Geometric Isotope Effect Research Articles

Phase Transition and Crystal Structure of CsHSeO4 and CsDSeO4 Crystals

DSC, TG-DTA and X-ray diffraction measurements have been performed on cesium hydrogen selenate CsHSeO 4 and deuterated CsDSeO 4 crystals. The superionic phase transitions for the proton and deuterated compounds were found to occur at 402.6 and 398.1 K, respectively. The thermal decomposition accompanied by hydrolysis in both compounds started at around the transition temperature, and the maximum rate of weight loss from the reaction was observed at around 490 K. The space group symmetry (monoclinic P 2 1 / c ) and structural parameters were determined at 298 and 355 K. The expansion of the O-H-O hydrogen bond at room temperature by the substitution of deuterium for hydrogen was observed to be 0.015(7) A. The geometric isotope effect on the hydrogen bond structure by deuteration was realized in the CsHSeO 4 crystal. The experimental results denied the existence of a phase transition from phase II to III in the proton and deuterated compounds.

Theoretical Study of H/D Isotope Effects on Nuclear Magnetic Shieldings Using an ab initio Multi-Component Molecular Orbital Method

We have theoretically analyzed the nuclear quantum effect on the nuclear magnetic shieldings for the intramolecular hydrogen-bonded systems of σ-hydroxy acyl aromatic species using the gauge-including atomic orbital technique combined with our multi-component density functional theory. The effect of H/D quantum nature for geometry and nuclear magnetic shielding changes are analyzed. Our study clearly demonstrated that the geometrical changes of hydrogen-bonds induced by H/D isotope effect (called geometrical isotope effect: GIE) is the dominant factor of deuterium isotope effect on 13C chemical shift.

Rh(111)に吸着したシクロヘキサンにおける速度論的および幾何学的同位体効果

Rh(111)に吸着したシクロヘキサンにおける速度論的および幾何学的同位体効果

Theoretical analysis of the geometrical isotope effect on the hydrogen bonds in photoactive yellow protein with multi-component density functional theory

To theoretically analyze the nuclear quantum effects of protons on two hydrogen bonds around the chromophore (CRO) in the photoactive yellow protein (PYP), we have calculated simple cluster model consisting of CRO, Glu46, and Tyr42 residues in PYP with the multi-component molecular orbital method and multi-component density functional theory, which can take account of quantum fluctuations of light mass particles. The average OO distances between CRO and Glu46 and between CRO and Tyr42 with our methods are shorter than the corresponding equilibrium ones, while the OH distances become longer due to the anharmonicity of the potential. The H/D geometrical isotope effect is also found, that is, the distances between oxygen atoms are elongated by the deuterium substitution, known as Ubbelohde effect.

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.

Hydrogen Bonding in Pyridine N-Oxide/Acid Systems: Proton Transfer and Fine Details Revealed by FTIR, NMR, and X-ray Diffraction

The H-bonded complexes of pyridine N-oxide (PyO) with H(2)O, acetic, cyanoacetic, propiolic, tribromoacetic, trichloroacetic, trifluoroacetic, hydrochloric, and methanesulfonic acids have been studied by FTIR and NMR spectroscopy, X-ray diffraction, and quantum chemical DFT calculations. Correlations between vibrational frequencies of the NO stretching and PyO ring modes and geometric parameters of the H-bond have been established. FTIR experiments show and DFT calculations confirm that definite discontinuity is present in the vicinity of the midpoint in the proton transfer pathway. The established correlations significantly aid in the understanding of fine effects such as the isotope (deuteration) effect, crystal-to-solution transition, or criticality of aqueous solutions induced by ionic pairs. Geometric isotope effect in the ionic H-bond aggregate of PyO·H(D)Cl was found to be extraordinary large. Measured FTIR, CP/MAS, and high-resolution (13)C NMR spectra indicate that H-bond in the PyO·HCl complex in polar solvent can potentially be more ionic than in the crystal. Vibrational modes of ionic pairs originating via proton transfer in H-bond complexes can provide new information concerning the interionic interaction and its role in the phase separation and mezo-structuring processes. The results are compared to the relevant data for PyO·HCl complex in argon matrix.

Kinetic and geometric isotope effects originating from different adsorption potential energy surfaces: Cyclohexane on Rh(111)

Novel isotope effects were observed in desorption kinetics and adsorption geometry of cyclohexane on Rh(111) by the use of infrared reflection absorption spectroscopy, temperature programmed desorption, photoelectron spectroscopy, and spot-profile-analysis low energy electron diffraction. The desorption energy of deuterated cyclohexane (C(6)D(12)) is lower than that of C(6)H(12). In addition, the work function change by adsorbed C(6)D(12) is smaller than that by adsorbed C(6)H(12). These results indicate that C(6)D(12) has a shallower adsorption potential than C(6)H(12) (vertical geometric isotope effect). The lateral geometric isotope effect was also observed in the two-dimensional cyclohexane superstructures as a result of the different repulsive interaction between interfacial dipoles. The observed isotope effects should be ascribed to the quantum nature of hydrogen involved in the C-H···metal interaction.

吸着分子における速度論的および構造的同位体効果：シクロヘキサン／Rh(111)

吸着分子における速度論的および構造的同位体効果：シクロヘキサン／Rh(111)

Geometrical and kinetic isotope effects on S N2 chemical reactions using multi-component molecular orbital method

To estimate the kinetic isotope effect (KIE) for nucleophilic substitution (S N2) reaction, F − + CH 4 → CH 3F + H −, and deuterated ones, we have considered the geometrical isotope effect (GIE) induced by the difference of the protonic and deuteronic wavefunctions using the multi-component molecular orbital (MC_MO) method. By replacing protons with deuterons, the C–D bond lengths are about 0.007 Å shorter than C–H. We estimated the ratio ( k a H / k a D ) of rate constants based on MC_MO results. The geometrical and energetic differences between H and D compounds are induced by relaxation of electronic structures due to the difference in the wavefunctions of the proton and deuteron.

Interpretation of Intermolecular Geometric Isotope Effect in Hydrogen Bonds: Nuclear Orbital plus Molecular Orbital Study

The intermolecular geometric isotope effect (GIE) in hydrogen bond A-X···B (X = H and D) is investigated theoretically using the nuclear orbital plus molecular orbital (NOMO) theory. To interpret the GIE in terms of physically meaningful energy components such as electrostatic and exchange-repulsion interactions, the reduced variational space self-consistent-field method is extended to the NOMO scheme. The intermolecular GIE is analyzed as a two-stage process: the intramolecular bond shrinkage and the intermolecular bond elongation. According to the isotopic shifts of energy components described by the NOMO/MP2 method, the intermolecular GIE is approximately interpreted as a process reducing the exchange-repulsion interaction after the decrease of electrostatic interaction.

H/D isotope effects on the geometry and infrared spectrum of the protonated ammonia dimer

The two isotopomers, N 2 H 7 + and N 2 D 7 + , have been investigated using a six-dimensional quantum mechanical model. In both cases a structural symmetrization due to zero point vibrational motion is observed. The probability distribution along the proton/deuteron transfer coordinate is found to have a single maximum, which is flattened in the deuterated case due to the energetic proximity of the barrier. Being a strong hydrogen bonding case, the secondary geometric isotope effect leads to a bond compression by 0.004 Å. Most notable changes in the infrared absorption spectrum in the range below 500 cm −1 concern a red-shift of the asymmetric proton stretching fundamental transition by about 47% for the fully deuterated case.

<i>Ab initio</i>経路積分法：量子多体系の第一原理計算

Nuclear quantum effects, such as zero-point vibration and tunneling, are important aspect in molecular systems containing light atoms like hydrogen, and it is considered to have substantial influence on their chemical behavior and physical properties. In this report, I will describe the basic idea of path integral molecular dynamics simulations which enables one to compute nuclear quantum effects in complex many-body systems. When the method is combined with ab initio electron structure calculations, the whole molecular entity composed of electrons and nuclei is treated quantum mechanically based on first principles within the framework of Born-Oppenheimer approximation. Using this technique, the quantum nature of strong hydrogen bonds in protonated and deprotonated water clusters have been studied, with a focus on the geometrical isotope effect.

Crystal structures and isotope effect on Na5H3(SeO4)4·2H2O and Na5D3(SeO4)4·2D2O crystals

AbstractDifferential scanning calorimetry (DSC) and X‐ray diffraction measurements have been performed on pentasodium trihydrogen tetraselenate dihydrate Na5H3(SeO4)4·2H2O and deuterated Na5D3(SeO4)4·2D2O crystals. Any distinct anomaly around 428 K in the DSC curves for both crystals is suggested to be caused by a chemical reaction of thermal decomposition with hydrolysis at high temperature. The space group symmetry (triclinic P$ \bar 1 $) and the structure parameters are determined at room temperature. The hydrogen atom in the centrosymmetric O‐H(D)‐O hydrogen bond of both crystals is found to be equally distributed at two equivalent sites in the bond. The expansions of two O‐H‐O hydrogen bonds by the substitution of deuterium are observed to be 0.016(6) and 0.011(4) Å. The geometric isotope effect on hydrogen bonds is confirmed to be existed in Na5H3(SeO4)4·2H2O. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Efficient ab initio path integral hybrid Monte Carlo based on the fourth-order Trotter expansion: Application to fluoride ion-water cluster

We propose an efficient path integral hybrid Monte Carlo (PIHMC) method based on fourth-order Trotter expansion. Here, the second-order effective force is employed to generate short trial trajectories to avoid computationally expensive Hessian matrix, while the final acceptance is judged based on fourth-order effective potential. The computational performance of our PIHMC scheme is compared with that of conventional PIHMC and PIMD methods based on second- and fourth-order Trotter expansions. Our method is applied to on-the-fly ab initio PIHMC calculation of fluoride ion-water complexes, F(-)(H(2)O) and F(-)(D(2)O), at ambient temperature, particularly focusing on the geometrical isotope effect.

Geometric Isotope Effect on Low Barrier Hydrogen-Bonding Systems of Acetic Acid Dimer, Formic Acid Dimer, and Their Anionic Clusters by Using the Multi-Component Molecular Orbital Method

The geometric isotope effect (GIE) on low barrier hydrogen-bonded systems of acetic acid dimer, formic acid dimer, and their anion clusters is analyzed by HF and hybrid DFT levels of the multi-component molecular orbital (MC_MO) method, which directly includes nuclear quantum effect of proton/deuteron. Our optimized geometries for both neutral and anionic species with HF level of MC_MO method have reproduced the overall tendency of the GIE of the corresponding experimental ones. On the other hand, the results for anionic clusters with hybrid BHandHLYP functional of MC_MO method give poor agreement due to the underestimation of the barrier height of hydrogen-bonding. Our multi-component analysis clearly demonstrates that the hydrogen-bonding interaction energy is strongly affected by the distribution of nuclear wavefunction.

Change in compressibility of -AlOOH and -AlOOD at high pressure: A study of isotope effect and hydrogen-bond symmetrization

The compression behaviors of δ-AlOOH and δ-AlOOD were investigated under quasi-hydrostatic conditions at pressures up to 63.5 and 34.9 GPa, respectively, using results from synchrotron X-ray diffraction experiments conducted at ambient temperature. Because of the geometric isotope effect, at ambient pressure, the a and b axes of δ-AlOOD, which define the plane in which the hydrogen bond lies, are longer than those of δ-AOOH. Under increasing pressure, the a and b axes of δ-AlOOH stiffen at 10 GPa, although the c axis shows no marked change. Identical behavior was found in δ-AlOOD, but the change in compressibility was observed at a slightly higher pressure of 12 GPa. Axial ratios a / c and b / c first decrease rapidly with increasing pressure, then begin to increase at pressures >10 GPa in δ-AlOOH and >12 GPa in δ-AlOOD. At these pressures, the pressure dependence of a / b also changes from increasing to decreasing. The unit-cell volumes of δ-AlOOH and δ-AlOOD become slightly less compressible at high pressures. Assuming K ′ = 4, the calculated bulk moduli of δ-AlOOH below and above 10 GPa are 152(2) and 219(3) GPa, respectively. Those of δ-AlOOD below and above 12 GPa are 151(1) and 207(2) GPa, respectively.

Hydrogen bond dynamics in the active site of photoactive yellow protein

Hydrogen bonds play major roles in biological structure and function. Nonetheless, hydrogen-bonded protons are not typically observed by X-ray crystallography, and most structural studies provide limited insight into the conformational plasticity of individual hydrogen bonds or the dynamical coupling present within hydrogen bond networks. We report the NMR detection of the hydrogen-bonded protons donated by Tyr-42 and Glu-46 to the chromophore oxygen in the active site of the bacterial photoreceptor, photoactive yellow protein (PYP). We have used the NMR resonances for these hydrogen bonds to probe their conformational properties and ability to rearrange in response to nearby electronic perturbation. The detection of geometric isotope effects transmitted between the Tyr-42 and Glu-46 hydrogen bonds provides strong evidence for robust coupling of their equilibrium conformations. Incorporation of a modified chromophore containing an electron-withdrawing cyano group to delocalize negative charge from the chromophore oxygen, analogous to the electronic rearrangement detected upon photon absorption, results in a lengthening of the Tyr-42 and Glu-46 hydrogen bonds and an attenuated hydrogen bond coupling. The results herein elucidate fundamental properties of hydrogen bonds within the complex environment of a protein interior. Furthermore, the robust conformational coupling and plasticity of hydrogen bonds observed in the PYP active site may facilitate the larger-scale dynamical coupling and signal transduction inherent to the biological function that PYP has evolved to carry out and may provide a model for other coupled dynamic systems.

Review of multicomponent molecular orbital method for direct treatment of nuclear quantum effect

AbstractWe present the methodology and applications of multicomponent molecular orbital (MC_MO) method, which can take into account of the quantum effect of light particles, such as proton and deuteron, directly. We summarize the equations of the MC_MO method at the Hartree–Fock (HF) level and beyond the HF. The methodology of the MC_MO with fragment molecular orbital (FMO) method for large molecular systems is also described. We discuss the development of nuclear basis function based on the GTF, which is used in MC_MO and FMO‐MC_MO calculations. We present the applications of MC_MO and FMO‐MC_MO method for the analysis of geometrical isotope effect and kinetic isotope effect induced by H/D isotope effect. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

Mechanism of quantum effects in hydrogen-bonded crystals of theK3H(SO4)2group

The complete isotope effect and quantum paraelectricity in hydrogen-bonded crystals of the ${\text{K}}_{3}\text{H}{({\text{SO}}_{4})}_{2}$ group are usually attributed to the proton tunneling and geometric isotope effect. However, a mechanism of the quantum effects is not unambiguously determined because neutron-scattering experiments indicate different forms of hydrogen-bond proton potential. The quantum effects and contradictory experimental results are accounted for by the model where the proton potential is strongly affected by a low-frequency heavy-atom mode.

Theoretical analysis of H/D geometric isotope effect on adenine–thymine base pair using multi-component molecular orbital method

The H/D isotope effect on adenine(A)–thymine(T) DNA base pair has been analyzed at Hartree–Fock/3-21G** level of multi-component molecular orbital (MC_MO) method, which can directly take account of the quantum effect of proton/deuteron. The difference of quantum nature between proton and deuteron in A–T base pair causes the geometric isotope effect (GIE) on the backbone structure of respective monomers, as well as the hydrogen-bonded structure (primary and secondary GIEs). Our MC_MO results clearly suggest the importance of the quantum nature in hydrogen-interacting systems.