The Journal of Physical Chemistry B 2019

DOI: 10.1021/acs.jpcb.8b10767

The RNA virus Influenza A is a serious public health problem with every year
epidemics resulting in more than 250,000 deaths. A protein cavity was identified
on the HA2 subunit of the hemagglutinin responsible for the entry of the virus into
the host cell by endocytosis. The binding of a ligand in this zone rich in invariant
residues and synthetic lethal couples, could prevent therapeutic escape and inhibit the
conformational change at pH=5 initiating the membrane fusion in the endosome. Two
pentapeptides, a linear peptide (EQRRS) and a cyclic peptide (DQRRD) have been
proposed as potential ligands. Complex stability and the interactions between the
ligand and the protein have been studied with the help of molecular dynamics and
quantum chemistry methods. A high stability of the interactions has been obtained
for these two ligands at both pH=7 and pH=5. Indeed, these two peptides present
two cooperative modes of actio...

Journal of Computational Chemistry 2018

DOI: 10.1002/jcc.25750 pdf

With the aim of offering new computational tools helping in the description of photochemical reactions and phenomena occurring at the excited state, we present in this work the capability of a density based index (Π) in locating decay channels from higher to lower excited states. The Π index, previously applied to disclose non‐radiative decay channels from the first excited state to the ground state, is very simple in its formulation and can be evaluated, practically with no extra computational cost, and coupled to any quantum method able to provide excited states densities. Indeed, this index relies only on the knowledge of energetics and electron densities of the different electronic states involved in the decay. In the present work, we show the proficiency of the Π index in the general case of decay between excited states by applying it to two model systems well characterized both theoretically and experimentally. In b...

International Journal of Quantum Chemistry

DOI: 10.1002/qua.25831

Gradient‐regulated connection (GRAC) is a generalized gradient approximation exchange density functional designed by combining the revPBE and PW91 exchange functionals to impose their behaviors in the slowly‐ and fast‐varying density regions, respectively. Such a construction allows one single density functional to accurately estimate both covalent and weak interactions occurring in main‐group‐based molecular systems. For the first time, the assessment of the performance of the GRAC exchange functional is extended to the modeling of various metal bond energy and structure properties. This assessment shows that when GRAC is coupled with the Perdew, Burke, Ernzerhof (PBE) correlation, the resulting exchange‐correlation density functional is an excellent alternative to global hybrids to model bond dissociation energy, atomic electronic excitation energy, and bond length structure properties of single‐reference metal bonds. It...

Inorganic Chemistry 2018

DOI: 10.1021/acs.inorgchem.8b02845

Azobenzene has become a ubiquitous component of functional molecules and polymeric materials because of the light-induced trans → cis isomerization of the diazene group. In contrast, there are very few applications utilizing azobenzene luminescence, since the excitation energy typically dissipates via nonradiative pathways. Inspired by our earlier studies with 2,2′-bis[N,N′-(2-pyridyl)methyl]diaminoazobenzene (AzoAMoP) and related compounds, we investigated a series of five aminoazobenzene derivatives and their corresponding silver complexes. Four of the aminoazobenzene ligands, which exhibit no emission under ambient conditions, form silver coordination polymers that are luminescent at room temperature. AzoAEpP (2,2′-bis[N,N′-(4-pyridyl)ethyl]diaminoazobenzene) assembles into a three-dimensional coordination polymer (AgAAEpP) that undergoes a reversible loss of emission upon the addition of metal-coordinating analytes such as p...

Langmuir 2018

DOI: 10.1021/acs.langmuir.8b02245

In the past few years, core–shell nanoparticles have opened new perspectives for the optoelectronic applications of semiconductor quantum dots. In particular, it has become possible to localize electrons in either part of these heterostructures. Understanding and controlling this phenomenon require a thorough characterization of the interfaces. In this study, we prepared quasi-2D CdSeS/ZnS core–shell nanoplatelets (NPLs) by colloidal atomic layer deposition. This technique allows fine control over the quantum confinement, the surfaces, and the interfaces. The layer-by-layer formation of a the ZnS shell around the CdSeS core was monitored using UV–vis absorption, XRD, and Raman spectroscopy. The measured band gaps and structural distortions were compared with results obtained from density functional theory (DFT) calculations. Modeling has also shown that 34% of the photoexcited electrons are delocalized into the ZnS shell. The herein present...

Chemical Physics Letters 2019

DOI: 10.1016/j.cplett.2018.10.060

A modified version of the DCT index, based on total density analysis and evaluation of the particle-hole distance for a given excited state, which enables the consideration of only the contributions of a user-defined subset of atoms is presented. This index allows one to measure partial charge transfer in parts of molecular systems and can be used to analyze charge transfer in symmetric push-pull systems.

This index (DCTP) has been computed for three families of model symmetric compounds characterized by the presence of a single donor unit and several (2–4) acceptor moieties

Journal of Chemical Theory and Computation 2018

DOI: 10.1021/acs.jctc.8b00762

We present the implementation of an implicit solvation model in the CRYSTAL code. The solvation energy is separated into two components: the electrostatic contribution arising from a self-consistent reaction field treatment obtained within a generalized finite-difference Poisson model, augmented by a nonelectrostatic contribution proportional to the solvent-accessible surface area of the solute. A discontinuous dielectric boundary is used, along with a solvent-excluded surface built from interlocking atom-centered spheres on which apparent surface point charges are mapped. The procedure is general and can be performed at both the Hartree–Fock and density functional theory levels, with pure or hybrid functionals, for systems periodic in 0, 1, and 2 directions, that is, for isolated molecules and extended polymers and surfaces. The Poisson equation resolution and apparent surface charge formalism is first validat...

Physical Chemistry Chemical Physics 2019

DOI: 10.1039/c8cp04730h

We report a QM (TD-DFT) and QM/QM′ (ONIOM) study of the modulation of emission in a series of thiazolo[5,4,b]thieno[3,2-e]pyridine (TTP) derivatives [Huang et al., J. Mater. Chem. C, 2017, 14, 3456]. By computing the excitation energy transfer couplings and the Huang–Rhys (HR) factors, we rationalize the aggregation-caused quenching (ACQ) observed for the parent molecule and the crystallization-induced emission (CIE) observed for the derivatives presenting intra-molecular H-bonding. We also show that the CIE strategy relying on the rigidification of the arch-bridge-like stator should be considered with caution since it can promote the energy dissipation through vibrational motions.

Journal of Computational Chemistry 2018

DOI:10.1002/jcc.25553

Recently, exciton‐controlled hybridization‐sensitive fluorescent oligonucleotide (ECHO) probe, which shows strong emission in the near‐infrared region via hybridization to the target DNA and/or RNA strand, has been developed. In this work, photophysical properties of the chromophores of these probes and the fluorescent mechanism have been investigated by the SAC‐CI and TD‐DFT calculations. Three fluorescent cyanine chromophores whose excitation is challenging for TD‐DFT methods, have been examined regarding the photo‐absorption and emission spectra. The SAC‐CI method well reproduces the experimental values with respect to transition energies, while the quantitative prediction by TD‐DFT calculations is difficult for these chromophores. Some stable structures of H‐aggregate system were computationally located and two of the configurations were examined for the photo‐absorption. The present results support for the assumption base...