Fragment‐based quantum mechanical calculation of protein–protein binding affinities

The electrostatically embedded generalized molecular fractionation with conjugate caps (EE‐GMFCC) method has been successfully utilized for efficient linear‐scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE‐GMFCC method for calculation of binding affinity of Endonuclease colicin–immunity protein complex. The binding free energy changes between the wild‐type and mutants of the complex calculated by EE‐GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0.906 at the B3LYP/6‐31G*‐D level, based on the snapshot whose binding affinity is closest to the average result from the molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) calculation. The inclusion of the QM effects is important for accurate prediction of protein–protein binding affinities. Moreover, the self‐consistent calculation of PB solvation energy is required for accurate calculations of protein–protein binding free energies. This study demonstrates that the EE‐GMFCC method is capable of providing reliable prediction of relative binding affinities for protein–protein complexes. © 2018 Wiley Periodicals, Inc.     

Dissipaton Equation of Motion Theory versus Fokker-Planck Quantum Master Equation

The quest of exact and nonperturbative methods on quantum dissipation with nonlinear coupling environments remains in general a great challenge. In this review we present a comprehensive account on two approaches to the entangled system-and-environment dynamics, in the presence of linear-plus-quadratic coupling bath. One is the dissipaton-equation-ofmotion (DEOM) theory that has been extended recently to treat the nonlinear coupling environment. Another is the extended Fokker-Planck quantum master equation (FP-QME) approach that will be constructed in this work, based on its DEOM correspondence. We closely compare these two approaches, with the focus on the underlying quasi-particle picture, physical implications, and implementations.     

Quantum chemical electron impact mass spectrum prediction for de novo structure elucidation: Assessment against experimental reference data and comparison to competitive fragmentation modeling

We investigate the success of the quantum chemical electron impact mass spectrum (QCEIMS) method in predicting the electron impact mass spectra of a diverse test set of 61 small molecules selected to be representative of common fragmentations and reactions in electron impact mass spectra. Comparison with experimental spectra is performed using the standard matching algorithms, and the relative ranking position of the actual molecule matching the spectra within the NIST‐11 library is examined. We find that the correct spectrum is ranked in the top two matches from structural isomers in more than 50% of the cases. QCEIMS, thus, reproduces the distribution of peaks sufficiently well to identify the compounds, with the RMSD and mean absolute difference between appropriately normalized predicted and experimental spectra being at most 9% and 3% respectively, even though the most intense peaks are often qualitatively poorly reproduced. We also compare the QCEIMS method to competitive fragmentation modeling for electron ionization, a training‐based mass spectrum prediction method, and remarkably we find the QCEIMS performs equivalently or better. We conclude that QCEIMS will be very useful for those who wish to identify new compounds which are not well represented in the mass spectral databases.     

Perturbed structures generated using coordinates derived from compliance constants in internal vibrations for QTAIM dual functional analysis: Intrinsic dynamic nature of interactions

Perturbed structures for QTAIM dual functional analysis (QTAIM‐DFA) are proposed to generate using the coordinates corresponding to the compliance force constants in internal vibrations (CIV). In QTAIM‐DFA, total electron energy densities H_b( r _c) are plotted versus H_b( r _c) – V_b( r _c)/2 at bond critical points (BCPs) of interactions in question, where V_b( r _c) are potential energy densities at BCPs. Each plot of an interaction based on the data from both perturbed structures and fully optimized one takes the form (θ_p, κ_p), where θ_p corresponds to the tangent line of the plot and κ_p is the curvature. The θ_p values evaluated with CIV are equal to those obtained by partial optimizations with the interaction distance in question being fixed suitably, within the calculation errors. Very high applicability of CIV is demonstrated to generate the perturbed structures for QTAIM‐DFA. Dynamic nature of interactions based on (θ_p, κ_p) with CIV is called “intrinsic dynamic nature of interactions.”     

Toward a universal quantum QSPR operator

This article presents a discussion about the formalism, which might be associated to a general Quantum quantitative structure–properties relations operator, appearing in a Boltzmann‐like exponential form, which is based in turn on the definition of the concept of thermal voltage, applied to thermally scaled electronic density functions. Three practical numerical examples are presented, corresponding to the calculation of the polarization angle in assorted chiral molecules, the estimation of fish toxicity for perchlorobenzene within the set of chlorobenzenes and a typical quantum QSAR study on the popular Cramer steroid set.     

Accurate spectroscopic constants of the lowest three electronic states in halonitrenes with multireference configuration interaction

Internally contracted multireference configuration interaction (icMRCI) calculations of the ground state (X³Σ⁻), the first excited state (a¹Δ) as well as the second excited state (b¹Σ⁺) have been performed for a series of halogenated nitrenes NXs (X = Cl, Br, and I). Accurate spectroscopic constants of these lowest three electronic states of each NX were obtained in this work using MRCI methods with aug‐cc‐pVXZ (X = T, Q, 5) basis sets and complete basis set (CBS) limit. In addition, various corrections, including the Davidson correction, scalar relativistic effect, core‐valence correlation, and spin‐orbit coupling effect, have been studied in calculating spectroscopic constants, especially for heavy‐atom nitrenes. Comparisons have been made with previous computational and experimental results where available. The icMRCI + Q calculations presented in this work provide a comprehensive series of results at a consistent high level of theory for all of the halogenated nitrenes.     

Inversion of Optical Activity in the Synthesis of Mercury Sulfide Nanoparticles: Role of Ligand Coordination

Optical activity in inorganic colloidal materials was controlled through interactions of chiral molecules with the nanoparticle (NP) surface. An inversion of optical activity in the synthesis of mercury sulfide (HgS) NPs was demonstrated with an intrinsically chiral crystalline system in the presence of an identical chiral capping ligand. A continuous decrease in the positive first Cotton effect and an eventual reversal of CD profile were observed upon heating the aqueous solution of HgS NPs capped with N‐acetyl‐l ‐cysteine (Ac‐l ‐Cys) at 80 °C. Ac‐l ‐Cys afforded two bidentate coordination configurations with an almost mirror image of each other using the thiolate and either of carboxylate or acetyl–carbonyl groups on the HgS core. Experiment and calculation suggest that a shift in the distribution of the NP formation with energy in response to the combinations of ligand coordination structure and chiral crystalline surface is responsible for the inversion of optical activity.     

Coordination compounds of some transition metal ions with new Schiff base ligand derived from dibenzoyl methane. Structural characterization,thermal behavior,molecular structure,antimicrobial, anticancer activity and molecular docking studies

Series of Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) complexes were prepared with tetradentate Schiff base ligand derived by condensation of 2‐aminophenol with dibenzoylmethane. The novel Schiff base H₂L (2–2′‐((1Z,1Z’)‐(1,3‐diphenyl propane‐1,3 diylidene) bis (azanylylidene) diphenol) and its binary metal complexes were characterized by physicochemical procedures i.e. elemental analysis, FT‐IR, UV–Vis, thermal analyses (TGA/DTG), mass spectrometry, magnetic susceptibility and conductometric measurements. On the basis of these studies, an octahedral geometry for all these complexes was proposed expect Ni(II) complex which had tetrahedral geometry. Molar conductivity values revealed that the complexes were electrolytes except Mn(II), Zn(II) and Cd(II) complexes were non electrolytes. The ligand bound to the metal ions via two azomethine N and two phenolic OH as indicated from the IR and ¹H NMR spectral study. The molecular and electronic structures of H₂L and its zinc complex were optimized theoretically and the quantum chemical parameters were calculated. The antimicrobial activity against a number of bacterial organisms as Streptococcus pneumonia, Bacillus Subtilis, Pseudomonas aeruginosa and Escherichia coli and fungi as Aspergillus fumigates, Syncephalastrum racemosum, Geotricum candidum and Candida albicans by disk diffusion method were screened for the Schiff base and its complexes. The Cd(II) complex has potent antimicrobial activity. Anticancer activity of the Schiff base ligand and its metal complexes were evaluated in human cancer (MCF‐7 cells viability). The Cr(III) complex exhibited higher activity than other complexes and ligand. Molecular docking was used to predict the binding between Schiff base ligand (H₂L) and its Zn(II) complex and the receptors of RNA of amikacin antibiotic (4P20) and human‐DNA‐Topo I complex (1SC7). The docking study provided useful structural information for inhibition studies.     

基于重叠栅工艺的硅量子点阵列的制备与调控

利用半导体量子点阵列结构实现近邻耦合是规模化扩展自旋量子比特的主要方案之一.随着量子点数目的增加,量子点阵列器件的制作工艺及参数调控均愈加复杂.本文介绍了一种重叠栅工艺结构,利用多层相互重叠且具有不同功能的栅极定义量子点,制作出结构紧凑、调控性好的量子点阵列器件,解决了工艺扩展的难题.此外,本文发展了一套高效可靠的调控方法,按顺序逐个添加量子点并建立虚拟电极,实现了对量子点参数的独立控制,并且能够高效且独立地调控各量子点中的电子数目,克服了大规模量子点阵列中电压参数配置的困难.这些方法为未来实现大规模自旋比特阵列提供了一种标准化的方案.