Theoretical study on the structures and electronic spectra of TCNE2-.

Investigations into the charge-separated states and electron-transfer transitions in tetracyanoethylene (TCNE) complexes have recently generated much interest. In this work we present theoretical calculations showing that the most stable structure of the dianion TCNE2- has D2d symmetry in vacuum as well as in the solvents dichloromethane and acetonitrile. By means of the coupled cluster linear response, we compute the vertical electronic spectrum in both the gas phase and solution. The theoretical results are compared to the experimental data and good agreement is achieved.     

Ultrafast shape recognition to search compound databases for similar molecular shapes

Finding a set of molecules, which closely resemble a given lead molecule, from a database containing potentially billions of chemical structures is an important but daunting problem. Similar molecular shapes are particularly important, given that in biology small organic molecules frequently act by binding into a defined and complex site on a macromolecule. Here, we present a new method for molecular shape comparison, named ultrafast shape recognition (USR), capable of screening billions of compounds for similar shapes using a single computer and without the need of aligning the molecules before testing for similarity. Despite its extremely fast comparison rate, USR will be shown to be highly accurate at describing, and hence comparing, molecular shapes.     

Conformational and electronic properties of a microperoxidase in aqueous solution: a computational study.

A theoretical study of the conformational properties of a small heme peptide in aqueous solution is carried out by classical, long-timescale molecular dynamics simulations. The electronic properties of this species, that is, the relative energies of its excited electronic states and the redox potential, are reproduced and related to the conformational behavior using the perturbed matrix method and basic statistical mechanics. Our results show an interesting coupling between the conformational transitions and the electronic properties. These investigations, beyond the biophysically relevant results addressing the long-standing question of the actual role of the enzyme structure on the enzyme activity, are also of some methodological interest since they offer a further computational perspective for including the electronic degrees of freedom into the modeling of rather complex molecular systems.     

A theoretical study of solvent effects on tautomerism and electronic absorption spectra of 3-hydroxy-2-mercaptopyridine and 2,3-dihydroxypyridine

The tautomerization equilibria of 3-hydroxy-2-mercaptopyridine (HMP) and 2,3-dihydroxypyridine (DHP) in vacuo and in ethanol solution have been studied using the density functional theory (DFT) at B3LYP/6-31Gd level. The results indicate that the thione form of HMP and the keto form of DHP are the most stable tautomers in the equilibrium, and the energy barrier for the thiol-thione and enol-keto proton transfer decreases significantly when the tautomerism is mediated by a specific ethanol molecule in solution. The time-dependent density functional theory--polarizable continuum model (TDDFT-PCM) calculations on all tautomers of HMP and DHP in vacuo and in ethanol have assigned the lowest pi --> pi* excitations of thione and keto tautomers to the observed absorption bands of HMP and DHP in solutions. The solvation is predicted to have relatively small effect on these pi --> pi* excitations in ethanol.     

Effect of peripheral substitution on the electronic absorption and fluorescence spectra of metal-free and zinc phthalocyanines

The effect of substituents on the position and intensity of the electronic absorption and fluorescence spectra of phthalocyanines (Pcs) was examined for 35 Pc compounds. When electron-releasing groups are bound to four alpha-benzo positions of the Pc skeleton, the B and Q bands shift to longer wavelength. Relative to this shift, the effect of introducing the same electron-releasing groups at the other four alpha positions amounts to about 1.6-2.0. Although the effect is not always clearly seen, introduction of electron-releasing groups in the beta-benzo positions of the Pc skeleton generally shifts the Q band to shorter wavelength. The effect of electron-withdrawing groups is exactly the opposite with respect to the alpha and beta positions. These effects can be reasonably explained by considering the magnitude of the atomic orbital coefficients of the carbon atoms derived from molecular orbital (MO) calculations. In addition, the following intriguing phenomena were observed in the experiments, although not all were explained theoretically: 1) the splitting of the Q band of metal-free Pcs decreases with increasing wavelength of the Q band, 2) the ring currents of Pcs with Q bands at longer wavelength are generally smaller, and 3) the absorption coefficients of the Q band of Pc compounds with 16-electron-releasing substituents are larger than those of the corresponding tetra- and octasubstituted Pcs by several tens of percent. 4) Our PPP calculations suggested that the absorption coefficient of the Q band of Pcs with more strongly electron releasing substituents is larger. 5) The second HOMO of the Pcs with the Q band at longer wavelength has b(1u) symmetry, as opposed to the a(2u) symmetry of normal Pcs. 6) Pcs showing S1 emission maxima at wavelengths longer than about 740 nm generally have quantum yields of less than 0.1.     

Computer simulation of the shape of absorption bands in electronic spectra ofJ-aggregates

The shape of absorption bands of aggregates formed by two, four, and nine molecules of a polymethine dye was calculated by the Monte-Carlo method. The energy of interaction of the molecules in the ground state was simulated using atom-atom potentials, and the energies of interaction between dipole moments of electronic transitions of the monomers were estimated by quantum-chemical methods. In the dimer aggregate the dipole moments of the electronic transitions in the monomers interact weakly; therefore, the electron absorption spectrum should be similar to that of the monomer. On going from the dimer to the aggregates consisting of four and nine monomers, the relative positions of monomers change and this, in turn, increases the energy of interaction between the dipole moments of their electronic transitions, resulting in a red shift characteristic ofJ-aggregates and narrowing of the absorption bands. Translated fromIzvestiya Akademii Nauk Seriya Khimicheskaya. No. 1, pp. 67–69, January, 1997.     

A simple scheme for calculating the energy levels and the spectra of molecular crystals

A simple matrix method for calculating the vibrational and electron energy levels and spectra in molecular crystals is proposed.     

X-ray photoelectron spectroscopy-based valence band spectra of passive films on titanium

Titanium (Ti) is always covered by thin passive films. Thus, valence band (VB) spectra, obtained using X-ray photoelectron spectroscopy (XPS), are superpositions of the VB spectra of passive films and that of the metallic Ti substrate. In this study, to obtain the VB spectra only of passive films, angular resolution (for eliminating the substrate Ti contribution) and argon ion sputtering (for removing passive films) were used along with XPS. The passive film on Ti was determined to consist of a very thin TiO₂layer with small amounts of Ti₂O₃, TiO, hydroxyl groups, and water with a thickness of 5.9 nm. The VB spectra of Ti were deconvoluted into four peak components: a peak at ~1 eV, attributed to the Ti metal substrate; a broad peak in the 3–10 eV range, mainly attributed to O 2p (~6 eV) and O 2p-Ti 3d hybridized states (~8 eV), owing to the π (non-bonding) and σ (bonding) orbitals in the passive oxide film; and a peak at ~13 eV, attributed to the 3σ orbital of O 2p as OH⁻or H₂O. The VB region spectrum between approximately 3 and 14 eV from Ti is originating from the passive film on Ti. In particular, characterization of VB spectrum obtained with a takeoff angle of less than 24° is effective to obtain VB spectrum only from the passive film on Ti. The property as n-type semiconductor of the passive film on Ti is probably higher than that of rutile TiO₂ceramics.     

Structures and electronic absorption spectra of a recently synthesised class of photodynamic therapy agents

A theoretical study was performed on a novel class of boron-containing molecules (various substituted tetraarylazadipyrromethenes), which show in vitro activity for application in photodynamic therapy. Geometric optimisation of the structures for the singlet and triplet electronic states was carried out on compounds in vacuo at the density functional level of theory, by employing the PBE0 hybrid functional and the split-valence plus polarisation basis set. The absorbance properties in the UV-visible region were examined by means of time-dependent density functional response theory, using the same functional as mentioned above. To evaluate the influence of the solvent on the excitation energies, the continuum polarisable model was applied. Calculated electronic excitations, such as those regarding the Q-like band, were found to be in good agreement (within 0.01-0.1 eV) with experimental values and experimental trends on changing both the substituents and solvent.     

Modeling of heavy-atom-ligand NMR spin-spin coupling in solution: molecular dynamics study and natural bond orbital analysis of Hg-C coupling constants

Ab initio molecular dynamics (MD) and relativistic density functional NMR methods were applied to calculate the one‐bond Hg? C NMR indirect nuclear spin–spin coupling constants (J) of [Hg(CN)₂] and [CH₃HgCl] in solution. The MD averages were obtained as J(¹⁹⁹Hg? ¹³C)=3200 and 1575 Hz, respectively. The experimental Hg? C spin–spin coupling constants of [Hg(CN)₂] in methanol and [CH₃HgCl] in DMSO are 3143 and 1674 Hz, respectively. To deal with solvent effects in the calculations, finite “droplet” models of the two systems were set up. Solvent effects in both systems lead to a strong increase of the Hg? C coupling constant. From a relativistic natural localized molecular orbital (NLMO) analysis, it was found that the degree of delocalization of the Hg 5d_σ nonbonding orbital and of the Hg? C bonding orbital between the two coupled atoms, the nature of the trans Hg? C/Cl bonding orbital, and the s character of these orbitals, exhibit trends upon solvation of the complexes that, when combined, lead to the strong increase of J(Hg? C).     

Computer simulation of band shapes in electronic absorption spectra of dimers of organic dyes

The band shapes in the absorption spectra of dimers of cyanine dyes were simulated using a combination of an empirical molecular force field for the ground state with quantum-chemical calculations of the electron excitation energy as a function of normal nuclear coordinates. The shape and the width of an absorption band strongly depend on the mutual arrangement of the monomers. If the monomers are located one directly above the other, the sublevels arising from intramolecular vibrations disappear in the spectrum, and a large hypsochromic shift of the 0-0-transition band is observed, which results mainly from through-space interaction of monomer orbitals. If the monomers are strongly shifted relative to each other, the sublevels mentioned are also absent in the spectrum, but the bathochromic shift of the 0-0-transition band is small and results from interaction of dipole moments of electron transitions. A rather broad region of intermediate structures is found between these dimer forms, where the interaction of dipole moments of electron transitions in monomers is low, and the shapes of absorption bands are similar to those of the monomers.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1705–1710, September, 1995.This work was financially supported by the Russian Foundation for Basic Research (Project No. 94-03-08539) and the International Science Foundation (Grant M1Z 000).     

呋喃查尔酮结构与电子光谱的密度泛函理论研究

在密度泛函理论的PBE1PBE/6-31G(d)水平上对呋喃查尔酮及其衍生物的几何结构进行优化计算.在获得基态稳定结构的基础上,应用含时密度泛函理论计算其电子吸收光谱,探讨了取代基和溶剂对电子吸收光谱的影响,计算结果与实验结果吻合很好,平均绝对偏差仅为3.3nm(0.04eV).结果表明,取代基的引入和溶剂极性的增大均使光谱发生红移.通过前线轨道分析,揭示了该类化合物的主要吸收峰均源自分子中HOMO→LUMO电子跃迁.     

Ab initio simulations of two‐dimensional electronic spectra: The SOS//QM/MM approach

Two‐dimensional electronic spectroscopy (2DES) is a cutting‐edge technique for investigating with high temporal resolution energy transfer, structure, and dynamics in a wide range of systems in physical chemistry, energy sciences, biophysics, and biocatalysis. However, the interpretation of 2DES is challenging and requires computational modeling. This perspective provides a roadmap for the development of computational tools that could be routinely applied to simulate 2DES spectra of multichromophoric systems active in the UV region (2DUV) using state‐of‐the‐art ab initio electronic structure methods within a quatum mechanics/molecular mechanics (QM/MM) scheme and the sum‐over‐states (SOS) approach (here called SOS//QM/MM). Multiconfigurational and multireference perturbative methods, such as the complete active space self‐consistent field and second‐order multireference perturbation theory (CASPT2) techniques, can be applied to reliably calculate the electronic properties of multichromophoric systems. Hybrid QM/MM method and molecular dynamics techniques can be used to assess environmental and conformational effects, respectively, that shape the 2D electronic spectra. DNA and proteins are important biological targets containing UV chromophores. We report ab initio simulation of 2DUV spectra of a cyclic tetrapeptide containing two interacting aromatic side chains, a model system for the study of protein structure and dynamics by means of 2DUV spectroscopy. © 2013 Wiley Periodicals, Inc.     

Nonlinear optical properties of dicyanomethylene‐derived heteroaromatic dyes: Semiempirical molecular orbital calculations and experimental investigations

The effect of conformation (E/Z isomerism), nature (donor/acceptor) of substituents, and endgroups (indandione, pyrazolone, pyrazoledione) on the molecular hyperpolarizability β_vec of dicyanomethylene (hetero)aromatic dyes is investigated by means of semiempirical (AM1, ZINDO) molecular orbital calculations. Unless Z isomers are stabilized by intramolecular hydrogen bonding, generally E conformers have larger β_vec's. Replacement of one nitrile group of the dicyanomethylene moiety by p‐aminoaryl rather than p‐R‐arylamino (R=NMe₂, MeO, H, NO₂) is found to be advantageous. Increasing the acceptor strength of 29 by successively replacing the carbonyl with dicyanovinyl groups leads to a maximum of β_vec for the derivative with one rather than two C(CN)₂ groups. With respect to endgroups, the indandione moiety generally is the least active group. Solvent effects are treated within the framework of the self‐consistent reaction field approximation. In most cases gas‐phase tendencies are either parallel or even reinforced if solvent effects are taken into account. The calculated results are compared with electric field induced second harmonic generation (EFISH) measurements. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 253–266, 2000     

Vital significance of addition of “shape similarity” between solutes to shape complementarity for more precise molecular recognition in aqueous binary solvents

Precise and specific molecular recognition is vital to living systems. Discrimination has mainly been studied by using particular host molecules (e.g., crown ethers, cyclodextrin and urea derivatives). Several studies in various fields have pointed out that the famous “lock‐and‐key theory” (the concept of shape complementarity) is, at present, insufficient for understanding precise discrimination. This seems to come from the fact that various types of intermolecular interactions are decisive in such discrimination. This Review intends to describe the novel concept that “shape similarity” between interacting solutes should be added to “shape complementarity” for more precise discrimination to be achieved. Further, the role of shape similarity between solvent and solute molecules is also described. In relation to precise molecular recognition, weak interactions, which depend on the three‐dimensional shape of substituents (shape‐specific weak interactions), are described. Possibility of alterations in solvent structures is discussed in aqueous binary solvents. DOI 10.1002/tcr.201100001     

Physical versus non-physical effective nuclear masses for non-adiabatic corrections to molecular spectra

Two types of developments for very accurate non-adiabatic corrections to rovibrational molecular energy levels, one of a formal nature and the other of a heuristic nature, lead to fundamentally different approaches for effective nuclear masses. The former yields effective masses that have non-physical interpretation at some ranges of nuclear distances. The later uses physical masses obtained from electronic structure calculations. This paper contains a brief review of the subject and proposes procedures to improve and generalize the heuristic approach. Comparisons are made of the results obtained by the two approaches for the H ${}_2$ molecule, since no further calculations were found with the proper accuracy, but some issues involving the HeH ${}^{+}$ ion and the water molecule are discussed. The conclusion is that the heuristic approach has many advantages over the formal one, namely, equivalent accuracy and physically grounded qualitative interpretation. But, moreover, it seems to be presently the only method that allows non-adiabatic calculations for well isolated states of larger molecules.     

Quantifying intermolecular interactions: guidelines for the molecular recognition toolbox

Molecular recognition events in solution are affected by many different factors that have hampered the development of an understanding of intermolecular interactions at a quantitative level. Our tendency is to partition these effects into discrete phenomenological fields that are classified, named, and divorced: aromatic interactions, cation-pi interactions, CH-O hydrogen bonds, short strong hydrogen bonds, and hydrophobic interactions to name a few.1 To progress in the field, we need to develop an integrated quantitative appreciation of the relative magnitudes of all of the different effects that might influence the molecular recognition behavior of a given system. In an effort to navigate undergraduates through the vast and sometimes contradictory literature on the subject, I have developed an approach that treats theoretical ideas and experimental observations about intermolecular interactions in the gas phase, the solid state, and solution from a single simplistic viewpoint. The key features are outlined here, and although many of the ideas will be familiar, the aim is to provide a semiquantitative thermodynamic ranking of these effects in solution at room temperature.     

Generalized electronic diabatic scheme: Diagonalizing the electronic Hamiltonian for artificial molecular systems. How do molecular meccanos move?

A quantum–classic model is presented and used to describe systems ranging from normal molecules up to electronic systems sensed in real space. The quantum system is a set of n‐electrons; a positive background in real space completes the model. A generalized electronic diabatic (GED) theory is introduced. The diabatic functions diagonalize the electronic Hamiltonian for any arrangement of the positive background. Physical quantum states are represented as linear superpositions in the diabatic basis; this latter is always fixed. For systems sensed in real space, the coefficients of the linear superposition are functions of the real space configuration coordinates. Physical changes are produced by interactions with external sources/sinks of energy. An interaction couples different diabatic states; diagonalizing the electronic Hamiltonian plus the couplings leads to new coefficients describing physical states. Among other things, these couplings can be used to simulate the effects produced by scanning tunneling microscopy, atomic force, and transmission electron microscopy on substrates located in real space. The important thing is that time–evolution in electronic Hilbert space can be related to actual motion in real space. The experiment of lateral hopping of a substrate on a metallic surface induced by vibration excitation and followed with scanning tunneling microscope is discussed. A result of the present work is that motion of molecular meccanos reflects then time–evolution in electronic Hilbert space. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

氢键对分子器件电学特性的影响

利用密度泛函理论和弹性散射格林函数方法,研究了被不同官能团取代后的联苯分子的电输运特性.计算结果表明,由于氢键的影响,使得分子的电子结构发生了变化,特别是对电子在分子结内的跃迁几率影响较大,从而直接影响了分子器件的伏安特性.