A comparison of techniques for embedding defect cluster calculations

Cluster calculations have proved one of the most fruitful means of extracting useful information about solid-state defect properties at finite computational expense, but large clusters are necessary to obtain reliable results and uncertainty always remains concerning the effects of edge states, with ad hoc boundary conditions such as the saturation of the surface with hydrogen atoms being frequently employed. Recently methods have been developed for embedding the cluster in the perfect crystal so that the solution obtained from the cluster calculation is the same as would have been obtained from a full calculation on the whole defective solid. Here the relationships of these methods with each other and with perturbed crystal methods which modify the perfect crystal solution to account for the presence of the defect are explored. It is shown that the embedding potential technique is preferable and is equivalent to methods that have been used in other fields.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     

Application of the linear interaction energy method for rational design of artemisinin analogues as haeme polymerisation inhibitors

The anti-malarial activity of artemisinin-derived drugs appears to be mediated by an interaction of the drug's endoperoxide bridge with intra-parasitic haeme. The binding affinity of artemisinin analogues with haeme were computed using linear interaction energy with a surface generalised Born (LIE-SGB) continuum solvation model. Low levels of root mean square error (0.348 and 0.415 kcal/mol) as well as significant correlation coefficients (r ² = 0.868 and 0.892) between the experimental and predicted free energy of binding (FEB) based on molecular dynamics and hybrid Monte Carlo sampling techniques establish the SGB-LIE method as an efficient tool for generating more potent inhibitors of haeme polymerisation inhibition.     

A mathematical model of the logical structure of chemistry. A bridge between theoretical and experimental chemistry and a general tool for computer-assisted molecular design

Summary A mathematical model of the logical structure of chemistry is suggested. The model is based on the phenomenon of convertibility between chemical species which is expressed by the so-called convertibility function . In the center of the model there is the potential energy (hyper)surface, PES. A heuristic modification of the general convertibility function is presented. Several algorithms have been developed for an analysis of PES which is described by paths, and for heuristic obtaining of PES paths. The notion ofK-barrier of conformational PES is introduced as well as an algorithm for its computation.     

Spherical‐harmonics expansion method for density‐matrix simulations of quantum electron dynamics in continuum states

Spherical‐harmonics expansion method is proposed to solve the quantum time‐evolution equations for density matrices numerically in momentum space. This method facilitates efficient real‐time simulations of quantum electron dynamics in continuum states through extension of our previous formalism developed for discrete states. Numerical accuracy and efficiency are demonstrated through two examples: (i) multiphoton ionization of a one‐electron atom in intense laser field, and (ii) real‐time dynamics of plasma oscillations in electron liquids. In case (i), coupled dynamics of density matrices for bound and continuum states reveals an enhancement of multiphoton ionization over the Keldysh approximation through resonant intermediate states. © 2015 Wiley Periodicals, Inc.     

Coupled‐cluster theory for the polarizable continuum model. III. A response theory for molecules in solution

A coupled‐cluster (CC) response functions theory for molecular solutes described with the framework of the polarizable continuum model (PCM) is presented. The theory is an extension to the dynamical molecular properties of the PCM‐CC analytic derivatives recently proposed for the calculation of static molecular properties (Cammi, Jr Chem Phys 2009, 131, 164104). The theory is presented for linear and quadratic response functions, and the operative expressions of these response functions can accurately account for the nonequilibrium solvation effects. The excitation energies and transition moments of the solvated chromophores have been determined from the linear response functions. Accurate expressions for gradients of excitation energies for the evaluation of the excited state properties have been also discussed. © 2012 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

A sparse algorithm for the evaluation of the local energy in quantum Monte Carlo

A new algorithm is presented for the sparse representation and evaluation of Slater determinants in the quantum Monte Carlo (QMC) method. The approach, combined with the use of localized orbitals in a Slater-type orbital basis set, significantly extends the size molecule that can be treated with the QMC method. Application of the algorithm to systems containing up to 390 electrons confirms that the cost of evaluating the Slater determinant scales linearly with system size.     

Simple method for the precise calculation of atomic energy levels of IB elements in the periodic table

Due to the complicated and typical electronic structure of atoms and ions of the IB group in the periodic table, theoretical calculation of their atomic energy levels has important theoretical and practical significance. In this article, the theoretical calculation of atomic energy levels of the atoms of IB group in the periodic table was completed for the first time within the scheme of the weakest bound electron potential model theory. The results were compared with experimental values and the deviations are about 0.1–1 cm^?1. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

P.‐O. Löwdin and the International Journal of Quantum Chemistry: A kaleidoscopic agenda for quantum chemistry

This is a article about P.‐O. Löwdin's life, his work in shaping quantum chemistry into a mature discipline at the intersection of mathematics, physics, chemistry, and biology, and his founding of the International Journal of Quantum Chemistry in 1967. Unavoidably, it is, also, a article reflecting our views about the history of quantum chemistry. We attempt to convey the complexities in the becoming of a subdiscipline, like quantum chemistry, where a variety of factors will have to be taken into consideration for a comprehensive understanding of its historical developments: the relations of chemists to the Heisenberg‐Schrödinger formulation of quantum mechanics after 1926, the institutional dynamics centered around the establishment of new courses and chairs, the research agendas and the vying for dominance within the community of quantum chemists, the methodological, and philosophical issues that have never left the quantum chemists indifferent, and, of course, the dramatic role of the computer in transforming the culture for actually practicing quantum chemistry. Furthermore, attracted by American history, culture, and ways of life, Löwdin suggested in the late 1970s that the post‐WWII character of quantum chemistry was dependent on its ability to hub a “scientific melting pot,” much like the United States of America which he viewed as a fusion of people from diverse provenances and cultures. In this article, we attempt to investigate another metaphor, that of the “kaleidoscope.” Löwdin believed that quantum chemistry's strength arose from its ability to nurture a multiplicity of heterogeneous cultural elements/subcultures and practices, interacting with each other, exchanging perspectives and modes of action, which circulated in an increasingly extended network of actors and institutional frameworks. © 2013 Wiley Periodicals, Inc.     

A homogeneous assay for highly sensitive detection of CaMV35S promoter in transgenic soybean by förster resonance energy transfer between nitrogen-doped graphene quantum dots and Ag nanoparticles

In this work, a novel homogeneous assay for DNA quantitative analysis based on förster resonance energy transfer (FRET) was developed for cauliflwer mosaic virus 35s (CaMV35S) promoter of transgenic soybean detection. The homogenous FRET of fluorescence signal was fabricated by DNA hybridization with probe modified nitrogen-doped graphene quantum dots (NGQDs) and silver nanoparticles (AgNPs), which acted the donor-acceptor pairs for the first time. The highly efficient FRET and unique properties of the NGQDs made the proposed FRET system as a functionalized detection platform for labelling of DNA. Upon the recognition of specific target DNA (tDNA), the FRET between NGQDs and AgNPs was triggered to produce fluorescence quenching, which could be used for tDNA detection. The fabricated homogeneous FRET assay displayed a wide linear range of 0.1–500.0 nM and a low limit of detection 0.03 nM for the detection of CaMV35S (S/N = 3). This proposed biosensor revealed high specificity to detect tDNA, with acceptable intra-assay precision and excellent stability. This method was successfully applied to identify the real sample of 0.5% containing transgenic soybean, which achieved the most of national law regulations. This assay was further validated by polymerase chain reaction as the genetically modified organisms, suggesting that the proposed FRET system is a feasible tool for the further daily genetically modified organism detection.