Multi-component Molecular Orbital Method Research Articles

Stability and bonding nature of positronic lithium molecular dianion.

We studied the stability of a system consisting of a positron (e+) and two lithium anions, [Li-; e+; Li-], using first-principles quantum Monte Carlo calculations combined with the multi-component molecular orbital method. While diatomic lithium molecular dianions Li22- are unstable, we found that its positronic complex can form a bound state with respect to the lowest energy decay into the dissociation channel Li2- and a positronium (Ps). The [Li-; e+; Li-] system has the minimum energy at the internuclear distance of ∼3 Å, which is close to the equilibrium internuclear distance of Li2-. At the minimum energy structure both an excess electron and a positron are delocalized as orbiting around the Li2- molecular anion core. A dominant feature of such a positron bonding structure is described as the Ps fraction bound to Li2-, unlike the covalent positron bonding scheme for the electronically isovalent [H-; e+; H-] complex.

Positron Binding and Annihilation Properties of Amino Acid Systems.

Despite the fact that the positron annihilation has been used in biomedical applications, the detailed mechanism of the positron annihilation on biological molecules remains poorly understood so far. In this work, we investigated the positron binding and positron annihilation properties for both global minimum and hydrogen-bonded structures of 20 amino acid molecules using the multicomponent molecular orbital method. By regression analysis, we confirmed that positron affinity can increase with an increase of the permanent dipole moment of the parent amino acids as reported in previous studies, while the annihilation rate linearly increases with respect to the square root of positron affinity. By the one-particle property analyses for probabilities of electron–positron contacts, we found that delocalization characteristics of both electrons and positrons play key roles to enhance the positron annihilation rate arising from both the valence electrons in σ- and π-type molecular orbitals from 2p atomic orbitals but not from the highest occupied molecular orbital electrons, particularly for comparatively weakly bound positronic amino acid systems.

Large amplitude motion in 9-methylanthracene: High-resolution spectroscopy and Ab Initio theoretical calculation

CH3 internal rotation is one of the typical large amplitude motions in polyatomic molecules, the spectral analysis and theoretical calculations of which, were developed by Li-Hong Xu and Jon Hougen. We observed a Doppler-free high-resolution and high-precision spectrum of 9-methylanthracene (9MA) by using the collimated supersonic jet and optical frequency comb techniques. The potential energy curve of CH3 internal rotation is expressed by a six-fold symmetric sinusoidal function. It was previously shown that the barrier height (V6) of 9MA-d12 was considerably smaller than that of 9MA-h12 [M. Baba, et al., J. Phys. Chem. A 113, 2366 (2009)]. We performed ab initio theoretical calculations of the multicomponent molecular orbital method. The barrier reduction by deuterium substitution was partly attributed to the difference between the wave functions of H and D atomic nuclei.

H/D isotope effect on charge-inverted hydrogen-bonded systems: Systematic classification of three different types in H3XH···YH3 (X = C, Si, or Ge, and Y = B, Al, or Ga) with multicomponent calculation.

Three different H/D isotope effect in nine H3 XH(D)···YH3 (X = C, Si, or Ge, and Y = B, Al, or Ga) hydrogen-bonded (HB) systems are classified using MP2 level of multicomponent molecular orbital method, which can take account of the nuclear quantum nature of proton and deuteron. First, in the case of H3 CH(D)···YH3 (Y = B, Al, or Ge) HB systems, the deuterium (D) substitution induces the usual H/D geometrical isotope effect such as the contraction of covalent R(C-H(D)) bonds and the elongation of intermolecular R(H(D)···Y) and R(C···Y) distances. Second, in the case of H3 XH(D)···YH3 (X = Si or Ge, and Y = Al or Ge) HB systems, where H atom is negatively charged called as charge-inverted hydrogen-bonded (CIHB) systems, the D substitution leads to the contraction of intermolecular R(H(D)···Y) and R(X···distances. Finally, in the case of H3 XH(D)···BH3 (X = Si or Ge) HB systems, these intermolecular R(H(D)···Y) and R(X···Y) distances also contract with the D substitution, in which the origin of the contraction is not the same as that in CIHB systems. The H/D isotope effect on interaction energies and spatial distribution of nuclear wavefunctions are also analyzed.

H/D isotope effect on structures, binding energies, and basis set superposition errors in F−(H2O)n (n = 1–3) clusters

The H/D isotope effects on structures, binding energies, and basis set superposition errors (BSSEs) of hydrated fluoride anion clusters, F−(H2O)n (n=1–3), are theoretically analyzed by using the MP2 level of multi-component molecular orbital (MC_MO-MP2) method, in which quantum nature of proton/deuteron and electron–electron correlation are directly taken account. Our results clearly show that the additional water molecule to F−(H2O)n−1 cluster forms stronger water–water hydrogen bond than that in simple water cluster, whereas the additional F−–water hydrogen bond formation in F−(H2O)n cluster weakens the original F−–water hydrogen bonds in F−(H2O)n−1 cluster. The BSSEs estimated in the MC_MO-MP2 calculations are slightly larger than those in the conventional MP2 calculations, due to the H/D geometrical isotope effect on the intermolecular distances. Consequently, the order of stability in several F−(H2O)3 cluster isomers cannot be adequately evaluated without BSSE corrections in our MC_MO-MP2 calculations, rather than the conventional MP2 ones.

Positron-attachment to acetonitrile, acetaldehyde, and acetone molecules: Vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach

To theoretically demonstrate the binding of a positron to acetonitrile, acetaldehyde, and acetone molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local CN or CO vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic – single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential. For acetonitrile, acetaldehyde, and acetone molecules, the PA values after averaging over the 1st vibrational state are 136, 55, and 96 meV, which can be compared with the corresponding experimental vlues of 180, 90, and 173 meV, respectively.

Theoretical investigation of a positron binding to an aspartame molecule using the ab initio multicomponent molecular orbital approach

The feature of positron binding to aspartame molecule was analyzed using the ab initio multicomponent molecular orbital method. All nine stable conformers for aspartame molecule have positive positron affinity (the binding energy of a positron) values, which means that a positron can be attached to parent aspartame molecule. Analyzing the positronic orbitals of positronic aspartame conformers and the electrostatic potential maps of the corresponding parent molecules, we found that long‐range electrostatic interaction is the most crucial role in positron binding to aspartame molecule. We theoretically confirmed the possibility of positron binding to the conformers of aspartame molecule with strong dipole moment. © 2014 Wiley Periodicals, Inc.

Corrigendum: Vibrational enhancement of positron affinities for nonpolar carbon dioxide and carbon disulfide molecules: Multi-component molecular orbital study for vibrational excited states

To demonstrate the binding of a positron to nonpolar CX2 (X = O and S) molecules, we have estimated the vibrational averaged positron affinity (PA) values for the harmonic asymmetric stretching vibrational coordinate with the multi-component molecular orbital method. A positron can be attached at higher vibrational excitation levels, and vibrational averaged PA values become greater as the number of vibrational quantum number increases. The resultant PA values of carbon disulfide (CS2) molecule are greater than those of CO2, which is consistent with the corresponding property such as infrared (IR) intensity and polarizability of the parent species. © 2012 Wiley Periodicals, Inc.

Positron-attachment to nonpolar or small dipole CXY (X, Y = O, S, and Se) molecules: vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach

To theoretically demonstrate the binding of a positron to a nonpolar or small dipole molecule, we have calculated the vibrational averaged positron affinity (PA) values along the harmonic asymmetric stretching vibrational coordinate with the configuration interaction level of multi-component molecular orbital method for CXY (X, Y = O, S, and Se) molecules. For CSe2 and CSSe molecules, a positron can even be attached at the equilibrium structures, due to the effect of the induced dipole moment with large polarizability values. For a CS2 molecule, the positive PA value is obtained at the lowest vibrational excited state in our scheme. Although there is no direct experimental evidence for the positron-binding to CO2, COS, and COSe molecules, we have predicted positron-binding for these molecules at higher vibrational excited states.

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.

Theoretical Study on the Phase Transition and the H/D Isotope Effect of Squaric Acid

We investigated the phase transition and the isotope effect in squaric acid (H2C4O4, abbreviated H2SQ), a hydrogen-bonded dielectric material. Using first-principles calculation, we found that Jahn-Teller distortion of the unit structure (C4H4O4) was the major driving force for the phase transition in the H2SQ crystal. In order to elucidate the isotope effect on the phase transition in deuterated squaric acid (D2SQ), we employed the multi-component molecular orbital (MC_MO) method, which directly takes into account the quantum effects of protons and deuterons. Using this model, we successfully predicted the difference between the phase transition temperature of H2SQ and that of D2SQ to be 192K, which is in reasonable agreement with the experimental value of 145 K. We found that the isotope effect in the H2SQ/D2SQ system was based more on shrinking distribution of the deuteron wave rather than that of the proton wave. When the MC_MO method was coupled with adequate cluster models, first-principles calculations were effective to determining the origin of the phase transition and the H/D isotope effect in hydrogen-bonded dielectric materials.

Systematic theoretical investigation of a positron binding to amino acid molecules using the ab initio multi-component molecular orbital approach

The feature of positron binding to twenty neutral amino acid molecules with the global minimum (GM) and intramoleculear hydrogen-bonded (HB) structures was analysed using the ab initio multi-component molecular orbital method. All amino acid molecules in the intramoleculear HB structures have positive positron affinity (PA, the binding energy of a positron) values, which means that a positron can be attached to parent molecules, while in the GM structures only three amino acid molecules of Gln, Trp, and His have positive PA values. Analysing the positronic orbitals of each positronic amino acid molecule and the electrostatic potential maps of the corresponding parent molecules, we found that long-range electrostatic interaction is the most crucial role in positron binding to neutral amino acid molecules. The strong correlation is observed between the PA and dipole moment, that is, a polar molecule with a large dipole moment has a large PA value. The critical dipole moment of neutral amino acid molecules for binding a positron was found at about 3.46 Debye. From the systematic analysis of twenty kinds of amino acid molecule, we theoretically confirmed the possibility of positron binding to conformers of amino acid molecules with strong dipole moment.

Theoretical Study on Isotope Effect for Phase Transition Temperature of Mixed K3H1-xDx(SO4)2, Mixed (H1-xDx)2SQ, Tritiated TKHS, and T2SQ Crystals

We theoretically investigated the phase transition temperature (Tc ) and geometrical changes of mixed K3H1-xDx(SO4)2 and mixed (H1-xDx)2SQ crystals by using the first-principle multi-component molecular orbital method, which can take account of the quantum effect of light nucleus. The O…O distances in K3H1-xDx(SO4)2 and (H1-xDx)2SQ crystals gradually elongate and the electronic charge density around the light nucleus becomes greater, as the deuterium concentration increases. We have also predicted the Tc values of TKHS and T2SQ, with the hydrogen substituted by the tritium, as about 190 and 680 K, respectively.

Molecular dynamics simulation based on the multi-component molecular orbital method: Application to [formula omitted

We propose a molecular dynamics (MD) method based on the multi-component molecular orbital (MC_MO) method, which takes into account the quantum effect of proton directly, for the detailed analyses of proton transfer in hydrogen bonding system. The MC_MO based MD (MC_MO-MD) method is applied to the basic structures, H 5 O 2 + (called “Zundel ion”), and its isotopomers ( D 5 O 2 + and T 5 O 2 + ). We clearly demonstrate the geometrical difference of hydrogen bonded O ⋯ O distance induced by H/D/T isotope effect because the O ⋯ O in H-compound was longer than that in D- or T-compound. We also find the strong relation between stretching vibration of O ⋯ O and the distribution of hydrogen bonded protonic wavefunction because the protonic wavefunction tends to delocalize when the O ⋯ O distance becomes short during the dynamics. Our proposed MC_MO-MD simulation is expected as a powerful tool to analyze the proton dynamics in hydrogen bonding systems.

Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born-Oppenheimer approximation. This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on (15)N nuclear shielding, (1)Δ(15)N(D), in ammonium and amines decrease as a counterion or water molecule moves closer to the nitrogen. (1)Δ(15)N(D) and (2)Δ(1)H(D) of the NH(3)(+) groups of lysine residues in the B1 domain of protein G have been calculated using truncated side chains and also determined experimentally by NMR. Comparisons show that the structures in solution are different from those in the crystal and that solvation plays an important role in weakening the hydrogen bonds.

Stability and hydration structure of model perfluorosulfonic acid compound systems, CF 3SO 3H(H 2O) n ( n = 1–4), and its isotopomer by the direct treatment of H/D nuclear quantum effects

We theoretically analyzed the stability and hydration structures of perfluorosulfonic acid (PFSA) for polymer electrolyte fuel cell (PEFC) by using model compound systems, CF 3SO 3H and its D isotopomer with one to four water molecules (H 2O/D 2O). We applied to the systems the multi-component molecular orbital method that takes into account the quantum effects of H and D nuclei directly. By comparing the results of H/D isotopomers, we clearly demonstrated the geometrical difference in hydrogen bonds due to the difference of H/D quantum behavior. The interaction energy of deuterated hydrogen bonds became small due to the weakness of hydrogen bond by the deuterium substitution. When four water molecules are hydrated, only the proton transfer structure for H compound was obtained due to the drastic change of the potential. We also analyzed the details of geometry and electronic charge of H/D isotopic oxonium ions, H 3O +, H 2DO +, HD 2O +, and D 3O +, in proton transfer structures.

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.

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.

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

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.