The equivalent potential of water molecules for electronic structure of cysteine

In order to get more reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. The first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of Cys. The process consists of three steps. First, the electronic structure of the cluster containing Cys and water molecules is calculated. Then, based on the structure, the electronic structure of Cys with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Cys with the potential of dipoles is calculated. The dipoles are adjusted so the electronic structure of Cys with the potential of dipoles is close to that of water molecules. The calculations show that the major effect of water molecules on Cys' electronic structure is lowering the occupied electronic states by about 0.032 Ry, and broadening energy gap by 16%. The effect of water molecules on the electronic structure of Cys can be simulated by dipoles potential.     

The equivalent potential of water molecules for electronic structure of lysine

In order to get more reliable electronic structures of proteins in aqueous solution, it is necessary to construct a potential of water molecules for protein’s electronic structure calculation. The lysine is a hydrophilic amino acid. It is positively charged (Lys+) in neutral water solution. The first-principles, all-electron, ab initio calcula-tions, based on the density functional theory, have been performed to construct such an equivalent potential of water molecules for lysine (Lys+). The process consists of three parts. First, the electronic structure of the cluster containing Lys+ and water molecules is calculated. By adjusting the positions of water molecules, the geometric structure of the cluster having minimum total energy is determined. Then, based on the structure, the electronic structure of Lys+ with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method. Finally, the electronic structure of Lys+ with the potential of dipoles is calculated. The dipoles are adjusted so that the electronic structure of Lys+ with the potential of dipoles is close to that of water molecules. Thus the equivalent potential of water molecules for the electronic structure of lysine is obtained. The major effect of water molecules on lysine’s electronic structure is raising the occupied eigenvalues about 0.5032 eV, and broadening energy gap 89%. The effect of water molecules on the electronic structure of lysine can be simulated by dipoles potential.     

带电荷C60分子的电子结构及其非线性光学性质

应用Su-Schrieffer-Heeget(SSH)模型研究带电荷C₆₀分子的结构和电子结构.分析所带电荷量对结构的影响,计算带不同电荷数时C₆₀分子的电子结构,进一步对三阶非线性光学极化率进行了研究.     

The equivalent potential of water molecules for electronic structure of alanine

Using ab initio calculations based on density functional theory, an equivalent potential of water molecules for the electronic structure of Ala in solution has been obtained. The calculation process consists of three steps: first, the geometric structure of Ala + nH₂O system is determined by searching for the lowest energy of the system using free cluster calculation method. Second, based on the geometric structure obtained, the electronic structure of Ala with the potential of water molecules is calculated using a self-consistent cluster-embedding method. Finally, after replacing water molecules with dipoles, the electronic structure of Ala with the potential of dipoles is calculated. The dipoles are adjusted so the electronic structure of Ala with the potential of dipoles is close to that of water molecules. The calculated results show that the main effect of water molecules is to raise the state for methyl CH₃ by about 0.14 Ry, raising all other eigenvalues by about 0.059 Ry, and widening the energy gap by about 25%. In contrast, the replacement of water molecules by dipoles is comparatively efficient, showing that the effect of water molecules on the electronic structure of Ala can be simulated by a dipole potential, which would be a shortcut calculation.     

Electronic energy exchange in high-temperature air

Kinetic processes with the participation of electronic states of atoms and molecules in air behind the shock wave front were analyzed. All metastable levels of molecular and atomic oxygen and nitrogen and nitrogen oxide molecules situated below the dissociation energy were analyzed. In high-temperature air, atom and molecule electronic states are formed in dissociation and recombination, electronic energy exchange in collisions of particles, and chemical exchange reactions. The formation of excited electronic states in the recombination of atoms and isoenergy vibrational energy transfer from highly excited vibrational levels into electronic energy is the fastest process. The quenching of metastable particles occurs in collisions between particles, dissociation and recombination, and chemical exchange reactions. A database on electronic energy exchange rate constants in high-temperature air is presented.     

Hydration effect on the electronic transport properties of oligomeric phenylene ethynylene molecular junctions

A first-principles computational method based on the hybrid density functional theory is developed to simulate the electronic transport properties of oligomeric phenylene ethynylene molecular junctions with H₂O molecules accumulated in the vicinity as recently reported by Na {\it et al.} [\wx{Nanotechnology}{18} 424001 (2007)]. The numerical results show that the hydrogen bonds between the oxygen atoms of the oligomeric phenylene ethynylene molecule and H₂O molecules result in the localisation of the molecular orbitals and lead to the lower transition peaks. The H₂O molecular chains accumulated in the vicinity of the molecular junction can not only change the electronic structure of the molecular junctions, but also open additional electronic transport pathways. The obvious influence of H₂O molecules on the electronic structure of the molecular junction and its electronic transport properties is thus demonstrated.     

Electrostatic investigation into the bonding of poly(phenylene) thiols to gold

The advancement of nanotechnology relies on the understanding of electrical connection to individual molecules. Electrostatic surface potential measurements of self-assembled monolayers can provide insight into the structural and electronic properties of molecules attached to surfaces. In this paper we report on the electrostatic potential of poly(phenylene) thiol molecules bound to gold surfaces. Kelvin force microscopy is used to probe self-assembled monolayers of a series of phenyl, biphenyl, and triphenyl thiol molecules. The dipole moments of the isolated molecules have been determined and show similar electronic trends. A difference in polarity between the isolated molecules and the electrostatic surface potential of a monolayer attached to gold reflects the electron transfer on to the bound molecule.     

Electronic States and Photoprocesses in Bichromophore Systems

We present the results of quantumchemical investigation of energy transfer in organic molecules and systems and the inferences drawn. The Förster theory has been subjected to a critical analysis in order that the energy transfer could be described in the context of the current theory of nonradiative transitions and the incorrectness of the basic premises of the Förster theory has been demonstrated. A new variant of the mechanism of electronic energy transfer on the basis of the theory of electron transitions and of the quantum mechanics of molecules has been suggested. It is shown that the interaction of the molecules of the donor and acceptor perturbs the electronic states of isolated molecules even before the excitation of the donor molecule. A characteristic feature of the manifestation of intermolecular interaction is the spatial delocalization of the wave functions of the electronic states of interacting molecules, leading to the possibility of occurrence of conventional photophysical processes with participation of the electronic states of various molecules of the bimolecular system. In experimental investigations, the result of the intermolecular nonradiative transition is recorded as evidence of the spatial transfer of the energy of electronic excitation from the donor molecule to the acceptor molecule.     

Molecular scale electronic devices using single molecules and molecular monolayers

Molecular electronic devices that utilize single molecules or molecular monolayers as active electronic components represent a promising approach in the ongoing miniaturization and integration of electronic devices. Rapid advances in technology have enabled us to engineer molecular electronic devices with diverse functionalities. Significant progress has been made in understanding charge transport in molecular systems at the single-molecule level, and concomitantly, new device concepts have emerged. This review article focuses on experimental aspects of electronic devices made with single molecules or molecular monolayers, with a primary focus on the characterization and manipulation of charge transport.     

Relaxation Processes at High Levels of Vibrational Excitation of Polyatomic Molecules in the Ground Electronic State

By the spectral and kinetic characteristics of the luminescence of vapors of polyatomic molecules (anthracene, anthraquinone, fluorenone) initiated by selective IR multiphoton excitation (IR MPE) of molecules in the ground electronic state S ₀ the relaxation processes proceeding under vibrational excitation of molecules to energies exceeding the energies of the lower excited electronic states have been investigated. The changes in the spectral and kinetic characteristics with increasing CO₂ laser energy density and vapor P _v and foreign gas pressure P _FG are analyzed. They are similar to the characteristics obtained for normal fluorescence of these molecules with changing vibrational energy E _vib content. On the basis of experimental data and model calculations it has been concluded that at the laser radiation densities used in the case of IR MPE the molecules reach energies considerably exceeding the energies of the electronic levels. It is shown that a nonadiabatic connection between the electronic states leads to the population of mixed electronic states isoenergetic to the vibrational levels of the ground electronic state and to emission of delayed luminescence spectrally identical to the normal luminescence of these molecules. It has been found that when high vibrational levels are populated, new relaxation channels, such as reverse electron relaxation, emission from high vibrational levels of the ground electronic state, and multiquantum vibrational energy transfer at collisions leading to a rapid establishment of vibrational equilibrium become important.     

Effects of partial charge-transfer solute – solvent interactions in absorption spectra of aromatic hydrocarbons in aqueous and alcoholic solutions

A method for study of charge-transfer interactions between solute molecules and solvent based on the comparison of the ratios of spectral shifts of different electronic transitions in solute molecules in chemically inert solvent is proposed. The method is applicable to molecules that do not change their dipole moment on excitation. As an example, a presence of charge transfer interactions in higher electronic states of aromatic hydrocarbons (benzene, phenanthrene, and naphthalene) dissolved in water and alcohols was demonstrated.     

A Theory of Electronic Energy Transfer in Complex Molecular Systems

The Förster theory for energy transfer is critically reviewed in the context of the present-day theory of nonradiative transitions, and the fundamental tenets of the Förster theory are shown to be erroneous. A new theory of electronic energy transfer is constructed taking into account the electronic transition theory. The intermolecular interaction between donor and acceptor molecules is assumed to perturb electron states of isolated molecules before the donor-molecule excitation. A distinguishing characteristic of the intermolecular interaction is spatial delocalization of the wave functions of electron states of the interacting molecules. It is this fact that has made it possible to realize ordinary photophysical processes between electron states of various molecules in a bimolecular system. In the experiments under study, the result of the intermolecular nonradiative photoprocess is given as evidence of electronic energy transfer from the donor molecule to the acceptor molecule.     

Design of perylene-diimides-based small-molecules semiconductors for organic solar cells

A series of perylene-diimide-based small molecules have been designed to explore their optical, electronic and charge transport properties as organic solar cell materials. The frontier molecular orbitals analysis has turned out that the vertical electronic transitions of absorption are characterised as intramolecular charge transfer between perylene diimide moieties and substituent aromatic groups. Our results suggest that the optical and electronic properties and reorganisation energies are affected by the introduction of different aromatic groups to these molecules. The calculation results showed that the designed molecules own the large longest wavelength of absorption spectrum, the oscillator strength and absorption region values. On the basis of the investigated results, the designed molecules could be used as solar cell material with intense broad absorption spectra. Furthermore, they are expected to be the promising candidates for hole and/or electron transport materials.     

ELECTRONIC TRANSITIONS OF DI-HYDROXY NAPHTHALENE MOLECULES

The electronic transitions of di-hydroxy naphthalene molecules are found to be shifted towards higher wavelength side, when hydroxyl groups are substituted in the naphthalene molecule. The changes in the position and intensity of the electronic bands depend upon the charge transfer property of the substituent. The present paper correlates the electronic transitions observed in the photoacoustic spectra of naphthalene, 1,3-dihydroxy naphthalene (DHN), 1,4-DHN and 1,5-DHN in the region 250–400 nm. The electronic transitions of these molecules have been interpreted using the optimised geometries and CNDO/S-CI methods. Assignments of the observed electronic transitions are made on the basis of radiative and non-radiative transitions. A good agreement is found between the experimental and calculated results.     

Correlation of electronic and optical transitions: Mo(CO)6 adsorbed on clean and K-preadsorbed Si(111)7 × 7

Electron energy loss spectroscopy (EELS) is used to measure the electronic structure of adsorbed Mo(CO)₆ molecules on clean and potassium-preadsorbed Si(111)7 × 7 at 82 K. The electronic structure of physisorbed MoCCO)₆ is found to be not significantly (within 0.1 eV) perturbed from that of free molecules. The implication of electronic EELS measurements to surface photochemistry is discussed in this paper.     

Electron energy loss spectroscopy (eels) of organic molecules in vapour phase: Design and fabrication of an indigenouseel spectrometer

An indigenous electron energy loss spectrometer has been designed and fabricated for the study of free molecules. The spectrometer enables the recording of low-resolution electronic spectra of molecules in the vapour phase with ready access to the vacuum ultraviolet region. Electron energy loss spectra of aliphatic alcohols and carbonyl compounds as well as of benzene derivatives have been recorded with the indigenous spectrometer and the electronic transitions in these molecules discussed. Contribution No. 274 from the Solid State and Structural Chemistry Unit, dedicated to Dr. Raja Ramanna on his 60th birthday.     

Population redistribution in optically trapped polar molecules

We investigate the rovibrational population redistribution of polar molecules in the electronic ground state induced by spontaneous emission and blackbody radiation. As a model system we use optically trapped LiCs molecules formed by photoassociation in an ultracold two-species gas. The population dynamics of vibrational and rotational states is modeled using an ab initio electric dipole moment function and experimental potential energy curves. Comparison with the evolution of the v″ = 3 electronic ground state yields good qualitative agreement. The analysis provides important input to assess applications of ultracold LiCs molecules in quantum simulation and ultracold chemistry.     

Calculation and interpretation of the vibronic spectra of pyridine and <Emphasis Type="Italic">trans</Emphasis>-1,2-di(2′-pyridyl)ethylene in the second approximation of the parametric method

The structures of pyridine and dipyridylethylene molecules in an excited state and their vibronic spectra are calculated within the second approximation of the parametric method. The system of parameters obtained, including parameters of the σ and π types, ensures a quantitative agreement between the theoretical and experimental spectra of the pyridine and dipyridylethylene molecules. This agreement indicates that the proposed model is adequate to the real structure of the molecules. The parameterization is sufficiently complete and provides a means for quantitatively modeling the vibrational structure of the spectra of complex molecules containing fragments similar to those characterized by the σπ* and ππ* transitions. It is demonstrated that, after such essential substitutions of atoms in the molecules, the system of parameters of the acene and polyene fragments retains the high stability. The vibrational structure of the electronic spectra of the pyridine and dipyridylethylene molecules is interpreted, and the changes observed in the geometry of these molecules under electronic excitation are analyzed.     

Stabilizing photoassociated Cs2 molecules by optimal control

We demonstrate theoretically that photoassociated molecules can be stabilized to deeply bound states. This process is achieved by transferring the population from the outer well to the inner well using the optimal control theory, the Cs 2 molecule is taken as an example. Numerical calculations show that weakly bound molecules formed in the outer well by a pump pulse can be compressed to the inner well via a vibrational level of the ground electronic state as an intermediary by an additionally optimized laser pulse. The positively chirped pulse can enhance the population of the target state. With a transform-limited dump pulse, nearly all the photoassociated molecules in the inner well of the excited electronic state can be transferred to the deeply vibrational level of the ground electronic state.