Aromatic-carbohydrate interactions: an NMR and computational study of model systems

The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar-aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl beta-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent-sugar and aromatic-sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations.     

Strategies for targeting protein-protein interactions with synthetic agents

The development of small-molecule modulators of protein-protein interactions is a formidable goal, albeit one that possesses significant potential for the discovery of novel therapeutics. Despite the daunting challenges, a variety of examples exists for the inhibition of two large protein partners with low-molecular-weight ligands. This review discusses the strategies for targeting protein-protein interactions and the state of the art in the rational design of molecules that mimic the structures and functions of their natural targets.     

Ultrafast voltammetry for probing interfacial electron transfer in molecular wires.

Electron transfer inside self-assembled monolayers made from complex redox-active oligophenylenevinylene molecular wires is examined by ultrafast cyclic voltammetry. Rate constants above 10(6) s(-1) are measured when the electroactive moieties are easily accessible to counterions from the electrolyte. These counterion movements are necessary to compensate the local charge created upon electron transfer. Conversely, if the redox center is buried within long hydrophobic diluents, the counterion movement towards the redox entity becomes rate limiting, thus drastically altering the rate magnitude and its physical meaning. This change in the mechanism is examined both for superexchange or when one electron-hopping step is involved.     

A new extension of classical molecular dynamics: An electron transfer algorithm

The molecular dynamics is one of the most widely used methods for the simulation of the properties corresponding to ionic motion. Unfortunately, classical molecular dynamics cannot be applied for electron transfer simulation. Suggested modification of the molecular dynamics allows performing the electron transfer from one particle to another during simulation runtime. All additional data structure and the corresponding algorithms are presented in this article. The method can be applied to the systems with pair Van der Waals and Coulomb interactions. Moreover, it may be extended for many‐bodied interatomic interactions. In addition, an algorithm of transference numbers calculation has been designed. This extension is not an independent method but it can be useful for simulating the systems with high concentration of electron donors and acceptors. © 2017 Wiley Periodicals, Inc.     

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: ab initio fragment molecular orbital study

The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP-cAMP with each base pair, DNA duplex with each amino acid residue, and each base pair with each residue. In addition, base-base interactions were analyzed including hydrogen bonding and stacking of DNA. In the interaction between DNA and CRP-cAMP, there was a significant charge transfer (CT) from the DNA to CRP, and this CT interaction played an important role as well as the electrostatic interactions. It is necessary to apply a quantum mechanical approach beyond the "classical" force-field approach to describe the sequence specificity. In the DNA intramolecular interaction, the dispersion interactions dominated the stabilization of the base-pair stacking interactions. Strong, attractive 1,2-stacking interactions and weak, repulsive 1,3-stacking interactions were observed. Comparison of the intramolecular interactions of free and complexed DNA revealed that the base-pairing interactions were stronger, and the stacking interactions were weaker, in the complexed structure. Therefore, the DNA duplex stability appears to change due to both the electrostatic and the CT interactions that take place under conditions of DNA-CRP binding.     

Quantum chemical approach to electron transfer in molecular systems

A theoretical treatment of electron transfer in and between molecules is presented. The nuclei are assumed to move classically. A time-dependent electron probability density is calculated using general equations given by Nikitin. Variational methods of different kinds may be employed in these equations. In the present paper some examples are studied at the extended Hückel level for the systems H₂-H ₂ ⁺ , H₂-O^2–-H ₂ ⁺ , H₂-S^2–-H ₂ ⁺ and H₂-H₂-H ₂ ⁺ .     

Non-adiabatic molecular dynamics simulation of ultrafast solar cell electron transfer

A non-adiabatic (NA) molecular dynamics (MD) simulation of the photoinduced electron transfer (ET) from a molecular electron donor to the TiO₂ acceptor is carried out. The system under study is typical of the dye sensitized semiconductor nanomaterials used in solar cells, photocatalysis and photoelectrolysis. The electronic structure of the dye-semiconductor system and the adiabatic dynamics are simulated by ab initio density functional theory MD, while the NA effects are incorporated by the quantum-classical mean-field approach. A novel procedure separating the NA and adiabatic ET pathways is developed. The simulation provides a detailed picture of the ET process. For the specific system under study, ET occurs on a 30 fs time scale, in agreement with the ultrafast experimental data. Both adiabatic and NA pathways for the ET are observed. The NA transfer entirely dominates at short times and can occur due to strong localized avoided crossing as well as extended regions of weaker NA coupling. Although the adiabatic ET contribution accumulates more slowly, it approaches that of the NA ET pathway asymptotically. The electron acceptor states are formed by the d-orbital of Ti atoms of the semiconductor and are localized within the first 3–4 layers of the surface. About 20% of the acceptor state density is localized on a single Ti atom of the first surface layer. The simulation predicts a complex non-single-exponential time dependence of the ET process.     

Theoretical study on electron transfer in biological systems (III)

Iritramolwular electron transfer of nlctal-containing spiro π-electron system was studied by AM1 method in the MOPAC-ET program developed by the present group. The results indicated that with the increasing of the outer electric field F, the activation energy of the reaction decreased. When F reaches a certain threshold value, the activation energy barrirr becomcs zero and the rate of reaction achieves the largest value. The results also indicated that electron transfer matrix elements V_AB and reorganization energy λ were not obviously affected by outer electric field while the exothermicity ΔE was directly proportional to it.     

Theoretical investigation of electron transfer transition in tetracyanoethylene-contained organic complexes

In this work, the authors use complete active space self-consistent field method to investigate the photoinduced charge-separated states and the electron transfer transition in complexes ethylene-tetracyanoethylene and tetramethylethylene-tetracyanoethylene. Geometries of isolated tetracyanoethylene, ethylene, and tetramethylethylene have been optimized. The ground state and the low-lying excited states of ethylene and tetracyanoethylene have been optimized. The state energies in the gas phase have been obtained and compared with the experimentally observed values. The torsion barrier of tetracyanoethylene has been investigated through the state energy calculation at different conformations. Attention has been particularly paid to the charge-separated states and the electron transfer transition of complexes. The stacked conformations of the donor-acceptor complexes have been chosen for the optimization of the ground and low-lying excited states. Equilibrium solvation has been considered by means of conductor-like screening model both in water and in dichloromethane. It has been found that the donor and tetracyanoethylene remain neutral in complexes in ground state (1)A(1) and in lowest triplet state (3)B(1), but charge separation appears in excited singlet state (1)B(1). Through the correction of nonequilibrium solvation energy based on the spherical cavity approximation, pi-->pi* electron transfer transition energies have been obtained. Compared with the experimental measurements in dichloromethane, the theoretical results in the same solvent are found higher by about 0.5 eV.     

Processing energy and signals by molecular and supramolecular systems

Any kind of device or machine requires a substrate, energy, and information signals. If we wish to operate at the nanometer scale, we must use molecules as substrates. Energy- and signal-processing at a molecular level relies on cause/effect relationships between the input supplied and the kind of process obtained. We have classified energy- and signal-processing at the molecular level according to the nature of the input (electronic, photonic, or chemical) and the nature of the obtained effect (electronic, photonic, or chemical process that follows). By coupling the three kinds of inputs with the three types of resulting processes, nine types of molecular-based processes (electronic, photonic, chemionic, electrophotonic, electrochemionic, photoelectronic, photochemionic, chemiophotonic, and chemioelectronic) can be identified. In this concept article, looking at molecular transformations in an unconventional way, we have tried to give a flavor of some of the new features that project the old science of chemistry towards novel achievements.     

Biosensors based on direct electron transfer in redox proteins

In biosensors based on direct electron transfer in redox proteins, efficient electron-transfer pathways between the immobilized redox protein and the electrode surface have to be established so to allow a fast electron transfer and concomitantly avoiding free-diffusing redox species. In this review, prerequisites for the direct electron transfer of redox proteins and immobilization of redox proteins on the electrode surfaces are addressed. Based on the specific nature of different proteins and non-manual immobilization procedures, possible biosensor designs are discussed, namely biosensors based on (1) ferritin; (2) cytochrome c; (3) myoglobin; (4) hemoglobin; (5) horseradish peroxidase; (6) catalase; (7) glucose oxidase; and (8) xanthine oxidase.     

Photosensitized oxidation of sulfides: discriminating between the singlet-oxygen mechanism and electron transfer involving superoxide anion or molecular oxygen

The oxidation of diethyl and diphenyl sulfide photosensitized by dicyanoanthracene (DCA), N-methylquinolinium tetrafluoroborate (NMQ(+)), and triphenylpyrylium tetrafluoroborate (TPP(+)) has been explored by steady-state and laser flash photolysis studies in acetonitrile, methanol, and 1,2-dichloroethane. In the Et(2)S/DCA system sulfide-enhanced intersystem crossing leads to generation of (1)O(2), which eventually gives the sulfoxide via a persulfoxide; this mechanism plays no role with Ph(2)S, though enhanced formation of (3)DCA has been demonstrated. In all other cases an electron-transfer (ET) mechanism is involved. Electron-transfer sulfoxidation occurs with efficiency essentially independent of the sulfide structure, is subject to quenching by benzoquinone, and does not lead to Ph(2)SO cooxidation. Formation of the radical cations R(2)S(*+) has been assessed by flash photolysis (medium-dependent yield, dichloroethane>CH(3)CN>CH(3)OH) and confirmed by quenching with 1,4-dimethoxybenzene. Electron-transfer oxidations occur both when the superoxide anion is generated by the reduced sensitizer (DCA(*-), NMQ(*)) and when this is not the case (TPP(*)). Although it is possible that different mechanisms operate with different ET sensitizers, a plausible unitary mechanism can be proposed. This considers that reaction between R(2)S(*+) and O(2)(*-) mainly involves back electron transfer, whereas sulfoxidation results primarily from the reaction of the sulfide radical cation with molecular oxygen. Calculations indeed show that the initially formed fleeting complex RS(2)(+)...O-O(*) adds to a sulfide molecule and gives strongly stabilized R(2)S-O(*)-(+)O-SR(2) via an accessible transition state. This intermediate gives the sulfoxide, probably via a radical cation chain path. This mechanism explains the larger scope of ET sulfoxidation with respect to the singlet-oxygen process.     

Intermolecular and intramolecular electron transfer from eosin ester to viologen

The covalently -(CH2)10- linked eosin-butylviologen compound has been synthesized. The photoinduced electron transfer of eosin ester and butylviologen as well as the influence of addition of cyclodextrin or amylose into the solution of linked compound on the system have been studied by the absorption spectra, fluorescence spectra and fluorescence lifetime. The results indicated that the intramolecular electron transfer is much more efficient than the intermolecular one. Due to the formation of inclusion complex, the process of intramolecular electron transfer was changed after adding cydodextrin or amylose.     

环糊精与烷基钴配合物分子识别作用的DFT研究

用密度泛函理论(DFT)的B3LYP方法对Costa型烷基钴配合物[n-C6H13Co(C11H19N4O2)·H2O]+(A)和烷基钴肟配合物n-C6H13Co(C8H14N4O4)·H2O(B)进行计算研究,探讨了环糊精对它们的分子识别作用与其电荷分布之间的关系.结果表明,由于A和B的轴向烷基都是中性的,而且它们的烷基均插入环糊精腔内,而使A或B与环糊精形成包结物,因此,在环糊精边上修饰负离子不能加强其对+1价的Costa型配合物的识别作用,平面配体的类型及电荷对分子识别影响也不大.