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.     

Interpretation of conformational effects on 2-endo-norborneol by natural chemical shielding analysis

This paper represents an extension of our work on the (1)H and (13)C NMR chemical shifts of norbornane and 2-endo-norborneol. NCS-NBO analysis was employed to probe contributions of bond orbitals and orbitals of lone pairs to nuclear shielding in conformers of the alcohol generated by rotation of the C-O bond. Variations in (1)H and (13)C chemical shifts with the dihedral angle are discussed in terms of Lewis and non-Lewis partitioning and their respective importance is evaluated. In addition to hyperconjugation of the lone pair in a p orbital of oxygen that was previously reported, a sizable participation of the lone pair which is in an sp orbital is also observed and their combined effect dominates the carbon chemical shifts of the C(1)-C(2)-OH and C(3)-C(2)-OH fragments. Both lone pairs on oxygen also contribute to localized, though-space effects on nuclei in the vicinity, these effects answering for the largest deviations in hydrogen chemical shifts on rotation around the C-O bond. On the other hand, for conformers in which nonbonded repulsions lead to distortions in the molecular framework, variations in chemical shifts may be attributed to angular effects.     

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.     

Photoemission and near-edge X-ray absorption fine structure studies of the bacterial surface protein layer of Bacillus sphaericus NCTC 9602

The electronic structure of the regular, two-dimensional bacterial surface protein layer of Bacillus sphaericus NCTC 9602 has been examined by photoemission (PE) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Both the O 1s and the N 1s core-level PE spectra show a single structure, whereas the C 1s core-level spectrum appears manifold, suggesting similar chemical states for each oxygen atom and also for each nitrogen atom, while carbon atoms exhibit a range of chemical environments in the different functional groups of the amino acids. This result is supported by the element-specific NEXAFS spectra of the unoccupied valence electronic states, which exhibit a series of characteristic NEXAFS peaks that can be assigned to particular molecular orbitals of the amino acids by applying a phenomenological building-block model. The relative contributions of the C-O, C-N, and C-C bond originating signals into the C 1s PE spectrum are in good agreement with the number ratios of the corresponding bonds calculated from the known primary structure of the bacterial surface protein. First interpretation of the PE spectrum of the occupied valence states is achieved on the basis of electronic density-of-states calculations performed for small peptides. It was found that mainly the pi clouds of the aromatic rings contribute to both the lowest unoccupied and the highest occupied molecular orbitals.     

Cu^2＋诱导甘氨酸质子迁移机理的理论研究

采用CCSD/6-31＋＋G＊＊//B3LYP/6-31＋＋G＊＊方法研究了Cu2＋诱导甘氨酸质子迁移的机理.优化得到了7个中性配合物和1个两性配合物,其中两性配合物最稳定,结合能为215.93 kcal mol-1.中性构型间通过分子内单键的旋转相互转化,C-N、C-C和C-O键旋转的能垒范围分别为1.62～2.49、0.27～7.80和2.27～16.97 kcal mol-1;中性构型N6经质子迁移变为两性构型,能垒为33.82 kcal mol-1.Cu2＋作用于甘氨酸,使甘氨酸N5原子负电荷减少超过0.5,降低了N5对H6原子的库仑吸引,钝化了共价键B（O3–H6）,动力学上不利于H6质子迁移;但是H6质子迁移后,形成的两性构型Z1却是热力学最稳定体系.     

The rotational barrier in ethane: a molecular orbital study

The energy change on each Occupied Molecular Orbital as a function of rotation about the C-C bond in ethane was studied using the B3LYP, mPWB95 functional and MP2 methods with different basis sets. Also, the effect of the ZPE on rotational barrier was analyzed. We have found that σ and π energies contribution stabilize a staggered conformation. The σ(s) molecular orbital stabilizes the staggered conformation while the stabilizes the eclipsed conformation and destabilize the staggered conformation. The π(z) and molecular orbitals stabilize both the eclipsed and staggered conformations, which are destabilized by the π(v) and molecular orbitals. The results show that the method of calculation has the effect of changing the behavior of the energy change in each Occupied Molecular Orbital energy as a function of the angle of rotation about the C-C bond in ethane. Finally, we found that if the molecular orbital energy contribution is deleted from the rotational energy, an inversion in conformational preference occurs.     

New diagnostic of the most populated conformer of tetrahydrofuran in the gas phase

The most populated conformer of tetrahydrofuran (C(4)H(8)O) has been diagnosed as the Cs conformer in the present study, jointly using experimental electron momentum spectroscopy (EMS) and quantum mechanics. Our B3LYP/6-311++G** model indicates that the C1 conformation, which is one of the three possible conformations of tetrahydrofuran produced by pseudorotation in the gas phase, is a transition state due to its imaginary frequencies, in agreement with the prediction from a recent ab initio MP2/aug-cc-pVTZ study (J. Chem. Phys. 2005, 122, 204303). The study has identified the fingerprint of the highest occupied molecular orbital (HOMO) of the C(s) (12a') conformer as the most populated conformer. The identification of the C(s) structure, therefore, leads to the orbital-based assignment of the ionization binding energy spectra of tetrahydrofuran for the first time, on the basis of the outer valence Green function OVGF/6-31G* model and the density functional theory (DFT) SAOP/ET-PVQZ model. The present study explores an innovative approach to study molecular stabilities. It also indicates that energetic properties are not always the most appropriate means to study conformer-rich biological systems.     

Investigation of valence orbitals of propene by electron momentum spectroscopy

The binding energy spectra and momentum distributions of all valence orbitals of propene were studied by electron momentum spectroscopy (EMS) as well as Hartree-Fock and density functional theoretical calculations. The experiment was carried out at impact energies of 1200 eV and 600 eV on the state-of-the-art EMS spectrometer developed at Tsinghua University recently. The experimental momentum profiles of the valence orbitals were obtained and compared with the various theoretical calculations. Moreover, the experiment with a new analysis method presents a strong support for the correct ordering of the orbital 8a' and 1a', i.e., 9a' < 8a' < 1a' < 7a'.     

Valence electronic structures of CH2BrCl and CF2BrCl: binding energy spectra and electron momentum distributions

The binding energy spectra (BES) of valence shells of CH2BrCl and CF2BrCl have been measured at a series of different azimuthal angles by an (e, 2e) electron momentum spectrometer employing noncoplanar symmetric geometry at an impact energy of 1200 eV plus binding energy. The experimental momentum profiles (XMPs) are extracted from the sequential BES and compared with the theoretical ones calculated by using Hartree-Fock (HF) and density functional theory (DFT-B3LYP) calculations with 6-311G, 6-311++G**, and aug-cc-pVTZ basis sets. In general, the DFT-B3LYP calculations using the larger basis sets 6-311++G** and aug-cc-pVTZ describe the XMPs well for both molecules. Moreover, the pole strengths of main ionizations from the inner valence orbitals 2a', 3a', and 1a' of CH2BrCl are determined, and the controversial ordering of two outer valence orbitals 3a' ' and 6a' of CF2BrCl has also been assigned unambiguously.     

Methyl 3-methyl-2H-azirine-2-carboxylate photochemistry studied by matrix-isolation FTIR and DFT calculations

The aliphatic 2H-azirine, methyl 3-methyl-2H-azirine-2-carboxylate (MMAC), has been synthesized and its monomeric form investigated by IR spectroscopy in an argon matrix, at 10 K, as well as theoretically (DFT/B3LYP/6-311++G(d,p)). Two low-energy conformers of MMAC (Ct and Cc) were found in the matrix, both exhibiting the cis conformation around the C-O bond but differing in the arrangement around the C-C(alpha) bond. The two conformers were photoreactive upon in situ broadband UV excitation (lambda > 235 nm), yielding nitrile ylide (P1) and ketene imine (P2) type products, which resulted from cleavage of the C-C or C-N bond, respectively. The kinetics of the reactions leading to the formation of P1 and P2 are of first order, with the processes being favored when the reactant is in the Cc conformation. Very interestingly, the C-N bond photocleavage, which is unusual for aliphatic 2H-azirines, was found to be preferred over the generally favored in 2H-azirines C-C bond breakage. This behavior is attributed to the presence in the molecule of the electron-withdrawing methoxycarbonyl substituent, which accelerates the intersystem crossing toward the T(1) triplet state and, in this way, favors the C-N bond cleavage. In addition to the primary photoprocesses leading to formation of P1 and P2, secondary photoprocesses leading to the decarboxylation and decarbonylation of P2 have been also observed.     

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.     

Ionization Energies and Dyson Orbials of Allyl Alcohol and Allyl Mercaptan Conformers

The conformers of allyl alcohol and allyl mercaptan were studied with B3LYP/aug-cc-pVTZ method. Their relative energies were calculated at MP3, MP4(SDQ), and CCSD(T) levels. The most stable conformers for these two molecules are Gauche-gauche' (Gg'). The theo-retical photoelectron spectra simulated with the calculated ionization energies demonstrate that there are at least four conformers in allyl alcohol and four conformers in allyl mercaptan in the gas-phase experiments. The Dyson orbitals of the highest occupied molecular orbital (HOMO) and the next HOMO (HOMO-1) of allyl mercaptan Gg' conformer show strongly mixing n_S and π_C=C characteristics, which may be due to the resonance and inductive effects between π_C=C and n_S in HOMO-1 and HOMO.     

Why is there a molecular relativistic effect?

The almost exclusive association of the molecular geometry dependence of the relativistic correction with the valence orbital contribution to the mass-velocity and Darwin terms is investigated using SCF and MCSCF wavefunctions. The requirement of orthogonality of the valence orbitals to the core orbitals is confirmed to be the mechanism responsible for the increase in (the absolute value of) relativistic energy upon decrease of the internuclear distance. Certain “fingerprint”-type features of the valence relativistic correction, revealing the identity of the particular core orbital giving rise to it, are identified.     

A “double-zeta” type wavefunction for an organometallic: Bis-(π-allyl)nickel

A wavefunction which is of double-zeta quality at the level of the valence orbitals [based on a (11, 7, 5/8, 4/4) gaussian basis set contracted to (4, 3, 2/3, 2/2)] is reported for thebis-(π-allyl)nickel molecule. Independant SCF calculations for two ionized states substantiate the conclusion reached previously for a number of organometallics with a minimal basis set that Koopmans' theorem is not valid for these molecules, namely that the highest occupied orbital from the ground state calculation for the neutral molecule is mostly a ligand π orbital whereas the lowest ionization potential corresponds to the removal of an electron from a molecular orbital which is mostly a metal 3d orbital. The nature of the bonding inbis-(π-allyl)nickel is discussed on the basis of the possible interactions between the metal orbitals and the π orbitals of the allyl group. The interaction between the filled nonbonding π orbital of the allyl group and the empty 3d _xz orbital of the Ni atom appears responsible for most of the bonding, together with some backbonding through an interaction between the 3d x ²?y ²and 3d xyorbitals and the σ and π orbitals of the ligands. The computed value for the rotation barrier about the C-C allyl bond, 90 kcal/mole, rules out this rotation as one of the possible mechanisms which account for the equivalence of the terminal hydrogens in the proton magnetic resonance spectra of π-allyl complexes.     

Conformation-specific Raman bands and electronic conjugation in substituted thioanisoles

Nonresonant Raman spectra and conformational stability are studied for thioanisole (TA) and substituted analogues [4-XTA, X = NO(2) (1), CN (2), H (3), CH(3) (4), and NH(2) (5)] at the 4-position. The ring-substituent (SCH(3)) vibrational modes of out-of-plane bending and torsional types are calculated to have strong Raman scattering activities only for the vertical conformers. Agreement between observed and calculated Raman spectra is analyzed numerically. The conformational stability of the SCH(3) rotation changes systematically to the electron-withdrawing character of the substituents. The rotational barrier is calculated satisfactorily by B3LYP/6-31++G(d,p) calculations, whereas the second- to fourth-order M?ller-Presset perturbation theory and coupled-cluster with single- and double-excitation calculations tend to overestimate conformational energy barriers with respect to coplanar forms. The coplanar form is obtained for 1 and 2, whereas the vertical conformer is favorable for 4 and 5. The origin of the conformational energy difference, DeltaE, is demonstrated on the basis of canonical molecular orbitals and natural bond orbitals (NBOs) of the ground state. The natural bond orbital interaction between a nonbonding n(S) orbital of the S atom and a pi orbital of the benzene ring is shown to stabilize the coplanar form predominantly. A linear relationship is obtained between the energy of the highest occupied molecular orbitals and DeltaE. The n(S)-pi interaction energy, E(2), based on the NBO representation and the Hammet constants also change linearly with respect to DeltaE.     

Molecule intrinsic minimal basis sets. I. Exact resolution of ab initio optimized molecular orbitals in terms of deformed atomic minimal-basis orbitals

A method is presented for expressing the occupied self-consistent-field (SCF) orbitals of a molecule exactly in terms of chemically deformed atomic minimal-basis-set orbitals that deviate as little as possible from free-atom SCF minimal-basis orbitals. The molecular orbitals referred to are the exact SCF orbitals, the free-atom orbitals referred to are the exact atomic SCF orbitals, and the formulation of the deformed "quasiatomic minimal-basis-sets" is independent of the calculational atomic orbital basis used. The resulting resolution of molecular orbitals in terms of quasiatomic minimal basis set orbitals is therefore intrinsic to the exact molecular wave functions. The deformations are analyzed in terms of interatomic contributions. The Mulliken population analysis is formulated in terms of the quasiatomic minimal-basis orbitals. In the virtual SCF orbital space the method leads to a quantitative ab initio formulation of the qualitative model of virtual valence orbitals, which are useful for calculating electron correlation and the interpretation of reactions. The method is applicable to Kohn-Sham density functional theory orbitals and is easily generalized to valence MCSCF orbitals.     

Photoelectron spectroscopy of the doubly-charged anions [MIVO(mnt)2]2- (M = Mo, W; mnt = S2C2(CN)2(2-): access to the ground and excited states of the [MVO(mnt)2]- anion

Photodetachment photoelectron spectroscopy was used to investigate the electronic structure of the doubly charged complexes [MIVO(mnt)2]2- (M = Mo, W; mnt = 1,2-dicyanoethenedithiolato). These dianions are stable in the gas phase and are minimal models for the active sites of the dimethyl sulfoxide reductase family of molybdenum enzymes and of related tungsten enzymes. Adiabatic and vertical electron binding energies for both species were measured, providing detailed information about molecular orbital energy levels of the parent dianions as well as the ground and excited states of the product anions [MVO(mnt)2]-. Density functional theory calculations were used to assist assignment of the detachment features. Differences in energy between these features provided the energies of ligand-to-metal charge-transfer transitions from S(pi) and S(sigma) molecular orbitals to the singly occupied metal-based orbital of the products [MVO(mnt)2]-. These unique data for the M(V) species were obtained at the C(2)(v)() geometry of the parent M(IV) dianions. However, theoretical calculations and available condensed phase data suggested that a geometry featuring differentially folded dithiolene ligands (Cs point symmetry) was slightly lower in energy. The driving force for ligand folding is a favorable covalent interaction between the singly occupied metal-based molecular orbital (a1 in C2v) point symmetry; highest occupied molecular orbital (HOMO)) and the least stable of the occupied sulfur-based molecular orbitals (b1 in C2v point symmetry, HOMO-1) that is only possible upon reduction to the lower symmetry. This ligand folding induces a large increase in the intensity predicted for the a' S(pi) --> a' dx2 - y2 charge-transfer transition originating from the HOMO-2 of [MVO(mnt)2](-) under Cs point symmetry. Electronic absorption spectra are available for the related species [MoVO(bdt)2]- (bdt = 1,2-benzenedithiolato) and for the oxidized form of dimethyl sulfoxide reductase. The intense absorptions at approximately 1.7 eV have been assigned previously to S(sigma) --> Mo transitions, assuming C2v geometry. The present work indicates that the alternative a' S(pi) --> a' dx2 - y2 of Cs geometry must be considered. Overall, this study confirms that the electronic structure of the M-dithiolene units are exquisitely sensitive to dithiolene ligand folding, reinforcing the proposal that these units are tunable conduits for electron transfer in enzyme systems.     

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.     

Electronic structures of acyl nitrites and nitrates

The gas phase electronic structures of CM(3)C(O)ONO and CM(3)C(O)ONO(2) (M=H, Cl, F) are studied by photoelectron spectroscopy (PES) combined with the outer valence Green's function (OVGF) calculations at 6-311+G(d, p) basis sets. The highest occupied molecular orbital (HOMO) for each compound is the carbonyl oxygen lone pair (n(O)), the ionizations of these orbitals are associated with the vibrational frequency about 1750 and 1820 cm(-1) reflected on the first band, respectively, for acyl nitrites and nitrate. Comparing with the calculated energies, it can be concluded that the syn conformers with Cs overall symmetry, a planar CC(O)ONO skeleton in nitrites, and a planar CC(O)ON skeleton in nitrates, respectively, are the most stable in the gas phase.