Imaging Molecular Orbitals of Single Picene Molecules Adsorbed on Cu（111） Surface： a Combined Experimental and Theoretical Study

Picene, which attracts the great interest of researchers, not only can be used to fabricate thin film transistors with high hole mobilities, but also is the parent material of a new type organic superconductor. Here, we investigate the electronic properties of individual picene molecules directly adsorbed on Cu（111） surface by a combination of experimental scanning tunneling microscopy/spectroscopy measurements and theoretical calculations based on the density functional theory. At low coverage, the picene molecules exhibit mono-dispersed adsorption behavior with the benzene ring planes parallel to the surface. The highest occupied state around -1.2 V and the lowest unoccupied state around 1.6 V with an obvious energy gap of the singly adsorbed picene molecule are identified by the dI/dV spectra and maps. In addition, we observe the strong dependence of the dI/dV signal of the unoccupied states on the intramolecular positions. Our first-principles calculations reproduce the above experimental results and interpret them as a specific molecule-substrate interaction and energy/spatial distributions of hybrid states mainly derived from different molecular orbitals of picene with some intermixing between them. This work provides direct information on the local electronic structure of individual picene on a metallic substrate and will facilitate the understanding the dependence of electron transport properties on the coupling between molecules and metal electrodes in single-molecule devices.

VALENCE STATE OF C AtOMS AND σ_t-η_n SEPARABILITY OF MOLECULAR ORBITALS IN THE (BUCKMINSTER)FULLERENE C_(50)

The valence state of C atoms and the structure of molecular orbitals of the (Buckminster)Fullerene C_(60)have been demonstrated. It has been shown that when a motion-coordinate system is adopted, in which the coordinate origin is at every C atom, the z axis is in the direction of the normal and the (x,y) axes are in the direction of tangents of C_(60)'s spherical surface, 240 valence atomic orbitals of C_(60) can be divided into two groups. All (P_x, P_y)atomic orbitals named as Pt ones and all the other P_z atomic orbitals named as p. ones, That is to say that if we name the molecular orbital linearly combined of P_t atomic orbitals as σ_t and the molecular orbital linearly combined of P_n atomic orbitals as π_n, the 240 valence molecular orbitals are of the property of σ_t-π_n separability. It has also been shown that the frontier and nearby frontier molecular orbitals are π_n ones, and therefore the essential physical and chemical properties of C_(60) are determined by its π_n molecular orbitals.

Conformation effects on the molecular orbitals of serine

This paper calculates the five most stable conformers of serine with Hartree-Fock theory, density functional theory （B3LYP）, Moller-Plesset perturbation theory （MP4（SDQ）） and electron propagation theory with the 6-311＋＋G（2d,2p） basis set. The calculated vertical ionization energies for the valence molecular orbitals of each conformer are in agreement with the experimental data, indicating that a range of molecular conformations would coexist in an equilibrium sample. Information of the five outer valence molecular orbitals for each conformer is explored in coordinate and momentum spaces using dual space analysis to investigate the conformational processes, which are generated from the global minimum conformer Serl by rotation of C2-C3 （Ser4）, C1 C2 （Ser5） and C1-O2 （Set2 and Ser3）. Orbitals 28a, 27a and 26a are identified as the fingerprint orbitals for all the conformational processes.

Role of highest occupied molecular orbitals in molecular field-free alignment by a femtosecond pulse

This paper studies the molecular rotational excitation and field-free spatial alignment in a nonresonant intense laser field numerically and analytically by using the time-dependent SchrSdinger equation. The broad rotational wave packets excited by the femtosecond pulse are defined in conjugate angle space, and their coefficients are obtained by solving a set of coupled linear equations. Both single molecule orientation angles and an ensemble of O2 and CO molecule angular distributions are calculated in detail. The numerical results show that, for single molecule highest occupied molecular orbital （HOMO） symmetry σ tends to have a molecular orientation along the laser polarization direction and the permanent dipole moment diminishes the mean of the orientation angles; for an ensemble of molecules, angular distributions provide more complex and additional information at times where there are no revivals in the single molecule plot. In particular, at the revival peak instant, with the increase of temperature of the molecular ensemble, the anisotropic angular distributions with respect to the laser polarization direction of the πg orbital gradually transform to the symmetrical distributions regarding the laser polarization vector and for two HOMO configurations angular distributions of all directions are confined within a smaller angle when the temperature of the molecular ensemble is higher.

Assessment of delocalized and localized molecular orbitals through electron momentum spectroscopy

Recently, there was a hot controversy about the concept of localized orbitals, which was triggered by Grushow＇s work titled ＂Is it time to retire the hybrid atomic orbital？＂ [J. Chem. Educ. 88, 860 （2011）]. To clarify the issue, we assess the delocalized and localized molecular orbitals from an experimental view using electron momentum spectroscopy. The delocalized and localized molecular orbitals based on various theoretical models for CH4, NH3, and H20 are compared with the experimental momentum distributions. Our results show that the delocalized molecular orbitals rather than the localized ones can give a direct interpretation of the experimental （e, 2e） results.

Coordination of neighboring C——H bond to transition metal center——III. Study on localized molecular orbitals of the binucleate ion [Fe_2(CH_3)(CO) (Ph_2pCH_2PPh_2)Cp_2]^+

A localized INDO method was used to calculate the ion [Fe_2 (CH_3) (CO) (Ph_2PCH_2PPh_2)- Cp_2]^+. Based on the analysis of the localized molecular orbitals (LMO), bond orders and contour maps, it was pointed out that the LMO no. 20 corresponds to the coordination of C(1)-H(I) σbond to Fe(2) atom. Non occurrence of metal-metal bond between Fe(1) and Fe(2) atoms was found and the covalence of irons was numerated, which coincides with the value in ref 17.

Direct Imaging of Molecular Orbitals of Metal Phthalocyanines on Metal Surfaces with an O2-Functionalized Tip of a Scanning Tunneling Microscope

High-resolution scanning tunneling microscope images of iron phthalocyanine and zinc phthalocyanine molecules on Au（111） have been obtained using a functionalized tip of a scanning tunneling microscope （STM）, and show rich intramolecular features that are not observed using clean tips. Ab initio density functional theory calculations and extended Huckel theory calculations revealed that the imaging of detailed electronic states is due specifically to the decoration of the STM tip with O2. The detailed structures are differentiated only when interacting with the highly directional orbitals of the oxygen molecules adsorbed on a truncated, [111]-oriented tungsten tip. Our results indicate a method for increasing the resolution in generic scans and thus, have potential applications in fundamental research based on high-resolution electronic states of molecules on metals, concerning, for example, chemical reactions, and catalysis mechanisms.

Investigating molecular orbitals with submolecular precision on pristine sites and single atomic vacancies of monolayer h-BN

Understanding the influence of adsorption sites to the electronic properties of adsorbed molecules on two-dimensional(2D)ultrathin insulator is of essential importance for future organic-inorganic hybrid nanodevices.Here,the adsorption and electronic states of manganese phthalocyanine(MnPc)on a single layer of hexagonal boron nitride(h-BN)have been comprehensively studied by low-temperature scanning tunneling microscopy/spectroscopy and tight binding calculations.The frontier orbitals of the MnPc can change drastically by reversible manipulation of individual MnPc molecules onto and away from the single atomic vacancies at the h-BN surface.Particularly,the change of the molecular electronic configuration can be controlled depending on whether the atomic vacancy is below the metal center or the ligand of the MnPc.These findings give new insight into defect-engineering of the organic-inorganic hybrid nanodevices down to submolecular level.

S-matrix study on alignment dependence of single ionization of molecular ions with different active orbitals

The single ionization rate of the diatomic molecular ion H2^＋ with different active orbitals in an intense field is studied by using S-matrix theory. Our results show that the orientation-dependent single ionization probability of H2^＋ is greatly dependent on the symmetry and the electron density distribution of its initial states, and it can be used to identify the excited state of the molecular ion in the dissociation process.

Understanding Bonding Nature ofα-Keggin Polyoxometalates[XW_(12)O_(40)]^(n−)(X=Al,Si,P,S):A Generalized Superatomic Perspective

α-Keggin polyoxometalates(POMs)[XW_(12)O_(40)]^(n−)(X=Al,Si,P,S)are widely used in batteries owing to their remarkable redox activity.However,the mechanism underlying the applications appears inconsistent with the widely accepted covalent bonding nature.Here,first-principles calculations show that XW_(12)are core–shell structures composed of a shell and an XO_(4)^(n−)core,both are stabilized by covalent interactions.Interestingly,owing to the presence of a substantial number of electrons in W_(12)O_(36)shell,the frontier molecular orbitals of XW_(12)are not only strongly delocalized but also exhibit superatomic properties with high-angular momentum electrons that do not conform to the Jellium model.Detailed analysis indicates that energetically high lying filled molecular orbitals(MOs)have reached unusually high-angular momentum characterized by quantum number K or higher,allowing for the accommodation of numerous electrons.This attribute confers strong electron acceptor ability and redox activity to XW_(12).Moreover,electrons added to XW_(12)still occupy the K orbitals and will not cause rearrangement of the MOs,thereby maintaining the stability of these structures.Our findings highlight the structure–activity relationship and provide a direction for tailor-made POMs with specific properties at atomic level.

Biomedical overview of melanin.2.Updating molecular modeling,synthesis mechanism,and supramolecular properties regarding melanoma therapy

Melanins represent one of the most ancient and important group of natural macromolecular pigments.They have multiple biological roles in almost all organisms across the Phyla,examples being photoprotection,anti-oxidative action,radical scavenger activity,and heavy metal removal.From the biomedical point of view,melanocytes are involved in the origin of melanoma tumors,and the main therapeutic advances for their treatment have been revised in Part 1 of this review.The chemical structure of eumelanin is a biological concern of great importance,and therefore,exploring theoretical molecular models and synthesis mechanisms will be here described,as well as molecular orbital features and supramolecular organization,which are responsible for the key properties that make these biological pigments so important,and so fascinating.Ultimately,this updated overview is devoted to describe present structural models and physico-chemical characteristics of eumelanin,in order to explain and utilize melanin properties on which new photothermal and ultrasonic protocols for melanoma treatment can be devised and applied.

SEMI-EMPIRICAL CALCULATION FOR ELECTRONIC STRUCTURE OF C60 CLUSTER BY MOLECULAR DYNAMICS AND MNDO APPROACH

The electronic structure for C 60 was semi empirically investigated by using MD (molecular dynamics) and MNDO (modified neglect of diatomic overlap) approach of quantum chemistry.Especially,taking both σ and π orbitals into account,one electron energy levels,those symmetries and π orbital occupancies as well as electron excitation energies for different select rules,cohesive energy,ionization energies and electronic affinity forces were calculated.The obtained molecular orbital ratio shows a wide separation of σ and π types,and near HOMO and LUMO levels there are π orbitals mainly.The calculated semi empirical calculation results are in good agreement with experimental and ab initio calculation data.

Maximum Overlap Symmetry Molecular Orbital Calculation under CNDO／2 Approximation

A basic calculation procedure for the MOSMO method under CNDO/2 approximation is presented in this paper,and performed by using the same parameters as those used in the ordinary CNDO/2 LCAO-MO calculation.The calculated results on the whole are close to those obtained by use of the ordinary CNDO/2 LCAO-MO calculation,illustrating that the presented procedure is reasonable.Due to its simplicity,the presented calculation procedure may be feasible even in very large molecular s ystems.

Strength of Intramolecular Hydrogen Bonds

The concept of resonance-assisted hydrogen bonds(RAHBs)highlights the synergistic interplay between theπ-resonance and hydrogen bonding interactions.This concept has been well-accepted in academia and is widely used in practice.However,it has been argued that the seemingly enhanced intramolecular hydrogen bonding(IMHB)in unsaturated compounds may simply be a result of the constraints imposed by theσ-skeleton framework.Thus,it is crucial to estimate the strength of IMHBs.In this work,we used two approaches to probe the resonance effect and estimate the strength of the IMHBs in the two exemplary cases of the enol forms of acetylacetone and o-hydroxyacetophenone.One approach is the block-localized wavefunction(BLW)method,which is a variant of the ab initio valence bond(VB)theory.Using this approach,it is possible to derive the geometries and energetics with resonance shut down.The other approach is Edmiston’s truncated localized molecular orbital(TLMO)technique,which monitors the energy changes by removing the delocalization tails from localized molecular orbitals.The integrated BLW and TLMO studies confirmed that the hydrogen bonding in these two molecules is indeed enhanced byπ-resonance,and that this enhancement is not a result ofσconstraints.

Electronic Couplings for Singlet Oxygen Photosensitization and Its Molecular Orbital Overlap Description

The reaction of triplet fusion,also named triplet-triplet annihilation,has attracted a lot of research interests because of its wide applications in photocatalytic,solar cells,and bioimaging.As for the singlet oxygen photosensitization,the reactive singlet oxygen species are generated through the energy transfers from photosensitizer(PS)to ground triplet oxygen molecule.In this work,we computed the electronic coupling for singlet oxygen photosensitization using the nonadiabatic coupling from the quantum chemical calculation.Then we utilized the molecular orbital(MO)overlaps to approximate it,where the MOs were computed from isolated single molecules.As demonstrated with quantitative results,this approach well describes the distribution of the coupling strength as the function of the intermolecular distance between the sensitizer and O_(2),providing us a simple but effective way to predict the coupling of triplet fusion reactions.

APPLICATION OF MOLECULAR ORBITAL THEORY TO ANALYSIS OF PHASE STABILITY FOR ALLOYS

The critical _d vahues ( _ ) of the γ/(γ+σ).γ/(γ+μ) and γ/(γ+γ') phase boundaries in some ternar alloy phase diagrams at various temperatures are calculated by averaging the _d values of sererai selected characteristic points at the phase boundaries.Approxmate equations for the temperature dependence of the critical _d of γ/(γ+σ).γ/(γ+μ) and γ/(γ+γ') phase boundaries are established.The accuracy of the analysis is discussed in detail. It is found for the first time that the average value of the bond order _ at the phase boundaries ts also approximatelr a constant and therefore a critical average bond order _ like - can be introduced for the analysts of phase stability

LOCALIZED MOLECULAR ORBITAL STUDY ON ELECTRONIC STRUCTURES OF BOWL-SHAPED AROMATIC HYDROCARBONS

The localized molecular orbitals for typical bowl-shaped circulenes are obtained by the use of INDO-LMO method. It is found that these bowl-shaped circulenes with strained π-electron systems are still aromatic and the rim π-bonds with larger localization form reactive regions for formation of buckminsterfullerene.

Quasi-aromaticity in Cluster Chemistry Ⅲ. Localized Molecular Orbital Study on Electron-rich Cobalt-sulfur Cluster Compounds[Co_6(μ_3-X)_8L_6]￣(n+)(X=S,Se;L=PPh_3,PEt_3,CO;n=0,1)

The localized molecular orbitals and energy levels for [Co_6 (μ_3-S)_8 (PH_3)_6]￣(n+)(n=0, 1) as model molecules of the electron-rich [Co_6 (μ_3-S)_8 (PPh_3)_6]￣(n+) (n=0,1) cluster compounds have been calculated by using Edmiston-Ruedenberg energy localization scheme under the spin-unrestricted CNDO/2 approximation. It is shown that the cluster skeletons of these two isostructural molecules consist of the edge-localized two-centered two-electron (Co-S) bonds plus a pair of the skeleton electrons delocalized on the whole cluster core,leading an extra stability of the cluster core.The one-electron oxidation for the neutral molecule gives rise to a one-electron σ (Co-Co) bond.which further resonates among the three diagonal lines of the {Co_6} octahedron. The comparison between [Co_6 (μ_3-S)_8(PPh_3)_6] and [Co_6(μ_3-CO)_8(CO)_6]￣(4-) indicates that the latter possesses face-localized bridging-bonds which are further delocalized on the whole surface of the cluster octahedron by the back-donation bonds from the lone electron pairs on the Co atoms to the capping carbonyl CO ligands. The structural features of the series of the [Co6(μ_3-X)_8L_6]￣(n+)(X =S, Se; L=PPh_3,PEt_3, CO;n=0, 1) cluster compounds are briefly rationalized on the basis of the localization description as well.

Crystal Structure and Molecular Orbital Calculation of(1R,2S)-N-Methylephedine Benzoate Hydrochloride

The title compound was synthesized and its crystal structure was determined. C_(13)H(21)NO_2·HCl, orthorhombic, space group P2_12_12_1 with dimensions:a =10. 635(2), b=26.942(6), c=6.193(2), V=1774.5(8),Z=4,Mr=319. 83 and Dc=1.20g/cm￣3. The final residual factor R=0.048, Rw=0.062. The C atoms except those in rings has a distorted tetrahedron structure.The dihedral angle between the phenyl rings in the molecule is 74. 56°. There is no bond between HCl and ester.The molecules join each other by van der Waals force. Its molecular orbital calculations were carried out by means of extended Huckel molecular orbital method.

Bonding Energy of a Molecular Orbital(Ⅱ)——Ab initio Calculation

Calculation of the bonding energy of a molecular orbital for a series of small molecules has been carried out by using ab initio STO-3G method. The results obtained demonstrate that the concept of the molecular orbital bonding energy is applicable for judging whether a molecular orbital is bonding, nonbonding or antibonding besides Mulliken overlap criterion.