Excited states of TAPT-PDA COF spectra based on first principles and quantum chemical calculations

Improving two-dimensional (2D) materials is crucial for achieving integrated, intelligent, and multifunctional development of optoelectronic materials. Thus, it is essential to have a comprehensive understanding of the excitation mechanisms of covalent organic framework (COF) materials in order to prepare and modify 2D materials. This study focuses primarily on the optoelectronic properties of TAPT-PDA COF. First, the geometric structure of TAPT-PDA COF, which has a pore size of 32.4 Å and a width of 1.75 Å, was determined using first principles and quantum chemical methods. Second, the hole–electron distribution of each excited state of TAPT-PDA COF was analyzed for oscillator strengths exceeding 0.01. Additionally, the electron transition mechanism for each excited state following photon absorption was investigated. Finally, the study presents the UV–Vis and electronic circular dichroism spectra of TAPT-PDA COF based on quantitative calculations. To validate the results, the chirality of TAPT-PDA COF was experimentally confirmed. The graphs and data obtained from the experiments demonstrate that TAPT-PDA COF exhibits excellent optoelectronic performance and has significant potential for application in optoelectronic devices.     

Storage management strategies in large-scale quantum dynamics calculations

We discuss the computational strategies related to memory and disk storage and to data movement between memory and disk in large-scale quantum dynamics calculations. The discussion includes practical implementations of various strategies for handling large data sets on various supercomputer architectures.This paper was presented at the International Conference on The Impact of Supercomputers on Chemistry, held at the University of London, London, UK, 13–16 April 1987     

Electrostatic field-adapted molecular fractionation with conjugated caps for energy calculations of charged biomolecules

An electrostatic field-adapted molecular fractionation with conjugated caps (EFA-MFCC) approach is implemented for treating macromolecules with several charge centers. The molecular fragmentation is performed in an "electrostatic field," which is described by putting point charges on charge centers, directly affecting the Hamiltonians of both fragments and conjugated caps. So the present method does not need truncation during the calculation of electrostatic interactions. Our test calculations on a series of charged model systems and biological macromolecules using the HF and B3LYP methods have demonstrated that this approach is capable of describing the electronic structure with accuracy comparable to other fragment-based methods. The EFA-MFCC approach is an alternative way for predicting the total energies of charged macromolecules with acyclic, loop, and intersectional loop structures and interaction energies between two molecules.     

Ewald mesh method for quantum mechanical calculations

The Fourier transform Coulomb (FTC) method has been shown to be effective for the fast and accurate calculation of long-range Coulomb interactions between diffuse (low-energy cutoff) densities in quantum mechanical (QM) systems. In this work, we split the potential of a compact (high-energy cutoff) density into short-range and long-range components, similarly to how point charges are handled in the Ewald mesh methods in molecular mechanics simulations. With this linear scaling QM Ewald mesh method, the long-range potential of compact densities can be represented on the same grid as the diffuse densities that are treated by the FTC method. The new method is accurate and significantly reduces the amount of computational time on short-range interactions, especially when it is compared to the continuous fast multipole method.     

Site specific interaction between ZnO nanoparticles and tryptophan: a first principles quantum mechanical study

First principles density functional theory calculations are performed on tryptophan-ZnO nanoparticles complex in order to study site specific interactions between tryptophan and ZnO. The calculated results find the salt bridge structure involving the -COOH group and ZnO cluster to be energetically more favorable than other interacting sites, such as indole and amine groups in tryptophan. The interaction between tryptophan and ZnO appears to be mediated by both ionic and hydrogen bonds. The calculated molecular orbital energy levels and charge distributions suggest non-radiative energy transfer from an excited state of tryptophan to states associated with ZnO, which may lead to a reduction in the emission intensity assigned to the π-π* transition of the indole functional group of tryptophan.     

Oxygen vacancies on TiO2 (110) from first principles calculations

We have carried out a systematic study of oxygen vacancy formation on the TiO2 (110) surface by means of plane-wave pseudopotential density-functional theory calculations. We have used models with the mean number of vacancies per surface unit cell being theta=0.25 and theta=0.5. The study comprises several kind of vacancies within the outermost layers of the surface. The use of a suitable set of technical parameter is often essential in order to get accurate results. We find that the presence of bridging vacancies is energetically favored in accordance to experimental data, although the formation of sub-bridging vacancies might be possible at moderate temperatures. Surprisingly, the spin state of the vacancy has little influence on the results. Atomic displacements are also analyzed and found to be strongly dependent on the particular arrangement of vacancies.     

Chemisorption of barrelene on Si(100) from first principles calculations

The chemisorption of C8H8 bicyclo[2.2.2]-2,5,7-octatriene (barrelene) on the Si(100) surface is studied from first principles calculations. We find that, in the most stable configuration, barrelene is bonded to Si(100) through four Si-C bonds, with the C-C bonds which are orthogonal to the underlying Si dimers. The chemisorption reaction responsible for this structure is driven by the biradical nature of the Si-Si dimer bond. Two others, slightly less stable configurations, exist which are also characterized by four Si-C bonds but have a different orientation or location with respect to the Si(100) surface. The properties of these and other, less stable configurations have been investigated. For the most stable structures, the effect of different surface coverages has been also studied, showing a tendency to easily form complete monolayers of barrelene on the Si surface. On the basis of energetic and kinetic considerations, we expect that chemisorption of barrelene monolayers on the Si(100) surface will be characterized however by a certain amount of disorder. Finally, several possible reaction pathways, leading from one stable structure to another of lower energy or from a molecule in the gas phase to a chemisorbed configuration, have been investigated in detail and estimates of the relative energy barriers are given.     

Predicting cyclic peptide chemical shifts using quantum mechanical calculations

A hybrid sequential molecular mechanics and quantum mechanical approach to modeling cyclic peptides has led to an effective method for predicting their ¹H and ¹³C NMR chemical shift values. The method was first developed to predict chemical shifts in chloroform before being adapted to a more peptide friendly solvent, DMSO. Finally the effectiveness of this method was tested in a blind fashion and excellent agreement with the experimental NMR chemical shifts was observed.     

Structural and dynamical stability of cadmium nitride using first principles calculations

We report the results of a theoretical study on the behavior of the structural parameters, electronic band structure, vibrational and thermodynamical properties of transition metal nitride, CdN in the rocksalt (RS), NiAs (P63/mmc) and CuS (B₁₈) phases at ambient pressure. The calculations are based on the ab-initio plane-wave pseudopotential density functional theory (DFT), within the generalized gradient approximations (GGA) for the exchange and correlation functional. The calculated values of lattice parameters, bulk modulus and its first order pressure derivative are in good agreement with other reports. A linear response approach to the density functional theory is used to derive the phonon frequencies, phonon densities of states and thermodynamical properties. We discuss the contribution of the phonons in the dynamical stability of CdN and detailed analysis of thermodynamical properties of specific heat and Debye temperature for CdN in all considered structures.     

High pressure reactivity of propene by first principles molecular dynamics calculations

The reactivity of propene under high pressure has been investigated in the framework of Car-Parrinello molecular dynamics. Changes in structural and electronic properties due to pressure have been analyzed in systems with a density ranging from 0.855 to 2.151 g/cm(3). A ionic collective mechanism which leads to the formation of oligomers has been found by both spin restricted and spin polarized formalism. The maximally localized Wannier centers analysis has allowed us to characterize the addition scheme and to identify a Wannier center with a high spread value involved in the formation of the principal reaction products.     

The effects of solvent screening in quantum mechanical calculations in protein systems

We report on an implementation of quantum mechanical density functional calculations carried out in a dielectric medium. The dielectric medium is introduced by integrating the solution of the Poisson-Boltzmann equations into the density functional calculation. The calculations are carried out for a simple amide in vacuum, in the field of an ion, and in the ion field in several dielectric environments. The environment was constructed to include a low dielectric interior embedded in a high dielectric continuum of dielectric 80 (corresponding to aqueous solution). The energies and electron densities of formamide in the ion field were calculated at various configurations in this system, including at the low dielectric–high dielectric interface. The systems were designed to simulate situations which are similar to those that occur in proteins (i.e., the protein constitutes the low dielectric medium surrounded by aqueous solution). The system mimics situations in which charges in such proteins located in various regions interact with other parts of the protein and with ligands which mainly bind to the surface. © 1994 by John Wiley & Sons, Inc.     

Quantum mechanical embedding theory based on a unique embedding potential

We remove the nonuniqueness of the embedding potential that exists in most previous quantum mechanical embedding schemes by letting the environment and embedded region share a common embedding (interaction) potential. To efficiently solve for the embedding potential, an optimized effective potential method is derived. This embedding potential, which eschews use of approximate kinetic energy density functionals, is then used to describe the environment while a correlated wavefunction (CW) treatment of the embedded region is employed. We first demonstrate the accuracy of this new embedded CW (ECW) method by calculating the van der Waals binding energy curve between a hydrogen molecule and a hydrogen chain. We then examine the prototypical adsorption of CO on a metal surface, here the Cu(111) surface. In addition to obtaining proper site ordering (top site most stable) and binding energies within this theory, the ECW exhibits dramatic changes in the p-character of the CO 4σ and 5σ orbitals upon adsorption that agree very well with x-ray emission spectra, providing further validation of the theory. Finally, we generalize our embedding theory to spin-polarized quantum systems and discuss the connection between our theory and partition density functional theory.