Orbital signatures of methyl in L-alanine

Molecular orbital signatures of the methyl substituent in L-alanine have been identified with respect to those of glycine from information obtained in coordinate and momentum space, using dual space analysis. Electronic structural information in coordinate space is obtained using ab initio (MP2/TZVP) and density functional theory (B3LYP/TZVP) methods, from which the Dyson orbitals are simulated based on the plane wave impulse approximation into momentum space. In comparison to glycine, relaxation in geometry and valence orbitals in L-alanine is found as a result of the attachment of the methyl group. Five orbitals rather than four orbitals are identified as methyl signatures. That is, orbital 6a in the core shell, orbitals 11a and 12a in the inner valence shell, and orbitals 19a and 20a in the outer valence shell. In the inner valence shell, the attachment of methyl to glycine causes a splitting of its orbital 10a' into orbitals 11a and 12a of L-alanine, whereas in the outer valence shell the methyl group results in an insertion of an additional orbital pair of 19a and 20a. The frontier molecular orbitals, 24a and 23a, are found without any significant role in the methylation of glycine.     

饱和烷烃分子C_nH_(2n+2)(n=4-6)的电子动量光谱(英文)

使用B3LYP/TZVP//B3LYP/aug-cc-pVTZ方法系统研究了饱和烷烃分子CnH2n+2(n=4-6)的轨道电子动量光谱,比较了同分异构体CnH2n+2(n=4-6)对轨道动量分布的影响.结合二维空间分析方法对电子在坐标空间中的密度分布进行了系统的研究.计算结果表明,最内价壳层电荷分布主要由s电子贡献,第二近邻芯价壳层则主要由p电子贡献,而其余的价壳层则为sp杂化.最内价轨道表现出最大的谱线强度并且远大于其它轨道的谱线强度,而且正烷烃的谱线强度要大于异烷烃等同分异构体的谱线强度,表现出了明显的与甲基移动的个数有关的性质.     

Effects of solvation and core switching on the photoelectron angular distributions from (CO2)n(-) and (CO2)(n)(-).H2O

Photoelectron images are recorded in the photodetachment of two series of cluster anions, (CO(2))(n)(-), n=4-9 and (CO(2))(n)(-).H(2)O, n=2-7, with linearly polarized 400 nm light. The energetics of the observed photodetachment bands compare well with previous studies, showing evidence for switching between two anionic core structures: The CO(2)(-) monomer and covalent (CO(2))(2)(-) dimer anions. The systematic study of photoelectron angular distributions (PADs) sheds light on the electronic structure of the different core anions and indicates that solvation by several CO(2) molecules and/or one water molecule has only moderate effect on the excess-electron orbitals. The observed PAD character is reconciled with the symmetry properties of the parent molecular orbitals. The most intriguing result concerns the PADs showing remarkable similarities between the monomer and dimer anion cluster-core types. This observation is explained by treating the highest-occupied molecular orbital of the covalent dimer anion as a linear combination of two spatially separated monomeric orbitals.     

Theoretical study of isomerism in protonated forms of N2O,NPO, and P2O

The geometric parameters of the isomers HN₂O⁺, HPNO⁺, and HP₂O⁺ were calculated by the nonempirical SCF/3-21G* method and their relative energies were determined with consideration of the electronic correlation in the MP3/DEHD + PS approximation. According to the calculations, protonation of N₂O, PNO, and P₂O molecules should preferably take place at the oxygen atom. Isomers with a quasilinear NNO and PNO backbone are most advantageous in HN₂O⁺ and HPNO⁺, and cyclic isomers are 60 and 30 kcal/mole less stable, respectively. On the contrary, the cyclic form is more stable for HPO ₂ ⁺ (by 10 kcal/mole). The bond at the attacked atom usually weakens (breaks) and the neighboring (opposite) bonds are strengthened in protonation. Protonation of P₂O stabilizes the cyclic isomer by 15 kcal/mole more strongly than the "open" isomer, resulting in inversion of their position on the energy scale. In the case of N₂O and PNO, the relative position of the cyclic and basic isomers virtually does not change, but the linear NPO isomer is destabliized. The stability of the cyclic isomers in comparison to the "open" isomers increases on substitution of N atoms by P atoms in both molecules of N₂O, PNO, and P₂O and in their ions HN₂O⁺, HPNO⁺, and HP₂O⁺. This tendency probably holds in subsequent transition to As and Sb atoms.Institute of New Chemical Problems, Russian Academy of Sciences, 142432 Chernogolovka. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 1, pp. 126–134, January, 1992.     

Valence orbital response to pseudorotation of tetrahydrofuran: a snapshot using dual space analysis

The pseudorotation of tetrahydrofuran (THF) (C(4)H(8)O) has been studied using density functional theory, with respect to the valence orbital responses to the ionization potentials and to orbital electron and momentum distributions. Three conformations of THF, the global minimum structure C(s), local minimum structure C(2), and a transition state structure C(1), which are characteristic configurations on the potential energy surface, are examined using the SAOP/et-pVQZ//B3LYP/6-311++G** models with the aforementioned dual space analysis. It is noted in the ionization energy spectra that the minimum structures C(s) and C(2) are not directly connected by pseudorotation, but through the transition state structure C(1). As a result, some orbitals of the C(s) conformer are able to "correlate" to orbitals of the C(2) conformer without a strict symmetry constraint, i.e., orbital 7a' of the C(s) conformer is correlated to orbital 5b of the C(2) conformer. It is also noted that although the valence orbital ionization potentials are not significantly altered by the pseudorotation of THF, their spectra (mainly due to excitation) are quite different indeed. Detailed orbital analysis based on dual space analysis is given. The valence orbital behavior of the conformations is orbital dependent. It can be approximately divided into three groups: the "signature group" is associated with orbitals experiencing significant changes. The frontier orbitals are in this group. The "nearly identical group" includes orbitals without apparent changes across the conformations. Most of the orbitals showing a certain degree of distortion during the pseudorotation process belong to the third group. The present study demonstrates that a comprehensive understanding of the pseudorotation of THF and its dynamics requires multidimensional information and that the information gained from momentum space is complementary to that from the more familiar coordinate space.     

Investigation into the valence electronic structure of norbornene using electron momentum spectroscopy, Green's function, and density functional theories

Results of a study of the valence electronic structure of norbornene (C(7)H(10)), up to binding energies of 30 eV, are reported. Experimental electron momentum spectroscopy (EMS) and theoretical Green's function and density functional theory approaches were utilized in this investigation. A stringent comparison between the electron momentum spectroscopy and theoretical orbital momentum distributions found that, among the tested models, the combination of the Becke-Perdew functional and a polarized valence basis set of triple-zeta quality provides the best representation of the electron momentum distributions for all 19 valence orbitals of norbornene. This experimentally validated model was then used to extract other molecular properties of norbornene (geometry, infrared spectrum). When these calculated properties are compared to corresponding results from independent measurements, reasonable agreement is typically found. Due to the improved energy resolution, EMS is now at a stage to very finely image the effective topology of molecular orbitals at varying distances from the molecular center, and the way the individual atomic components interact with each other, often in excellent agreement with theory. This will be demonstrated here. Green's Function calculations employing the third-order algebraic diagrammatic construction scheme indicate that the orbital picture of ionization breaks down at binding energies larger than about 22 eV. Despite this complication, they enable insights within 0.2 eV accuracy into the available ultraviolet emission and newly presented (e,2e) ionization spectra. Finally, limitations inherent to calculations of momentum distributions based on Kohn-Sham orbitals and employing the vertical depiction of ionization processes are emphasized, in a formal discussion of EMS cross sections employing Dyson orbitals.     

Structural and electronic properties of hetero-transition-metal Keggin anions: a DFT Study of alpha/beta-[XW12O40]n- (X = CrVI, VV, TiIV, FeIII, CoIII, NiIII, CoII, and ZnII) relative stability

Density functional theory calculations have been carried out to investigate the electronic structures and the alpha/beta relative stability of Keggin-typed [XW(12)O(40)]n- anions with transition metal as heteroatom X (X = Cr(VI), V(V), Ti(IV), Fe(III), Co(III), Ni(III), Co(II) and Zn(II)). Nice agreement in geometries between computation and experiment has been obtained, and the higher stability of the alpha isomer over the beta one has been confirmed. Structural parameter analysis reveals that the {M(3)O(13)} triads in both alpha and beta isomers contract considerably with the increase of the negative anionic charge, while the overall size of both isomers shrinks only slightly. Fragment molecular orbital analysis shows that except alpha/beta-[TiW(12)O(40)]4-, the electronic structures of Keggin anions can be described by the insertion of the e and/or t2 orbital of XO4n- into the frontier orbitals of W(12)O(36) cage, and this leads to the specific redox property, which is different from that of the Keggin anions with main-group elements as heteroatoms. Energy decomposition analysis shows that the enhanced intrinsic stability of the alpha isomer in Td arrangement of W(12)O(36) shell and the larger deformation of the alpha over the beta isomer are two dominating factors and contribute oppositely to the alpha/beta relative stability.     

A systematic multireference perturbation-theory study of the low-lying states of SiC3

The three known lowest-energy isomers of SiC(3), two cyclic singlets (2s and 3s) and a linear triplet (1t), have been reinvestigated using multireference second-order perturbation theory (MRPT2). The dependence of the relative energies of the isomers upon the quality of the basis sets and the sizes of the reference active spaces is explored. When using a complete-active-space self-consistent-field reference wave function with 12 electrons in 11 orbitals [CASSCF (12, 11)] together with basis sets that increase in size up to the correlation-consistent polarized core-valence quadruple zeta basis set (cc-pCVQZ), the MRPT2 method consistently predicts the linear triplet to be the most stable isomer. A new parallel direct determinant MRPT2 code has been used to systematically explore reference spaces that vary in size from CASSCF (8,8) to full optimized reaction space [FORS or CASSCF (16,16)] with the cc-pCVQZ basis. It is found that the relative energies of the isomers change substantially as the active space is increased. At the best level of theory, MRPT2 with a full valence FORS reference, the 2s isomer is predicted to be more stable than 3s and 1t by 4.7 and 2.2 kcal/mol, respectively.     

Calculation of X-ray absorption near edge structure of CeO2 using a model cluster

We report result of a first-principle molecular orbital calculation using discrete-variational (DV)-X method on a model of CeO₂ ([CeO₈]¹²⁻), and compare them with experimental date on X-ray absorption-near-edge structure. Even using a small cluster model, we can reproduce the two-peak structure near edge and explain the origin of the peaks. The two-peak structure is relially interpreted from the viewpoint of interactions between atomic orbitals. The theoretical spectra are obtained with the dipole approximation. In addition, we calculate the wave functions, which indicate that the low-energy peak in the two-peak structure originates from a quasi-bound state composed of localized Ce d and O component. The orgin of the high-energy peak is the phase shift between localized Ce d orbital and that of the delocalized standing wave of O atomic orbitals.     

Electron Momentum Spectroscopy of Valence Orbitals of Cyclopentene: Nuclear Dynamics and Distorted Wave Effect

We report a measurement of electron momentum distributions of valence orbitals of cyclopentene employing symmetric noncoplanar (e, 2e) kinematics at impact energies of 1200 and 1600 eV plus the binding energy. Experimental momentum profiles for individual ionization bands are obtained and compared with theoretical calculations considering nuclear dynamics by harmonic analytical quantum mechanical and thermal sampling molecular dynamics approaches. The results demonstrate that molecular vibrational motions including ring-puckering of this flexible cyclic molecule have obvious influences on the electron momentum profiles for the outer valence orbitals, especially in the low momentum region. For π*-like molecular orbitals 3a'', 2a'', and 3a', the impact-energy dependence of the experimental momentum profiles indicates a distorted wave effect.     

Electronic structure of the benzene dimer cation

The benzene and benzene dimer cations are studied using the equation-of-motion coupled-cluster model with single and double substitutions for ionized systems. The ten lowest electronic states of the dimer at t-shaped, sandwich, and displaced sandwich configurations are described and cataloged based on the character of the constituent fragment molecular orbitals. The character of the states, bonding patterns, and important features of the electronic spectrum are explained using qualitative dimer molecular orbital linear combination of fragment molecular orbital framework. Relaxed ground state geometries are obtained for all isomers. Calculations reveal that the lowest energy structure of the cation has a displaced sandwich structure and a binding energy of 20 kcal/mol, while the t-shaped isomer is 6 kcal/mol higher. The calculated electronic spectra agree well with experimental gas phase action spectra and femtosecond transient absorption in liquid benzene. Both sandwich and t-shaped structures feature intense charge resonance bands, whose location is very sensitive to the interfragment distance. Change in the electronic state ordering was observed between sigma and piu states, which correlate to the B and C bands of the monomer, suggesting a reassignment of the local excitation peaks in the gas phase experimental spectrum.     

Electron propagator theory study of N-/O-methylglycine conformers

The low-lying conformers of N-/O-methylglycine are studied by ab initio calculations at the B3LYP, MP3, and MP4(SDQ) levels of theory with the aug-cc-pVDZ basis set. The conformers having the intramolecular hydrogen bonds N-H...O=C or O-H...N are more stable than the others. Vertical ionization energies for the valence molecular orbitals of each conformer predicted with the electron propagator theory in the partial third-order quasiparticle approximation are in good agreement with the experimental data available in the literatures. The relative energies of the conformers and comparison between the simulated and the experimental photoelectron spectra demonstrate that there are at least three and two conformers of N- and O-methylglycine, respectively, in the gas-phase experiments. The intramolecular hydrogen bonding O-H...N effects on the molecular electronic structures are discussed for the glycine methyl derivatives, on the basis of the ab initio electronic structure calculations, natural orbital bond, and atoms-in-molecules analyses. The intramolecular hydrogen bonding O-H...N interactions hardly affect the electronic structures of the O-NH2-CH2-C(=O)-O-CH3 and alpha-methylated NH2-CH2-C(CH3)OOH conformers, while the similar intramolecular interactions lead to the significantly lower-energy levels of the highest occupied molecular orbitals for the N-(CH3-NH-CH2-COOH) and beta-methylated (NH2-CH2-CH2-COOH) conformers.     

Coexistence of 1,3-butadiene conformers in ionization energies and Dyson orbitals

The minimum-energy structures on the torsional potential-energy surface of 1,3-butadiene have been studied quantum mechanically using a range of models including ab initio Hartree-Fock and second-order M?ller-Plesset theories, outer valence Green's function, and density-functional theory with a hybrid functional and statistical average orbital potential model in order to understand the binding-energy (ionization energy) spectra and orbital cross sections observed by experiments. The unique full geometry optimization process locates the s-trans-1,3-butadiene as the global minimum structure and the s-gauche-1,3-butadiene as the local minimum structure. The latter possesses the dihedral angle of the central carbon bond of 32.81 degrees in agreement with the range of 30 degrees-41 degrees obtained by other theoretical models. Ionization energies in the outer valence space of the conformer pair have been obtained using Hartree-Fock, outer valence Green's function, and density-functional (statistical average orbital potentials) models, respectively. The Hartree-Fock results indicate that electron correlation (and orbital relaxation) effects become more significant towards the inner shell. The spectroscopic pole strengths calculated in the Green's function model are in the range of 0.85-0.91, suggesting that the independent particle picture is a good approximation in the present study. The binding energies from the density-functional (statisticaly averaged orbital potential) model are in good agreement with photoelectron spectroscopy, and the simulated Dyson orbitals in momentum space approximated by the density-functional orbitals using plane-wave impulse approximation agree well with those from experimental electron momentum spectroscopy. The coexistence of the conformer pair under the experimental conditions is supported by the approximated experimental binding-energy spectra due to the split conformer orbital energies, as well as the orbital momentum distributions of the mixed conformer pair observed in the orbital cross sections of electron momentum spectroscopy.     

Binary (e,2e) spectroscopic study of carbonyl sulfide and the momentum-space chemistry of CO2, CS2 and OCS

The valence-shell binding energy spectra (8–44 eV) and molecular orbital momentum distributions of OCS have been studied by non-coplanar symmetric binary (e,2e) spectroscopy. Existing theoretical binding energy spectra calculated using the many-body 2ph-TDA Green's function (GF) method and using the symmetry-adapted cluster (SAC) on method are compared with the experiment. Intense many-body structure in the measured and calculated binding energy spectra indicates the general breakdown of the independent particle ionization picture. Experimental momentum distributions are compared with those calculated using ab initio SCF wavefunctions of minimal basis set quality and of near Hartree—Fock quality. Excellent agreement between the experimental momentum distributions and those calculated by the near Hartree—Fock wavefunction is obtained for the three innermost valence orbitals: 8σ, 7σ and 6σ. The correct order of the close lying outer-valence 2π and 9σ orbitals is unambiguously identified from the shapes of the measured momentum distributions. Momentum and position contour density maps computed from theoretical wavefunctions of near Hartree—Fock quality are used to interpret the shapes and atomic characters of the observed momentum distributions. The momentum densities of the outermost-valence antibonding π orbitals and of the outermost-valence bonding σ orbitals of the linear triatomic group: CO₂, CS₂ and OCS are compared respectively with each other. The associated chemical trends are discussed within the existing framework of momentum-space chemical principles.     

Experimental and theoretical electron momentum spectroscopic study of the valence electronic structure of tetrahydrofuran under pseudorotation

The most populated structure of tetrahydrofuran (THF) has been investigated in our previous study using electron momentum spectroscopy (EMS). Because of the relatively low impact energy (600 eV) and low energy resolution (DeltaE = 1.20 eV) in the previous experiment, only the highest occupied molecular orbital (HOMO) of THF was investigated. The present study reports the most recent high-resolution EMS of THF in the valence space for the first time. The binding energy spectra of THF are measured at 1200 and 2400 eV plus the binding energies, respectively, for a series of azimuthal angles. The experimentally obtained binding energy spectra and orbital momentum distributions (MDs) are employed to study the orbital responses of the pseudorotation motion of THF. The outer valence Greens function (OVGF), the OVGF/6-311++G** model, and density function theory (DFT)-based SAOP/et-pVQZ model are employed to simulate the binding energy spectra. The orbital momentum distributions (MDs) are produced using the DFT-based B3LYP/aug-cc-pVTZ model, incorporating thermodynamic population analysis. Good agreement between theory and experiment is achieved. Orbital MDs of valence orbitals exhibit only slight differences with respect to the impact energies at 1200 and 2400 eV, indicating validation of the plane wave impulse approximation (PWIA). The present study has further discovered that the orbital MDs of the HOMO in the low-momentum region (p < 0.70 a.u) change significantly with the pseudorotation angle, phi, giving a v-shaped cross section, whereas the innermost valence orbital of THF does not vary with pseudorotation, revealing a very different bonding mechanism from the HOMO. The present study explores an innovative approach to study pseudorotation of sugar puckering, which sheds a light to study other biological systems with low energy barriers among ring-puckering conformations.     

Efficient evaluation of nonlocal pseudopotentials via Euler exponential spline interpolation.

An Euler exponential spline (EES) based formalism is employed to derive new expressions for the electron-atom nonlocal pseudopotential interaction (NL) in electronic structure calculations performed using a plane wave basis set that can be computed more rapidly than standard techniques. Two methods, one that is evaluated by switching between real and reciprocal space via fast Fourier transforms, and another that is evaluated completely in real space, are described. The reciprocal-space or g-space-based technique, NLEES-G, scales as NMlogM approximately N2logN, where N is the number of electronic orbitals and M is the number of plane waves. The real-space based technique, NLEES-R, scales as N2. The latter can potentially be used within a maximally spatially localized orbital method to yield linear scaling, while the former could be employed within a maximally delocalized orbital method to yield NlogN scaling. This behavior is to be contrasted with standard techniques, which scale as N3. The two new approaches are validated using several examples, including solid silicon and liquid water, and demonstrated to be improvements on other, reduced-order nonlocal techniques. Indeed, the new methods have a low overhead and become more efficient than the standard technique for systems with roughly 20 or more atoms. Both NLEES methods are shown to work stably and efficiently within the Car-Parrinello ab initio molecular dynamics framework, owing to the existence of p-2 continuous derivatives of a pth-order spline.     

MRCI investigation of different isomers of Ni2O2H2(+)

The geometrical and electronic structures of different isomers of Ni(2)O(2)H(2)(+) are investigated by multireference configuration interaction (MRCI) calculations using natural atomic orbital basis sets. The lowest-lying isomer, Ni(2)(OH)(2)(+), has a rhombic shape with two OH groups bridging the Ni atoms. The next isomer in energetic order with a relative energy of 0.29 eV consists of a linear NiONi(OH(2))(+) chain. Other structures with a rhombic shape, (NiH)(2)O(2)(+), with H bound to the Ni atoms have considerably higher energies, above 4 eV. Especially the low-lying isomers are characterised by a large number of low-lying electronic terms. The product Ni(2)O(2)H(2)(+) of the reaction of Ni(2)O(2)(+) with small alkanes is likely to have the rhombic Ni(2)(OH)(2)(+) structure. The reaction energy of the reaction Ni(2)O(2)(+) + H(2)→ Ni(2)(OH)(2)(+) is estimated to be about -3.5 eV.     

Plane wave/pseudopotential implementation of excited state gradients in density functional linear response theory: a new route via implicit differentiation

This work presents the formalism and implementation of excited state nuclear forces within density functional linear response theory using a plane wave basis set. An implicit differentiation technique is developed for computing nonadiabatic coupling between Kohn-Sham molecular orbital wave functions as well as gradients of orbital energies which are then used to calculate excited state nuclear forces. The algorithm has been implemented in a plane wave/pseudopotential code taking into account only a reduced active subspace of molecular orbitals. It is demonstrated for the H(2) and N(2) molecules that the analytical gradients rapidly converge to the exact forces when the active subspace of molecular orbitals approaches completeness.