Ab Initio Molecular Orbital Research Articles

Chemical significance of x-ray photoelectron spectroscopy binding energy shifts: A Perspective

The principal intent of this Perspective is to review the mechanisms that are responsible for the shifts of binding energies, ΔBE, observed in x-ray photoelectron spectroscopy (XPS) measurements and so to relate the shifts to the electronic structure and the chemical bonding in the systems studied. To achieve this goal, several theoretical considerations are necessary beyond just the calculation of XPS BEs. Though briefly discussed here, we are not primarily interested in absolute values of BE or quantitation using relative intensities. Within the molecular orbital (MO) theory framework, it is shown that the analysis of orbital properties is critical for the correct interpretation of XPS. In particular, rigorous definitions are given for the initial state and final state contributions to BEs and to BE shifts, ΔBE. It is first shown how the BEs of core levels are related to the electronic structure by consideration of the BEs for a model atomic system to establish the origins and magnitudes of BE shifts. The mechanisms established for the model system are then applied to a review of XPS measurements and MO theory on a set of real examples. An important focus of the paper is to demonstrate that, in many cases, initial state mechanisms allow for a definitive interpretation of the XPS BE shifts and that an important role of theory is to provide qualitative explanations rather than quantitative agreement with XPS measurements. The mechanisms established are a guide to the interpretation of XPS measurements and consideration of these mechanisms may suggest additional calculations that would be useful. It is concluded that there is still a bright future for the coupling of ab initio MO theory with XPS measurements.

Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations.

The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), prevents the reproduction of Mycobacteria. To propose potent inhibitors of FtsZ, the binding properties of FtsZ with various derivatives of Zantrin ZZ3 were investigated at an electronic level, using molecular simulations. We here employed protein–ligand docking, classical molecular mechanics (MM) optimizations, and ab initio fragment molecular orbital (FMO) calculations. Based on the specific interactions between FtsZ and the derivatives, as determined by FMO calculations, we proposed novel ligands, which can strongly bind to FtsZ and inhibit its aggregations. The introduction of a hydroxyl group into ZZ3 was found to enhance its binding affinity to FtsZ.

A New Lipid Force Field (FUJI).

To explore inhomogeneous and anisotropic systems such as lipid bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method has been applied without a conventional isotropic dispersion correction. As the popular AMBER and CHARMM lipid force fields were developed using a cutoff scheme, their lipid bilayers unacceptably shrink when using the LJ-PME method. In this study, a new all-atom lipid force field (FUJI) was developed on the basis of the AMBER force-field scheme including the Lipid14 van der Waals parameters. Point charges were calculated using the restrained electrostatic potentials of many lipid conformers. Further, torsion energy profiles were calculated using high-level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ), following which the molecular mechanical dihedral parameters were derived through a fast Fourier transform. By incorporation of these parameters into a new lipid force field without fitting experimental data, the desired lipid characteristics such as the area per lipid and lateral diffusion coefficients were obtained through GROMACS molecular dynamics simulations using the LJ-PME method and virtual hydrogen sites. The calculated area per lipid and lateral diffusion coefficients showed satisfactory agreement with experimental data. Furthermore, the electron-density profiles along the membrane normal were calculated for pure lipid bilayers, and the resulting membrane thicknesses agreed well with the experimental values. As the new lipid force field is compatible with FUJI for protein and small molecules, the new FUJI force field will offer accurate modeling for complex systems consisting of various membrane proteins and lipids.

Quasi-Atomic Bond Analyses in the Sixth Period: I. Relativistic Accurate Atomic Minimal Basis Sets for the Elements Cesium to Radon

Full-valence relativistic accurate atomic minimal basis set (AAMBS) orbitals are developed for the sixth-row elements from cesium to radon, including the lanthanides. Saturated primitive atomic basis sets are developed and subsequently used to form the AAMBS orbitals. By virtue of the use of a saturated basis, properties computed based on the AAMBS orbitals are basis set independent. In molecules, the AAMBS orbitals can be used to construct valence virtual orbitals (VVOs) that provide chemically meaningful ab initio lowest unoccupied molecular orbitals (LUMOs) with basis set independent orbital energies. The optimized occupied molecular orbitals complemented with the VVOs form a set of full-valence molecular orbitals. They can be transformed into a set of oriented quasi-atomic orbitals (QUAOs) that provide information on intramolecular bonding via an intrinsic density analysis. In the present work, the development of the AAMBS for the sixth row is presented.

Ab Initio Molecular Orbital Study of the First Four Si/C Alternately Substituted Annulenes.

The ground and low-lying excited states of four alternating Si/C annulenes, H nSi n/2C n/2 with n = 4, 6, 8, and 10, have been investigated by ab initio molecular orbital methods and compared to those of their all-carbon and all-silicon analogues. In the ground state, all of the Si/C-mixed annulenes, except for the largest 10-membered annulene (H10Si5C5), assume equal-bond-length structures by adopting a closed-shell electronic structure in the possible highest symmetry. For the largest H10Si5C5, the trend of the bond delocalization still remains but the circular structure is considerably distorted and nonplanar due to severe angle strain. In the low-lying singlet (S1) and triplet (T1) states, the geometry of the compounds tends to be nonplanar as the excitations produce silyl radical character. Relative energies of the T1 and S1 states of the 6-membered ring, compared to those of the respective ground states (S0), are higher than those of the 4- and 8-membered rings, suggesting a special stability for H6Si3C3. The planar rhombus shape of the formally antiaromatic H4Si2C2 suggests that a synthetic effort is merited. Bonding analyses are given to support the conclusions reached on the basis of geometric structures and excited-state energetics.

Theoretical Study of the Formation Methane in the Reaction of Methyl Radical with Propanol-2

Theoretical Study of the Formation Methane in the Reaction of Methyl Radical with Propanol-2

Theoretical Study on Reaction Pathways of Methyl Radical with Ethylamine

Theoretical Study on Reaction Pathways of Methyl Radical with Ethylamine

New high-pressure tetragonal polymorphs of SrTiO3—molecular orbital and Raman band change under pressure

The vibrational and structural properties of SrTiO3 were investigated using Raman spectroscopy, synchrotron x-ray powder diffraction up to 55 GPa at 300 K, and ab initio quantum chemical molecular orbital (MO) calculations. These measurements and calculations revealed the structure transformation from cubic to tetragonal phase at about 9 GPa. Above 9 GPa, sharper new peaks were associated with a tetragonal structure. At about 30 GPa some bands disappeared and several new bands emerged. Structure transformation from I4/mcm to a new structure of P4/mbm was found at above 30 GPa by Rietveld profile fitting analysis. The diffraction pattern gave no indication of a Cmcm orthorhombic phase. Ab initio MO calculation proved the change of the molecular orbital coupling with a structure transformation. The Mulliken charge of Ti is increased with increasing pressure in the cubic phase, but the Sr charge continuously decreased. The d–p–π hybridization of the Ti–O bond and localizing the electron density are decreased with increasing pressure. The Ti–O bond becomes shorted in the P4/mbm phase and the change in the Ti charge accelerated more. All present investigations by x-ray diffraction, Raman spectra study and MO calculation show consistent results.

Pressure dependence of electron density distribution and d-p- π hybridization in titanate perovskite ferroelectrics

Electron density distributions of $\mathrm{PbTi}{\mathrm{O}}_{3}, \mathrm{BaTi}{\mathrm{O}}_{3}$, and $\mathrm{SrTi}{\mathrm{O}}_{3}$ were determined by synchrotron x-ray powder diffraction up to 55 GPa at 300 K and ab initio quantum chemical molecular orbital (MO) calculations, together with a combination of maximum entropy method calculations. The intensity profiles of Bragg peaks reveal split atoms in both ferroelectric $\mathrm{PbTi}{\mathrm{O}}_{3}$ and $\mathrm{BaTi}{\mathrm{O}}_{3}$, reflecting the two possible positions occupied by the Ti atom. The experimentally obtained atomic structure factor was used for the determination of the deformation in electron density and the d-p-$\ensuremath{\pi}$ hybridization between ${d}_{xz}$ (and ${d}_{yz}$) of Ti and ${p}_{x}$ (and ${p}_{y}$) of O in the Ti-O bond. Ab initio MO calculations proved the change of the molecular orbital coupling and of Mulliken charges with a structure transformation. The Mulliken charge of Ti in the $\mathrm{Ti}{\mathrm{O}}_{6}$ octahedron increased in the ionicity with increasing pressure in the cubic phase. The bonding nature is changed with a decrease in the hybridization of the Ti-O bond and the localization of the electron density with increasing pressure. The hybridization decreases with pressure and disappears in the cubic paraelectric phase, which has a much more localized electron density distribution.

Determination of Structures and Energetics of Small- and Medium-Sized One-Carbon-Bridged Twisted Amides using ab Initio Molecular Orbital Methods: Implications for Amidic Resonance along the C-N Rotational Pathway.

Twisted amides containing nitrogen at the bridgehead position are attractive practical prototypes for the investigation of the electronic and structural properties of nonplanar amide linkages. Changes that occur during rotation around the N-C(O) axis in one-carbon-bridged twisted amides have been studied using ab initio molecular orbital methods. Calculations at the MP2/6-311++G(d,p) level performed on a set of one-carbon-bridged lactams, including 20 distinct scaffolds ranging from [2.2.1] to [6.3.1] ring systems, with the C═O bond on the shortest bridge indicate significant variations in structures, resonance energies, proton affinities, core ionization energies, frontier molecular orbitals, atomic charges, and infrared frequencies that reflect structural changes corresponding to the extent of resonance stabilization during rotation along the N-C(O) axis. The results are discussed in the context of resonance theory and activation of amides toward N-protonation (N-activation) by distortion. This study demonstrates that one-carbon-bridged lactams-a class of readily available, hydrolytically robust twisted amides-are ideally suited to span the whole spectrum of the amide bond distortion energy surface. Notably, this study provides a blueprint for the rational design and application of nonplanar amides in organic synthesis. The presented findings strongly support the classical amide bond resonance model in predicting the properties of nonplanar amides.

S=12ferromagnetic-antiferromagnetic alternating Heisenberg chain in a zinc-verdazyl complex

We successfully synthesized the zinc-verdazyl complex $[{\text{Zn(hfac)}}_{2}]\ifmmode\cdot\else\textperiodcentered\fi{}(o\ensuremath{-}\mathrm{Py}\ensuremath{-}V)$ [hfac = 1,1,1,5,5,5-hexafluoroacetylacetonate; $o$-Py-V = 3-(2-pyridyl)-1,5-diphenylverdazyl], which is an ideal model compound with an $S=\frac{1}{2}$ ferromagnetic-antiferromagnetic alternating Heisenberg chain (F-AF AHC). Ab initio molecular-orbital (MO) calculations indicate that two dominant interactions ${J}_{\mathrm{F}}$ and ${J}_{\mathrm{AF}}$ form the $S=\frac{1}{2}$ F-AF AHC in this compound. The magnetic susceptibility and magnetic specific heat of the compound exhibit thermally activated behavior below approximately 1 K. Furthermore, its magnetization curve is observed up to the saturation field and directly indicates a zero-field excitation gap of 0.5 T. These experimental results provide evidence for the existence of a Haldane gap. We successfully explain the results in terms of the $S=\frac{1}{2}$ F-AF AHC through quantum Monte Carlo calculations with $|{J}_{\mathrm{AF}}/{J}_{\mathrm{F}}|=0.22$. The ab initio MO calculations also indicate a weak AF interchain interaction ${J}^{\ensuremath{'}}$ and that the coupled F-AF AHCs form a honeycomb lattice. The ${J}^{\ensuremath{'}}$ dependence of the Haldane gap is calculated, and the actual value of ${J}^{\ensuremath{'}}$ is determined to be less than $0.01|{J}_{\mathrm{F}}|$.

Neutral-Fragmentation Paths of Methane Induced by Intense Ultrashort IR Laser Pulses: Ab Initio Molecular Orbital Approach

Instantaneous (laser-field-dependent) potential energy curves leading to neutral fragmentations of methane were calculated at several laser intensities from 1.4 × 10(13) to 1.2 × 10(14) W/cm(2) (from 1.0 × 10(10) to 3.0 × 10(10) V/m) using ab initio molecular orbital (MO) methods to validate the observation of neutral fragmentations induced by intense femtosecond IR pulses (Kong et al. J. Chem. Phys. 2006, 125, 133320). Two fragmentation paths, CH(2) + 2H and CH(2) + H(2), in (1)T(2) superexcited states that are located in the energy range of 12-16 eV were considered as the reaction paths because these states are responsible for Jahn-Teller distortion opening up reaction paths during ultrashort pulses. As field intensity increased, the low-lying excited (1)A(1) states originated from the Jahn-Teller (1)T(2) states were substantially stabilized along the neutral-fragment path CH(4) → CH(2) + 2H and were located below the ionization threshold. On the other hand, the low-lying excited (1)B(1) states, which also originate from the Jahn-Teller (1)T(2) states, were embedded on the ionized state along the dissociation path to CH(2) + H(2). This indicates that ionic fragments, rather than neutral ones, are produced along the CH(2) + H(2) path. The computational results support neutral fragmentations through superexcited states proposed by Kong et al.

Development of Calculation and Analysis Methods for the Dynamic First Hyperpolarizability Based on the Ab Initio Molecular Orbital – Quantum Master Equation Method

We develop novel calculation and analysis methods for the dynamic first hyperpolarizabilities β [the second-order nonlinear optical (NLO) properties at the molecular level] in the second-harmonic generation based on the quantum master equation method combined with the ab initio molecular orbital (MO) configuration interaction method. As examples, we have evaluated off-resonant dynamic β values of donor (NH(2))- and/or acceptor (NO(2))-substituted benzenes using these methods, which are shown to reproduce those by the conventional summation-over-states method well. The spatial contributions of electrons to the dynamic β of these systems are also analyzed using the dynamic β density and its partition into the MO contributions. The present results demonstrate the advantage of these methods in unraveling the mechanism of dynamic NLO properties and in building the structure-dynamic NLO property relationships of real molecules.

Effect of fluoro substitution on the fragmentation of the K‐shell excited/ionized pyridine studied by electron impact

Fragmentation of the pyridine ring followed by K-shell excitation/ionization has been studied with 2-fluoropyridine (2FPy) by electron impact. Ab initio molecular orbital (MO) calculations were also carried out to investigate the electronic states correlating with specific fragment ions. The fragment ions are produced characteristically at the N 1s edge, while the spectra observed at the F 1s and C 1s edges exhibit a small difference from that at the valence ionization. The production of the C(4)H(2)(+), C(4)H(3)(+) and C(4)H(2)F(+) ions indicates that the cleavage of the N-C6 and C2-C3 bonds or the N-C2 and C5-C6 bonds is likely to occur after the N 1s excitation/ionization. Ab initio MO calculations indicate that the former fission is likely to proceed through the n(N)(1)π(2)(1)π(3)(2) and n(N)(0)π(2)(2)π(3)(2) excited states of the parent molecular dication. On the other hand, the breakage of the N-C2 and C4-C5 bonds, which specifically proceeds at the N 1s edge for 2-methylpyridine, does not occur for 2FPy. The present calculation reveals that the products of this channel are unstable by the electronegativity of fluorine and that the relative energy of the Auger-final states of 2FPy is lowered by the reorganization and electron correlation effects.

An optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework

For the purpose of executing direct dynamic and statistical calculation of chemical reactions in solution, we proposed an optimum strategy using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRPs), that is, the NDDO-SSRP method. It has been further extended to develop the NDDO-MAIS-SSRP method, which is the NDDO-SSRP method reinforced with the method adopted for intermolecular studies (MAIS), to correct the description of the intermolecular core-core repulsion interaction energy. In this strategy, the empirical parameters of the semiempirical MO method are optimized individually for a target chemically reacting molecular system by reference to the ab initio MO calculation data for a lot of instantaneous geometries on the potential energy surface near the reaction path. For demonstration, the NDDO-MAIS-SSRP method was applied, within the QM/MM framework, to a molecular cluster, that is, a couple of a QM solute NH(3)-H(2)O molecule pair and a MM solvent H(2)O molecule. The NDDO-MAIS-SSRP method can reproduce the electrostatic energy in the region R > 4.0 A, though the electrostatic energy shows large difference with those of MP2 level calculations in the region R < 4.0 A in some cases. Both the NDDO-SSRP and the NDDO-MAIS-SSRP methods could promise in the dynamical application to chemical reaction in solution (Takenaka et al., Chem Phys Lett 2010, 485, 119; Koyano et al., Bull Chem Soc Jpn, in press).

Mechanism of Orientational Isomerism of Unsymmetrical Guests in a Heterodimeric Capsule: Analysis by Ab Initio Molecular Orbital Calculations

The geometries and interaction energies of the heterodimeric capsule [tetrakis(4-hydroxyhphenyl)-cavitand 1 and tetra(4-pyridyl)-cavitand 2] complexes with methyl p-acetoxybenzoate 3, methyl p-ethoxybenzeoate 4, and p-ethoxyiodobenzene 5 were studied by ab initio molecular orbital calculations. The optimized structures and charge distributions of the complexes suggest that the electrostatic interactions of oxygen atoms in the guest molecules with the hydrogen atoms of aromatic rings and methylene-bridge rim in the heterodimeric capsule stabilize the complexes. The calculated relative energies of the two orientational isomers of the complexes well reproduce the experimentally observed orientational selectivity of the guest molecules. The calculated stabilization energies for the major orientational isomers of the heterodimeric capsule (1.2) complexes with guest molecules (3, 4, and 5) are -21.6, -19.6, and -19.4 kcal/mol, respectively. Those for the minor orientational isomers are 1.5, 3.5, and 3.7 kcal/mol smaller (less negative), respectively. The magnitude of the calculated energy differences agrees well with the order of the experimental population of the major orientational isomer (3 < 4 approximately 5). The large electron correlation contributions to the attraction (-27.0 to -31.8 kcal/mol) show that the dispersion interactions are the major source of the attraction in the complexes, while the electrostatic interactions (-4.9 to -12.5 kcal/mol) are also an important source of the attraction. Although the electrostatic interactions are weaker than the dispersion interactions, the highly orientation dependent electrostatic interactions mainly determine the orientation of the unsymmetrical guest molecules in the complexes. The electrostatic interactions in the major orientational isomer are 2.6-3.9 kcal/mol larger (more negative) than those in the minor orientational isomer, while the differences of other energy terms are small (less than 1.1 kcal/mol). The interaction energies calculated for model complexes show that the CH/pi interactions are not playing important roles in controlling the orientation of the guest molecules in the complexes.

Specific fragmentation of the K-shell excited/ionized pyridine derivatives studied by electron impact: 2-, 3- and 4-methylpyridine

Fragmentation of the pyridine ring upon K-shell excitation/ionization has been studied with gaseous 2-, 3- and 4-methylpyridine by the electron-impact method. Ab initio molecular orbital (MO) calculations were also carried out to explore electronic states correlating with specific fragments. Some specific fragmentation channels were identified from the ionic fragments enhanced characteristically at the N 1s edge. Yields of the C(2)HN(+) and C(5)H(5)(+)/C(5)H(6)(+) ions show that the fission of the N-C2 and C4-C5/C5-C6 bonds of the ring is likely to occur after the N 1s excitation and ionization. Ab initio MO calculations for the 2-methylpyridine molecule indicate that the dissociation channels to produce these ions are only accessible through the excited states of the parent molecular dication, which can be formed by Auger decays after the N 1s ionization. Fragment ions via hydrogen rearrangement are produced as well, but the rearrangement is not a phenomenon specific to the K-shell excitation/ionization.

Ab initio MO Study of Hydrogen Bonding and Spectral Characteristics of HCN-H2O-HCN Trimer: Comparison between Dimer and Trimer

Hydrogen bonding of HCN-H2O-HCN trimer has been studied by means of ab initio molecular orbital (MO) calculations. The changes in intermolecular interaction energy and vibrational frequency induced by addition of HCN molecule to HCN-H2O or H2O-HCN dimer are especially focused. The distances of hydrogen bonds in the trimer are calculated to be shorter than those in the corresponding dimers. The hydrogen bond distances are hence shortened by addition of another HCN. The interaction energies of the hydrogen bonds are also increased by addition of HCN. The dipole moment of the trimer is smaller than the sum of the dipole moments of the separate moieties (HCN + H2O + HCN). This is opposite of the previous result for H2O-HCN-H2O. The spectral shift of the stretching modes induced by hydrogen bond formation has been predicted by vibrational frequency analysis. The vibrational frequency of the asymmetric stretching mode of HCN included in the H2O-HCN part of the trimer is remarkably red-shifted from that of the H2O-HCN dimer. This information is expected to be useful for experimental detection of the trimer.

Ab initio MO–CI based quantum master equation approach: Exciton dynamics of weakly and strongly coupled J-type aggregates

In order to investigate the time evolutions of electron and hole distributions in weakly and strongly coupled H 2 dimer models, we employ a novel dynamic exciton expression derived from the exciton density matrices calculated by the quantum master equation combined with the ab initio molecular orbital (MO)–configuration interaction (CI) method. The oscillation of exciton distribution over the monomers is observed in case of small inter-monomer distance, where the coupled dipole approximation is invalid. The result originates in the covalent character of inter-monomer interaction in the first excited state, i.e., delocalized character of LUMO distribution.

An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution

For the purpose to execute direct dynamics calculation in solution chemistry, we propose an optimum strategy for solution chemistry using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRP), i.e., the NDDO-SSRP method. In this strategy, the empirical parameters of the semi-empirical MO method were optimized individually for target molecule or ion by reference to the ab initio MO calculation data for many configurations on the potential energy surface near the reaction path. For demonstration, the NDDO-SSRP method was applied to two molecules and two ions (OH(-), H(2)O, NH(3), NH(4)(+)) at their equilibrium states in aqueous solution, respectively. Accordingly, it was verified that both the potential energy surface and the charge distribution of these solutes in aqueous solution are dramatically improved to reproduce themselves accurately at ab initio MO calculation level. In conclusion, it is expected that the NDDO-SSRP method should become quite useful for dynamic and statistical applications to chemical reaction systems in solution.