcosine sarcosinium bromide

The crystal and molecular structures and vibrational spectra of sarcosine sarcosinium chloride (I) and sarcosine sarcosinium bromide (II) have been determined and are discussed. In the case of sarcosine sarcosinium bromide (II), an old publication exists, where the structure is reported, but the data given are less accurate and hydrogen positions have not been determined at all. Both salts are isotypic and crystallize in the orthorhombic system (space group Pca21), the asymmetric unit contains two formula units. The O⋯O distances in dimeric cations are equal to 2.469(2)Å and 2.463(2)Å in (I) and 2.453(3)Å and 2.464(3)Å in (II). The presence of these short hydrogen bonds is reflected in the infrared spectra. The vibrational spectra of sarcosinium chloride and sarcosinium bromide are shown for comparison.

Design of a Qubit and a Decoder in Quantum Computing Based on a Spin Field Effect

In this paper we present a new method for designing a qubit and decoder in quantum computing based on the field effect in nuclear spin. In this method, the position of hydrogen has been studied in different external fields. The more we have different external field effects and electromagnetic radiation, the more we have different distribution ratios. Consequently, the quality of different distribution ratios has been applied to the suggested qubit and decoder model. We use the nuclear property of hydrogen in order to find a logical truth value. Computational results demonstrate the accuracy and efficiency that can be obtained with the use of these models.